RNF39 (ring finger protein 39) - Rat Genome Database

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Gene: RNF39 (ring finger protein 39) Homo sapiens
Analyze
Symbol: RNF39
Name: ring finger protein 39
RGD ID: 1604283
HGNC Page HGNC:18064
Description: Predicted to enable ubiquitin protein ligase activity. Predicted to be involved in protein ubiquitination. Predicted to be active in cytoplasm. Biomarker of cholangiocarcinoma.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: FAP216; HZF; HZFW; LIRF; LTP (long-term potentiation) induced RING finger protein
RGD Orthologs
Mouse
Rat
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Orthologs
More Info more info ...
Allele / Splice: See ClinVar data
Latest Assembly: GRCh38 - Human Genome Assembly GRCh38
Position:
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38630,070,270 - 30,075,769 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl630,070,266 - 30,075,849 (-)EnsemblGRCh38hg38GRCh38
GRCh37630,038,047 - 30,043,546 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 36630,146,022 - 30,151,607 (-)NCBINCBI36Build 36hg18NCBI36
Celera631,636,296 - 31,641,881 (-)NCBICelera
Cytogenetic Map6p22.1NCBI
HuRef629,836,215 - 29,841,800 (-)NCBIHuRef
CHM1_1630,040,092 - 30,045,677 (-)NCBICHM1_1
T2T-CHM13v2.0629,934,544 - 29,940,043 (-)NCBIT2T-CHM13v2.0
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View

Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Cellular Component

Molecular Function

Phenotype Annotations     Click to see Annotation Detail View

Human Phenotype
References

References - curated
# Reference Title Reference Citation
1. Identification of key genes and pathways associated with cholangiocarcinoma development based on weighted gene correlation network analysis. Liu J, etal., PeerJ. 2019 Oct 31;7:e7968. doi: 10.7717/peerj.7968. eCollection 2019.
2. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
3. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:8889548   PMID:10585558   PMID:11006080   PMID:11076863   PMID:11130983   PMID:11716498   PMID:12477932   PMID:14574404   PMID:17719541   PMID:19050382   PMID:19115949   PMID:19693088  
PMID:19851445   PMID:20041166   PMID:20593013   PMID:20875797   PMID:21873635   PMID:24489884   PMID:28149331   PMID:28729889   PMID:32296183  


Genomics

Comparative Map Data
RNF39
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38630,070,270 - 30,075,769 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl630,070,266 - 30,075,849 (-)EnsemblGRCh38hg38GRCh38
GRCh37630,038,047 - 30,043,546 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 36630,146,022 - 30,151,607 (-)NCBINCBI36Build 36hg18NCBI36
Celera631,636,296 - 31,641,881 (-)NCBICelera
Cytogenetic Map6p22.1NCBI
HuRef629,836,215 - 29,841,800 (-)NCBIHuRef
CHM1_1630,040,092 - 30,045,677 (-)NCBICHM1_1
T2T-CHM13v2.0629,934,544 - 29,940,043 (-)NCBIT2T-CHM13v2.0
Rnf39
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391737,253,943 - 37,258,878 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1737,253,810 - 37,258,878 (+)EnsemblGRCm39 Ensembl
GRCm381736,943,051 - 36,947,986 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1736,942,918 - 36,947,986 (+)EnsemblGRCm38mm10GRCm38
MGSCv371737,079,996 - 37,084,931 (+)NCBIGRCm37MGSCv37mm9NCBIm37
Celera1740,366,596 - 40,371,525 (+)NCBICelera
Cytogenetic Map17B1NCBI
cM Map1719.16NCBI
Rnf39
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8201,610,027 - 1,615,516 (-)NCBIGRCr8
mRatBN7.2201,604,794 - 1,610,283 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl201,604,794 - 1,610,283 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx201,657,567 - 1,663,054 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0201,661,064 - 1,666,549 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0201,602,535 - 1,608,038 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.0202,098,375 - 2,103,864 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl202,098,375 - 2,103,864 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0204,135,089 - 4,140,578 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4201,697,530 - 1,703,019 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.1201,697,529 - 1,703,019 (-)NCBI
Celera202,313,358 - 2,318,849 (-)NCBICelera
Cytogenetic Map20p12NCBI
Rnf39
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0NW_004955583201,638 - 206,754 (-)NCBIChiLan1.0ChiLan1.0
RNF39
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v2544,663,536 - 44,669,354 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan1640,626,537 - 40,632,281 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v0629,848,055 - 29,853,659 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.1630,518,327 - 30,523,597 (-)NCBIpanpan1.1PanPan1.1panPan2
RNF39
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.13526,292,218 - 26,296,980 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl3526,292,781 - 26,297,083 (-)EnsemblCanFam3.1canFam3CanFam3.1
ROS_Cfam_1.03526,600,790 - 26,605,478 (-)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl3526,601,338 - 26,605,630 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.13526,255,356 - 26,260,068 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.03526,316,600 - 26,320,753 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.03527,786,250 - 27,790,957 (-)NCBIUU_Cfam_GSD_1.0
Rnf39
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440494632,619,246 - 32,624,624 (-)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_004936723967,263 - 975,952 (+)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_004936723967,376 - 972,496 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
RNF39
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl722,637,732 - 22,642,612 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1722,637,732 - 22,642,427 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2724,985,817 - 24,990,520 (+)NCBISscrofa10.2Sscrofa10.2susScr3
RNF39
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11742,423,486 - 42,429,631 (+)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl1742,424,126 - 42,428,787 (+)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_02366604429,725,245 - 29,731,196 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Rnf39
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_00462475425,331,070 - 25,335,153 (+)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_00462475425,331,126 - 25,348,957 (+)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in RNF39
21 total Variants

Clinical Variants
Name Type Condition(s) Position(s) Clinical significance
GRCh38/hg38 6p22.3-21.33(chr6:18120520-30767516)x1 copy number loss Developmental Delay and additional significant developmental and morphological phenotypes referred for genetic testing [RCV000052180]|Developmental delay and additional significant developmental and morphological phenotypes referred for genetic testing [RCV000052180]|See cases [RCV000052180] Chr6:18120520..30767516 [GRCh38]
Chr6:18120751..30735293 [GRCh37]
Chr6:18228730..30843272 [NCBI36]
Chr6:6p22.3-21.33		 pathogenic
NM_021959.2(PPP1R11):c.361C>T (p.Pro121Ser) single nucleotide variant Malignant melanoma [RCV000061381] Chr6:30069286 [GRCh38]
Chr6:30037063 [GRCh37]
Chr6:30145042 [NCBI36]
Chr6:6p22.1		 not provided
NM_021959.2(PPP1R11):c.332C>T (p.Pro111Leu) single nucleotide variant Malignant melanoma [RCV000067266] Chr6:30069257 [GRCh38]
Chr6:30037034 [GRCh37]
Chr6:30145013 [NCBI36]
Chr6:6p22.1		 not provided
GRCh38/hg38 6p25.2-21.33(chr6:3224310-30657190)x3 copy number gain See cases [RCV000138956] Chr6:3224310..30657190 [GRCh38]
Chr6:3224544..30624967 [GRCh37]
Chr6:3169543..30732946 [NCBI36]
Chr6:6p25.2-21.33		 pathogenic
GRCh38/hg38 6p25.3-12.3(chr6:156974-46789291)x3 copy number gain See cases [RCV000143497] Chr6:156974..46789291 [GRCh38]
Chr6:156974..46757028 [GRCh37]
Chr6:101974..46864987 [NCBI36]
Chr6:6p25.3-12.3		 pathogenic
chr6:29910378..30075843 complex variant complex Breast ductal adenocarcinoma [RCV000207211] Chr6:29910378..30075843 [GRCh37]
Chr6:6p22.1		 uncertain significance
GRCh37/hg19 6p25.3-q27(chr6:156975-170919482)x3 copy number gain See cases [RCV000512067] Chr6:156975..170919482 [GRCh37]
Chr6:6p25.3-q27		 pathogenic
GRCh37/hg19 6p25.3-q27(chr6:156975-170919482) copy number gain See cases [RCV000510595] Chr6:156975..170919482 [GRCh37]
Chr6:6p25.3-q27		 pathogenic
GRCh37/hg19 6p22.1-q14.1(chr6:29455465-81447367) copy number gain not provided [RCV000767714] Chr6:29455465..81447367 [GRCh37]
Chr6:6p22.1-q14.1		 pathogenic
GRCh37/hg19 6p25.3-q27(chr6:60107-171054786)x3 copy number gain not provided [RCV000745400] Chr6:60107..171054786 [GRCh37]
Chr6:6p25.3-q27		 pathogenic
GRCh37/hg19 6p25.3-q27(chr6:165632-170919470)x3 copy number gain not provided [RCV000745404] Chr6:165632..170919470 [GRCh37]
Chr6:6p25.3-q27		 pathogenic
GRCh37/hg19 6p25.3-q27(chr6:108666-170980171)x3 copy number gain not provided [RCV000745403] Chr6:108666..170980171 [GRCh37]
Chr6:6p25.3-q27		 pathogenic
GRCh37/hg19 6p22.1-21.32(chr6:28130359-32108367)x3 copy number gain not provided [RCV000745592] Chr6:28130359..32108367 [GRCh37]
Chr6:6p22.1-21.32		 uncertain significance
GRCh37/hg19 6p22.1(chr6:29730504-30202199)x3 copy number gain not provided [RCV002473460] Chr6:29730504..30202199 [GRCh37]
Chr6:6p22.1		 uncertain significance
GRCh37/hg19 6p22.1(chr6:29162783-30236331)x3 copy number gain not provided [RCV002472477] Chr6:29162783..30236331 [GRCh37]
Chr6:6p22.1		 uncertain significance
NC_000006.11:g.28005012_31683185del deletion Megacolon [RCV001290055] Chr6:28005012..31683185 [GRCh37]
Chr6:6p22.1-21.33		 likely pathogenic
NM_025236.4(RNF39):c.-131C>T single nucleotide variant not specified [RCV004317995] Chr6:30075716 [GRCh38]
Chr6:30043493 [GRCh37]
Chr6:6p22.1		 uncertain significance
NM_025236.4(RNF39):c.1025G>C (p.Arg342Pro) single nucleotide variant not specified [RCV004300744] Chr6:30071145 [GRCh38]
Chr6:30038922 [GRCh37]
Chr6:6p22.1		 uncertain significance
NM_025236.4(RNF39):c.937G>A (p.Gly313Ser) single nucleotide variant not specified [RCV004214974] Chr6:30071233 [GRCh38]
Chr6:30039010 [GRCh37]
Chr6:6p22.1		 uncertain significance
NM_025236.4(RNF39):c.1042G>C (p.Val348Leu) single nucleotide variant not specified [RCV004205635] Chr6:30071128 [GRCh38]
Chr6:30038905 [GRCh37]
Chr6:6p22.1		 uncertain significance
NM_025236.4(RNF39):c.271C>G (p.Leu91Val) single nucleotide variant not specified [RCV004115484] Chr6:30075315 [GRCh38]
Chr6:30043092 [GRCh37]
Chr6:6p22.1		 uncertain significance
NM_025236.4(RNF39):c.-47C>A single nucleotide variant not specified [RCV004113034] Chr6:30075632 [GRCh38]
Chr6:30043409 [GRCh37]
Chr6:6p22.1		 uncertain significance
NM_025236.4(RNF39):c.986G>A (p.Gly329Glu) single nucleotide variant not specified [RCV004164383] Chr6:30071184 [GRCh38]
Chr6:30038961 [GRCh37]
Chr6:6p22.1		 uncertain significance
NM_025236.3(RNF39):c.18G>C (p.Leu6Phe) single nucleotide variant not specified [RCV004226527] Chr6:30075772 [GRCh38]
Chr6:30043549 [GRCh37]
Chr6:6p22.1		 uncertain significance
NM_025236.4(RNF39):c.-17C>G single nucleotide variant not specified [RCV004234430] Chr6:30075602 [GRCh38]
Chr6:30043379 [GRCh37]
Chr6:6p22.1		 uncertain significance
NM_025236.4(RNF39):c.443A>T (p.Tyr148Phe) single nucleotide variant not specified [RCV004205541] Chr6:30073192 [GRCh38]
Chr6:30040969 [GRCh37]
Chr6:6p22.1		 uncertain significance
NM_025236.4(RNF39):c.353T>C (p.Leu118Pro) single nucleotide variant not specified [RCV004155276] Chr6:30075233 [GRCh38]
Chr6:30043010 [GRCh37]
Chr6:6p22.1		 likely benign
NM_025236.4(RNF39):c.-23C>A single nucleotide variant not specified [RCV004132561] Chr6:30075608 [GRCh38]
Chr6:30043385 [GRCh37]
Chr6:6p22.1		 uncertain significance
NM_025236.4(RNF39):c.542G>A (p.Ser181Asn) single nucleotide variant not specified [RCV004168781] Chr6:30071628 [GRCh38]
Chr6:30039405 [GRCh37]
Chr6:6p22.1		 uncertain significance
NM_025236.4(RNF39):c.715G>C (p.Glu239Gln) single nucleotide variant not specified [RCV004258784] Chr6:30071455 [GRCh38]
Chr6:30039232 [GRCh37]
Chr6:6p22.1		 uncertain significance
NM_025236.4(RNF39):c.253G>A (p.Val85Met) single nucleotide variant not specified [RCV004274294] Chr6:30075333 [GRCh38]
Chr6:30043110 [GRCh37]
Chr6:6p22.1		 uncertain significance
NM_025236.4(RNF39):c.-132G>T single nucleotide variant not specified [RCV004317994] Chr6:30075717 [GRCh38]
Chr6:30043494 [GRCh37]
Chr6:6p22.1		 uncertain significance
NM_025236.4(RNF39):c.983T>C (p.Leu328Pro) single nucleotide variant not specified [RCV004347772] Chr6:30071187 [GRCh38]
Chr6:30038964 [GRCh37]
Chr6:6p22.1		 uncertain significance
NM_025236.4(RNF39):c.736G>A (p.Gly246Ser) single nucleotide variant not specified [RCV004362299] Chr6:30071434 [GRCh38]
Chr6:30039211 [GRCh37]
Chr6:6p22.1		 uncertain significance
NM_025236.4(RNF39):c.872A>G (p.Glu291Gly) single nucleotide variant not provided [RCV003428776] Chr6:30071298 [GRCh38]
Chr6:30039075 [GRCh37]
Chr6:6p22.1		 likely benign
NM_025236.4(RNF39):c.900C>T (p.Asp300=) single nucleotide variant not provided [RCV003431707] Chr6:30071270 [GRCh38]
Chr6:30039047 [GRCh37]
Chr6:6p22.1		 likely benign
NM_025236.4(RNF39):c.242T>G (p.Leu81Arg) single nucleotide variant not specified [RCV004446749] Chr6:30075344 [GRCh38]
Chr6:30043121 [GRCh37]
Chr6:6p22.1		 uncertain significance
NM_025236.4(RNF39):c.250G>C (p.Glu84Gln) single nucleotide variant not specified [RCV004446750] Chr6:30075336 [GRCh38]
Chr6:30043113 [GRCh37]
Chr6:6p22.1		 uncertain significance
NM_025236.4(RNF39):c.460A>G (p.Met154Val) single nucleotide variant not specified [RCV004446751] Chr6:30073175 [GRCh38]
Chr6:30040952 [GRCh37]
Chr6:6p22.1		 uncertain significance
NM_025236.4(RNF39):c.610G>C (p.Ala204Pro) single nucleotide variant not specified [RCV004446752] Chr6:30071560 [GRCh38]
Chr6:30039337 [GRCh37]
Chr6:6p22.1		 uncertain significance
NM_025236.4(RNF39):c.1031C>T (p.Pro344Leu) single nucleotide variant not specified [RCV004446748] Chr6:30071139 [GRCh38]
Chr6:30038916 [GRCh37]
Chr6:6p22.1		 uncertain significance
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:1251
Count of miRNA genes:329
Interacting mature miRNAs:348
Transcripts:ENST00000244360, ENST00000376751
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.

Markers in Region
G31541  
Human AssemblyChrPosition (strand)SourceJBrowse
GRCh37630,038,717 - 30,038,828UniSTSGRCh37
Build 36630,146,696 - 30,146,807RGDNCBI36
Celera631,636,970 - 31,637,081RGD
Cytogenetic Map6p21.3UniSTS
HuRef629,836,889 - 29,837,000UniSTS
RH99256  
Human AssemblyChrPosition (strand)SourceJBrowse
GRCh37630,041,144 - 30,041,302UniSTSGRCh37
Build 36630,149,123 - 30,149,281RGDNCBI36
Celera631,639,397 - 31,639,555RGD
Cytogenetic Map6p21.3UniSTS
HuRef629,839,316 - 29,839,474UniSTS
GeneMap99-GB4 RH Map6117.14UniSTS
RNF39_1552.2  
Human AssemblyChrPosition (strand)SourceJBrowse
GRCh37630,038,029 - 30,038,779UniSTSGRCh37
Build 36630,146,008 - 30,146,758RGDNCBI36
Celera631,636,282 - 31,637,032RGD
HuRef629,836,201 - 29,836,951UniSTS
G29206  
Human AssemblyChrPosition (strand)SourceJBrowse
GRCh37630,037,875 - 30,038,014UniSTSGRCh37
Build 36630,145,854 - 30,145,993RGDNCBI36
Celera631,636,128 - 31,636,267RGD
Cytogenetic Map6p21.3UniSTS
HuRef629,836,047 - 29,836,186UniSTS
STS-R63837  
Human AssemblyChrPosition (strand)SourceJBrowse
GRCh37630,041,559 - 30,041,681UniSTSGRCh37
Build 36630,149,538 - 30,149,660RGDNCBI36
Celera631,639,812 - 31,639,934RGD
Cytogenetic Map6p21.3UniSTS
HuRef629,839,731 - 29,839,853UniSTS
GeneMap99-GB4 RH Map6117.03UniSTS
NCBI RH Map6396.6UniSTS
STS-W44579  
Human AssemblyChrPosition (strand)SourceJBrowse
GRCh37630,037,733 - 30,037,892UniSTSGRCh37
Build 36630,145,712 - 30,145,871RGDNCBI36
Celera631,635,986 - 31,636,145RGD
Cytogenetic Map6p21.3UniSTS
HuRef629,835,905 - 29,836,064UniSTS
GeneMap99-GB4 RH Map6117.03UniSTS
NCBI RH Map6396.6UniSTS


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 sensory system adipose tissue appendage entire extraembryonic component
High
Medium 98 2 8 153 11 8 1317 4 16 23 387 80 148 12 699
Low 2022 1689 1250 134 1244 121 2090 930 3311 241 1029 1392 22 885 1387 3
Below cutoff 308 1278 452 326 635 326 942 1236 377 147 30 120 307 701 1

Sequence

Nucleotide Sequences
RefSeq Transcripts NM_025236 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  NM_170769 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017011325 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017011326 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_054328523 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_054329914 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_054330406 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_054330685 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_054330899 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_054331419 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_054356472 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
GenBank Nucleotide AB088087 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AB202082 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AF238315 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AF238316 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AF238317 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AL669914 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AL671859 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AL845439 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  BA000025 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  BX088647 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  BX927229 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CA311242 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CH471081 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CP068272 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CR388205 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CR759763 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CR759960 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CR933538 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  KY500606 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  KY500607 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  KY500608 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  KY500609 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  KY500610 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  KY500611 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  KY500612 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  KY500613 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  KY500614 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles

Reference Sequences
RefSeq Acc Id: ENST00000244360   ⟹   ENSP00000244360
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl630,070,270 - 30,075,769 (-)Ensembl
RefSeq Acc Id: ENST00000376751   ⟹   ENSP00000365942
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl630,070,266 - 30,075,849 (-)Ensembl
RefSeq Acc Id: NM_025236   ⟹   NP_079512
RefSeq Status: VALIDATED
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38630,070,270 - 30,075,769 (-)NCBI
GRCh37630,038,043 - 30,043,628 (-)RGD
Build 36630,146,022 - 30,151,607 (-)NCBI Archive
Celera631,636,296 - 31,641,881 (-)RGD
HuRef629,836,215 - 29,841,800 (-)RGD
CHM1_1630,040,092 - 30,045,677 (-)NCBI
T2T-CHM13v2.0629,934,544 - 29,940,043 (-)NCBI
Sequence:
RefSeq Acc Id: NM_170769   ⟹   NP_739575
RefSeq Status: VALIDATED
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38630,070,270 - 30,075,769 (-)NCBI
GRCh37630,038,043 - 30,043,628 (-)RGD
Build 36630,146,022 - 30,151,607 (-)NCBI Archive
Celera631,636,296 - 31,641,881 (-)RGD
HuRef629,836,215 - 29,841,800 (-)RGD
CHM1_1630,040,092 - 30,045,675 (-)NCBI
T2T-CHM13v2.0629,934,544 - 29,940,043 (-)NCBI
Sequence:
RefSeq Acc Id: XM_017011325   ⟹   XP_016866814
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38630,070,270 - 30,075,769 (-)NCBI
Sequence:
RefSeq Acc Id: XM_054356472   ⟹   XP_054212447
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
T2T-CHM13v2.0629,934,544 - 29,940,043 (-)NCBI
Protein Sequences
Protein RefSeqs NP_079512 (Get FASTA)   NCBI Sequence Viewer  
  NP_739575 (Get FASTA)   NCBI Sequence Viewer  
  XP_016866814 (Get FASTA)   NCBI Sequence Viewer  
  XP_054184498 (Get FASTA)   NCBI Sequence Viewer  
  XP_054185889 (Get FASTA)   NCBI Sequence Viewer  
  XP_054186381 (Get FASTA)   NCBI Sequence Viewer  
  XP_054186660 (Get FASTA)   NCBI Sequence Viewer  
  XP_054186874 (Get FASTA)   NCBI Sequence Viewer  
  XP_054187394 (Get FASTA)   NCBI Sequence Viewer  
  XP_054212447 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein AAG40628 (Get FASTA)   NCBI Sequence Viewer  
  AAG40629 (Get FASTA)   NCBI Sequence Viewer  
  AAG40630 (Get FASTA)   NCBI Sequence Viewer  
  AQY77078 (Get FASTA)   NCBI Sequence Viewer  
  AQY77079 (Get FASTA)   NCBI Sequence Viewer  
  AQY77080 (Get FASTA)   NCBI Sequence Viewer  
  AQY77081 (Get FASTA)   NCBI Sequence Viewer  
  AQY77082 (Get FASTA)   NCBI Sequence Viewer  
  AQY77083 (Get FASTA)   NCBI Sequence Viewer  
  AQY77084 (Get FASTA)   NCBI Sequence Viewer  
  AQY77085 (Get FASTA)   NCBI Sequence Viewer  
  AQY77086 (Get FASTA)   NCBI Sequence Viewer  
  BAB63333 (Get FASTA)   NCBI Sequence Viewer  
  BAC54920 (Get FASTA)   NCBI Sequence Viewer  
  BAE78602 (Get FASTA)   NCBI Sequence Viewer  
  EAX03255 (Get FASTA)   NCBI Sequence Viewer  
  EAX03256 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSP00000244360
  ENSP00000244360.7
  ENSP00000365941.2
  ENSP00000365942
  ENSP00000365942.4
  ENSP00000373106.2
  ENSP00000387930.2
  ENSP00000391822.2
  ENSP00000392508.2
  ENSP00000393560.2
  ENSP00000395696.2
  ENSP00000398512.2
  ENSP00000401131.2
  ENSP00000405340.2
  ENSP00000407248.2
  ENSP00000407291.2
  ENSP00000408539.2
  ENSP00000415281.2
GenBank Protein Q9H2S5 (Get FASTA)   NCBI Sequence Viewer  
Reference Protein Sequences
RefSeq Acc Id: NP_079512   ⟸   NM_025236
- Peptide Label: isoform 1
- UniProtKB: Q9H2S5 (UniProtKB/Swiss-Prot),   Q9H2S4 (UniProtKB/Swiss-Prot),   Q9H2S3 (UniProtKB/Swiss-Prot),   Q5SS29 (UniProtKB/Swiss-Prot),   Q5SRK1 (UniProtKB/Swiss-Prot),   Q5SRJ9 (UniProtKB/Swiss-Prot),   Q5SPN0 (UniProtKB/Swiss-Prot),   Q5SPM9 (UniProtKB/Swiss-Prot),   Q5SPM8 (UniProtKB/Swiss-Prot),   B0S858 (UniProtKB/Swiss-Prot),   A6NCD6 (UniProtKB/Swiss-Prot),   A2BEK3 (UniProtKB/Swiss-Prot),   Q96QB5 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: NP_739575   ⟸   NM_170769
- Peptide Label: isoform 2
- UniProtKB: A0A1U9X8G2 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_016866814   ⟸   XM_017011325
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: ENSP00000244360   ⟸   ENST00000244360
RefSeq Acc Id: ENSP00000365942   ⟸   ENST00000376751
RefSeq Acc Id: XP_054212447   ⟸   XM_054356472
- Peptide Label: isoform X1
Protein Domains
B30.2/SPRY   RING-type

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-Q9H2S5-F1-model_v2 AlphaFold Q9H2S5 1-420 view protein structure

Promoters
RGD ID:6872352
Promoter ID:EPDNEW_H9341
Type:initiation region
Name:RNF39_1
Description:ring finger protein 39
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Experiment Methods:Single-end sequencing.
Position:
Human AssemblyChrPosition (strand)Source
GRCh38630,075,769 - 30,075,829EPDNEW
RGD ID:6813068
Promoter ID:HG_ACW:67893
Type:CpG-Island
SO ACC ID:SO:0000170
Source:MPROMDB
Tissues & Cell Lines:CD4+TCell,   Lymphoblastoid
Transcripts:RNF39.CAPR07-UNSPLICED,   SPAKLUBU.AAPR07-UNSPLICED,   SPYKLUBU.AAPR07-UNSPLICED
Position:
Human AssemblyChrPosition (strand)Source
Build 36630,146,904 - 30,147,404 (-)MPROMDB
RGD ID:6804622
Promoter ID:HG_KWN:52795
Type:CpG-Island
SO ACC ID:SO:0000170
Source:MPROMDB
Tissues & Cell Lines:HeLa_S3
Transcripts:ENST00000376746,   OTTHUMT00000076625,   OTTHUMT00000076626
Position:
Human AssemblyChrPosition (strand)Source
Build 36630,151,496 - 30,151,996 (-)MPROMDB

Additional Information

Database Acc Id Source(s)
AGR Gene HGNC:18064 AgrOrtholog
COSMIC RNF39 COSMIC
Ensembl Genes ENSG00000204618 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot
  ENSG00000206500 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  ENSG00000227171 UniProtKB/Swiss-Prot
  ENSG00000230332 UniProtKB/Swiss-Prot
  ENSG00000230467 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  ENSG00000235022 UniProtKB/Swiss-Prot
  ENSG00000236967 UniProtKB/Swiss-Prot
  ENSG00000237733 UniProtKB/Swiss-Prot
Ensembl Transcript ENST00000244360 ENTREZGENE
  ENST00000244360.8 UniProtKB/Swiss-Prot
  ENST00000376750.6 UniProtKB/Swiss-Prot
  ENST00000376751 ENTREZGENE
  ENST00000376751.8 UniProtKB/Swiss-Prot
  ENST00000383611.2 UniProtKB/TrEMBL
  ENST00000417541.6 UniProtKB/Swiss-Prot
  ENST00000420562.2 UniProtKB/TrEMBL
  ENST00000425956.6 UniProtKB/Swiss-Prot
  ENST00000432647.2 UniProtKB/Swiss-Prot
  ENST00000441449.6 UniProtKB/Swiss-Prot
  ENST00000442063.2 UniProtKB/Swiss-Prot
  ENST00000442378.2 UniProtKB/Swiss-Prot
  ENST00000449145.2 UniProtKB/Swiss-Prot
  ENST00000450015.2 UniProtKB/Swiss-Prot
  ENST00000451425.6 UniProtKB/Swiss-Prot
  ENST00000456156.6 UniProtKB/Swiss-Prot
  ENST00000457092.6 UniProtKB/Swiss-Prot
Gene3D-CATH 2.60.120.920 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  3.30.40.10 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
GTEx ENSG00000204618 GTEx
  ENSG00000206500 GTEx
  ENSG00000227171 GTEx
  ENSG00000230332 GTEx
  ENSG00000230467 GTEx
  ENSG00000235022 GTEx
  ENSG00000236967 GTEx
  ENSG00000237733 GTEx
HGNC ID HGNC:18064 ENTREZGENE
Human Proteome Map RNF39 Human Proteome Map
InterPro B30.2/SPRY UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  B30.2/SPRY_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Butyrophylin_SPRY UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  ConA-like_dom_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  PRY UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SPRY_dom UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Znf-RING_euk UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Znf_RING UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Znf_RING/FYVE/PHD UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Znf_RING_CS UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report hsa:80352 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
NCBI Gene 80352 ENTREZGENE
OMIM 607524 OMIM
PANTHER E3 UBIQUITIN-PROTEIN LIGASE TRIM UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  RING FINGER PROTEIN 39 UniProtKB/TrEMBL
  RING-TYPE DOMAIN-CONTAINING PROTEIN UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Pfam PRY UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SPRY UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  zf-RING_UBOX UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PharmGKB PA134949953 PharmGKB
PRINTS BUTYPHLNCDUF UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PROSITE B302_SPRY UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  ZF_RING_1 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  ZF_RING_2 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
SMART PRY UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  RING UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SPRY UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Superfamily-SCOP RING/U-box UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SSF49899 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniProt A0A140T8Y9_HUMAN UniProtKB/TrEMBL
  A0A140T901_HUMAN UniProtKB/TrEMBL
  A0A1U9X8G2 ENTREZGENE, UniProtKB/TrEMBL
  A2BEK3 ENTREZGENE
  A6NCD6 ENTREZGENE
  B0S858 ENTREZGENE
  Q2L6J4_HUMAN UniProtKB/TrEMBL
  Q5SPM8 ENTREZGENE
  Q5SPM9 ENTREZGENE
  Q5SPN0 ENTREZGENE
  Q5SRJ9 ENTREZGENE
  Q5SRK1 ENTREZGENE
  Q5SS29 ENTREZGENE
  Q96QB5 ENTREZGENE, UniProtKB/TrEMBL
  Q9H2S3 ENTREZGENE
  Q9H2S4 ENTREZGENE
  Q9H2S5 ENTREZGENE, UniProtKB/Swiss-Prot
UniProt Secondary A2BEK3 UniProtKB/Swiss-Prot
  A6NCD6 UniProtKB/Swiss-Prot
  B0S858 UniProtKB/Swiss-Prot
  Q5SPM8 UniProtKB/Swiss-Prot
  Q5SPM9 UniProtKB/Swiss-Prot
  Q5SPN0 UniProtKB/Swiss-Prot
  Q5SRJ9 UniProtKB/Swiss-Prot
  Q5SRK1 UniProtKB/Swiss-Prot
  Q5SS29 UniProtKB/Swiss-Prot
  Q9H2S3 UniProtKB/Swiss-Prot
  Q9H2S4 UniProtKB/Swiss-Prot