Human Gene RAB39B (ENST00000369454.4) Description and Page Index
  Description: Homo sapiens RAB39B, member RAS oncogene family (RAB39B), mRNA. (from RefSeq NM_171998)
RefSeq Summary (NM_171998): This gene encodes a member of the Rab family of proteins. Rab proteins are small GTPases that are involved in vesicular trafficking. Mutations in this gene are associated with X-linked cognitive disability. [provided by RefSeq, Aug 2013]. Publication Note: This RefSeq record includes a subset of the publications that are available for this gene. Please see the Gene record to access additional publications. ##Evidence-Data-START## Transcript exon combination :: SRR1660807.93953.1, SRR1803612.57940.1 [ECO:0000332] RNAseq introns :: single sample supports all introns SAMEA1965299, SAMEA1966682 [ECO:0000348] ##Evidence-Data-END## ##RefSeq-Attributes-START## MANE Ensembl match :: ENST00000369454.4/ ENSP00000358466.3 RefSeq Select criteria :: based on single protein-coding transcript ##RefSeq-Attributes-END##
Gencode Transcript: ENST00000369454.4
Gencode Gene: ENSG00000155961.5
Transcript (Including UTRs)
   Position: hg38 chrX:155,258,235-155,264,491 Size: 6,257 Total Exon Count: 2 Strand: -
Coding Region
   Position: hg38 chrX:155,260,803-155,264,288 Size: 3,486 Coding Exon Count: 2 

Page IndexSequence and LinksUniProtKB CommentsMalaCardsCTDRNA-Seq Expression
Microarray ExpressionRNA StructureProtein StructureOther SpeciesGO AnnotationsmRNA Descriptions
PathwaysOther NamesGeneReviewsMethods
Data last updated: 2019-09-04

-  Sequence and Links to Tools and Databases
Genomic Sequence (chrX:155,258,235-155,264,491)mRNA (may differ from genome)Protein (213 aa)
Gene SorterGenome BrowserOther Species FASTAGene interactionsTable SchemaBioGPS
CGAPEnsemblEntrez GeneExonPrimerGeneCardsHGNC
ReactomeStanford SOURCEUniProtKBWikipedia

-  Comments and Description Text from UniProtKB
DESCRIPTION: RecName: Full=Ras-related protein Rab-39B;
FUNCTION: May be involved in vesicular trafficking. Plays a role in synapse formation (By similarity).
SUBCELLULAR LOCATION: Cell membrane; Lipid-anchor; Cytoplasmic side (Potential). Golgi apparatus. Note=Partial colocalization with markers that cycle from the cell surface to the trans-Golgi network (By similarity).
TISSUE SPECIFICITY: Highly expressed in the brain.
DISEASE: Defects in RAB39B are the cause of mental retardation X- linked type 72 (MRX72) [MIM:300271]. Mental retardation is characterized by significantly below average general intellectual functioning associated with impairments in adaptative behavior and manifested during the developmental period. MRX72 patients can manifest autism spectrum disorder, seizures and macrocephaly as additional features.
SIMILARITY: Belongs to the small GTPase superfamily. Rab family.

-  MalaCards Disease Associations
  MalaCards Gene Search: RAB39B
Diseases sorted by gene-association score: waisman syndrome* (1739), x-linked non-specific intellectual disability* (202), early-onset parkinson disease (20), chromosomal duplication syndrome (9), frontotemporal dementia and/or amyotrophic lateral sclerosis 1 (4), intellectual disability (2), autism spectrum disorder (1)
* = Manually curated disease association

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 9.11 RPKM in Brain - Cerebellar Hemisphere
Total median expression: 94.29 RPKM

View in GTEx track of Genome Browser    View at GTEx portal     View GTEx Body Map

+  Microarray Expression Data
  Press "+" in the title bar above to open this section.

-  mRNA Secondary Structure of 3' and 5' UTRs
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -87.70203-0.432 Picture PostScript Text
3' UTR -678.902568-0.264 Picture PostScript Text

The RNAfold program from the Vienna RNA Package is used to perform the secondary structure predictions and folding calculations. The estimated folding energy is in kcal/mol. The more negative the energy, the more secondary structure the RNA is likely to have.

-  Protein Domain and Structure Information
  InterPro Domains: Graphical view of domain structure
IPR005225 - Small_GTP-bd_dom
IPR001806 - Small_GTPase
IPR003579 - Small_GTPase_Rab_type

Pfam Domains:
PF00071 - Ras family

ModBase Predicted Comparative 3D Structure on Q96DA2
The pictures above may be empty if there is no ModBase structure for the protein. The ModBase structure frequently covers just a fragment of the protein. You may be asked to log onto ModBase the first time you click on the pictures. It is simplest after logging in to just click on the picture again to get to the specific info on that model.

-  Orthologous Genes in Other Species
  Orthologies between human, mouse, and rat are computed by taking the best BLASTP hit, and filtering out non-syntenic hits. For more distant species reciprocal-best BLASTP hits are used. Note that the absence of an ortholog in the table below may reflect incomplete annotations in the other species rather than a true absence of the orthologous gene.
MouseRatZebrafishD. melanogasterC. elegansS. cerevisiae
Genome BrowserGenome BrowserNo orthologGenome BrowserGenome BrowserNo ortholog
Gene Details     
Gene Sorter     
Protein SequenceProtein Sequence Protein SequenceProtein Sequence 
AlignmentAlignment AlignmentAlignment 

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0000166 nucleotide binding
GO:0003924 GTPase activity
GO:0005515 protein binding
GO:0005525 GTP binding
GO:0031489 myosin V binding

Biological Process:
GO:0006914 autophagy
GO:0010506 regulation of autophagy
GO:0015031 protein transport
GO:0016192 vesicle-mediated transport
GO:0050808 synapse organization

Cellular Component:
GO:0005622 intracellular
GO:0005794 Golgi apparatus
GO:0005886 plasma membrane
GO:0016020 membrane
GO:0030659 cytoplasmic vesicle membrane
GO:0031410 cytoplasmic vesicle
GO:0031982 vesicle
GO:0043005 neuron projection

-  Descriptions from all associated GenBank mRNAs
  LF211553 - JP 2014500723-A/19056: Polycomb-Associated Non-Coding RNAs.
MA447130 - JP 2018138019-A/19056: Polycomb-Associated Non-Coding RNAs.
AL834460 - Homo sapiens mRNA; cDNA DKFZp547N196 (from clone DKFZp547N196).
LF213834 - JP 2014500723-A/21337: Polycomb-Associated Non-Coding RNAs.
MA449411 - JP 2018138019-A/21337: Polycomb-Associated Non-Coding RNAs.
LF385333 - JP 2014500723-A/192836: Polycomb-Associated Non-Coding RNAs.
MA620910 - JP 2018138019-A/192836: Polycomb-Associated Non-Coding RNAs.
AK056209 - Homo sapiens cDNA FLJ31647 fis, clone NT2RI2003973.
JD357922 - Sequence 338946 from Patent EP1572962.
JD498871 - Sequence 479895 from Patent EP1572962.
JD494979 - Sequence 476003 from Patent EP1572962.
JD274043 - Sequence 255067 from Patent EP1572962.
JD274357 - Sequence 255381 from Patent EP1572962.
JD078872 - Sequence 59896 from Patent EP1572962.
JD403274 - Sequence 384298 from Patent EP1572962.
JD320688 - Sequence 301712 from Patent EP1572962.
JD429090 - Sequence 410114 from Patent EP1572962.
JD038092 - Sequence 19116 from Patent EP1572962.
JD102251 - Sequence 83275 from Patent EP1572962.
JD468845 - Sequence 449869 from Patent EP1572962.
JD479911 - Sequence 460935 from Patent EP1572962.
JD544431 - Sequence 525455 from Patent EP1572962.
JD174274 - Sequence 155298 from Patent EP1572962.
AY052478 - Homo sapiens RAB39 mRNA, complete cds.
BC009714 - Homo sapiens RAB39B, member RAS oncogene family, mRNA (cDNA clone MGC:9428 IMAGE:3900092), complete cds.
CU679459 - Synthetic construct Homo sapiens gateway clone IMAGE:100016779 5' read RAB39B mRNA.
KJ895317 - Synthetic construct Homo sapiens clone ccsbBroadEn_04711 RAB39B gene, encodes complete protein.
AM393847 - Synthetic construct Homo sapiens clone IMAGE:100001856 for hypothetical protein (RAB39B gene).
AB528219 - Synthetic construct DNA, clone: pF1KE0117, Homo sapiens RAB39B gene for RAB39B, member RAS oncogene family, without stop codon, in Flexi system.
LF381009 - JP 2014500723-A/188512: Polycomb-Associated Non-Coding RNAs.
MA616586 - JP 2018138019-A/188512: Polycomb-Associated Non-Coding RNAs.
LF381010 - JP 2014500723-A/188513: Polycomb-Associated Non-Coding RNAs.
MA616587 - JP 2018138019-A/188513: Polycomb-Associated Non-Coding RNAs.
LF381011 - JP 2014500723-A/188514: Polycomb-Associated Non-Coding RNAs.
MA616588 - JP 2018138019-A/188514: Polycomb-Associated Non-Coding RNAs.
JD462011 - Sequence 443035 from Patent EP1572962.
JD289325 - Sequence 270349 from Patent EP1572962.
JD125421 - Sequence 106445 from Patent EP1572962.
JD417093 - Sequence 398117 from Patent EP1572962.

-  Biochemical and Signaling Pathways
  Reactome (by CSHL, EBI, and GO)

Protein Q96DA2 (Reactome details) participates in the following event(s):

R-HSA-8870466 RGGT:CHM binds RABs
R-HSA-8877813 DENND5A,B exchange GTP for GDP on RAB39
R-HSA-8870469 RGGT geranylgeranylates RAB proteins
R-HSA-8873719 RAB geranylgeranylation
R-HSA-8876198 RAB GEFs exchange GTP for GDP on RABs
R-HSA-597592 Post-translational protein modification
R-HSA-9007101 Rab regulation of trafficking
R-HSA-392499 Metabolism of proteins
R-HSA-199991 Membrane Trafficking
R-HSA-5653656 Vesicle-mediated transport

-  Other Names for This Gene
  Alternate Gene Symbols: NM_171998, Q5JT79, Q8NEX3, Q96DA2, RB39B_HUMAN, uc004fne.1, uc004fne.2, uc004fne.3, uc004fne.4, uc004fne.5, uc004fne.6
UCSC ID: uc004fne.6
RefSeq Accession: NM_171998
Protein: Q96DA2 (aka RB39B_HUMAN or R39B_HUMAN)
CCDS: CCDS14766.1

-  GeneReviews for This Gene
  GeneReviews article(s) related to gene RAB39B:
xq28-dup (Xq28 Duplication Syndrome, Int22h1/Int22h2 Mediated)

-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.