Human Gene VCY (ENST00000250825.5_6) from GENCODE V47lift37

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Description: variable charge Y-linked (from RefSeq NM_004679.4)
Gencode Transcript: ENST00000250825.5_6
Gencode Gene: ENSG00000129864.7_7
Transcript (Including UTRs)
Position: hg19 chrY:16,097,652-16,098,353 Size: 702 Total Exon Count: 2 Strand: -
Coding Region
Position: hg19 chrY:16,097,751-16,098,320 Size: 570 Coding Exon Count: 2

Page Index	Sequence and Links	UniProtKB Comments	Primers	MalaCards	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 (chrY:16,097,652-16,098,353)			mRNA (may differ from genome)		Protein (125 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	BioGrid CRISPR DB

Comments and Description Text from UniProtKB


	ID: VCY1_HUMAN DESCRIPTION: RecName: Full=Testis-specific basic protein Y 1; AltName: Full=Basic charge, Y-linked 1; AltName: Full=Variably charged protein Y; FUNCTION: May mediate a process in spermatogenesis or may play a role in sex ratio distortion. TISSUE SPECIFICITY: Expressed exclusively in testis. SIMILARITY: Belongs to the VCX/VCY family.

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: VCY Diseases sorted by gene-association score: chronic laryngitis (2)

Comparative Toxicogenomics Database (CTD)


	The following chemicals interact with this gene D000535 Aluminum D019327 Copper Sulfate

Common Gene Haplotype Alleles


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


	Highest median expression: 0.00 RPKM in (null) Total median expression: 0.00 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	-7.40	33	-0.224	Picture	PostScript	Text
3' UTR	-23.50	99	-0.237	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
IPR026653 - VCX/VCY1

Pfam Domains:
PF15231 - Variable charge X/Y family

ModBase Predicted Comparative 3D Structure on O14598


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 Ontology (GO) Annotations with Structured Vocabulary


	Biological Process: GO:0007420 brain development

Descriptions from all associated GenBank mRNAs


	BC056508 - Homo sapiens variable charge, Y-linked 1B, mRNA (cDNA clone MGC:61936 IMAGE:6450744), complete cds. AF000979 - Homo sapiens testis-specific Basic Protein Y 1 (BPY1) mRNA, complete cds. BC096729 - Homo sapiens variable charge, Y-linked, mRNA (cDNA clone MGC:119817 IMAGE:40014422), complete cds. BC104154 - Homo sapiens variable charge, X-linked 3A, mRNA (cDNA clone MGC:125730 IMAGE:40029402), complete cds. JD210013 - Sequence 191037 from Patent EP1572962. HQ447627 - Synthetic construct Homo sapiens clone IMAGE:100070973; CCSB013357_01 variable charge, Y-linked 1B (VCY1B) gene, encodes complete protein. KJ896135 - Synthetic construct Homo sapiens clone ccsbBroadEn_05529 VCY1B gene, encodes complete protein. CU691160 - Synthetic construct Homo sapiens gateway clone IMAGE:100022360 5' read VCY1B mRNA.

Other Names for This Gene


	Alternate Gene Symbols: BPY1, BPY1B, ENST00000250825.1, ENST00000250825.2, ENST00000250825.3, ENST00000250825.4, NM_004679, O14598, uc317fci.1, uc317fci.2, VCY1A, VCY1B, VCY1_HUMAN UCSC ID: ENST00000250825.5_6 RefSeq Accession: NM_004679.4 Protein: O14598 (aka VCY1_HUMAN)

Gene Model Information


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Methods, Credits, and Use Restrictions


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