Human Gene SDF4 (ENST00000360001.12_13) from GENCODE V47lift37

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Description: stromal cell derived factor 4, transcript variant 2 (from RefSeq NM_016176.6)
Gencode Transcript: ENST00000360001.12_13
Gencode Gene: ENSG00000078808.20_15
Transcript (Including UTRs)
Position: hg19 chr1:1,152,311-1,167,381 Size: 15,071 Total Exon Count: 7 Strand: -
Coding Region
Position: hg19 chr1:1,152,892-1,164,152 Size: 11,261 Coding Exon Count: 6

Page Index	Sequence and Links	Primers	MalaCards	CTD	Gene Alleles
RNA-Seq Expression	Microarray Expression	RNA Structure	Other Species	mRNA Descriptions	Other Names
Model Information	Methods

Data last updated at UCSC: 2024-08-22 23:36:26

Sequence and Links to Tools and Databases

Genomic Sequence (chr1:1,152,311-1,167,381)			mRNA (may differ from genome)		Protein (355 aa)
Gene Sorter	Genome Browser	Other Species FASTA	Gene interactions	Table Schema	AlphaFold
BioGPS	Ensembl	Entrez Gene	ExonPrimer	GeneCards	HGNC
Malacards	MGI	OMIM	PubMed	UniProtKB	Wikipedia
BioGrid CRISPR DB

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

MalaCards Disease Associations


	MalaCards Gene Search: SDF4 Diseases sorted by gene-association score: bladder squamous cell carcinoma (2), cardiomyopathy, dilated, 1p (1), myopathy, tubular aggregate, 1 (1)

Comparative Toxicogenomics Database (CTD)


	The following chemicals interact with this gene D015127 9,10-Dimethyl-1,2-benzanthracene D016604 Aflatoxin B1 D000643 Ammonium Chloride D003993 Dibutyl Phthalate D004026 Dieldrin D004958 Estradiol D007854 Lead D008070 Lipopolysaccharides D008727 Methotrexate D010634 Phenobarbital more ... click here to view the complete list

Common Gene Haplotype Alleles


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RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)


	Highest median expression: 89.68 RPKM in Cells - Cultured fibroblasts Total median expression: 2886.71 RPKM View in GTEx track of Genome Browser View at GTEx portal View GTEx Body Map

Microarray Expression Data


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mRNA Secondary Structure of 3' and 5' UTRs

Region	Fold Energy	Bases	Energy/Base	Display As
5' UTR	-113.30	284	-0.399	Picture	PostScript	Text
3' UTR	-248.00	581	-0.427	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.

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.

Mouse	Rat	Zebrafish	D. melanogaster	C. elegans	S. cerevisiae
No ortholog	No ortholog	No ortholog	No ortholog	Genome Browser	No ortholog
Gene Details	Gene Details		Gene Details	Gene Details
Gene Sorter	Gene Sorter		Gene Sorter	Gene Sorter
	RGD	Ensembl		WormBase
				Protein Sequence
				Alignment

Descriptions from all associated GenBank mRNAs


	AK000717 - Homo sapiens cDNA FLJ20710 fis, clone KAIA1109. BC022375 - Homo sapiens stromal cell derived factor 4, mRNA (cDNA clone MGC:23934 IMAGE:4839718), complete cds. BC008917 - Homo sapiens stromal cell derived factor 4, mRNA (cDNA clone MGC:16111 IMAGE:3622725), complete cds. AK027277 - Homo sapiens cDNA FLJ14371 fis, clone HEMBA1001302, highly similar to Homo sapiens calcium binding protein precursor, mRNA. AK222521 - Homo sapiens mRNA for calcium binding protein Cab45 precursor variant, clone: adSE01609. AK075352 - Homo sapiens cDNA PSEC0034 fis, clone NT2RP1000713, highly similar to 45 KDA CALCIUM-BINDING PROTEIN PRECURSOR. BC007625 - Homo sapiens stromal cell derived factor 4, mRNA (cDNA clone MGC:15780 IMAGE:3503540), complete cds. BC011244 - Homo sapiens stromal cell derived factor 4, mRNA (cDNA clone MGC:18132 IMAGE:4153655), complete cds. BC006211 - Homo sapiens stromal cell derived factor 4, mRNA (cDNA clone MGC:852 IMAGE:3162764), complete cds. AF153686 - Homo sapiens calcium binding protein precursor, mRNA, complete cds. AF178986 - Homo sapiens calcium binding protein Cab45 precursor, mRNA, complete cds. AK126927 - Homo sapiens cDNA FLJ44980 fis, clone BRAWH3003573, highly similar to 45 kDa calcium-binding protein precursor (Stromal cell-derived factor 4) (SDF-4). AK055331 - Homo sapiens cDNA FLJ30769 fis, clone FEBRA2000733, highly similar to 45 KDA CALCIUM-BINDING PROTEIN PRECURSOR. JD384544 - Sequence 365568 from Patent EP1572962. JD054014 - Sequence 35038 from Patent EP1572962. JD396996 - Sequence 378020 from Patent EP1572962. JD415624 - Sequence 396648 from Patent EP1572962. JD210440 - Sequence 191464 from Patent EP1572962. JD391930 - Sequence 372954 from Patent EP1572962. JD129602 - Sequence 110626 from Patent EP1572962. AK223079 - Homo sapiens mRNA for calcium binding protein Cab45 precursor variant, clone: KAT02235. JD021082 - Sequence 2106 from Patent EP1572962. JD020639 - Sequence 1663 from Patent EP1572962. JD023101 - Sequence 4125 from Patent EP1572962. JD033391 - Sequence 14415 from Patent EP1572962. L79912 - Homo sapiens EF-hand calcium-binding protein of 45 kDa mRNA, complete cds. AK315517 - Homo sapiens cDNA, FLJ96583, highly similar to Homo sapiens stromal cell derived factor 4 (SDF4), mRNA. AF132749 - Homo sapiens calcium-binding protein Cab45b mRNA, complete cds. HQ448229 - Synthetic construct Homo sapiens clone IMAGE:100071630; CCSB000374_02 stromal cell derived factor 4 (SDF4) gene, encodes complete protein. KJ898839 - Synthetic construct Homo sapiens clone ccsbBroadEn_08233 SDF4 gene, encodes complete protein. JD322776 - Sequence 303800 from Patent EP1572962. JD075294 - Sequence 56318 from Patent EP1572962. CU679896 - Synthetic construct Homo sapiens gateway clone IMAGE:100017107 5' read SDF4 mRNA. AK299810 - Homo sapiens cDNA FLJ59162 complete cds, highly similar to 45 kDa calcium-binding protein precursor. JD114782 - Sequence 95806 from Patent EP1572962. JD419348 - Sequence 400372 from Patent EP1572962. JD372732 - Sequence 353756 from Patent EP1572962. JD103975 - Sequence 84999 from Patent EP1572962. JD155149 - Sequence 136173 from Patent EP1572962.

Other Names for This Gene


	Alternate Gene Symbols: A0A5F9UP49, A0A5F9UP49_HUMAN, ENST00000360001.1, ENST00000360001.10, ENST00000360001.11, ENST00000360001.2, ENST00000360001.3, ENST00000360001.4, ENST00000360001.5, ENST00000360001.6, ENST00000360001.7, ENST00000360001.8, ENST00000360001.9, NM_016176, SDF4 , uc318bij.1, uc318bij.2 UCSC ID: ENST00000360001.12_13 RefSeq Accession: NM_016176.6

Gene Model Information


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Methods, Credits, and Use Restrictions


	Click here for details on how this gene model was made and data restrictions if any.