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SYNCRIP synaptotagmin binding cytoplasmic RNA interacting protein [ Homo sapiens (human) ]

Gene ID: 10492, updated on 3-Jan-2019

Summary

Official Symbol
SYNCRIPprovided by HGNC
Official Full Name
synaptotagmin binding cytoplasmic RNA interacting proteinprovided by HGNC
Primary source
HGNC:HGNC:16918
See related
Ensembl:ENSG00000135316 MIM:616686
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
Also known as
PP68; NSAP1; GRYRBP; HNRNPQ; HNRPQ1; GRY-RBP; hnRNP-Q
Summary
This gene encodes a member of the cellular heterogeneous nuclear ribonucleoprotein (hnRNP) family. hnRNPs are RNA binding proteins that complex with heterogeneous nuclear RNA (hnRNA) and regulate alternative splicing, polyadenylation, and other aspects of mRNA metabolism and transport. The encoded protein plays a role in multiple aspects of mRNA maturation and is associated with several multiprotein complexes including the apoB RNA editing-complex and survival of motor neurons (SMN) complex. Alternatively spliced transcript variants encoding multiple isoforms have been observed for this gene, and a pseudogene of this gene is located on the short arm of chromosome 20. [provided by RefSeq, Dec 2011]
Expression
Ubiquitous expression in thyroid (RPKM 21.7), appendix (RPKM 18.1) and 25 other tissues See more
Orthologs

Genomic context

See SYNCRIP in Genome Data Viewer
Location:
6q14.3
Exon count:
13
Annotation release Status Assembly Chr Location
109 current GRCh38.p12 (GCF_000001405.38) 6 NC_000006.12 (85607784..85643862, complement)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 6 NC_000006.11 (86317502..86353568, complement)

Chromosome 6 - NC_000006.12Genomic Context describing neighboring genes Neighboring gene 5'-nucleotidase ecto Neighboring gene sorting nexin 14 Neighboring gene pyruvate kinase M1/2 pseudogene 3 Neighboring gene small nucleolar RNA, C/D box 50A Neighboring gene small nucleolar RNA host gene 5

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 Apr 4 07:08:55 2018

Bibliography

GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

HIV-1 interactions

Protein interactions

Protein Gene Interaction Pubs
Envelope surface glycoprotein gp120 env Tandem affinity purification and mass spectrometry analysis identify heterogeneous nuclear ribonucleoprotein Q (HNRNPQ; SYNCRIP), HIV-1 Gag, Gag/Pol, gp120, and Nef incorporated into staufen1 RNP complexes isolated from HIV-1-expressing cells PubMed
Gag-Pol gag-pol Tandem affinity purification and mass spectrometry analysis identify heterogeneous nuclear ribonucleoprotein Q (HNRNPQ; SYNCRIP), HIV-1 Gag, Gag/Pol, gp120, and Nef incorporated into staufen1 RNP complexes isolated from HIV-1-expressing cells PubMed
Nef nef Tandem affinity purification and mass spectrometry analysis identify heterogeneous nuclear ribonucleoprotein Q (HNRNPQ; SYNCRIP), HIV-1 Gag, Gag/Pol, gp120, and Nef incorporated into staufen1 RNP complexes isolated from HIV-1-expressing cells PubMed
Pr55(Gag) gag hnRNP Q overexpression in HIV-1 infected HeLa cells increases levels of the HIV-1 Gag-p24 protein, while levels of viral Rev-dependent mRNAs are not affected PubMed
gag Tandem affinity purification and mass spectrometry analysis identify heterogeneous nuclear ribonucleoprotein Q (HNRNPQ; SYNCRIP), HIV-1 Gag, Gag/Pol, gp120, and Nef incorporated into staufen1 RNP complexes isolated from HIV-1-expressing cells PubMed
Rev rev hnRNP Q overexpression increases levels of reporter proteins in a Rev-dependent manner PubMed
rev HIV-1 Rev interacting protein, synaptotagmin binding, cytoplasmic RNA interacting protein, is identified by the in-vitro binding experiments involving cytosolic or nuclear extracts from HeLa cells. The interaction of Rev with SYNCRIP is increased by RRE PubMed
rev HIV-1 Rev involves its amino acids 9-14 for specific binding to the heterogeneous nuclear ribonucleoproteins (hnRNP) Q PubMed
capsid gag hnRNP Q overexpression in HIV-1 infected HeLa cells increases levels of the HIV-1 Gag-p24 protein, while levels of viral Rev-dependent mRNAs are not affected PubMed

Go to the HIV-1, Human Interaction Database

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Clone Names

  • FLJ31626

Gene Ontology Provided by GOA

Function Evidence Code Pubs
RNA binding HDA PubMed 
RNA binding IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
mRNA 5'-UTR binding IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
mRNA binding IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
poly(A) binding IEA
Inferred from Electronic Annotation
more info
 
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
Process Evidence Code Pubs
CRD-mediated mRNA stabilization IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
CRD-mediated mRNA stabilization IMP
Inferred from Mutant Phenotype
more info
PubMed 
RNA processing TAS
Traceable Author Statement
more info
PubMed 
RNA splicing TAS
Traceable Author Statement
more info
PubMed 
cellular response to interferon-gamma IDA
Inferred from Direct Assay
more info
PubMed 
mRNA splicing, via spliceosome IC
Inferred by Curator
more info
PubMed 
negative regulation of translation IDA
Inferred from Direct Assay
more info
PubMed 
negative regulation of translation IMP
Inferred from Mutant Phenotype
more info
PubMed 
osteoblast differentiation HDA PubMed 
viral process IEA
Inferred from Electronic Annotation
more info
 
Component Evidence Code Pubs
CRD-mediated mRNA stability complex IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
CRD-mediated mRNA stability complex IDA
Inferred from Direct Assay
more info
PubMed 
GAIT complex IDA
Inferred from Direct Assay
more info
PubMed 
catalytic step 2 spliceosome IDA
Inferred from Direct Assay
more info
PubMed 
endoplasmic reticulum IEA
Inferred from Electronic Annotation
more info
 
histone pre-mRNA 3'end processing complex ISS
Inferred from Sequence or Structural Similarity
more info
 
membrane HDA PubMed 
nucleoplasm IEA
Inferred from Electronic Annotation
more info
 
nucleus IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
ribonucleoprotein complex IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
ribonucleoprotein complex IDA
Inferred from Direct Assay
more info
PubMed 

General protein information

Preferred Names
heterogeneous nuclear ribonucleoprotein Q
Names
NS1-associated protein 1
glycine- and tyrosine-rich RNA-binding protein

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_031848.1 RefSeqGene

    Range
    5001..40542
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001159673.1NP_001153145.1  heterogeneous nuclear ribonucleoprotein Q isoform 2

    See identical proteins and their annotated locations for NP_001153145.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) differs in the 5' UTR, 3' UTR, and coding region and initiates translation at an alternate in-frame start codon, compared to variant 1. The resulting isoform (2) is shorter and has distinct N- and C-termini, compared to isoform 1.
    Source sequence(s)
    AB209098, AF037448, AL136082, BF221524
    Consensus CDS
    CCDS75491.1
    UniProtKB/Swiss-Prot
    O60506
    UniProtKB/TrEMBL
    B7Z645, Q59GL1
    Related
    ENSP00000484577.1, ENST00000616122.4
    Conserved Domains (1) summary
    cl25617
    Location:5459
    LSM_int_assoc; LSM-interacting associated unstructured
  2. NM_001159674.1NP_001153146.1  heterogeneous nuclear ribonucleoprotein Q isoform 3

    See identical proteins and their annotated locations for NP_001153146.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) differs in the 5' UTR, 3' UTR, and coding region compared to variant 1. The resulting isoform (3) is shorter and has a distinct C-terminus, compared to isoform 1.
    Source sequence(s)
    AB209098, AF037448, AL136082, BC032643, BF221524
    UniProtKB/Swiss-Prot
    O60506
    UniProtKB/TrEMBL
    Q59GL1
    Conserved Domains (1) summary
    cl25617
    Location:103522
    LSM_int_assoc; LSM-interacting associated unstructured
  3. NM_001159675.1NP_001153147.1  heterogeneous nuclear ribonucleoprotein Q isoform 4

    See identical proteins and their annotated locations for NP_001153147.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (4) differs in the 5' UTR and coding region compared to variant 1. The resulting isoform (4) is shorter, compared to isoform 1.
    Source sequence(s)
    AL136082, AY034482, BC015575, DB160837
    UniProtKB/Swiss-Prot
    O60506
    Conserved Domains (1) summary
    cl25617
    Location:103580
    LSM_int_assoc; LSM-interacting associated unstructured
  4. NM_001159676.1NP_001153148.1  heterogeneous nuclear ribonucleoprotein Q isoform 5

    See identical proteins and their annotated locations for NP_001153148.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (5) differs in the 5' UTR, 3' UTR, and coding region compared to variant 1. The resulting isoform (5) is shorter and has a distinct C-terminus, compared to isoform 1.
    Source sequence(s)
    AB209098, AL136082, AY034483, BC015575, BF221524
    UniProtKB/Swiss-Prot
    O60506
    UniProtKB/TrEMBL
    Q59GL1
    Conserved Domains (1) summary
    cl25617
    Location:103553
    LSM_int_assoc; LSM-interacting associated unstructured
  5. NM_001159677.1NP_001153149.1  heterogeneous nuclear ribonucleoprotein Q isoform 6

    See identical proteins and their annotated locations for NP_001153149.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (6) differs in the 3' UTR and coding region compared to variant 1. The resulting isoform (6) is shorter and has a distinct C-terminus, compared to isoform 1.
    Source sequence(s)
    AB209098, AF037448, AF155568, AL136082, BF221524, DA845413
    Consensus CDS
    CCDS55041.1
    UniProtKB/Swiss-Prot
    O60506
    UniProtKB/TrEMBL
    Q59GL1
    Related
    ENSP00000347380.6, ENST00000355238.10
    Conserved Domains (1) summary
    cl25617
    Location:103557
    LSM_int_assoc; LSM-interacting associated unstructured
  6. NM_001253771.1NP_001240700.1  heterogeneous nuclear ribonucleoprotein Q isoform 7

    See identical proteins and their annotated locations for NP_001240700.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (7) differs in the 3' UTR, lacks an internal exon, uses an alternate splice site in the coding region and initiates translation at an alternate start codon, compared to variant 1. The encoded isoform (7) is shorter and has distinct N- and C-termini, compared to isoform 1.
    Source sequence(s)
    AA411631, AB209098, BC040844, BF221524, CV806885
    UniProtKB/Swiss-Prot
    O60506
    UniProtKB/TrEMBL
    Q59GL1
    Conserved Domains (4) summary
    cd12489
    Location:89173
    RRM2_hnRNPQ; RNA recognition motif 2 in vertebrate heterogeneous nuclear ribonucleoprotein Q (hnRNP Q)
    cd12495
    Location:185256
    RRM3_hnRNPQ; RNA recognition motif 3 in vertebrate heterogeneous nuclear ribonucleoprotein Q (hnRNP Q)
    cl17169
    Location:1187
    RRM_SF; RNA recognition motif (RRM) superfamily
    cl17173
    Location:358401
    AdoMet_MTases; S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy). ...
  7. NM_006372.4NP_006363.4  heterogeneous nuclear ribonucleoprotein Q isoform 1

    See identical proteins and their annotated locations for NP_006363.4

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) encodes the longest isoform (1).
    Source sequence(s)
    AF037448, AL136082, DA117533, DA845413, DB160837
    Consensus CDS
    CCDS5005.1
    UniProtKB/Swiss-Prot
    O60506
    Related
    ENSP00000358635.3, ENST00000369622.7
    Conserved Domains (1) summary
    cl25617
    Location:103615
    LSM_int_assoc; LSM-interacting associated unstructured

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 109

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

Reference GRCh38.p12 Primary Assembly

Genomic

  1. NC_000006.12 Reference GRCh38.p12 Primary Assembly

    Range
    85607784..85643862 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_017010178.2XP_016865667.1  heterogeneous nuclear ribonucleoprotein Q isoform X4

    UniProtKB/Swiss-Prot
    O60506
    Conserved Domains (1) summary
    cl25617
    Location:103557
    LSM_int_assoc; LSM-interacting associated unstructured
  2. XM_017010179.1XP_016865668.1  heterogeneous nuclear ribonucleoprotein Q isoform X5

    Conserved Domains (1) summary
    cl25617
    Location:103553
    LSM_int_assoc; LSM-interacting associated unstructured
  3. XM_005248635.4XP_005248692.1  heterogeneous nuclear ribonucleoprotein Q isoform X5

    See identical proteins and their annotated locations for XP_005248692.1

    Conserved Domains (1) summary
    cl25617
    Location:103553
    LSM_int_assoc; LSM-interacting associated unstructured
  4. XM_017010177.1XP_016865666.1  heterogeneous nuclear ribonucleoprotein Q isoform X2

    Conserved Domains (1) summary
    cl25617
    Location:103592
    LSM_int_assoc; LSM-interacting associated unstructured
  5. XM_017010176.1XP_016865665.1  heterogeneous nuclear ribonucleoprotein Q isoform X1

    Conserved Domains (1) summary
    cl25617
    Location:103592
    LSM_int_assoc; LSM-interacting associated unstructured
  6. XM_005248637.2XP_005248694.1  heterogeneous nuclear ribonucleoprotein Q isoform X3

    See identical proteins and their annotated locations for XP_005248694.1

    UniProtKB/Swiss-Prot
    O60506
    Conserved Domains (1) summary
    cl25617
    Location:103615
    LSM_int_assoc; LSM-interacting associated unstructured
  7. XM_005248636.3XP_005248693.1  heterogeneous nuclear ribonucleoprotein Q isoform X6

    See identical proteins and their annotated locations for XP_005248693.1

    Conserved Domains (1) summary
    cl25617
    Location:5517
    LSM_int_assoc; LSM-interacting associated unstructured
  8. XM_017010180.2XP_016865669.1  heterogeneous nuclear ribonucleoprotein Q isoform X7

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