Format

Send to:

Choose Destination

SDF2 stromal cell derived factor 2 [ Homo sapiens (human) ]

Gene ID: 6388, updated on 1-Jun-2020

Summary

Official Symbol
SDF2provided by HGNC
Official Full Name
stromal cell derived factor 2provided by HGNC
Primary source
HGNC:HGNC:10675
See related
Ensembl:ENSG00000132581 MIM:602934
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 believed to be a secretory protein. It has regions of similarity to hydrophilic segments of yeast mannosyltransferases. Its expression is ubiquitous and the gene appears to be relatively conserved among mammals. Alternate splicing results in both coding and non-coding variants. A pseudogene of this gene is located on chromosome 15. [provided by RefSeq, Dec 2011]
Expression
Ubiquitous expression in adrenal (RPKM 19.5), placenta (RPKM 16.0) and 25 other tissues See more
Orthologs

Genomic context

See SDF2 in Genome Data Viewer
Location:
17q11.2
Exon count:
5
Annotation release Status Assembly Chr Location
109.20200522 current GRCh38.p13 (GCF_000001405.39) 17 NC_000017.11 (28648346..28662189, complement)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 17 NC_000017.10 (26975374..26989207, complement)

Chromosome 17 - NC_000017.11Genomic Context describing neighboring genes Neighboring gene SPAG5 antisense RNA 1 Neighboring gene ribosomal protein S6 kinase related Neighboring gene KIAA0100 Neighboring gene ribosomal protein S12 pseudogene 28 Neighboring gene SPT6 homolog, histone chaperone and transcription elongation factor Neighboring gene Sharpr-MPRA regulatory region 10516 Neighboring gene protein interacting with cyclin A1

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 Functions

What's a GeneRIF?

HIV-1 interactions

Protein interactions

Protein Gene Interaction Pubs
Envelope surface glycoprotein gp120 env HIV-1 gp120 is identified to have a physical interaction with stromal cell-derived factor 2 (SDF2) in human HEK293 and/or Jurkat cell lines by using affinity tagging and purification mass spectrometry analyses PubMed
Envelope surface glycoprotein gp160, precursor env HIV-1 gp160 is identified to have a physical interaction with stromal cell-derived factor 2 (SDF2) in human HEK293 and/or Jurkat cell lines by using affinity tagging and purification mass spectrometry analyses 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

  • FLJ17932

Gene Ontology Provided by GOA

Function Evidence Code Pubs
dolichyl-phosphate-mannose-protein mannosyltransferase activity TAS
Traceable Author Statement
more info
PubMed 
Process Evidence Code Pubs
protein O-linked mannosylation IEA
Inferred from Electronic Annotation
more info
 
protein glycosylation TAS
Traceable Author Statement
more info
PubMed 
Component Evidence Code Pubs
extracellular space TAS
Traceable Author Statement
more info
PubMed 
membrane IEA
Inferred from Electronic Annotation
more info
 

General protein information

Preferred Names
stromal cell-derived factor 2
Names
SDF-2

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.

mRNA and Protein(s)

  1. NM_006923.4NP_008854.2  stromal cell-derived factor 2 precursor

    See identical proteins and their annotated locations for NP_008854.2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) represents the longer transcript and encodes the functional protein.
    Source sequence(s)
    AC005726, AW026433, BC001406, BQ056236
    Consensus CDS
    CCDS11238.1
    UniProtKB/Swiss-Prot
    Q99470
    UniProtKB/TrEMBL
    Q6IBU4
    Related
    ENSP00000247020.3, ENST00000247020.9
    Conserved Domains (1) summary
    cl25703
    Location:14188
    PMT_4TMC; C-terminal four TMM region of protein-O-mannosyltransferase

RNA

  1. NR_045585.1 RNA Sequence

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) contains an alternate 5' exon, compared to variant 1. This variant is represented as non-coding because it lacks a large portion of the coding region, including the translational start codon, found in variant 1.
    Source sequence(s)
    AC005726, AC010761, AW026433, BC001406, CD673481
    Related
    ENST00000592250.5

RefSeqs of Annotated Genomes: Homo sapiens Updated Annotation Release 109.

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

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000017.11 Reference GRCh38.p13 Primary Assembly

    Range
    28648346..28662189 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_011525106.2XP_011523408.1  stromal cell-derived factor 2 isoform X1

    See identical proteins and their annotated locations for XP_011523408.1

    Conserved Domains (1) summary
    smart00472
    Location:83157
    MIR; Domain in ryanodine and inositol trisphosphate receptors and protein O-mannosyltransferases
Support Center