RAB39A (RAB39A, member RAS oncogene family) - Rat Genome Database

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Gene: RAB39A (RAB39A, member RAS oncogene family) Homo sapiens
Analyze
Symbol: RAB39A
Name: RAB39A, member RAS oncogene family
RGD ID: 1322661
HGNC Page HGNC
Description: Predicted to have GTPase activity. Involved in phagosome acidification and phagosome-lysosome fusion. Localizes to phagocytic vesicle; INTERACTS WITH acrylamide; benzo[a]pyrene; silicon dioxide.
Type: protein-coding
RefSeq Status: VALIDATED
Also known as: rab-39; rab-related GTP-binding protein; RAB39; RAB39, member RAS oncogene family; ras-related protein Rab-39A
RGD Orthologs
Mouse
Rat
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Allele / Splice: See ClinVar data
Latest Assembly: GRCh38 - Human Genome Assembly GRCh38
Position:
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl11107,928,448 - 107,963,482 (+)EnsemblGRCh38hg38GRCh38
GRCh3811107,928,448 - 107,963,482 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh3711107,799,174 - 107,834,208 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 3611107,304,487 - 107,339,418 (+)NCBINCBI36hg18NCBI36
Build 3411107,304,486 - 107,339,416NCBI
Celera11104,953,680 - 104,988,614 (+)NCBI
Cytogenetic Map11q22.3NCBI
HuRef11103,724,396 - 103,759,321 (+)NCBIHuRef
CHM1_111107,682,503 - 107,717,462 (+)NCBICHM1_1
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View

Gene-Chemical Interaction 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
1. GOA_HUMAN data from the GO Consortium
2. RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:9119394   PMID:12477932   PMID:15489334   PMID:16923123   PMID:19833722   PMID:20379614   PMID:21255211   PMID:21832049   PMID:21873635   PMID:23246001   PMID:24349490   PMID:25416956  
PMID:26163492   PMID:26186194   PMID:26824392   PMID:26841866   PMID:26972000   PMID:27103069   PMID:27173435   PMID:27494456   PMID:29449217   PMID:29648608   PMID:29845934   PMID:30021884  
PMID:31073040   PMID:31091453   PMID:32296183  


Genomics

Comparative Map Data
RAB39A
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl11107,928,448 - 107,963,482 (+)EnsemblGRCh38hg38GRCh38
GRCh3811107,928,448 - 107,963,482 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh3711107,799,174 - 107,834,208 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 3611107,304,487 - 107,339,418 (+)NCBINCBI36hg18NCBI36
Build 3411107,304,486 - 107,339,416NCBI
Celera11104,953,680 - 104,988,614 (+)NCBI
Cytogenetic Map11q22.3NCBI
HuRef11103,724,396 - 103,759,321 (+)NCBIHuRef
CHM1_111107,682,503 - 107,717,462 (+)NCBICHM1_1
Rab39
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39953,595,410 - 53,617,532 (-)NCBIGRCm39mm39
GRCm39 Ensembl953,595,410 - 53,617,532 (-)Ensembl
GRCm38953,684,110 - 53,706,232 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl953,684,110 - 53,706,232 (-)EnsemblGRCm38mm10GRCm38
MGSCv37953,492,215 - 53,514,337 (-)NCBIGRCm37mm9NCBIm37
MGSCv36953,446,505 - 53,468,627 (-)NCBImm8
Celera950,943,745 - 50,965,823 (-)NCBICelera
Cytogenetic Map9A5.3NCBI
Rab39a
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2854,088,744 - 54,105,756 (-)NCBI
Rnor_6.0 Ensembl858,272,098 - 58,293,102 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.0858,275,984 - 58,292,995 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.0856,857,848 - 56,874,859 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4857,153,452 - 57,173,146 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1857,175,070 - 57,228,689 (-)NCBI
Celera853,579,185 - 53,596,351 (-)NCBICelera
Cytogenetic Map8q24NCBI
Rab39a
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495541210,224,074 - 10,240,270 (+)EnsemblChiLan1.0
ChiLan1.0NW_00495541210,224,074 - 10,240,270 (+)NCBIChiLan1.0ChiLan1.0
RAB39A
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.111106,291,348 - 106,326,587 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl11106,291,348 - 106,326,587 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v011102,814,825 - 102,851,700 (+)NCBIMhudiblu_PPA_v0panPan3
RAB39A
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1524,516,541 - 24,546,743 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl524,519,240 - 24,546,606 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha524,440,396 - 24,472,421 (-)NCBI
ROS_Cfam_1.0524,543,996 - 24,576,058 (-)NCBI
UMICH_Zoey_3.1524,591,329 - 24,623,183 (-)NCBI
UNSW_CanFamBas_1.0524,492,978 - 24,524,815 (-)NCBI
UU_Cfam_GSD_1.0524,551,508 - 24,583,580 (-)NCBI
Rab39a
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440494790,758,066 - 90,785,866 (+)NCBI
SpeTri2.0NW_004936551750,940 - 778,432 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
RAB39A
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl936,341,339 - 36,403,696 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1936,341,339 - 36,403,690 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2940,452,457 - 40,480,041 (+)NCBISscrofa10.2Sscrofa10.2susScr3
RAB39A
(Chlorocebus sabaeus - African green monkey)
Vervet AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1199,353,125 - 99,388,429 (+)NCBI
ChlSab1.1 Ensembl199,353,210 - 99,387,262 (+)Ensembl
Rab39a
(Heterocephalus glaber - naked mole-rat)
Molerat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046247842,679,281 - 2,709,514 (+)NCBI

Position Markers
D11S1828  
Human AssemblyChrPosition (strand)SourceJBrowse
GRCh3711107,827,391 - 107,827,478UniSTSGRCh37
Build 3611107,332,601 - 107,332,688RGDNCBI36
Celera11104,981,797 - 104,981,884RGD
Cytogenetic Map11q22.3UniSTS
HuRef11103,752,504 - 103,752,591UniSTS
RAB39_2302  
Human AssemblyChrPosition (strand)SourceJBrowse
GRCh3711107,833,552 - 107,834,281UniSTSGRCh37
Build 3611107,338,762 - 107,339,491RGDNCBI36
Celera11104,987,958 - 104,988,687RGD
HuRef11103,758,665 - 103,759,394UniSTS

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:429
Count of miRNA genes:341
Interacting mature miRNAs:359
Transcripts:ENST00000320578
Prediction methods:Miranda, Rnahybrid
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.


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 visual system adipose tissue appendage entire extraembryonic component pharyngeal arch
High
Medium 8 1 4 2 64 2 168 11 55 1 14 86
Low 426 493 465 112 1051 84 954 145 2176 151 577 584 32 1 653 434 6 2
Below cutoff 1804 2101 1031 396 725 270 2572 1571 1460 228 688 785 128 537 1869

Sequence


Reference Sequences
RefSeq Acc Id: ENST00000320578   ⟹   ENSP00000322594
RefSeq Status:
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p13 Ensembl11107,928,448 - 107,963,482 (+)Ensembl
RefSeq Acc Id: NM_017516   ⟹   NP_059986
RefSeq Status: VALIDATED
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh3811107,928,448 - 107,963,482 (+)NCBI
GRCh3711107,799,277 - 107,834,208 (+)RGD
Build 3611107,304,487 - 107,339,418 (+)NCBI Archive
Celera11104,953,680 - 104,988,614 (+)RGD
HuRef11103,724,396 - 103,759,321 (+)ENTREZGENE
CHM1_111107,682,503 - 107,717,462 (+)NCBI
Sequence:
Protein Sequences
Protein RefSeqs NP_059986 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein AAH28064 (Get FASTA)   NCBI Sequence Viewer  
  BAF85658 (Get FASTA)   NCBI Sequence Viewer  
  CAA68227 (Get FASTA)   NCBI Sequence Viewer  
  EAW67100 (Get FASTA)   NCBI Sequence Viewer  
  Q14964 (Get FASTA)   NCBI Sequence Viewer  
Reference Sequences
RefSeq Acc Id: NP_059986   ⟸   NM_017516
- UniProtKB: Q14964 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: ENSP00000322594   ⟸   ENST00000320578

Promoters
RGD ID:6789428
Promoter ID:HG_KWN:14107
Type:CpG-Island
SO ACC ID:SO:0000170
Source:MPROMDB
Tissues & Cell Lines:Lymphoblastoid
Transcripts:NM_017516,   UC001PJR.1
Position:
Human AssemblyChrPosition (strand)Source
Build 3611107,304,021 - 107,304,542 (-)MPROMDB
RGD ID:7222003
Promoter ID:EPDNEW_H16747
Type:initiation region
Name:RAB39A_1
Description:RAB39A, member RAS oncogene family
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Alternative Promoters:null; see alsoEPDNEW_H16748  
Experiment Methods:Single-end sequencing.; Paired-end sequencing.
Position:
Human AssemblyChrPosition (strand)Source
GRCh3811107,928,448 - 107,928,508EPDNEW
RGD ID:7222005
Promoter ID:EPDNEW_H16748
Type:initiation region
Name:RAB39A_2
Description:RAB39A, member RAS oncogene family
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Alternative Promoters:null; see alsoEPDNEW_H16747  
Experiment Methods:Single-end sequencing.
Position:
Human AssemblyChrPosition (strand)Source
GRCh3811107,928,552 - 107,928,612EPDNEW

Clinical Variants
Name Type Condition(s) Position(s) Clinical significance
GRCh38/hg38 11q22.1-25(chr11:100348599-135040246)x3 copy number gain See cases [RCV000053638] Chr11:100348599..135040246 [GRCh38]
Chr11:100219331..134910140 [GRCh37]
Chr11:99724541..134415350 [NCBI36]
Chr11:11q22.1-25
pathogenic
GRCh38/hg38 11q22.3(chr11:107479091-108222532)x1 copy number loss See cases [RCV000136500] Chr11:107479091..108222532 [GRCh38]
Chr11:107349817..108093259 [GRCh37]
Chr11:106855027..107598469 [NCBI36]
Chr11:11q22.3
pathogenic
GRCh38/hg38 11q14.3-22.3(chr11:91086659-109595582)x1 copy number loss See cases [RCV000138038] Chr11:91086659..109595582 [GRCh38]
Chr11:90819827..109466308 [GRCh37]
Chr11:90459475..108971518 [NCBI36]
Chr11:11q14.3-22.3
pathogenic
GRCh38/hg38 11q22.3(chr11:107656034-107998014)x3 copy number gain See cases [RCV000139982] Chr11:107656034..107998014 [GRCh38]
Chr11:107526760..107868740 [GRCh37]
Chr11:107031970..107373950 [NCBI36]
Chr11:11q22.3
likely benign
GRCh37/hg19 11q22.3(chr11:107554267-108004957)x3 copy number gain Premature ovarian failure [RCV000225269] Chr11:107554267..108004957 [GRCh37]
Chr11:11q22.3
benign
GRCh37/hg19 11q22.3(chr11:107537962-107950512)x3 copy number gain See cases [RCV000449345] Chr11:107537962..107950512 [GRCh37]
Chr11:11q22.3
likely benign
GRCh37/hg19 11q22.3(chr11:107537206-107925627)x3 copy number gain See cases [RCV000448378] Chr11:107537206..107925627 [GRCh37]
Chr11:11q22.3
likely benign
GRCh37/hg19 11q14.2-22.3(chr11:88152458-109414650)x1 copy number loss See cases [RCV000510457] Chr11:88152458..109414650 [GRCh37]
Chr11:11q14.2-22.3
pathogenic
GRCh37/hg19 11p15.5-q25(chr11:230616-134938470) copy number gain See cases [RCV000511729] Chr11:230616..134938470 [GRCh37]
Chr11:11p15.5-q25
pathogenic
GRCh37/hg19 11p15.5-q25(chr11:230616-134938470)x3 copy number gain See cases [RCV000510881] Chr11:230616..134938470 [GRCh37]
Chr11:11p15.5-q25
pathogenic
GRCh37/hg19 11q13.4-23.3(chr11:71588805-116680918)x3 copy number gain not provided [RCV000683374] Chr11:71588805..116680918 [GRCh37]
Chr11:11q13.4-23.3
pathogenic
GRCh37/hg19 11p15.5-q25(chr11:198510-134934063)x3 copy number gain not provided [RCV000737348] Chr11:198510..134934063 [GRCh37]
Chr11:11p15.5-q25
pathogenic
GRCh37/hg19 11p15.5-q25(chr11:70864-134938470)x3 copy number gain not provided [RCV000749874] Chr11:70864..134938470 [GRCh37]
Chr11:11p15.5-q25
pathogenic
GRCh37/hg19 11q14.1-23.2(chr11:80053454-113316236)x1 copy number loss not provided [RCV000737595] Chr11:80053454..113316236 [GRCh37]
Chr11:11q14.1-23.2
pathogenic
GRCh37/hg19 11q22.3(chr11:107530277-107904646)x1 copy number loss not provided [RCV000737677] Chr11:107530277..107904646 [GRCh37]
Chr11:11q22.3
benign
GRCh37/hg19 11q22.3(chr11:107753547-107943124)x3 copy number gain not provided [RCV000750197] Chr11:107753547..107943124 [GRCh37]
Chr11:11q22.3
benign
GRCh37/hg19 11q22.3(chr11:107757018-107938578)x3 copy number gain not provided [RCV000750198] Chr11:107757018..107938578 [GRCh37]
Chr11:11q22.3
benign
GRCh37/hg19 11q22.3(chr11:107799785-107933087)x3 copy number gain not provided [RCV000750200] Chr11:107799785..107933087 [GRCh37]
Chr11:11q22.3
benign
GRCh37/hg19 11q22.3(chr11:107546688-108077391)x3 copy number gain not provided [RCV000849110] Chr11:107546688..108077391 [GRCh37]
Chr11:11q22.3
uncertain significance
GRCh37/hg19 11q22.3-23.3(chr11:104101411-116680918)x1 copy number loss not provided [RCV000848741] Chr11:104101411..116680918 [GRCh37]
Chr11:11q22.3-23.3
pathogenic
GRCh37/hg19 11q22.3(chr11:107789951-107950571)x3 copy number gain not provided [RCV000845968] Chr11:107789951..107950571 [GRCh37]
Chr11:11q22.3
uncertain significance
GRCh37/hg19 11q22.3(chr11:107744785-107950571)x3 copy number gain not provided [RCV000849237] Chr11:107744785..107950571 [GRCh37]
Chr11:11q22.3
uncertain significance
GRCh37/hg19 11q22.3-23.2(chr11:103320065-114349787)x1 copy number loss not provided [RCV001006439] Chr11:103320065..114349787 [GRCh37]
Chr11:11q22.3-23.2
pathogenic
GRCh37/hg19 11q22.3-23.3(chr11:105699599-114524876)x1 copy number loss not provided [RCV001006445] Chr11:105699599..114524876 [GRCh37]
Chr11:11q22.3-23.3
pathogenic
Single allele deletion Intellectual disability [RCV001293382] Chr11:118359328..118372573 [GRCh37]
Chr11:11p15.3-q23.3
pathogenic

Additional Information

Database Acc Id Source(s)
AGR Gene HGNC:16521 AgrOrtholog
COSMIC RAB39A COSMIC
Ensembl Genes ENSG00000179331 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Protein ENSP00000322594 ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Transcript ENST00000320578 ENTREZGENE, UniProtKB/Swiss-Prot
GTEx ENSG00000179331 GTEx
HGNC ID HGNC:16521 ENTREZGENE
Human Proteome Map RAB39A Human Proteome Map
InterPro P-loop_NTPase UniProtKB/Swiss-Prot
  Rab39 UniProtKB/Swiss-Prot
  Small_GTP-bd_dom UniProtKB/Swiss-Prot
  Small_GTPase UniProtKB/Swiss-Prot
KEGG Report hsa:54734 UniProtKB/Swiss-Prot
NCBI Gene 54734 ENTREZGENE
Pfam Ras UniProtKB/Swiss-Prot
PharmGKB PA34130 PharmGKB
PROSITE RAB UniProtKB/Swiss-Prot
Superfamily-SCOP SSF52540 UniProtKB/Swiss-Prot
TIGRFAMs small_GTP UniProtKB/Swiss-Prot
UniProt Q14964 ENTREZGENE, UniProtKB/Swiss-Prot
UniProt Secondary A8KAA4 UniProtKB/Swiss-Prot
  Q8N6W2 UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2011-11-29 RAB39A  RAB39A, member RAS oncogene family  RAB39  RAB39, member RAS oncogene family  Symbol and/or name change 5135510 APPROVED