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ONTOLOGY REPORT - ANNOTATIONS


Term:vitamin D metabolic process
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Accession:GO:0042359 term browser browse the term
Definition:The chemical reactions and pathways involving vitamin D, any of a group of related, fat-soluble compounds that are derived from delta-5,7 steroids and play a central role in calcium metabolism. Specific forms of vitamin D include calciferol (ergocalciferol; vitamin D2) and cholecalciferol (calciol; vitamin D3).
Synonyms:exact_synonym: vitamin D metabolism
 narrow_synonym: calciferol metabolic process;   calciferol metabolism;   cholecalciferol metabolic process;   cholecalciferol metabolism;   ergocalciferol metabolic process;   ergocalciferol metabolism


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vitamin D metabolic process term browser
Symbol Object Name Evidence Notes Source PubMed Reference(s) RGD Reference(s) Position
G Calb1 calbindin 1 TAS RGD PMID:2792772 RGD:68751 NCBI chr 5:29,538,380...29,562,774
Ensembl chr 5:29,538,380...29,562,773
JBrowse link
G Cyp24a1 cytochrome P450, family 24, subfamily a, polypeptide 1 IDA
ISO
TAS
MGI:MGI:2182338 (MGI:MGI:3046628|PMID:15225763) RGD PMID:15225763, PMID:1991512, PMID:12372434 MGI:MGI:3046628, RGD:1298844, RGD:734870 NCBI chr 3:168,097,484...168,111,920
Ensembl chr 3:168,097,485...168,111,920
JBrowse link
G Cyp27b1 cytochrome P450, family 27, subfamily b, polypeptide 1 TAS
ISO
IDA
(PMID:9415400) RGD PMID:9415400, PMID:11316734, PMID:9371776 RGD:68680, RGD:69372 NCBI chr 7:70,333,150...70,340,006
Ensembl chr 7:70,335,061...70,340,005
JBrowse link
G Cyp2r1 cytochrome P450, family 2, subfamily r, polypeptide 1 ISO (MGI:MGI:2677973|PMID:12867411) RGD PMID:12867411 MGI:MGI:2677973 NCBI chr 1:184,060,521...184,106,604
Ensembl chr 1:184,093,920...184,106,200
JBrowse link
G Fgf23 fibroblast growth factor 23 IEP RGD PMID:15531762 RGD:1598934 NCBI chr 4:159,622,404...159,630,082
Ensembl chr 4:159,622,404...159,630,082
JBrowse link
G Gc GC, vitamin D binding protein ISO
IEA
(MGI:MGI:3046628|PMID:15225763)
GO_REF:0000107
RGD
Ensembl
PMID:15225763 GO_REF:0000107, MGI:MGI:3046628 NCBI chr14:20,267,023...20,302,577
Ensembl chr14:20,266,891...20,302,581
JBrowse link
calcitriol biosynthetic process from calciol term browser
Symbol Object Name Evidence Notes Source PubMed Reference(s) RGD Reference(s) Position
G Cyp27a1 cytochrome P450, family 27, subfamily a, polypeptide 1 IEA
IBA
ISO
GO_REF:0000107
PMID:21873635
(PMID:15465040)
Ensembl
RGD
PMID:15465040, PMID:21873635 GO_REF:0000107, RGD:13792537 NCBI chr 9:81,968,285...81,998,213
Ensembl chr 9:81,968,332...81,998,169
JBrowse link
G Cyp27b1 cytochrome P450, family 27, subfamily b, polypeptide 1 ISO
IBA
(PMID:15795327), (PMID:16549446), (PMID:17023519), (PMID:22862690), (PMID:9415400)
PMID:21873635
(MGI:MGI:3590419|PMID:15972816)
RGD PMID:9415400, PMID:15795327, PMID:15972816, PMID:16549446, PMID:17023519, PMID:22862690, PMID:21873635 MGI:MGI:3590419, RGD:13792537 NCBI chr 7:70,333,150...70,340,006
Ensembl chr 7:70,335,061...70,340,005
JBrowse link
G Cyp2r1 cytochrome P450, family 2, subfamily r, polypeptide 1 ISO (PMID:15465040), (PMID:18511070) RGD PMID:15465040, PMID:18511070 NCBI chr 1:184,060,521...184,106,604
Ensembl chr 1:184,093,920...184,106,200
JBrowse link
G LOC100909462 25-hydroxyvitamin D-1 alpha hydroxylase, mitochondrial-like IBA PMID:21873635 GO_Central PMID:21873635 RGD:13792537
negative regulation of calcidiol 1-monooxygenase activity term browser
Symbol Object Name Evidence Notes Source PubMed Reference(s) RGD Reference(s) Position
G Cyp27b1 cytochrome P450, family 27, subfamily b, polypeptide 1 ISO (PMID:16549446) RGD PMID:16549446 NCBI chr 7:70,333,150...70,340,006
Ensembl chr 7:70,335,061...70,340,005
JBrowse link
G Gfi1 growth factor independent 1 transcriptional repressor ISO (PMID:15947108) RGD PMID:15947108 NCBI chr14:3,058,035...3,073,332
Ensembl chr14:3,058,993...3,068,371
JBrowse link
G Nfkb1 nuclear factor kappa B subunit 1 ISO
IEA
(PMID:15243130)
GO_REF:0000107
RGD
Ensembl
PMID:15243130 GO_REF:0000107 NCBI chr 2:240,773,520...240,890,053
Ensembl chr 2:240,773,456...240,866,689
JBrowse link
negative regulation of vitamin D biosynthetic process term browser
Symbol Object Name Evidence Notes Source PubMed Reference(s) RGD Reference(s) Position
G Snai1 snail family transcriptional repressor 1 ISO (PMID:19502595) RGD PMID:19502595 NCBI chr 3:164,274,710...164,279,199
Ensembl chr 3:164,274,710...164,279,378
JBrowse link
G Snai2 snail family transcriptional repressor 2 ISO (PMID:18485278), (PMID:19502595) RGD PMID:18485278, PMID:19502595 NCBI chr11:90,404,421...90,406,730
Ensembl chr11:90,403,333...90,406,797
JBrowse link
positive regulation of calcidiol 1-monooxygenase activity term browser
Symbol Object Name Evidence Notes Source PubMed Reference(s) RGD Reference(s) Position
G Ifng interferon gamma ISO (PMID:9282826) RGD PMID:9282826 NCBI chr 7:61,337,383...61,341,419
Ensembl chr 7:61,337,381...61,341,419
JBrowse link
G Il1b interleukin 1 beta IEA
ISO
GO_REF:0000107
(PMID:16720713), (PMID:17023519)
Ensembl
RGD
PMID:16720713, PMID:17023519 GO_REF:0000107 NCBI chr 3:121,876,256...121,882,637
Ensembl chr 3:121,876,263...121,882,726
JBrowse link
G Tnf tumor necrosis factor ISO (PMID:1690216) RGD PMID:1690216 NCBI chr20:5,189,382...5,192,000
Ensembl chr20:5,189,390...5,192,000
JBrowse link
positive regulation of vitamin D biosynthetic process term browser
Symbol Object Name Evidence Notes Source PubMed Reference(s) RGD Reference(s) Position
G Ifng interferon gamma ISO (PMID:9282826) RGD PMID:9282826 NCBI chr 7:61,337,383...61,341,419
Ensembl chr 7:61,337,381...61,341,419
JBrowse link
G Tnf tumor necrosis factor ISO (PMID:1690216) RGD PMID:1690216 NCBI chr20:5,189,382...5,192,000
Ensembl chr20:5,189,390...5,192,000
JBrowse link
regulation of calcidiol 1-monooxygenase activity term browser
Symbol Object Name Evidence Notes Source PubMed Reference(s) RGD Reference(s) Position
G Vdr vitamin D receptor ISO
IEA
(MGI:MGI:1097206|PMID:9295274)
GO_REF:0000107
RGD
Ensembl
PMID:9295274 GO_REF:0000107, MGI:MGI:1097206 NCBI chr 7:139,344,452...139,394,138
Ensembl chr 7:139,342,063...139,394,166
JBrowse link
vitamin D catabolic process term browser
Symbol Object Name Evidence Notes Source PubMed Reference(s) RGD Reference(s) Position
G Cyp24a1 cytochrome P450, family 24, subfamily a, polypeptide 1 TAS
IBA
IDA
ISO
PMID:21873635
PMID:16617161
PMID:10231362
(PMID:16617161), (PMID:24893882), (PMID:8679605)
RGD PMID:8679605, PMID:16617161, PMID:24893882, PMID:12048211, PMID:21873635, PMID:16617161, PMID:10231362 RGD:625496, RGD:13792537, RGD:14995311, RGD:14995316 NCBI chr 3:168,097,484...168,111,920
Ensembl chr 3:168,097,485...168,111,920
JBrowse link
G Cyp27b1 cytochrome P450, family 27, subfamily b, polypeptide 1 IDA
IBA
ISO
PMID:9333115
PMID:21873635
(MGI:MGI:1097206|PMID:9295274)
RGD PMID:9295274, PMID:9333115, PMID:21873635 MGI:MGI:1097206, RGD:69373, RGD:13792537 NCBI chr 7:70,333,150...70,340,006
Ensembl chr 7:70,335,061...70,340,005
JBrowse link
G Fgf23 fibroblast growth factor 23 ISO (PMID:15040831) RGD PMID:15040831 NCBI chr 4:159,622,404...159,630,082
Ensembl chr 4:159,622,404...159,630,082
JBrowse link
G LOC100909462 25-hydroxyvitamin D-1 alpha hydroxylase, mitochondrial-like IBA PMID:21873635 GO_Central PMID:21873635 RGD:13792537
vitamin D3 metabolic process term browser
Symbol Object Name Evidence Notes Source PubMed Reference(s) RGD Reference(s) Position
G Fgfr1 Fibroblast growth factor receptor 1 ISO
IEA
MGI:MGI:95525 (MGI:MGI:5548021|PMID:24259513)
GO_REF:0000107
RGD
Ensembl
PMID:24259513 GO_REF:0000107, MGI:MGI:5548021 NCBI chr16:71,265,390...71,319,046
Ensembl chr16:71,266,248...71,319,449
JBrowse link
G Fgfr4 fibroblast growth factor receptor 4 ISO MGI:MGI:95522 (MGI:MGI:5548021|PMID:24259513) RGD PMID:24259513 MGI:MGI:5548021 NCBI chr17:9,990,072...10,004,339
Ensembl chr17:9,990,078...10,004,321
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
        organic hydroxy compound metabolic process 538
          vitamin D metabolic process 18
            vitamin D biosynthetic process + 12
            vitamin D catabolic process + 4
            vitamin D2 metabolic process 0
            vitamin D3 metabolic process + 6
            vitamin D4 metabolic process 0
            vitamin D5 metabolic process 0
Path 2
Term Annotations click to browse term
  biological_process 20014
    metabolic process 12256
      small molecule metabolic process 1870
        vitamin metabolic process 81
          fat-soluble vitamin metabolic process 39
            vitamin D metabolic process 18
              vitamin D biosynthetic process + 12
              vitamin D catabolic process + 4
              vitamin D2 metabolic process 0
              vitamin D3 metabolic process + 6
              vitamin D4 metabolic process 0
              vitamin D5 metabolic process 0
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.