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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 chrNW_004936566:1,630,698...1,632,607 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 chrNW_004936691:650,753...694,362 JBrowse link
G Prtfdc1 phosphoribosyl transferase domain containing 1 NOT|involved_in ISO (PMID:21054786) UniProt PMID:21054786 NCBI chrNW_004936484:568,056...650,820 JBrowse link
heme A biosynthetic process term browser
Symbol Object Name Qualifiers Evidence Notes Source PubMed Reference(s) RGD Reference(s) Position
G LOC101959085 cytochrome c oxidase assembly protein COX15 homolog involved_in ISO (PMID:12474143) HGNC-UCL PMID:12474143 NCBI chrNW_004936636:385,198...401,090 JBrowse link
G LOC101967907 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 chrNW_004936724:783,591...905,625 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 chrNW_004936569:1,628,649...1,635,599 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 chrNW_004936484:20,154,467...20,179,748 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 chrNW_004936559:226,481...237,258 JBrowse link
G Alas2 5'-aminolevulinate synthase 2 involved_in ISO (MGI:3694153|PMID:9446639) UniProt PMID:9446639 MGI:3694153 NCBI chrNW_004936751:1,818,255...1,841,028 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 chrNW_004936474:12,396,416...12,399,760 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 chrNW_004936630:4,412,099...4,424,867 JBrowse link
G Fech ferrochelatase acts_upstream_of_or_within
involved_in
ISO (MGI:79136|PMID:8611576)
(MGI:3620268|PMID:16503645), (MGI:3696634|PMID:15496139)
(MGI:1327758|PMID:9989256)
(MGI:3794459|PMID:16306232)
(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 chrNW_004936497:6,755,626...6,788,568 JBrowse link
G Hmbs hydroxymethylbilane synthase involved_in ISO (PMID:18936296) UniProt PMID:18936296 NCBI chrNW_004936542:4,037,888...4,046,089 JBrowse link
G Hnf1a HNF1 homeobox A acts_upstream_of_or_within ISO (MGI:1352605|PMID:10617683) MGI PMID:10617683 MGI:1352605 NCBI chrNW_004936668:62,103...81,549 JBrowse link
G Pgrmc1 progesterone receptor membrane component 1 involved_in ISO (PMID:27599036) UniProt PMID:27599036 NCBI chrNW_004936479:10,625,989...10,634,058 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 chrNW_004936903:470,317...474,705 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 chrNW_004936512:8,590,302...8,622,121 JBrowse link
G Urod uroporphyrinogen decarboxylase acts_upstream_of_or_within ISO (MGI:3703836|PMID:17360334) MGI PMID:17360334 MGI:3703836 NCBI chrNW_004936474:26,207,169...26,210,599 JBrowse link
G Uros uroporphyrinogen III synthase involved_in ISO (PMID:3805019) UniProt PMID:3805019 NCBI chrNW_004936486:13,792,354...13,816,744 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 chrNW_004936530:2,217,713...2,224,070 JBrowse link
G Prps1 phosphoribosyl pyrophosphate synthetase 1 involved_in ISO (PMID:17701896) UniProt PMID:17701896 NCBI chrNW_004936499:7,114,838...7,136,468 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 chrNW_004936691:650,753...694,362 JBrowse link
melanin biosynthetic process term browser
Symbol Object Name Qualifiers Evidence Notes Source PubMed Reference(s) RGD Reference(s) Position
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 chrNW_004936762:1,387,354...1,392,955 JBrowse link
G Dct dopachrome tautomerase acts_upstream_of_or_within ISO (MGI:76308|PMID:7665913) MGI PMID:7665913 MGI:76308 NCBI chrNW_004936472:15,074,947...15,110,427 JBrowse link
G LOC101978402 agouti signaling protein acts_upstream_of_or_within ISO (MGI:76308|PMID:7665913) MGI PMID:7665913 MGI:76308 NCBI chrNW_004936561:6,341,667...6,346,440 JBrowse link
G Mc1r melanocortin 1 receptor acts_upstream_of_or_within ISO (MGI:76308|PMID:7665913) MGI PMID:7665913 MGI:76308 NCBI chrNW_004936641:193,885...198,730 JBrowse link
G Myo5a myosin VA acts_upstream_of_or_within ISO (MGI:76308|PMID:7665913) MGI PMID:7665913 MGI:76308 NCBI chrNW_004936471:14,105,832...14,257,386 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 chrNW_004936471:38,612,450...38,952,150 JBrowse link
G Pmel premelanosome protein acts_upstream_of_or_within ISO (MGI:76308|PMID:7665913) MGI PMID:7665913 MGI:76308 NCBI chrNW_004936646:368,064...379,085 JBrowse link
G Trpc1 transient receptor potential cation channel subfamily C member 1 involved_in ISO (PMID:8126111) CACAO PMID:8126111 NCBI chrNW_004936540:4,340,672...4,417,655 JBrowse link
G Tyr tyrosinase involved_in
acts_upstream_of_or_within
ISO (PMID:8126111)
(MGI:1202196|PMID:9548375)
(MGI:76308|PMID:7665913)
CACAO
MGI
PMID:7665913 PMID:8126111 PMID:9548375 MGI:1202196 MGI:76308 NCBI chrNW_004936736:421,623...519,085 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 chrNW_004936472:15,074,947...15,110,427 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 chrNW_004936588:2,011,838...2,019,119 JBrowse link
G Opn3 opsin 3 involved_in ISO (PMID:31097585) UniProt PMID:31097585 NCBI chrNW_004936526:8,833,495...8,876,631 JBrowse link
G Rapgef2 Rap guanine nucleotide exchange factor 2 involved_in ISO (MGI:5499726|PMID:16272156) UniProt PMID:16272156 MGI:5499726 NCBI chrNW_004936576:5,583,847...5,746,583 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 chrNW_004936471:10,470,078...10,492,334 JBrowse link
G Wnt5a Wnt family member 5A involved_in ISO (MGI:5619434|PMID:23569434) CACAO PMID:23569434 MGI:5619434 NCBI chrNW_004936473:6,031,627...6,052,211 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 chrNW_004936683:1,224,703...1,326,761 JBrowse link
G Slc6a9 solute carrier family 6 member 9 involved_in ISO (MGI:6450351|PMID:28495915) ARUK-UCL PMID:28495915 MGI:6450351 NCBI chrNW_004936474:25,312,544...25,344,993 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 chrNW_004936473:7,580,495...7,647,471 JBrowse link
G Atp7a ATPase copper transporting alpha involved_in ISO (PMID:11092760) UniProt PMID:11092760 NCBI chrNW_004936683:2,874,022...2,936,214 JBrowse link
G Cdh3 cadherin 3 involved_in ISO (PMID:23334344) UniProt PMID:23334344 NCBI chrNW_004936475:18,908,031...18,954,402 JBrowse link
G Gipc1 GIPC PDZ domain containing family member 1 involved_in ISO (PMID:21291857) UniProt PMID:21291857 NCBI chrNW_004936659:3,019,829...3,030,280 JBrowse link
G LOC101978402 agouti signaling protein involved_in ISO (MGI:5294257|PMID:21949658) CACAO PMID:21949658 MGI:5294257 NCBI chrNW_004936561:6,341,667...6,346,440 JBrowse link
G Opn3 opsin 3 involved_in ISO (PMID:28842328) UniProt PMID:28842328 NCBI chrNW_004936526:8,833,495...8,876,631 JBrowse link
G Pmel premelanosome protein involved_in ISO (MGI:5294257|PMID:21949658) CACAO PMID:21949658 MGI:5294257 NCBI chrNW_004936646:368,064...379,085 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 chrNW_004936539:6,537,448...6,555,440 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 chrNW_004936630:4,412,099...4,424,867 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 chrNW_004936471:36,547,552...36,601,327 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 chrNW_004936741:1,849,239...1,877,724 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 chrNW_004936657:1,104,833...1,112,854 JBrowse link
G Tmem14c transmembrane protein 14C acts_upstream_of_or_within ISO (MGI:5581691|PMID:25157825) MGI PMID:25157825 MGI:5581691 NCBI chrNW_004936534:2,233,467...2,240,223 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 chrNW_004936677:342,964...360,890 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 chrNW_004936588:2,011,838...2,019,119 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 chrNW_004936535:9,177,305...9,242,743 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 chrNW_004936530:2,217,713...2,224,070 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 chrNW_004936591:3,347,346...3,368,062 JBrowse link

Term paths to the root
Path 1
Term Annotations click to browse term
  biological_process 12170
    metabolic process 7647
      pigment metabolic process 57
        pigment biosynthetic process 49
          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 + 21
          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