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ONTOLOGY REPORT - ANNOTATIONS


Term:ncRNA transcription
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Accession:GO:0098781 term browser browse the term
Definition:The transcription of non (protein) coding RNA from a DNA template.


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ncRNA transcription term browser
Symbol Object Name Evidence Notes Source PubMed Reference(s) RGD Reference(s) Position
G Celf3 CUGBP, Elav-like family member 3 ISO (MGI:MGI:5755769|PMID:25145264) RGD PMID:25145264 MGI:MGI:5755769 NCBI chr 2:195,716,373...195,732,872
Ensembl chr 2:195,719,543...195,730,274
JBrowse link
G Topaz1 testis and ovary specific PAZ domain containing 1 ISO MGI:MGI:5700076 (MGI:MGI:5697228|PMID:26358182) RGD PMID:26358182 MGI:MGI:5697228 NCBI chr 8:131,788,816...131,843,668
Ensembl chr 8:131,789,575...131,843,713
JBrowse link
5S class rRNA transcription by RNA polymerase III term browser
Symbol Object Name Evidence Notes Source PubMed Reference(s) RGD Reference(s) Position
G Gtf3c1 general transcription factor IIIC subunit 1 IBA PMID:21873635 GO_Central PMID:21873635 RGD:13792537 NCBI chr 1:197,032,473...197,098,676
Ensembl chr 1:197,032,474...197,098,649
JBrowse link
negative regulation of transcription of nucleolar large rRNA by RNA polymerase I term browser
Symbol Object Name Evidence Notes Source PubMed Reference(s) RGD Reference(s) Position
G Dedd death effector domain-containing ISO (MGI:MGI:1306907|PMID:9774341) RGD PMID:9774341 MGI:MGI:1306907 NCBI chr13:89,706,932...89,721,825
Ensembl chr13:89,718,066...89,721,454
JBrowse link
G Macroh2a1 macroH2A.1 histone ISO UniProtKB:Q9P0M6 (PMID:24071584)
(MGI:MGI:5559643|PMID:24071584)
RGD PMID:24071584 MGI:MGI:5559643 NCBI chr17:9,282,109...9,344,698
Ensembl chr17:9,282,675...9,344,678
JBrowse link
G Macroh2a2 macroH2A.2 histone ISO UniProtKB:P0C0S8 (PMID:24071584) RGD PMID:24071584 NCBI chr20:31,352,924...31,402,483
Ensembl chr20:31,352,960...31,402,483
JBrowse link
G Nop53 NOP53 ribosome biogenesis factor ISO (PMID:27729611) RGD PMID:27729611 NCBI chr 1:77,836,522...77,843,991
Ensembl chr 1:77,836,196...77,844,189
JBrowse link
nucleolar large rRNA transcription by RNA polymerase I term browser
Symbol Object Name Evidence Notes Source PubMed Reference(s) RGD Reference(s) Position
G Polr1e RNA polymerase I subunit E ISO
IBA
(PMID:24207024)
PMID:21873635
RGD PMID:24207024, PMID:21873635 RGD:13792537 NCBI chr 5:60,572,573...60,588,097
Ensembl chr 5:60,572,577...60,588,240
JBrowse link
G Taf1b TATA-box binding protein associated factor, RNA polymerase I subunit B IBA PMID:21873635 GO_Central PMID:21873635 RGD:13792537 NCBI chr 6:43,644,931...43,722,124
Ensembl chr 6:43,644,830...43,722,113
JBrowse link
G Tcof1 treacle ribosome biogenesis factor 1 ISO
IBA
MGI:MGI:2386185 (MGI:MGI:3047194|PMID:15249688)
PMID:21873635
RGD PMID:15249688, PMID:21873635 MGI:MGI:3047194, RGD:13792537 NCBI chr18:56,081,863...56,115,719
Ensembl chr18:56,082,195...56,115,593
JBrowse link
positive regulation of snRNA transcription by RNA polymerase II term browser
Symbol Object Name Evidence Notes Source PubMed Reference(s) RGD Reference(s) Position
G Larp7 La ribonucleoprotein 7, transcriptional regulator ISS
ISO
IEA
GO_REF:0000024
(PMID:28254838)
GO_REF:0000107
UniProt
RGD
Ensembl
PMID:28254838 GO_REF:0000024, GO_REF:0000107 NCBI chr 2:231,866,888...231,882,002
Ensembl chr 2:231,867,135...231,881,939
JBrowse link
G Mepce methylphosphate capping enzyme ISO (PMID:28254838) RGD PMID:28254838 NCBI chr12:21,721,246...21,725,965
Ensembl chr12:21,721,837...21,725,435
JBrowse link
G Myod1 myogenic differentiation 1 ISS
IEA
ISO
GO_REF:0000024
GO_REF:0000107
(MGI:MGI:6148658|PMID:25217815)
UniProt
Ensembl
RGD
PMID:25217815 GO_REF:0000024, GO_REF:0000107, MGI:MGI:6148658 NCBI chr 1:102,396,538...102,399,248
Ensembl chr 1:102,396,538...102,399,248
JBrowse link
G Zfp143 zinc finger protein 143 ISO (PMID:9009278) RGD PMID:9009278 NCBI chr 1:174,702,310...174,738,133
Ensembl chr 1:174,702,373...174,738,126
JBrowse link
positive regulation of transcription of nucleolar large rRNA by RNA polymerase I term browser
Symbol Object Name Evidence Notes Source PubMed Reference(s) RGD Reference(s) Position
G Ddx11 DEAD/H-box helicase 11 ISO (PMID:26089203) RGD PMID:26089203 NCBI chr 9:114,113,642...114,133,908
Ensembl chr 9:114,111,580...114,132,492
JBrowse link
G Ippk inositol-pentakisphosphate 2-kinase IEA
ISO
GO_REF:0000107
(PMID:23203802)
Ensembl
RGD
PMID:23203802 GO_REF:0000107 NCBI chr17:15,604,148...15,643,312
Ensembl chr17:15,604,145...15,643,489
JBrowse link
G Mars1 methionyl-tRNA synthetase 1 ISO (PMID:10791971) RGD PMID:10791971 NCBI chr 7:70,585,011...70,602,425
Ensembl chr 7:70,585,013...70,602,310
JBrowse link
G Mtor mechanistic target of rapamycin kinase ISO (PMID:24036451) RGD PMID:24036451 NCBI chr 5:165,263,813...165,373,967
Ensembl chr 5:165,263,800...165,373,967
JBrowse link
G Ncl nucleolin IEA
ISO
GO_REF:0000107
(PMID:24071584)
Ensembl
RGD
PMID:24071584 GO_REF:0000107 NCBI chr 9:93,369,119...93,377,643
Ensembl chr 9:93,368,932...93,377,643
JBrowse link
G Nol11 nucleolar protein 11 ISO (PMID:22916032) RGD PMID:22916032 NCBI chr10:95,388,223...95,408,053
Ensembl chr10:95,388,888...95,407,997
JBrowse link
G Pih1d1 PIH1 domain containing 1 ISO UniProtKB:P42345|UniProtKB:Q12824 (PMID:22368283), (PMID:24036451) RGD PMID:22368283, PMID:24036451 NCBI chr 1:101,151,240...101,156,806
Ensembl chr 1:101,152,734...101,156,805
JBrowse link
G Pwp1 PWP1 homolog, endonuclein ISO (PMID:29065309) RGD PMID:29065309 NCBI chr 7:23,988,776...24,004,774
Ensembl chr 7:23,988,776...24,004,774
JBrowse link
G Smarca4 SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 4 ISO
IEA
(PMID:22368283)
GO_REF:0000107
RGD
Ensembl
PMID:22368283 GO_REF:0000107 NCBI chr 8:22,648,323...22,739,468
Ensembl chr 8:22,648,323...22,739,468
JBrowse link
G Smarcb1 SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily b, member 1 ISO UniProtKB:Q9NWS0 (PMID:22368283) RGD PMID:22368283 NCBI chr20:13,679,955...13,702,821
Ensembl chr20:13,680,716...13,704,931
JBrowse link
regulation of transcription of nucleolar large rRNA by RNA polymerase I term browser
Symbol Object Name Evidence Notes Source PubMed Reference(s) RGD Reference(s) Position
G Sirt7 sirtuin 7 ISS
ISO
GO_REF:0000024
(PMID:24207024)
UniProt
RGD
PMID:24207024 GO_REF:0000024 NCBI chr10:109,796,046...109,802,821
Ensembl chr10:109,796,020...109,802,739
JBrowse link
rRNA transcription term browser
Symbol Object Name Evidence Notes Source PubMed Reference(s) RGD Reference(s) Position
G AABR07027088.1 IEA GO_REF:0000107 Ensembl GO_REF:0000107 Ensembl chr17:14,087,182...14,091,766 JBrowse link
G Ang angiogenin ISO (PMID:15735021) RGD PMID:15735021 NCBI chr15:28,022,926...28,028,636 JBrowse link
G Cavin1 caveolae associated protein 1 IEA
ISS
ISO
GO_REF:0000107
GO_REF:0000024
(MGI:MGI:5806011|PMID:27528195)
Ensembl
UniProt
RGD
PMID:27528195 GO_REF:0000024, GO_REF:0000107, MGI:MGI:5806011 NCBI chr10:88,862,513...88,874,495
Ensembl chr10:88,860,733...88,874,528
JBrowse link
G Cdkn2a cyclin-dependent kinase inhibitor 2A ISO MGI:MGI:98834 (MGI:MGI:3822232|PMID:18809582) RGD PMID:18809582 MGI:MGI:3822232 NCBI chr 5:107,823,323...107,832,405
Ensembl chr 5:107,823,330...107,841,175
JBrowse link
G LOC257642 rRNA promoter binding protein IDA RGD PMID:11713263 RGD:1299600 NCBI chr 6:30,638,801...30,639,289 JBrowse link
G Mars1 methionyl-tRNA synthetase 1 ISO (PMID:10791971) RGD PMID:10791971 NCBI chr 7:70,585,011...70,602,425
Ensembl chr 7:70,585,013...70,602,310
JBrowse link
G NEWGENE_1306210 spindlin 1 ISS GO_REF:0000024 UniProt GO_REF:0000024 NCBI chr17:14,078,821...14,103,338
Ensembl chr16:884,861...930,527
JBrowse link
G Npm1 nucleophosmin 1 IMP RGD PMID:21444791 RGD:11535018 NCBI chr10:18,080,949...18,091,062
Ensembl chr10:18,080,950...18,090,950
JBrowse link
G Npm3 nucleophosmin/nucleoplasmin, 3 ISO (MGI:MGI:3573985|PMID:15596447) RGD PMID:15596447 MGI:MGI:3573985 NCBI chr 1:265,504,105...265,506,080
Ensembl chr 1:265,504,575...265,506,046
JBrowse link
G Polr1a RNA polymerase I subunit A IDA RGD PMID:9422795 RGD:2312782 NCBI chr 4:99,822,964...99,903,969
Ensembl chr 4:99,823,252...99,887,132
JBrowse link
G Polr1b RNA polymerase I subunit B IDA
IEA
ISO
GO_REF:0000107
MGI:MGI:3774130 (MGI:MGI:3771267|PMID:18023416)
Ensembl
RGD
PMID:18023416, PMID:9422795 GO_REF:0000107, MGI:MGI:3771267, RGD:2312782 NCBI chr 3:121,632,043...121,656,506
Ensembl chr 3:121,632,043...121,656,506
JBrowse link
G Polr1g RNA polymerase I subunit G ISO (MGI:MGI:3047492|PMID:15226435) RGD PMID:15226435 MGI:MGI:3047492 NCBI chr 1:80,267,725...80,271,001
Ensembl chr 1:80,267,725...80,271,001
JBrowse link
G Sirt7 sirtuin 7 ISO (PMID:19174463) RGD PMID:19174463 NCBI chr10:109,796,046...109,802,821
Ensembl chr10:109,796,020...109,802,739
JBrowse link
G Spin1 spindlin 1 ISO
ISS
(PMID:21960006)
GO_REF:0000024
RGD
UniProt
PMID:21960006 GO_REF:0000024 NCBI chr16:884,854...930,527
Ensembl chr16:884,861...930,527
JBrowse link
G Top1 DNA topoisomerase I IMP RGD PMID:3033639 RGD:2317069 NCBI chr 3:156,635,688...156,717,686
Ensembl chr 3:156,642,464...156,717,686
JBrowse link
G Tp53 tumor protein p53 ISO MGI:MGI:104738 (MGI:MGI:3822232|PMID:18809582) RGD PMID:18809582 MGI:MGI:3822232 NCBI chr10:56,186,299...56,198,449
Ensembl chr10:56,187,020...56,198,449
JBrowse link
snRNA transcription term browser
Symbol Object Name Evidence Notes Source PubMed Reference(s) RGD Reference(s) Position
G Rpap2 RNA polymerase II associated protein 2 ISO
ISS
(PMID:22137580)
GO_REF:0000024
RGD
UniProt
PMID:22137580 GO_REF:0000024 NCBI chr14:3,125,595...3,204,590
Ensembl chr14:3,124,622...3,204,588
JBrowse link
G Uspl1 ubiquitin specific peptidase like 1 ISO (PMID:24413172) RGD PMID:24413172 NCBI chr12:6,930,018...6,957,027
Ensembl chr12:6,929,978...6,956,984
JBrowse link
snRNA transcription by RNA polymerase II term browser
Symbol Object Name Evidence Notes Source PubMed Reference(s) RGD Reference(s) Position
G Ell elongation factor for RNA polymerase II ISO (MGI:MGI:5582153|PMID:22195968)
(PMID:22195968), (PMID:23932780)
RGD PMID:22195968, PMID:23932780 MGI:MGI:5582153 NCBI chr16:20,594,129...20,641,441
Ensembl chr16:20,594,072...20,641,908
JBrowse link
G Ell2 elongation factor for RNA polymerase II 2 ISO (PMID:22195968) RGD PMID:22195968 NCBI chr 2:2,456,189...2,525,590
Ensembl chr 2:2,456,735...2,524,237
JBrowse link
G Ell3 elongation factor for RNA polymerase II 3 ISO
ISS
(PMID:22195968)
GO_REF:0000024
RGD
UniProt
PMID:22195968 GO_REF:0000024 NCBI chr 3:113,400,395...113,405,869
Ensembl chr 3:113,401,734...113,405,829
JBrowse link
G Ice1 interactor of little elongation complex ELL subunit 1 ISO (PMID:22195968), (PMID:23932780) RGD PMID:22195968, PMID:23932780 NCBI chr 1:35,280,481...35,322,769
Ensembl chr 1:35,280,701...35,319,182
JBrowse link
G Ice2 interactor of little elongation complex ELL subunit 2 ISO
IBA
(PMID:23932780)
PMID:21873635
RGD PMID:23932780, PMID:21873635 RGD:13792537 NCBI chr 8:75,625,147...75,666,959
Ensembl chr 8:75,625,174...75,666,866
JBrowse link
G Snapc1 small nuclear RNA activating complex, polypeptide 1 IBA PMID:21873635 GO_Central PMID:21873635 RGD:13792537 NCBI chr 6:96,871,675...96,893,422
Ensembl chr 6:96,871,625...96,893,444
JBrowse link
G Snapc3 small nuclear RNA activating complex, polypeptide 3 IBA PMID:21873635 GO_Central PMID:21873635 RGD:13792537 NCBI chr 5:101,526,591...101,554,015
Ensembl chr 5:101,526,551...101,553,489
JBrowse link
G Snapc4 small nuclear RNA activating complex, polypeptide 4 ISO (PMID:9418884) RGD PMID:9418884 NCBI chr 3:3,808,596...3,827,425
Ensembl chr 3:3,809,407...3,824,284
JBrowse link
G Snapc5 small nuclear RNA activating complex, polypeptide 5 ISO (PMID:9732265) RGD PMID:9732265 NCBI chr 8:69,127,708...69,131,539
Ensembl chr 8:69,127,708...69,131,539
JBrowse link
G Zc3h8 zinc finger CCCH type containing 8 ISO (PMID:23932780) RGD PMID:23932780 NCBI chr 3:121,471,836...121,488,528
Ensembl chr 3:121,471,810...121,488,540
JBrowse link
snRNA transcription by RNA polymerase III term browser
Symbol Object Name Evidence Notes Source PubMed Reference(s) RGD Reference(s) Position
G Ell elongation factor for RNA polymerase II ISO (PMID:23932780) RGD PMID:23932780 NCBI chr16:20,594,129...20,641,441
Ensembl chr16:20,594,072...20,641,908
JBrowse link
G Ice1 interactor of little elongation complex ELL subunit 1 ISO (PMID:23932780) RGD PMID:23932780 NCBI chr 1:35,280,481...35,322,769
Ensembl chr 1:35,280,701...35,319,182
JBrowse link
G Ice2 interactor of little elongation complex ELL subunit 2 ISO
IBA
(PMID:23932780)
PMID:21873635
RGD PMID:23932780, PMID:21873635 RGD:13792537 NCBI chr 8:75,625,147...75,666,959
Ensembl chr 8:75,625,174...75,666,866
JBrowse link
G Snapc1 small nuclear RNA activating complex, polypeptide 1 IBA PMID:21873635 GO_Central PMID:21873635 RGD:13792537 NCBI chr 6:96,871,675...96,893,422
Ensembl chr 6:96,871,625...96,893,444
JBrowse link
G Snapc3 small nuclear RNA activating complex, polypeptide 3 IBA PMID:21873635 GO_Central PMID:21873635 RGD:13792537 NCBI chr 5:101,526,591...101,554,015
Ensembl chr 5:101,526,551...101,553,489
JBrowse link
G Snapc4 small nuclear RNA activating complex, polypeptide 4 ISO (PMID:9418884) RGD PMID:9418884 NCBI chr 3:3,808,596...3,827,425
Ensembl chr 3:3,809,407...3,824,284
JBrowse link
G Snapc5 small nuclear RNA activating complex, polypeptide 5 ISO (PMID:9732265) RGD PMID:9732265 NCBI chr 8:69,127,708...69,131,539
Ensembl chr 8:69,127,708...69,131,539
JBrowse link
G Zc3h8 zinc finger CCCH type containing 8 ISO (PMID:23932780) RGD PMID:23932780 NCBI chr 3:121,471,836...121,488,528
Ensembl chr 3:121,471,810...121,488,540
JBrowse link
tRNA transcription by RNA polymerase III term browser
Symbol Object Name Evidence Notes Source PubMed Reference(s) RGD Reference(s) Position
G AABR07006025.1 IBA PMID:21873635 GO_Central PMID:21873635 RGD:13792537 Ensembl chr 1:214,015,219...214,024,153 JBrowse link
G AABR07042789.1 IBA PMID:21873635 GO_Central PMID:21873635 RGD:13792537 Ensembl chr19:8,943,753...8,943,956 JBrowse link
G AC109542.1 IBA PMID:21873635 GO_Central PMID:21873635 RGD:13792537 Ensembl chr 1:214,452,127...214,455,039 JBrowse link
G Polr2l-ps1 polymerase (RNA) II (DNA directed) polypeptide L, pseudogene 1 IBA PMID:21873635 GO_Central PMID:21873635 RGD:13792537 NCBI chr19:8,943,599...8,943,966 JBrowse link

Term paths to the root
Path 1
Term Annotations click to browse term
  biological_process 20014
    metabolic process 12256
      organic substance metabolic process 11636
        macromolecule metabolic process 10081
          gene expression 6295
            transcription, DNA-templated 3419
              ncRNA transcription 55
                ncRNA transcription associated with protein coding gene TSS/TES + 0
                rRNA transcription + 33
                snRNA transcription + 16
                snoRNA transcription + 0
                tRNA transcription + 4
Path 2
Term Annotations click to browse term
  biological_process 20014
    metabolic process 12256
      organic substance metabolic process 11636
        organic cyclic compound metabolic process 5931
          nucleobase-containing compound metabolic process 5483
            nucleic acid metabolic process 4980
              RNA metabolic process 4470
                RNA biosynthetic process 3478
                  nucleic acid-templated transcription 3464
                    transcription, DNA-templated 3419
                      ncRNA transcription 55
                        ncRNA transcription associated with protein coding gene TSS/TES + 0
                        rRNA transcription + 33
                        snRNA transcription + 16
                        snoRNA transcription + 0
                        tRNA transcription + 4
paths to the root

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