Human Gene SDF2 (ENST00000247020.9_7) from GENCODE V47lift37
  Description: stromal cell derived factor 2, transcript variant 1 (from RefSeq NM_006923.4)
Gencode Transcript: ENST00000247020.9_7
Gencode Gene: ENSG00000132581.10_10
Transcript (Including UTRs)
   Position: hg19 chr17:26,975,364-26,988,924 Size: 13,561 Total Exon Count: 3 Strand: -
Coding Region
   Position: hg19 chr17:26,976,007-26,988,894 Size: 12,888 Coding Exon Count: 3 

Page IndexSequence and LinksUniProtKB CommentsPrimersCTDGene Alleles
RNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther SpeciesGO Annotations
mRNA DescriptionsOther NamesModel InformationMethods
Data last updated at UCSC: 2024-08-22 23:36:26

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr17:26,975,364-26,988,924)mRNA (may differ from genome)Protein (211 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
AlphaFoldBioGPSEnsemblEntrez GeneExonPrimerGeneCards
HGNCMGIOMIMPubMedUniProtKBBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: SDF2_HUMAN
DESCRIPTION: RecName: Full=Stromal cell-derived factor 2; Short=SDF-2; Flags: Precursor;
SUBCELLULAR LOCATION: Secreted (Probable).
SIMILARITY: Contains 3 MIR domains.

-  Primer design for this transcript
 

Primer3Plus can design qPCR Primers that straddle exon-exon-junctions, which amplify only cDNA, not genomic DNA.
Click here to load the transcript sequence and exon structure into Primer3Plus

Exonprimer can design one pair of Sanger sequencing primers around every exon, located in non-genic sequence.
Click here to open Exonprimer with this transcript

To design primers for a non-coding sequence, zoom to a region of interest and select from the drop-down menu: View > In External Tools > Primer3


-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene           more ... click here to view the complete list

+  Common Gene Haplotype Alleles
  Press "+" in the title bar above to open this section.

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 23.21 RPKM in Adrenal Gland
Total median expression: 597.16 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 -1.1030-0.037 Picture PostScript Text
3' UTR -162.20643-0.252 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
IPR027005 - GlyclTrfase_39
IPR016093 - MIR_motif

Pfam Domains:
PF02815 - MIR domain

SCOP Domains:
82109 - MIR domain
49503 - Cupredoxins

ModBase Predicted Comparative 3D Structure on Q99470
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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
No orthologNo orthologNo orthologNo orthologGenome BrowserNo ortholog
Gene DetailsGene Details Gene DetailsGene Details 
Gene SorterGene Sorter Gene SorterGene Sorter 
 RGDEnsembl WormBase 
    Protein Sequence 
    Alignment 

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0004169 dolichyl-phosphate-mannose-protein mannosyltransferase activity

Biological Process:
GO:0006486 protein glycosylation
GO:0035269 protein O-linked mannosylation
GO:0071712 ER-associated misfolded protein catabolic process

Cellular Component:
GO:0005576 extracellular region
GO:0005615 extracellular space
GO:0005789 endoplasmic reticulum membrane
GO:0016020 membrane


-  Descriptions from all associated GenBank mRNAs
  D50645 - Homo sapiens mRNA for SDF2, complete cds.
BC000500 - Homo sapiens stromal cell-derived factor 2, mRNA (cDNA clone MGC:8443 IMAGE:2821329), complete cds.
BC001406 - Homo sapiens stromal cell-derived factor 2, mRNA (cDNA clone MGC:2977 IMAGE:3140716), complete cds.
JD359430 - Sequence 340454 from Patent EP1572962.
JD563282 - Sequence 544306 from Patent EP1572962.
JD202815 - Sequence 183839 from Patent EP1572962.
JD204281 - Sequence 185305 from Patent EP1572962.
JD346277 - Sequence 327301 from Patent EP1572962.
JD549307 - Sequence 530331 from Patent EP1572962.
JD543926 - Sequence 524950 from Patent EP1572962.
JD320362 - Sequence 301386 from Patent EP1572962.
JD062442 - Sequence 43466 from Patent EP1572962.
CU674240 - Synthetic construct Homo sapiens gateway clone IMAGE:100018022 5' read SDF2 mRNA.
KJ892119 - Synthetic construct Homo sapiens clone ccsbBroadEn_01513 SDF2 gene, encodes complete protein.
BT006709 - Homo sapiens stromal cell-derived factor 2 mRNA, complete cds.
DQ891990 - Synthetic construct clone IMAGE:100004620; FLH182120.01X; RZPDo839C10138D stromal cell-derived factor 2 (SDF2) gene, encodes complete protein.
DQ895180 - Synthetic construct Homo sapiens clone IMAGE:100009640; FLH182116.01L; RZPDo839C10137D stromal cell-derived factor 2 (SDF2) gene, encodes complete protein.
CR456708 - Homo sapiens full open reading frame cDNA clone RZPDo834F123D for gene SDF2, stromal cell-derived factor 2; complete cds, incl. stopcodon.
AK310890 - Homo sapiens cDNA, FLJ17932.
JD241693 - Sequence 222717 from Patent EP1572962.
JD520413 - Sequence 501437 from Patent EP1572962.
JD294599 - Sequence 275623 from Patent EP1572962.

-  Other Names for This Gene
  Alternate Gene Symbols: ENST00000247020.1, ENST00000247020.2, ENST00000247020.3, ENST00000247020.4, ENST00000247020.5, ENST00000247020.6, ENST00000247020.7, ENST00000247020.8, NM_006923, Q99470, Q9BQ79, SDF2_HUMAN, uc317eux.1, uc317eux.2
UCSC ID: ENST00000247020.9_7
RefSeq Accession: NM_006923.4
Protein: Q99470 (aka SDF2_HUMAN)

-  Gene Model Information
  Click here for a detailed description of the fields of the table above.

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