Human Gene SPATA2 (ENST00000289431.10_7) from GENCODE V47lift37

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Description: spermatogenesis associated 2, transcript variant 1 (from RefSeq NM_006038.4)
Gencode Transcript: ENST00000289431.10_7
Gencode Gene: ENSG00000158480.11_9
Transcript (Including UTRs)
Position: hg19 chr20:48,519,928-48,532,066 Size: 12,139 Total Exon Count: 3 Strand: -
Coding Region
Position: hg19 chr20:48,522,156-48,525,027 Size: 2,872 Coding Exon Count: 2

Page Index	Sequence and Links	UniProtKB Comments	Primers	CTD	Gene Alleles
RNA-Seq Expression	Microarray Expression	RNA Structure	Protein Structure	Other Species	GO Annotations
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 (chr20:48,519,928-48,532,066)			mRNA (may differ from genome)		Protein (520 aa)
Gene Sorter	Genome Browser	Other Species FASTA	VisiGene	Gene interactions	Table Schema
AlphaFold	BioGPS	Ensembl	Entrez Gene	ExonPrimer	GeneCards
HGNC	MGI	OMIM	PubMed	UniProtKB	Wikipedia
BioGrid CRISPR DB

Comments and Description Text from UniProtKB


	ID: SPAT2_HUMAN DESCRIPTION: RecName: Full=Spermatogenesis-associated protein 2; AltName: Full=Spermatogenesis-associated protein PD1; FUNCTION: May have a role in the regulation of spermatogenesis. SUBCELLULAR LOCATION: Nucleus. TISSUE SPECIFICITY: Highly expressed in Sertoli cells, but not detected in spermatogenic cells. Low expression in spleen, thymus and prostate. SIMILARITY: Belongs to the SPATA2 family. SEQUENCE CAUTION: Sequence=BAA34477.2; Type=Erroneous initiation;

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 C111118 2',3,3',4',5-pentachloro-4-hydroxybiphenyl D000082 Acetaminophen D000643 Ammonium Chloride D019327 Copper Sulfate D003993 Dibutyl Phthalate D004041 Dietary Fats D004051 Diethylhexyl Phthalate D005419 Flavonoids D013629 Tamoxifen D013749 Tetrachlorodibenzodioxin 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: 16.09 RPKM in Testis Total median expression: 307.91 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	-112.70	252	-0.447	Picture	PostScript	Text
3' UTR	-663.70	2228	-0.298	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

SCOP Domains:
143503 - PUG domain-like
57903 - FYVE/PHD zinc finger

ModBase Predicted Comparative 3D Structure on Q9UM82


Front	Top	Side

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.

Mouse	Rat	Zebrafish	D. melanogaster	C. elegans	S. cerevisiae
No ortholog	No ortholog	No ortholog	No ortholog	No ortholog	No ortholog
Gene Details	Gene Details
Gene Sorter	Gene Sorter
	RGD

Gene Ontology (GO) Annotations with Structured Vocabulary


	Molecular Function: GO:0003674 molecular_function GO:0005515 protein binding Biological Process: GO:0007275 multicellular organism development GO:0007283 spermatogenesis GO:0030154 cell differentiation Cellular Component: GO:0001650 fibrillar center GO:0005634 nucleus GO:0005737 cytoplasm

Descriptions from all associated GenBank mRNAs


	LF206032 - JP 2014500723-A/13535: Polycomb-Associated Non-Coding RNAs. AB018300 - Homo sapiens KIAA0757 mRNA for KIAA0757 protein. LF210770 - JP 2014500723-A/18273: Polycomb-Associated Non-Coding RNAs. LF341000 - JP 2014500723-A/148503: Polycomb-Associated Non-Coding RNAs. JD551474 - Sequence 532498 from Patent EP1572962. LF350698 - JP 2014500723-A/158201: Polycomb-Associated Non-Coding RNAs. LF340999 - JP 2014500723-A/148502: Polycomb-Associated Non-Coding RNAs. JD454843 - Sequence 435867 from Patent EP1572962. JD504995 - Sequence 486019 from Patent EP1572962. JD323759 - Sequence 304783 from Patent EP1572962. JD171797 - Sequence 152821 from Patent EP1572962. LF350699 - JP 2014500723-A/158202: Polycomb-Associated Non-Coding RNAs. LF340998 - JP 2014500723-A/148501: Polycomb-Associated Non-Coding RNAs. JD315966 - Sequence 296990 from Patent EP1572962. JD120224 - Sequence 101248 from Patent EP1572962. JD292122 - Sequence 273146 from Patent EP1572962. LF350700 - JP 2014500723-A/158203: Polycomb-Associated Non-Coding RNAs. LF340997 - JP 2014500723-A/148500: Polycomb-Associated Non-Coding RNAs. JD094370 - Sequence 75394 from Patent EP1572962. JD565245 - Sequence 546269 from Patent EP1572962. JD159843 - Sequence 140867 from Patent EP1572962. JD441689 - Sequence 422713 from Patent EP1572962. JD442096 - Sequence 423120 from Patent EP1572962. JD084493 - Sequence 65517 from Patent EP1572962. JD312352 - Sequence 293376 from Patent EP1572962. JD518361 - Sequence 499385 from Patent EP1572962. JD521008 - Sequence 502032 from Patent EP1572962. JD193118 - Sequence 174142 from Patent EP1572962. JD052567 - Sequence 33591 from Patent EP1572962. JD178165 - Sequence 159189 from Patent EP1572962. JD305330 - Sequence 286354 from Patent EP1572962. BC009481 - Homo sapiens spermatogenesis associated 2, mRNA (cDNA clone MGC:15312 IMAGE:3953522), complete cds. AK023229 - Homo sapiens cDNA FLJ13167 fis, clone NT2RP3003726, highly similar to Spermatogenesis-associated protein 2. U28164 - Homo sapiens spermatogenesis associated PD1 mRNA, complete cds. JD253375 - Sequence 234399 from Patent EP1572962. JD155314 - Sequence 136338 from Patent EP1572962. JD477707 - Sequence 458731 from Patent EP1572962. JD541760 - Sequence 522784 from Patent EP1572962. JD493113 - Sequence 474137 from Patent EP1572962. JD159967 - Sequence 140991 from Patent EP1572962. JD365690 - Sequence 346714 from Patent EP1572962. JD123759 - Sequence 104783 from Patent EP1572962. JD341176 - Sequence 322200 from Patent EP1572962. JD060620 - Sequence 41644 from Patent EP1572962. JD056580 - Sequence 37604 from Patent EP1572962. JD055600 - Sequence 36624 from Patent EP1572962. AK295536 - Homo sapiens cDNA FLJ50158 complete cds, highly similar to Spermatogenesis-associated protein 2. JD353257 - Sequence 334281 from Patent EP1572962. JD185786 - Sequence 166810 from Patent EP1572962. JD046003 - Sequence 27027 from Patent EP1572962. AK289644 - Homo sapiens cDNA FLJ78311 complete cds, highly similar to Homo sapiens spermatogenesis associated 2 (SPATA2), mRNA. JD275027 - Sequence 256051 from Patent EP1572962. JD095196 - Sequence 76220 from Patent EP1572962. DQ893485 - Synthetic construct clone IMAGE:100006115; FLH194082.01X; RZPDo839F0379D spermatogenesis associated 2 (SPATA2) gene, encodes complete protein. AB383978 - Synthetic construct DNA, clone: pF1KSDA0757, Homo sapiens SPATA2 gene for spermatogenesis-associated protein 2, complete cds, without stop codon, in Flexi system. KJ892859 - Synthetic construct Homo sapiens clone ccsbBroadEn_02253 SPATA2 gene, encodes complete protein. DQ896412 - Synthetic construct Homo sapiens clone IMAGE:100010872; FLH194078.01L; RZPDo839F0369D spermatogenesis associated 2 (SPATA2) gene, encodes complete protein. CU679377 - Synthetic construct Homo sapiens gateway clone IMAGE:100020699 5' read SPATA2 mRNA. LF350701 - JP 2014500723-A/158204: Polycomb-Associated Non-Coding RNAs. LF350702 - JP 2014500723-A/158205: Polycomb-Associated Non-Coding RNAs. JD487416 - Sequence 468440 from Patent EP1572962. JD185497 - Sequence 166521 from Patent EP1572962. JD216683 - Sequence 197707 from Patent EP1572962. MA586275 - JP 2018138019-A/158201: Polycomb-Associated Non-Coding RNAs. MA586276 - JP 2018138019-A/158202: Polycomb-Associated Non-Coding RNAs. MA586277 - JP 2018138019-A/158203: Polycomb-Associated Non-Coding RNAs. MA586278 - JP 2018138019-A/158204: Polycomb-Associated Non-Coding RNAs. MA586279 - JP 2018138019-A/158205: Polycomb-Associated Non-Coding RNAs. MA441609 - JP 2018138019-A/13535: Polycomb-Associated Non-Coding RNAs. MA446347 - JP 2018138019-A/18273: Polycomb-Associated Non-Coding RNAs. MA576577 - JP 2018138019-A/148503: Polycomb-Associated Non-Coding RNAs. MA576576 - JP 2018138019-A/148502: Polycomb-Associated Non-Coding RNAs. MA576575 - JP 2018138019-A/148501: Polycomb-Associated Non-Coding RNAs. MA576574 - JP 2018138019-A/148500: Polycomb-Associated Non-Coding RNAs.

Other Names for This Gene


	Alternate Gene Symbols: E1P626, ENST00000289431.1, ENST00000289431.2, ENST00000289431.3, ENST00000289431.4, ENST00000289431.5, ENST00000289431.6, ENST00000289431.7, ENST00000289431.8, ENST00000289431.9, KIAA0757 , NM_006038, O94857, PD1 , Q9UM82, SPAT2_HUMAN, SPATA2 , uc317ksc.1, uc317ksc.2 UCSC ID: ENST00000289431.10_7 RefSeq Accession: NM_006038.4 Protein: Q9UM82 (aka SPAT2_HUMAN or SPA2_HUMAN)

Gene Model Information


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Methods, Credits, and Use Restrictions


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