Afap1l2 (actin filament associated protein 1-like 2) - Chinchilla Research Resource Database
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Gene: Afap1l2 (actin filament associated protein 1-like 2) Rattus norvegicus
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Symbol: Afap1l2
Name: actin filament associated protein 1-like 2
CRRD ID: 1310668
Description: Predicted to have SH2 domain binding activity; SH3 domain binding activity; and protein tyrosine kinase activator activity. Predicted to be involved in several processes, including inflammatory response; positive regulation of epidermal growth factor receptor signaling pathway; and regulation of gene expression. Predicted to localize to cytosol and plasma membrane. Orthologous to human AFAP1L2 (actin filament associated protein 1 like 2); INTERACTS WITH 2,2',4,4'-Tetrabromodiphenyl ether; 2,3,7,8-tetrachlorodibenzodioxine; 2,3,7,8-Tetrachlorodibenzofuran.
Type: protein-coding
RefSeq Status: VALIDATED
Also known as: actin filament-associated protein 1-like 2; LOC292130; phosphatidylinositol 3-kinase-associated protein; RGD1310668; similar to expressed sequence AU041783
Orthologs:
Homo sapiens (human) : AFAP1L2 (actin filament associated protein 1 like 2)  HGNC  Alliance
Mus musculus (house mouse) : Afap1l2 (actin filament associated protein 1-like 2)  MGI  Alliance
Chinchilla lanigera (long-tailed chinchilla) : Afap1l2 (actin filament associated protein 1 like 2)
Pan paniscus (bonobo/pygmy chimpanzee) : AFAP1L2 (actin filament associated protein 1 like 2)
Canis lupus familiaris (dog) : AFAP1L2 (actin filament associated protein 1 like 2)
Ictidomys tridecemlineatus (thirteen-lined ground squirrel) : Afap1l2 (actin filament associated protein 1 like 2)
Sus scrofa (pig) : AFAP1L2 (actin filament associated protein 1 like 2)
Heterocephalus glaber (naked mole-rat) : Afap1l2 (actin filament associated protein 1 like 2)
more info ...
Latest Assembly: Rnor_6.0 - RGSC Genome Assembly v6.0
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Rnor_6.01277,730,760 - 277,827,299 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1277,730,760 - 277,827,269 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01285,110,704 - 285,206,347 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41263,220,056 - 263,256,132 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11263,431,340 - 263,470,406 (-)NCBI
Celera1251,661,305 - 251,756,440 (-)NCBICelera
Cytogenetic Map1q55NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View


Cellular Component
cytoplasm  (ISO)
cytosol  (IBA,ISO)
plasma membrane  (IEA,ISO)

Molecular Function

References

Additional References at PubMed
PMID:17412687   PMID:21084565   PMID:22496359   PMID:29330129  


Genomics

Comparative Map Data
Afap1l2
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Rnor_6.01277,730,760 - 277,827,299 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1277,730,760 - 277,827,269 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01285,110,704 - 285,206,347 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41263,220,056 - 263,256,132 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11263,431,340 - 263,470,406 (-)NCBI
Celera1251,661,305 - 251,756,440 (-)NCBICelera
Cytogenetic Map1q55NCBI
AFAP1L2
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl10114,294,824 - 114,404,756 (-)EnsemblGRCh38hg38GRCh38
GRCh3810114,280,760 - 114,404,672 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh3710116,041,248 - 116,164,515 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 3610116,044,573 - 116,154,505 (-)NCBINCBI36hg18NCBI36
Build 3410116,044,573 - 116,154,505NCBI
Celera10109,783,766 - 109,893,772 (-)NCBI
Cytogenetic Map10q25.3NCBI
HuRef10109,682,148 - 109,791,263 (-)NCBIHuRef
CHM1_110116,338,430 - 116,448,332 (-)NCBICHM1_1
Afap1l2
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391956,900,786 - 57,017,021 (-)NCBI
GRCm381956,912,354 - 57,028,589 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1956,912,361 - 57,008,228 (-)EnsemblGRCm38mm10GRCm38
MGSCv371956,986,844 - 57,083,065 (-)NCBIGRCm37mm9NCBIm37
MGSCv361956,965,609 - 57,061,427 (-)NCBImm8
Celera1959,103,348 - 59,201,420 (-)NCBICelera
Cytogenetic Map19D2NCBI
Afap1l2
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495543119,276,412 - 19,315,446 (-)EnsemblChiLan1.0
ChiLan1.0NW_00495543119,275,257 - 19,378,507 (-)NCBIChiLan1.0ChiLan1.0
AFAP1L2
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.110114,324,736 - 114,434,148 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl10114,324,736 - 114,434,148 (-)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v010110,894,774 - 111,004,373 (-)NCBI
AFAP1L2
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1 Ensembl2825,133,296 - 25,194,431 (-)EnsemblCanFam3.1canFam3CanFam3.1
CanFam3.12825,137,235 - 25,228,454 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
Afap1l2
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
SpeTri2.0NW_0049364864,606,529 - 4,697,481 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
AFAP1L2
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.114124,630,797 - 124,737,350 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.214135,751,428 - 135,862,187 (-)NCBISscrofa10.2Sscrofa10.2susScr3
Afap1l2
(Heterocephalus glaber - naked mole-rat)
No map positions available.

Position Markers
RH143842  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.01277,827,017 - 277,827,157NCBIRnor6.0
Rnor_5.01285,206,100 - 285,206,240UniSTSRnor5.0
Celera1251,756,188 - 251,756,328UniSTS
Cytogenetic Map1q55UniSTS
RH 3.4 Map11680.3UniSTS


QTLs in Region (Rnor_6.0)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
CRRD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1354646Kidm18Kidney mass QTL 185.7kidney mass (VT:0002707)calculated kidney weight (CMO:0000160)1161784169278228889Rat
1354661Bw33Body weight QTL 335.2body mass (VT:0001259)body weight (CMO:0000012)1161784169278228889Rat
1354610Bw34Body weight QTL 344.1body mass (VT:0001259)body weight (CMO:0000012)1161784169278228889Rat
1549837Hcar15Hepatocarcinoma resistance QTL 150.05liver integrity trait (VT:0010547)liver tumorous lesion number (CMO:0001068)1163796316282763074Rat
1354580Scort1Serum corticosterone level QTL 13.4blood corticosterone amount (VT:0005345)blood corticosterone level (CMO:0001172)1167394665278228889Rat
738032Hcas5Hepatocarcinoma susceptibility QTL 53.12liver integrity trait (VT:0010547)liver tumorous lesion number (CMO:0001068)1191825895279986079Rat
1354652Kidm20Kidney mass QTL 204.3kidney mass (VT:0002707)calculated kidney weight (CMO:0000160)1192639698278228889Rat
1354624Cm35Cardiac mass QTL355.7heart left ventricle mass (VT:0007031)calculated heart weight (CMO:0000073)1192639698278228889Rat
1578763Kidm29Kidney mass QTL 293.30.0001kidney mass (VT:0002707)both kidneys wet weight (CMO:0000085)1196395041282763074Rat
1600388Niddm67Non-insulin dependent diabetes mellitus QTL 675.840.000004blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)1213476630278978026Rat
1600395Niddm69Non-insulin dependent diabetes mellitus QTL 694.140.0002blood insulin amount (VT:0001560)plasma insulin level (CMO:0000342)1213476630278978026Rat
1600396Niddm68Non-insulin dependent diabetes mellitus QTL 684.970.0003blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)1213476630278978026Rat
634313Niddm43Non-insulin dependent diabetes mellitus QTL 43blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)1217054291281795785Rat
1358890Bp259Blood pressure QTL 2593.06arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)1230420627282645769Rat
734768Niddm59Non-insulin dependent diabetes mellitus QTL 59body mass (VT:0001259)body weight (CMO:0000012)1235850810280850810Rat
2302040Pia35Pristane induced arthritis QTL 353.80.001blood immunoglobulin amount (VT:0002460)serum immunoglobulin G1 level (CMO:0002115)1236265430281265430Rat
61327Eae7Experimental allergic encephalomyelitis QTL 75.6body mass (VT:0001259)change in body weight (CMO:0002045)1236265430281265430Rat
70211Niddm24Non-insulin dependent diabetes mellitus QTL 243.79blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)1236795785281795785Rat
1549910Bw54Body weight QTL 540.05body mass (VT:0001259)body weight (CMO:0000012)1236795785281795785Rat
1598821Rf55Renal function QTL 556.3renal blood flow trait (VT:2000006)ratio of change in renal blood flow to change in renal perfusion pressure (CMO:0001239)1238824734279986079Rat
724533Rf51Renal function QTL 515.30.0002kidney plasma flow trait (VT:0005524)renal plasma flow (CMO:0001914)1238830534278228767Rat
731175Uae20Urinary albumin excretion QTL 203.50.0018urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)1241482188281795785Rat
10053715Scort24Serum corticosterone level QTL 242.130.0088blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)1242302911282763074Rat
724552Glom2Glomerulus QTL 23.30.0001kidney glomerulus morphology trait (VT:0005325)count of superficial glomeruli directly contacting the kidney surface (CMO:0001001)1243272341282763074Rat
1600392Bw123Body weight QTL 1230.001body mass (VT:0001259)body weight (CMO:0000012)1244087148282763074Rat
7387289Uae45Urinary albumin excretion QTL 452.860.0021urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)1244148899282763074Rat
631843Bw116Body weight QTL 1164.10.016abdominal adipose amount (VT:1000220)abdominal fat pad weight (CMO:0000088)1244401175282365384Rat
734767Niddm57Non-insulin dependent diabetes mellitus QTL 57body mass (VT:0001259)body weight (CMO:0000012)1244401175282365384Rat
734769Niddm58Non-insulin dependent diabetes mellitus QTL 58body mass (VT:0001259)body weight (CMO:0000012)1244992467282365384Rat
631215Stl8Serum triglyceride level QTL 89.270.0001blood triglyceride amount (VT:0002644)serum triglyceride level (CMO:0000360)1245529606282763074Rat
1300108Rf8Renal function QTL 83.75renal blood flow trait (VT:2000006)absolute change in renal vascular resistance (CMO:0001900)1249206242281795785Rat
1581544Rf52Renal function QTL 520.05total urine protein amount (VT:0000032)urine protein excretion rate to body weight ratio (CMO:0001099)1252948438281795785Rat
631669Iddm9Insulin dependent diabetes mellitus QTL 92.80.039blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)1252955158280632620Rat
631536Lnnr2Liver neoplastic nodule remodeling QTL 22.90.0005liver integrity trait (VT:0010547)liver remodeling tumorous lesion number to liver total tumorous lesion number ratio (CMO:0001705)1255728828282763074Rat
631690Scl5Serum cholesterol level QTL 52.1blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)1258132568282763074Rat
631837Niddm35Non-insulin dependent diabetes mellitus QTL 350.01blood insulin amount (VT:0001560)serum insulin level (CMO:0000358)1258709726281795785Rat
631836Stl31Serum triglyceride level QTL 314.640.00000487blood triglyceride amount (VT:0002644)plasma triglyceride level (CMO:0000548)1259295704282763074Rat
1598839Rf56Renal function QTL 56renal blood flow trait (VT:2000006)ratio of change in renal blood flow to change in renal perfusion pressure (CMO:0001239)1266793821279986079Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:123
Count of miRNA genes:57
Interacting mature miRNAs:60
Transcripts:ENSRNOT00000023113, ENSRNOT00000073346
Prediction methods:Microtar, Miranda, Rnahybrid, Targetscan
Result types:miRGate_prediction

The detailed report is available here: Full Report CSV TAB Printer

miRNA Target Status data imported from miRGate (http://mirgate.bioinfo.cnio.es/).
For more information about miRGate, see PMID:25858286 or access the full paper here.


Expression


RNA-SEQ Expression
High: > 1000 TPM value   Medium: Between 11 and 1000 TPM
Low: Between 0.5 and 10 TPM   Below Cutoff: < 0.5 TPM

alimentary part of gastrointestinal system circulatory system endocrine system exocrine system hemolymphoid system hepatobiliary system integumental system musculoskeletal system nervous system renal system reproductive system respiratory system appendage
High
Medium 4 11 1 1 26 18 26 11 1
Low 3 39 57 41 8 41 7 10 48 17 15 7
Below cutoff

Sequence

Nucleotide Sequences
RefSeq Transcripts NM_001305184 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_008760580 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_008760581 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017588861 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017588862 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017588863 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
GenBank Nucleotide AABR07007027 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AABR07007028 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AABR07007029 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AABR07007030 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AAHX01000967 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AAHX01000968 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AAHX01000969 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AAHX01000970 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AAHX01000971 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AB568258 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CH473986 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles

Reference Sequences
RefSeq Acc Id: ENSRNOT00000023113   ⟹   ENSRNOP00000023113
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl1277,731,799 - 277,768,368 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000073346   ⟹   ENSRNOP00000064164
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl1277,730,760 - 277,827,269 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000084915   ⟹   ENSRNOP00000073158
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl1277,821,122 - 277,827,178 (-)Ensembl
RefSeq Acc Id: NM_001305184   ⟹   NP_001292113
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.01277,730,760 - 277,827,269 (-)NCBI
Celera1251,661,305 - 251,756,440 (-)NCBI
Sequence:
RefSeq Acc Id: XM_008760580   ⟹   XP_008758802
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.01277,730,760 - 277,827,299 (-)NCBI
Sequence:
RefSeq Acc Id: XM_008760581   ⟹   XP_008758803
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.01277,730,760 - 277,827,298 (-)NCBI
Sequence:
RefSeq Acc Id: XM_017588861   ⟹   XP_017444350
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.01277,730,760 - 277,827,298 (-)NCBI
Sequence:
RefSeq Acc Id: XM_017588862   ⟹   XP_017444351
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.01277,730,760 - 277,773,188 (-)NCBI
Sequence:
RefSeq Acc Id: XM_017588863   ⟹   XP_017444352
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.01277,730,760 - 277,827,298 (-)NCBI
Sequence:
Reference Sequences
RefSeq Acc Id: XP_008758802   ⟸   XM_008760580
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: XP_008758803   ⟸   XM_008760581
- Peptide Label: isoform X5
- Sequence:
RefSeq Acc Id: NP_001292113   ⟸   NM_001305184
- Sequence:
RefSeq Acc Id: XP_017444352   ⟸   XM_017588863
- Peptide Label: isoform X4
- Sequence:
RefSeq Acc Id: XP_017444350   ⟸   XM_017588861
- Peptide Label: isoform X2
- Sequence:
RefSeq Acc Id: XP_017444351   ⟸   XM_017588862
- Peptide Label: isoform X3
- Sequence:
RefSeq Acc Id: ENSRNOP00000073158   ⟸   ENSRNOT00000084915
RefSeq Acc Id: ENSRNOP00000064164   ⟸   ENSRNOT00000073346
RefSeq Acc Id: ENSRNOP00000023113   ⟸   ENSRNOT00000023113
Protein Domains
PH

Transcriptome

eQTL   View at Phenogen
WGCNA   View at Phenogen
Tissue/Strain Expression   View at Phenogen

Promoters
RGD ID:13691006
Promoter ID:EPDNEW_R1529
Type:multiple initiation site
Name:Afap1l2_2
Description:actin filament associated protein 1-like 2
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Alternative Promoters:null; see alsoEPDNEW_R1530  
Experiment Methods:Single-end sequencing.
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.01277,826,917 - 277,826,977EPDNEW
RGD ID:13691011
Promoter ID:EPDNEW_R1530
Type:single initiation site
Name:Afap1l2_1
Description:actin filament associated protein 1-like 2
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Alternative Promoters:null; see alsoEPDNEW_R1529  
Experiment Methods:Single-end sequencing.
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.01277,827,263 - 277,827,323EPDNEW

Strain Variation

Strain Sequence Variants (Rnor 6.0)
ACI/EurMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
ACI/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
ACI/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
BBDP/Wor (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
BN/SsN (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
Buf/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
COP/CrCrl (MCW & UW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
University of Wisconsin (Dr. James Shull)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Charles River Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob) and UW Madison (Dr. James Shull)
F344/NCrl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
F344/NRrrc (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
FHH/EurMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHH/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
FHL/EurMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHL/EurMcwi (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
GH/OmrMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
GK/Ox (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LE/Stm (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/Crl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/NCrlBR (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LH/MavRrrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LL/MavRrrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LN/MavRrrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
M520/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
MHS/Gib (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MNS/Gib (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MR/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
SBH/Ygl (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBH/Ygl sequenced by MCW
SBH/Ygl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SBN/Ygl (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBN/Ygl sequenced by MCW
SBN/Ygl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHR/NHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHRSP/Gcrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SR/JrHsd (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Harlan Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SR/JrHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SS/Jr (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SS/JrHsdMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SS/JrHsdMcwi (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WAG/Rij (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/Gcrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
WKY/NCrl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/NHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WN/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1310668 AgrOrtholog
Ensembl Genes ENSRNOG00000017164 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000023113 UniProtKB/TrEMBL
  ENSRNOP00000064164 ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOP00000073158 UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000023113 UniProtKB/TrEMBL
  ENSRNOT00000073346 ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOT00000084915 UniProtKB/TrEMBL
Gene3D-CATH 2.30.29.30 UniProtKB/TrEMBL
InterPro AFAP UniProtKB/TrEMBL
  AFAP1L2 UniProtKB/TrEMBL
  PH_like_dom UniProtKB/TrEMBL
  Pleckstrin_homology UniProtKB/TrEMBL
NCBI Gene 292130 ENTREZGENE
PANTHER PTHR14338 UniProtKB/TrEMBL
  PTHR14338:SF4 UniProtKB/TrEMBL
Pfam PF00169 UniProtKB/TrEMBL
PhenoGen Afap1l2 PhenoGen
PROSITE PH_DOMAIN UniProtKB/TrEMBL
SMART SM00233 UniProtKB/TrEMBL
UniGene Rn.161912 ENTREZGENE
UniProt A0A0G2K4S9_RAT UniProtKB/TrEMBL
  F1M5W8_RAT UniProtKB/TrEMBL
  M0R484_RAT UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2008-02-27 Afap1l2  actin filament associated protein 1-like 2  RGD1310668_predicted  similar to expressed sequence AU041783 (predicted)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2005-01-20 RGD1310668_predicted  similar to expressed sequence AU041783 (predicted)  LOC292130_predicted    Symbol and Name status set to approved 1331353 APPROVED
2005-01-12 LOC292130_predicted  similar to expressed sequence AU041783 (predicted)      Symbol and Name status set to provisional 70820 PROVISIONAL

 



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RGD is funded by grant HL64541 from the National Heart, Lung, and Blood Institute on behalf of the NIH.