Pmel (premelanosome protein) - Rat Genome Database

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Gene: Pmel (premelanosome protein) Rattus norvegicus
Analyze
Symbol: Pmel
Name: premelanosome protein
RGD ID: 1307513
Description: Predicted to enable identical protein binding activity. Predicted to be involved in melanosome organization and positive regulation of melanin biosynthetic process. Predicted to act upstream of or within melanin biosynthetic process. Predicted to be located in several cellular components, including cis-Golgi network membrane; cytoplasmic vesicle; and extracellular exosome. Predicted to be active in melanosome and plasma membrane. Orthologous to human PMEL (premelanosome protein); INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; acrylamide; atrazine.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: LOC362818; melanocyte protein PMEL; melanocyte protein Pmel 17; Si; Silv; silver; silver homolog; silver homolog (mouse)
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Orthologs
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr871,721,948 - 1,733,248 (+)NCBIGRCr8
mRatBN7.271,138,202 - 1,148,735 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl71,138,586 - 1,148,746 (+)EnsemblmRatBN7.2 Ensembl
Rnor_6.073,133,347 - 3,143,827 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl73,133,506 - 3,143,911 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.073,105,316 - 3,116,614 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.472,007,882 - 2,018,998 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.172,008,881 - 2,018,859 (+)NCBI
Celera71,008,541 - 1,019,007 (+)NCBICelera
Cytogenetic Map7q11NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Experimental Data Annotations    Click to see Annotation Detail View

Vertebrate Trait
Object SymbolSpeciesTermQualifierEvidenceWithReferenceNotesSourceOriginal Reference(s)
PmelRatcoat/hair pigmentation trait  ISOPMEL (Canis lupus familiaris)9068941Coat colour and merleOMIAPMID:12580795 more ...

Disease Annotations     Click to see Annotation Detail View
melanoma  (ISO)

Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Molecular Function

Experimental Data Annotations     Click to see Annotation Detail View

Vertebrate Trait

References

References - curated
# Reference Title Reference Citation
1. Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
2. Rat ISS GO annotations from GOA human gene data--August 2006 GOA data from the GO Consortium
3. Rat ISS GO annotations from MGI mouse gene data--August 2006 MGD data from the GO Consortium
4. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:7665913   PMID:11266470   PMID:11694580   PMID:15096515   PMID:15695812   PMID:19666488   PMID:21106765   PMID:21949658   PMID:35708352  


Genomics

Comparative Map Data
Pmel
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr871,721,948 - 1,733,248 (+)NCBIGRCr8
mRatBN7.271,138,202 - 1,148,735 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl71,138,586 - 1,148,746 (+)EnsemblmRatBN7.2 Ensembl
Rnor_6.073,133,347 - 3,143,827 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl73,133,506 - 3,143,911 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.073,105,316 - 3,116,614 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.472,007,882 - 2,018,998 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.172,008,881 - 2,018,859 (+)NCBI
Celera71,008,541 - 1,019,007 (+)NCBICelera
Cytogenetic Map7q11NCBI
PMEL
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh381255,954,105 - 55,966,709 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl1255,954,105 - 55,973,317 (-)EnsemblGRCh38hg38GRCh38
GRCh371256,347,889 - 56,360,493 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 361254,634,156 - 54,646,093 (-)NCBINCBI36Build 36hg18NCBI36
Build 341254,634,156 - 54,646,093NCBI
Celera1256,000,543 - 56,012,534 (-)NCBICelera
Cytogenetic Map12q13.2NCBI
HuRef1253,386,917 - 53,399,406 (-)NCBIHuRef
CHM1_11256,315,023 - 56,327,629 (-)NCBICHM1_1
T2T-CHM13v2.01255,921,167 - 55,933,772 (-)NCBIT2T-CHM13v2.0
Pmel
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm3910128,531,757 - 128,555,993 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl10128,540,064 - 128,556,107 (+)EnsemblGRCm39 Ensembl
GRCm3810128,695,888 - 128,720,238 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl10128,704,195 - 128,720,238 (+)EnsemblGRCm38mm10GRCm38
MGSCv3710128,143,314 - 128,157,294 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv3610128,109,207 - 128,123,073 (+)NCBIMGSCv36mm8
Celera10131,098,390 - 131,112,396 (+)NCBICelera
Cytogenetic Map10D3NCBI
cM Map1077.13NCBI
Pmel
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554583,544,961 - 3,554,619 (-)EnsemblChiLan1.0
ChiLan1.0NW_0049554583,544,855 - 3,555,453 (-)NCBIChiLan1.0ChiLan1.0
PMEL
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v21038,363,001 - 38,374,882 (+)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan11238,359,773 - 38,371,654 (+)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v01232,946,951 - 32,958,205 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.11233,196,656 - 33,207,610 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1233,196,040 - 33,207,610 (+)Ensemblpanpan1.1panPan2
PMEL
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.110292,595 - 327,618 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl10292,597 - 300,098 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha10354,530 - 362,031 (-)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.010299,404 - 334,246 (-)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl10299,405 - 306,904 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.110277,211 - 284,717 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.010519,995 - 527,495 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.010644,259 - 651,766 (-)NCBIUU_Cfam_GSD_1.0
Pmel
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440494558,491,116 - 58,502,171 (+)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_004936646365,809 - 379,130 (-)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_004936646368,064 - 379,085 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
PMEL
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl521,355,619 - 21,364,987 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1521,355,611 - 21,365,609 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
PMEL
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11151,892,131 - 51,905,073 (-)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl1151,887,730 - 51,904,324 (-)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_023666037194,082,197 - 194,095,017 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Pmel
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_00462480212,083,090 - 12,092,767 (+)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_00462480212,073,932 - 12,092,885 (+)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Pmel
63 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:199
Count of miRNA genes:147
Interacting mature miRNAs:161
Transcripts:ENSRNOT00000049972
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.


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
61410Bw19Body weight QTL 196.20.001body mass (VT:0001259)body weight (CMO:0000012)7144782185Rat
1300176Hrtrt10Heart rate QTL 103.19heart pumping trait (VT:2000009)heart rate (CMO:0000002)766427026029351Rat
2317047Wbc4White blood cell count QTL 40.01leukocyte quantity (VT:0000217)white blood cell count (CMO:0000027)7135342956Rat
2298550Neuinf6Neuroinflammation QTL 63.3nervous system integrity trait (VT:0010566)spinal cord RT1-B protein level (CMO:0002132)7127829089Rat
631503Bp102Blood pressure QTL 1021.9arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)7144822433Rat
634336Anxrr17Anxiety related response QTL 173.66locomotor behavior trait (VT:0001392)number of entries into a discrete space in an experimental apparatus (CMO:0000960)7924703115097879Rat
724560Plsm3Polydactyly-luxate syndrome (PLS) morphotypes QTL 30.0003tibia length (VT:0004357)tibia length (CMO:0000450)7134000259Rat
9590142Scort5Serum corticosterone level QTL 524.40.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)7131962314Rat
7411566Bw136Body weight QTL 13610.40.001body mass (VT:0001259)body weight gain (CMO:0000420)7131962314Rat

Markers in Region
RH127677  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.271,148,886 - 1,149,093 (+)MAPPERmRatBN7.2
Rnor_6.073,143,979 - 3,144,185NCBIRnor6.0
Rnor_5.073,116,627 - 3,116,833UniSTSRnor5.0
RGSC_v3.472,019,011 - 2,019,217UniSTSRGSC3.4
Celera71,019,159 - 1,019,365UniSTS
Cytogenetic Map7q11UniSTS
RH133773  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.271,147,512 - 1,148,644 (+)MAPPERmRatBN7.2
Rnor_6.073,142,605 - 3,143,736NCBIRnor6.0
Rnor_5.073,115,253 - 3,116,384UniSTSRnor5.0
RGSC_v3.472,017,637 - 2,018,768UniSTSRGSC3.4
Celera71,017,785 - 1,018,916UniSTS
Cytogenetic Map7q11UniSTS


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 2
Low 3 26 43 27 19 27 1 1 72 34 41 11 1
Below cutoff 17 14 14 14 7 10 1 7

Sequence


Ensembl Acc Id: ENSRNOT00000049972   ⟹   ENSRNOP00000048469
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl71,138,586 - 1,148,746 (+)Ensembl
Rnor_6.0 Ensembl73,133,506 - 3,143,911 (+)Ensembl
Ensembl Acc Id: ENSRNOT00000112501   ⟹   ENSRNOP00000082328
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl71,139,958 - 1,148,746 (+)Ensembl
RefSeq Acc Id: NM_001427188   ⟹   NP_001414117
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr871,723,243 - 1,733,248 (+)NCBI
RefSeq Acc Id: XM_039080007   ⟹   XP_038935935
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr871,723,372 - 1,733,243 (+)NCBI
mRatBN7.271,138,858 - 1,148,735 (+)NCBI
RefSeq Acc Id: XM_063263712   ⟹   XP_063119782
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr871,721,948 - 1,733,243 (+)NCBI
Protein Sequences
Protein RefSeqs NP_001414117 (Get FASTA)   NCBI Sequence Viewer  
  XP_038935935 (Get FASTA)   NCBI Sequence Viewer  
  XP_063119782 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein EDL84820 (Get FASTA)   NCBI Sequence Viewer  
  EDL84821 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000048469.3
  ENSRNOP00000082328.1
Ensembl Acc Id: ENSRNOP00000048469   ⟸   ENSRNOT00000049972
RefSeq Acc Id: XP_038935935   ⟸   XM_039080007
- Peptide Label: isoform X1
- UniProtKB: D3ZED8 (UniProtKB/TrEMBL),   A0A8I5ZTD1 (UniProtKB/TrEMBL)
Ensembl Acc Id: ENSRNOP00000082328   ⟸   ENSRNOT00000112501
RefSeq Acc Id: XP_063119782   ⟸   XM_063263712
- Peptide Label: isoform X2
RefSeq Acc Id: NP_001414117   ⟸   NM_001427188
- Peptide Label: precursor
- UniProtKB: D3ZED8 (UniProtKB/TrEMBL)
Protein Domains
PKD

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-D3ZED8-F1-model_v2 AlphaFold D3ZED8 1-680 view protein structure

Transcriptome

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


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1307513 AgrOrtholog
BioCyc Gene G2FUF-35336 BioCyc
Ensembl Genes ENSRNOG00000023085 Ensembl, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000049972.5 UniProtKB/TrEMBL
  ENSRNOT00000112501.1 UniProtKB/TrEMBL
Gene3D-CATH 2.60.40.10 UniProtKB/TrEMBL
InterPro Ig-like_fold UniProtKB/TrEMBL
  PKAT UniProtKB/TrEMBL
  PKAT_KLD UniProtKB/TrEMBL
  PKD/Chitinase_dom UniProtKB/TrEMBL
  PKD_dom UniProtKB/TrEMBL
  PKD_dom_sf UniProtKB/TrEMBL
KEGG Report rno:362818 UniProtKB/TrEMBL
NCBI Gene 362818 ENTREZGENE
PANTHER MELANOCYTE PROTEIN PMEL UniProtKB/TrEMBL
  PTHR11861 UniProtKB/TrEMBL
Pfam PKAT_KLD UniProtKB/TrEMBL
  PKD UniProtKB/TrEMBL
PhenoGen Pmel PhenoGen
PROSITE PKD UniProtKB/TrEMBL
RatGTEx ENSRNOG00000023085 RatGTEx
SMART PKD UniProtKB/TrEMBL
Superfamily-SCOP SSF49299 UniProtKB/TrEMBL
UniProt A0A8I5ZTD1 ENTREZGENE, UniProtKB/TrEMBL
  D3ZED8 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2010-12-17 Pmel  premelanosome protein  Silv  silver homolog (mouse)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-03-24 Silv  silver homolog (mouse)  Silv_predicted  silver homolog (mouse) (predicted)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2006-03-30 Silv_predicted  silver homolog (mouse) (predicted)  Si_predicted  silver (predicted)  Symbol and Name updated 1299863 APPROVED
2005-01-12 Si_predicted  silver (predicted)      Symbol and Name status set to approved 70820 APPROVED