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RPH3A rabphilin 3A [ Homo sapiens (human) ]

Gene ID: 22895, updated on 5-Aug-2018

Summary

Official Symbol
RPH3Aprovided by HGNC
Official Full Name
rabphilin 3Aprovided by HGNC
Primary source
HGNC:HGNC:17056
See related
Ensembl:ENSG00000089169 MIM:612159; Vega:OTTHUMG00000169713
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Summary
The protein encoded by this gene is thought to be an effector for RAB3A, which is a small G protein that acts in the late stages of neurotransmitter exocytosis. The encoded protein may be involved in neurotransmitter release and synaptic vesicle traffic. [provided by RefSeq, Dec 2016]
Expression
Biased expression in brain (RPKM 30.1) and adrenal (RPKM 1.7) See more
Orthologs

Genomic context

See RPH3A in Genome Data Viewer
Location:
12q24.13
Exon count:
27
Annotation release Status Assembly Chr Location
109 current GRCh38.p12 (GCF_000001405.38) 12 NC_000012.12 (112575097..112898881)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 12 NC_000012.11 (113229343..113336686)

Chromosome 12 - NC_000012.12Genomic Context describing neighboring genes Neighboring gene protein tyrosine phosphatase, non-receptor type 11 Neighboring gene ribosomal protein L6 Neighboring gene microRNA 1302-1 Neighboring gene 2'-5'-oligoadenylate synthetase 1 Neighboring gene 2'-5'-oligoadenylate synthetase 3

Genomic regions, transcripts, and products

Expression

  • Project title: HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Jun 15 11:32:44 2016

Bibliography

GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

Phenotypes

Copy number response

Description
Copy number response
Triplosensitivity

No evidence available (Last evaluated (2018-07-25)

ClinGen Genome Curation Page
Haploinsufficency

Little evidence for dosage pathogenicity (Last evaluated (2018-07-25)

ClinGen Genome Curation PagePubMed

NHGRI GWAS Catalog

Description
New gene functions in megakaryopoiesis and platelet formation.
NHGRI GWA Catalog

Pathways from BioSystems

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Clone Names

  • KIAA0985

Gene Ontology Provided by GOA

Function Evidence Code Pubs
Rab GTPase binding IEA
Inferred from Electronic Annotation
more info
 
calcium ion binding ISS
Inferred from Sequence or Structural Similarity
more info
 
calcium-dependent phospholipid binding ISS
Inferred from Sequence or Structural Similarity
more info
 
inositol 1,4,5 trisphosphate binding ISS
Inferred from Sequence or Structural Similarity
more info
 
phosphate ion binding ISS
Inferred from Sequence or Structural Similarity
more info
 
phosphatidylinositol phosphate binding TAS
Traceable Author Statement
more info
PubMed 
phosphatidylinositol-4,5-bisphosphate binding ISS
Inferred from Sequence or Structural Similarity
more info
 
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
protein-containing complex binding ISS
Inferred from Sequence or Structural Similarity
more info
 
selenium binding ISS
Inferred from Sequence or Structural Similarity
more info
 
zinc ion binding ISS
Inferred from Sequence or Structural Similarity
more info
 
Process Evidence Code Pubs
intracellular protein transport IEA
Inferred from Electronic Annotation
more info
 
Component Evidence Code Pubs
colocalizes_with Golgi apparatus ISS
Inferred from Sequence or Structural Similarity
more info
 
cell junction IEA
Inferred from Electronic Annotation
more info
 
cytosol ISS
Inferred from Sequence or Structural Similarity
more info
 
extrinsic component of membrane ISS
Inferred from Sequence or Structural Similarity
more info
 
neuron projection ISS
Inferred from Sequence or Structural Similarity
more info
 
protein-containing complex ISS
Inferred from Sequence or Structural Similarity
more info
 
secretory granule ISS
Inferred from Sequence or Structural Similarity
more info
 
synapse ISS
Inferred from Sequence or Structural Similarity
more info
 
synaptic vesicle TAS
Traceable Author Statement
more info
PubMed 
synaptic vesicle membrane ISS
Inferred from Sequence or Structural Similarity
more info
 

General protein information

Preferred Names
rabphilin-3A
Names
exophilin-1
rabphilin 3A homolog

NCBI Reference Sequences (RefSeq)

RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

Genomic

  1. NG_052871.1 RefSeqGene

    Range
    221648..328785
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001143854.1NP_001137326.1  rabphilin-3A isoform 1

    See identical proteins and their annotated locations for NP_001137326.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) encodes the longest isoform (1). Variants 1, 3, 4, and 5 all encode the same isoform (1).
    Source sequence(s)
    AB023202, BU738474, DA332963
    Consensus CDS
    CCDS44979.1
    UniProtKB/Swiss-Prot
    Q9Y2J0
    Related
    ENSP00000374036.4, OTTHUMP00000241932, ENST00000389385.8, OTTHUMT00000405561
    Conserved Domains (3) summary
    cd04035
    Location:393516
    C2A_Rabphilin_Doc2; C2 domain first repeat present in Rabphilin and Double C2 domain
    cd08384
    Location:553685
    C2B_Rabphilin_Doc2; C2 domain second repeat present in Rabphilin and Double C2 domain
    cd15762
    Location:92171
    FYVE_RP3A; FYVE-related domain found in rabphilin-3A and similar proteins
  2. NM_001347952.1NP_001334881.1  rabphilin-3A isoform 1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) differs in the 5' UTR compared to variant 1. Variants 1, 3, 4, and 5 all encode the same isoform (1).
    Source sequence(s)
    AC004216, AC004465, AC004551
    Consensus CDS
    CCDS44979.1
    UniProtKB/Swiss-Prot
    Q9Y2J0
    Related
    ENSP00000440384.2, ENST00000543106.6
  3. NM_001347953.1NP_001334882.1  rabphilin-3A isoform 1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (4) differs in the 5' UTR compared to variant 1. Variants 1, 3, 4, and 5 all encode the same isoform (1).
    Source sequence(s)
    AC004465, AC004551
    Consensus CDS
    CCDS44979.1
    UniProtKB/Swiss-Prot
    Q9Y2J0
    Related
    ENSP00000405357.3, ENST00000415485.7
  4. NM_001347954.1NP_001334883.1  rabphilin-3A isoform 1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (5) differs in the 5' UTR compared to variant 1. Variants 1, 3, 4, and 5 all encode the same isoform (1).
    Source sequence(s)
    AC004465, AC004551
    Consensus CDS
    CCDS44979.1
    UniProtKB/Swiss-Prot
    Q9Y2J0
  5. NM_001347955.1NP_001334884.1  rabphilin-3A isoform 3

    Status: REVIEWED

    Description
    Transcript Variant: This variant (6) differs in the 5' UTR and coding sequence compared to variant 1. The resulting isoform (3) is shorter at the N-terminus compared to isoform 1.
    Source sequence(s)
    AC004465, AC004551
  6. NM_014954.3NP_055769.2  rabphilin-3A isoform 2

    See identical proteins and their annotated locations for NP_055769.2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) lacks an alternate in-frame exon compared to variant 1. The resulting isoform (2) has the same N- and C-termini but is 4 aa shorter compared to isoform 1.
    Source sequence(s)
    AB023202, BU738474, DA332963
    Consensus CDS
    CCDS31904.1
    UniProtKB/Swiss-Prot
    Q9Y2J0
    Related
    ENSP00000448297.1, OTTHUMP00000241934, ENST00000551052.5, OTTHUMT00000405563
    Conserved Domains (4) summary
    cd04035
    Location:389512
    C2A_Rabphilin_Doc2; C2 domain first repeat present in Rabphilin and Double C2 domain
    cd08384
    Location:549681
    C2B_Rabphilin_Doc2; C2 domain second repeat present in Rabphilin and Double C2 domain
    cd15762
    Location:88167
    FYVE_RP3A; FYVE-related domain found in rabphilin-3A and similar proteins
    cl26386
    Location:165349
    DNA_pol3_gamma3; DNA polymerase III subunits gamma and tau domain III

RNA

  1. NR_145126.1 RNA Sequence

    Status: REVIEWED

    Source sequence(s)
    AC004465, AC004551
  2. NR_145127.1 RNA Sequence

    Status: REVIEWED

    Source sequence(s)
    AC004465, AC004551

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 109 details...Open this link in a new tab

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p12 Primary Assembly

Genomic

  1. NC_000012.12 Reference GRCh38.p12 Primary Assembly

    Range
    112575097..112898881
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_017019034.2XP_016874523.1  rabphilin-3A isoform X1

    UniProtKB/TrEMBL
    A0A024RBK6
    Conserved Domains (2) summary
    cd04035
    Location:45168
    C2A_Rabphilin_Doc2; C2 domain first repeat present in Rabphilin and Double C2 domain
    cd08384
    Location:205337
    C2B_Rabphilin_Doc2; C2 domain second repeat present in Rabphilin and Double C2 domain
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