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ONTOLOGY REPORT - ANNOTATIONS


Term:pigment biosynthetic process
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Accession:GO:0046148 term browser browse the term
Definition:The chemical reactions and pathways resulting in the formation of a pigment, any general or particular coloring matter in living organisms, e.g. melanin.
Synonyms:exact_synonym: pigment anabolism;   pigment biosynthesis;   pigment formation;   pigment synthesis


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pigment biosynthetic process term browser
Symbol Object Name Qualifiers Evidence Notes Source PubMed Reference(s) RGD Reference(s) Position
G SOX2 SRY-box transcription factor 2 acts_upstream_of_or_within ISO (MGI:2181477|PMID:12036291) MGI PMID:12036291 MGI:2181477 NCBI chr 3:178,744,881...178,747,392
Ensembl chr 3:186,922,705...186,923,662
JBrowse link
guanine salvage term browser
Symbol Object Name Qualifiers Evidence Notes Source PubMed Reference(s) RGD Reference(s) Position
G HPRT1 hypoxanthine phosphoribosyltransferase 1 involved_in ISO (PMID:19527031) UniProt PMID:19527031 NCBI chr  X:123,609,248...123,650,102
Ensembl chr  X:133,916,681...133,948,197
JBrowse link
G PRTFDC1 phosphoribosyl transferase domain containing 1 NOT|involved_in ISO (PMID:21054786) UniProt PMID:21054786 NCBI chr10:25,023,015...25,127,770
Ensembl chr10:25,393,227...25,497,054
JBrowse link
heme A biosynthetic process term browser
Symbol Object Name Qualifiers Evidence Notes Source PubMed Reference(s) RGD Reference(s) Position
G LOC100980340 protoheme IX farnesyltransferase, mitochondrial involved_in
acts_upstream_of_or_within
ISO (PMID:12928484)
(MGI:3640032|PMID:16782876)
(MGI:3604933|PMID:16103131)
HGNC-UCL
MGI
PMID:12928484 PMID:16103131 PMID:16782876 MGI:3604933 MGI:3640032 NCBI chr17:37,443,319...37,582,436
Ensembl chr17:42,091,452...42,274,762
JBrowse link
G LOC100993532 cytochrome c oxidase assembly protein COX15 homolog involved_in ISO (PMID:12474143) HGNC-UCL PMID:12474143 NCBI chr10:96,328,841...96,349,655
Ensembl chr10:99,820,763...99,841,554
JBrowse link
heme B biosynthetic process term browser
Symbol Object Name Qualifiers Evidence Notes Source PubMed Reference(s) RGD Reference(s) Position
G ABCB6 ATP binding cassette subfamily B member 6 (Langereis blood group) NOT|involved_in ISO (PMID:22655043) UniProt PMID:22655043 NCBI chr2B:106,467,345...106,476,614
Ensembl chr2B:225,058,771...225,067,626
JBrowse link
heme biosynthetic process term browser
Symbol Object Name Qualifiers Evidence Notes Source PubMed Reference(s) RGD Reference(s) Position
G ABCB10 ATP binding cassette subfamily B member 10 involved_in ISO (MGI:5648801|PMID:24421385) UniProt PMID:24421385 MGI:5648801 NCBI chr 1:205,061,329...205,103,568
Ensembl chr 1:210,094,355...210,134,496
JBrowse link
G ALAD aminolevulinate dehydratase acts_upstream_of_or_within
involved_in
ISO (MGI:53493|PMID:4959158), (MGI:53609|PMID:4981581), (MGI:63121|PMID:14050799)
(PMID:11032836)
RGD
MGI
UniProt
PMID:1764448 PMID:4959158 PMID:4981581 PMID:11032836 PMID:14050799 MGI:53493 MGI:53609 MGI:63121 RGD:1599020 NCBI chr 9:84,488,339...84,503,360
Ensembl chr 9:112,859,171...112,873,784
JBrowse link
G ALAS2 5'-aminolevulinate synthase 2 involved_in ISO (MGI:3694153|PMID:9446639) UniProt PMID:9446639 MGI:3694153 NCBI chr  X:47,219,588...47,241,592
Ensembl chr  X:55,451,794...55,473,680
JBrowse link
G ATP5IF1 ATP synthase inhibitory factor subunit 1 involved_in ISO (PMID:23135403)
(MGI:5447588|PMID:23135403)
UniProt PMID:23135403 MGI:5447588 NCBI chr 1:27,495,250...27,497,255
Ensembl chr 1:28,532,091...28,542,607
JBrowse link
G CPOX coproporphyrinogen oxidase acts_upstream_of_or_within ISO (MGI:77569|PMID:8407975) RGD
MGI
PMID:3955059 PMID:8407975 MGI:77569 RGD:1600961 NCBI chr 3:95,674,861...95,689,139
Ensembl chr 3:102,359,382...102,372,170
JBrowse link
G FECH ferrochelatase acts_upstream_of_or_within
involved_in
ISO (MGI:3620268|PMID:16503645), (MGI:3696634|PMID:15496139)
(MGI:79136|PMID:8611576)
(MGI:3794459|PMID:16306232)
(MGI:1327758|PMID:9989256)
(PMID:27599036)
RGD
MGI
UniProt
PMID:3955059 PMID:8611576 PMID:9989256 PMID:15496139 PMID:16306232 More... MGI:1327758 MGI:3620268 MGI:3696634 MGI:3794459 MGI:79136 RGD:1600961 NCBI chr18:50,934,520...50,977,132
Ensembl chr18:54,273,527...54,312,378
JBrowse link
G HMBS hydroxymethylbilane synthase involved_in ISO (PMID:18936296) UniProt PMID:18936296 NCBI chr11:113,923,004...113,931,732
Ensembl chr11:117,852,295...117,860,757
JBrowse link
G HNF1A HNF1 homeobox A acts_upstream_of_or_within ISO (MGI:1352605|PMID:10617683) MGI PMID:10617683 MGI:1352605 NCBI chr12:118,562,308...118,584,596
Ensembl chr12:121,932,671...121,955,911
JBrowse link
G PGRMC1 progesterone receptor membrane component 1 involved_in ISO (PMID:27599036) UniProt PMID:27599036 NCBI chr  X:108,282,958...108,291,187
Ensembl chr  X:118,711,495...118,719,714
JBrowse link
G PPOX protoporphyrinogen oxidase acts_upstream_of_or_within
involved_in
ISO (MGI:3687447|PMID:3346226)
(PMID:7713909)
RGD
MGI
UniProt
PMID:3346226 PMID:3955059 PMID:7713909 MGI:3687447 RGD:1600961 NCBI chr 1:136,578,846...136,590,466
Ensembl chr 1:140,491,667...140,502,328
JBrowse link
G SLC11A2 solute carrier family 11 member 2 acts_upstream_of_or_within ISO (MGI:3691553|PMID:11739192) MGI PMID:11739192 MGI:3691553 NCBI chr12:37,726,158...37,774,554
Ensembl chr12:38,629,686...38,677,377
JBrowse link
G UROD uroporphyrinogen decarboxylase acts_upstream_of_or_within ISO (MGI:3703836|PMID:17360334) MGI PMID:17360334 MGI:3703836 NCBI chr 1:44,315,912...44,319,356
Ensembl chr 1:45,679,744...45,683,185
JBrowse link
G UROS uroporphyrinogen III synthase involved_in ISO (PMID:3805019) UniProt PMID:3805019 NCBI chr10:122,346,072...122,384,405
Ensembl chr10:126,613,732...126,648,363
JBrowse link
hypoxanthine biosynthetic process term browser
Symbol Object Name Qualifiers Evidence Notes Source PubMed Reference(s) RGD Reference(s) Position
G ADA adenosine deaminase acts_upstream_of_or_within ISO (MGI:3640719|PMID:10720488) MGI PMID:10720488 MGI:3640719 NCBI chr20:40,950,238...40,982,481
Ensembl chr20:42,044,613...42,076,868
JBrowse link
G PRPS1 phosphoribosyl pyrophosphate synthetase 1 involved_in ISO (PMID:17701896) UniProt PMID:17701896 NCBI chr  X:96,720,988...96,743,594
Ensembl chr  X:107,094,898...107,117,117
JBrowse link
hypoxanthine salvage term browser
Symbol Object Name Qualifiers Evidence Notes Source PubMed Reference(s) RGD Reference(s) Position
G HPRT1 hypoxanthine phosphoribosyltransferase 1 involved_in ISO (PMID:19527031) UniProt PMID:19527031 NCBI chr  X:123,609,248...123,650,102
Ensembl chr  X:133,916,681...133,948,197
JBrowse link
melanin biosynthetic process term browser
Symbol Object Name Qualifiers Evidence Notes Source PubMed Reference(s) RGD Reference(s) Position
G ASIP agouti signaling protein acts_upstream_of_or_within ISO (MGI:76308|PMID:7665913) MGI PMID:7665913 MGI:76308 NCBI chr20:30,583,038...30,592,726
Ensembl chr20:31,718,169...31,727,217
JBrowse link
G CITED1 Cbp/p300 interacting transactivator with Glu/Asp rich carboxy-terminal domain 1 involved_in ISO (MGI:4412464|PMID:11434569) UniProt PMID:11434569 MGI:4412464 NCBI chr  X:61,537,949...61,543,545
Ensembl chr  X:71,621,785...71,625,702
JBrowse link
G DCT dopachrome tautomerase acts_upstream_of_or_within ISO (MGI:76308|PMID:7665913) MGI PMID:7665913 MGI:76308 NCBI chr13:75,590,366...75,730,956
Ensembl chr13:94,773,794...94,816,083
JBrowse link
G MYO5A myosin VA acts_upstream_of_or_within ISO (MGI:76308|PMID:7665913) MGI PMID:7665913 MGI:76308 NCBI chr15:31,246,192...31,470,040
Ensembl chr15:49,578,491...49,704,319
JBrowse link
G OCA2 OCA2 melanosomal transmembrane protein acts_upstream_of_or_within ISO (MGI:1202196|PMID:9548375), (MGI:76308|PMID:7665913) MGI PMID:7665913 PMID:9548375 MGI:1202196 MGI:76308 NCBI chr15:1,811,728...2,192,018
Ensembl chr15:25,181,386...25,523,774
JBrowse link
G PMEL premelanosome protein acts_upstream_of_or_within ISO (MGI:76308|PMID:7665913) MGI PMID:7665913 MGI:76308 NCBI chr12:32,946,951...32,958,205
Ensembl chr12:33,196,040...33,207,610
JBrowse link
G TRPC1 transient receptor potential cation channel subfamily C member 1 involved_in ISO (PMID:8126111) CACAO PMID:8126111 NCBI chr 3:139,757,408...139,841,006
Ensembl chr 3:147,349,056...147,432,332
JBrowse link
G TYR tyrosinase involved_in
acts_upstream_of_or_within
ISO (PMID:8126111)
(MGI:76308|PMID:7665913)
(MGI:1202196|PMID:9548375)
CACAO
MGI
PMID:7665913 PMID:8126111 PMID:9548375 MGI:1202196 MGI:76308 NCBI chr11:84,188,557...84,306,686
Ensembl chr11:87,769,606...87,888,138
JBrowse link
melanin biosynthetic process from tyrosine term browser
Symbol Object Name Qualifiers Evidence Notes Source PubMed Reference(s) RGD Reference(s) Position
G DCT dopachrome tautomerase involved_in ISO (MGI:3690794|PMID:2169885) UniProt PMID:2169885 MGI:3690794 NCBI chr13:75,590,366...75,730,956
Ensembl chr13:94,773,794...94,816,083
JBrowse link
negative regulation of melanin biosynthetic process term browser
Symbol Object Name Qualifiers Evidence Notes Source PubMed Reference(s) RGD Reference(s) Position
G MFSD12 major facilitator superfamily domain containing 12 involved_in ISO (MGI:5912387|PMID:29025994) CACAO PMID:29025994 MGI:5912387 NCBI chr19:2,570,068...2,583,505
Ensembl chr19:3,520,399...3,532,767
JBrowse link
G OPN3 opsin 3 involved_in ISO (PMID:31097585) UniProt PMID:31097585 NCBI chr 1:217,155,765...217,202,577
Ensembl chr 1:222,136,422...222,184,598
JBrowse link
G RAPGEF2 Rap guanine nucleotide exchange factor 2 involved_in ISO (MGI:5499726|PMID:16272156) UniProt PMID:16272156 MGI:5499726 NCBI chr 4:151,419,402...151,680,769
Ensembl chr 4:163,316,396...163,487,495
JBrowse link
G SLC24A5 solute carrier family 24 member 5 acts_upstream_of_or_within ISO (MGI:3775882|PMID:18166528) MGI PMID:18166528 MGI:3775882 NCBI chr15:27,069,937...27,091,619
Ensembl chr15:45,394,090...45,415,823
JBrowse link
G WNT5A Wnt family member 5A involved_in ISO (MGI:5619434|PMID:23569434) CACAO PMID:23569434 MGI:5619434 NCBI chr 3:55,396,279...55,418,579
Ensembl chr 3:56,621,380...56,638,051
JBrowse link
positive regulation of heme biosynthetic process term browser
Symbol Object Name Qualifiers Evidence Notes Source PubMed Reference(s) RGD Reference(s) Position
G ABCB7 ATP binding cassette subfamily B member 7 involved_in ISO (PMID:30765471)
(MGI:6695684|PMID:30765471)
UniProt PMID:30765471 MGI:6695684 NCBI chr  X:64,304,101...64,407,310
Ensembl chr  X:74,418,754...74,521,726
JBrowse link
G SLC6A9 solute carrier family 6 member 9 involved_in ISO (MGI:6450351|PMID:28495915) ARUK-UCL PMID:28495915 MGI:6450351 NCBI chr 1:43,298,326...43,333,345
Ensembl chr 1:44,664,839...44,704,882
JBrowse link
positive regulation of melanin biosynthetic process term browser
Symbol Object Name Qualifiers Evidence Notes Source PubMed Reference(s) RGD Reference(s) Position
G APPL1 adaptor protein, phosphotyrosine interacting with PH domain and leucine zipper 1 involved_in ISO (PMID:21291857) UniProt PMID:21291857 NCBI chr 3:57,161,299...57,206,672
Ensembl chr 3:58,370,430...58,415,258
JBrowse link
G ASIP agouti signaling protein involved_in ISO (MGI:5294257|PMID:21949658) CACAO PMID:21949658 MGI:5294257 NCBI chr20:30,583,038...30,592,726
Ensembl chr20:31,718,169...31,727,217
JBrowse link
G ATP7A ATPase copper transporting alpha involved_in ISO (PMID:11092760) UniProt PMID:11092760 NCBI chr  X:67,093,675...67,231,318
Ensembl chr  X:77,255,312...77,342,756
JBrowse link
G CDH3 cadherin 3 involved_in ISO (PMID:23334344) UniProt PMID:23334344 NCBI chr16:49,015,115...49,071,903
Ensembl chr16:68,407,625...68,465,287
JBrowse link
G GIPC1 GIPC PDZ domain containing family member 1 involved_in ISO (PMID:21291857) UniProt PMID:21291857 NCBI chr19:14,041,192...14,059,402
Ensembl chr19:14,885,185...14,889,701
JBrowse link
G OPN3 opsin 3 involved_in ISO (PMID:28842328) UniProt PMID:28842328 NCBI chr 1:217,155,765...217,202,577
Ensembl chr 1:222,136,422...222,184,598
JBrowse link
G PMEL premelanosome protein involved_in ISO (MGI:5294257|PMID:21949658) CACAO PMID:21949658 MGI:5294257 NCBI chr12:32,946,951...32,958,205
Ensembl chr12:33,196,040...33,207,610
JBrowse link
G TYRP1 tyrosinase related protein 1 involved_in ISO (PMID:21996312)
(MGI:5294257|PMID:21949658)
CACAO PMID:21949658 PMID:21996312 MGI:5294257 NCBI chr 9:12,502,610...12,550,203
Ensembl chr 9:12,950,831...12,996,799
JBrowse link
protoporphyrinogen IX biosynthetic process term browser
Symbol Object Name Qualifiers Evidence Notes Source PubMed Reference(s) RGD Reference(s) Position
G CPOX coproporphyrinogen oxidase ISO RGD PMID:3814086 RGD:4145128 NCBI chr 3:95,674,861...95,689,139
Ensembl chr 3:102,359,382...102,372,170
JBrowse link
G IREB2 iron responsive element binding protein 2 acts_upstream_of_or_within ISO (MGI:3695992|PMID:15831703) MGI PMID:15831703 MGI:3695992 NCBI chr15:57,367,314...57,430,322
Ensembl chr15:76,331,610...76,394,476
JBrowse link
purine nucleobase biosynthetic process term browser
Symbol Object Name Qualifiers Evidence Notes Source PubMed Reference(s) RGD Reference(s) Position
G SHMT1 serine hydroxymethyltransferase 1 involved_in ISO (PMID:11516159) UniProt PMID:11516159 NCBI chr17:32,870,949...32,905,690
Ensembl chr17:37,849,206...37,884,220
JBrowse link
regulation of heme biosynthetic process term browser
Symbol Object Name Qualifiers Evidence Notes Source PubMed Reference(s) RGD Reference(s) Position
G SRRD SRR1 domain containing involved_in ISO (MGI:6282940|PMID:28802827) UniProt PMID:28802827 MGI:6282940 NCBI chr22:7,545,779...7,559,431
Ensembl chr22:25,268,727...25,276,402
JBrowse link
G TMEM14C transmembrane protein 14C acts_upstream_of_or_within ISO (MGI:5581691|PMID:25157825) MGI PMID:25157825 MGI:5581691 NCBI chr 6:10,564,011...10,572,177
Ensembl chr 6:10,843,062...10,851,278
JBrowse link
regulation of melanin biosynthetic process term browser
Symbol Object Name Qualifiers Evidence Notes Source PubMed Reference(s) RGD Reference(s) Position
G CTNS cystinosin, lysosomal cystine transporter involved_in ISO (PMID:22649030) UniProt PMID:22649030 NCBI chr17:3,686,903...3,711,857
Ensembl chr17:3,683,575...3,708,253
JBrowse link
G MFSD12 major facilitator superfamily domain containing 12 involved_in ISO (PMID:31117290)
(MGI:6492453|PMID:33208952)
(PMID:33208952)
UniProt PMID:31117290 PMID:33208952 MGI:6492453 NCBI chr19:2,570,068...2,583,505
Ensembl chr19:3,520,399...3,532,767
JBrowse link
G SLC7A11 solute carrier family 7 member 11 acts_upstream_of_or_within ISO (MGI:3588610|PMID:16037214) MGI PMID:16037214 MGI:3588610 NCBI chr 4:130,529,677...130,601,396
Ensembl chr 4:141,849,343...141,959,849
JBrowse link
xanthine biosynthetic process term browser
Symbol Object Name Qualifiers Evidence Notes Source PubMed Reference(s) RGD Reference(s) Position
G ADA adenosine deaminase acts_upstream_of_or_within ISO (MGI:3640719|PMID:10720488) MGI PMID:10720488 MGI:3640719 NCBI chr20:40,950,238...40,982,481
Ensembl chr20:42,044,613...42,076,868
JBrowse link
zeaxanthin biosynthetic process term browser
Symbol Object Name Qualifiers Evidence Notes Source PubMed Reference(s) RGD Reference(s) Position
G RPE65 retinoid isomerohydrolase RPE65 involved_in ISO (PMID:28874556) UniProt PMID:28874556 NCBI chr 1:67,666,784...67,687,891
Ensembl chr 1:69,623,775...69,644,904
JBrowse link

Term paths to the root
Path 1
Term Annotations click to browse term
  biological_process 12656
    metabolic process 7929
      pigment metabolic process 56
        pigment biosynthetic process 48
          anthocyanin-containing compound biosynthetic process + 0
          aurone biosynthetic process 0
          carotenoid biosynthetic process + 1
          chlorophyll biosynthetic process + 0
          eye pigment biosynthetic process + 0
          flavone biosynthetic process + 0
          heme biosynthetic process + 21
          melanin biosynthetic process + 20
          ocellus pigment biosynthetic process + 0
          phlobaphene biosynthetic process 0
          phytochrome chromophore biosynthetic process 0
          pigment biosynthetic process involved in pigment accumulation + 0
          pteridine biosynthetic process 0
          purine nucleobase biosynthetic process + 5
paths to the root