Human Gene SDF2L1 (ENST00000248958.5_4) from GENCODE V47lift37
  Description: stromal cell derived factor 2 like 1 (from RefSeq NM_022044.3)
Gencode Transcript: ENST00000248958.5_4
Gencode Gene: ENSG00000128228.5_7
Transcript (Including UTRs)
   Position: hg19 chr22:21,996,591-21,998,588 Size: 1,998 Total Exon Count: 3 Strand: +
Coding Region
   Position: hg19 chr22:21,996,626-21,998,464 Size: 1,839 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 (chr22:21,996,591-21,998,588)mRNA (may differ from genome)Protein (221 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
AlphaFoldBioGPSEnsemblEntrez GeneExonPrimerGeneCards
HGNCMGIOMIMPubMedUniProtKBBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: SDF2L_HUMAN
DESCRIPTION: RecName: Full=Stromal cell-derived factor 2-like protein 1; Short=SDF2-like protein 1; AltName: Full=PWP1-interacting protein 8; Flags: Precursor;
SUBCELLULAR LOCATION: Endoplasmic reticulum lumen (Potential).
TISSUE SPECIFICITY: Ubiquitously expressed with high expression in testis, moderate expression in the pancreas, spleen, prostate, small intestine and colon. Very low expression is seen in brain and skeletal muscle.
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

+  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: 60.70 RPKM in Pituitary
Total median expression: 928.45 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 -19.3035-0.551 Picture PostScript Text
3' UTR -41.00124-0.331 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

ModBase Predicted Comparative 3D Structure on Q9HCN8
FrontTopSide
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 orthologNo orthologNo ortholog
Gene DetailsGene Details    
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-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0004169 dolichyl-phosphate-mannose-protein mannosyltransferase activity
GO:0051087 chaperone binding
GO:0051117 ATPase binding
GO:0051787 misfolded protein binding

Biological Process:
GO:0034976 response to endoplasmic reticulum stress
GO:0035269 protein O-linked mannosylation
GO:0042981 regulation of apoptotic process
GO:0071218 cellular response to misfolded protein
GO:0071712 ER-associated misfolded protein catabolic process

Cellular Component:
GO:0005783 endoplasmic reticulum
GO:0005788 endoplasmic reticulum lumen
GO:0005789 endoplasmic reticulum membrane
GO:0016020 membrane
GO:0034663 endoplasmic reticulum chaperone complex


-  Descriptions from all associated GenBank mRNAs
  BC132849 - Homo sapiens stromal cell-derived factor 2-like 1, mRNA (cDNA clone MGC:164480 IMAGE:40146871), complete cds.
BC132851 - Homo sapiens stromal cell-derived factor 2-like 1, mRNA (cDNA clone MGC:164482 IMAGE:40146873), complete cds.
AY359118 - Homo sapiens clone DNA96857 HGS_A135 (UNQ1941) mRNA, complete cds.
AB043007 - Homo sapiens SDF2L1 mRNA for SDF2 like protein 1, complete cds.
CR456570 - Homo sapiens SDF2L1 full length open reading frame (ORF) cDNA clone (cDNA clone C22ORF:pGEM.SDF2L1).
AF277316 - Homo sapiens PWP1-interacting protein 8 percursor (PWP1) mRNA, complete cds.
KJ893444 - Synthetic construct Homo sapiens clone ccsbBroadEn_02838 hypothetical protein, encodes complete protein.
AB528230 - Synthetic construct DNA, clone: pF1KE0541, Homo sapiens SDF2L1 gene for stromal cell-derived factor 2-like 1, without stop codon, in Flexi system.
CU013457 - Homo sapiens SDF2L1, mRNA (cDNA clone IMAGE:100000427), complete cds, without stop codon, in Gateway system.
BC139837 - Synthetic construct Homo sapiens clone IMAGE:100000523, MGC:164682 stromal cell-derived factor 2-like 1 (SDF2L1) mRNA, encodes complete protein.
CU013169 - Homo sapiens SDF2L1, mRNA (cDNA clone IMAGE:100000523), complete cds, with stop codon, in Gateway system.
JD020627 - Sequence 1651 from Patent EP1572962.
JD325818 - Sequence 306842 from Patent EP1572962.
JD152854 - Sequence 133878 from Patent EP1572962.
JD449737 - Sequence 430761 from Patent EP1572962.
JD156393 - Sequence 137417 from Patent EP1572962.
JD221231 - Sequence 202255 from Patent EP1572962.
JD225666 - Sequence 206690 from Patent EP1572962.
BC006248 - Homo sapiens stromal cell-derived factor 2-like 1, mRNA (cDNA clone IMAGE:3946057).

-  Other Names for This Gene
  Alternate Gene Symbols: A2RUD3, ENST00000248958.1, ENST00000248958.2, ENST00000248958.3, ENST00000248958.4, NM_022044, Q9BRI5, Q9HCN8, SDF2L_HUMAN, uc317eyk.1, uc317eyk.2, UNQ1941/PRO4424
UCSC ID: ENST00000248958.5_4
RefSeq Accession: NM_022044.3
Protein: Q9HCN8 (aka SDF2L_HUMAN or SDFL_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.