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SPATA41 spermatogenesis associated 41 [ Homo sapiens (human) ]

Gene ID: 388182, updated on 10-Oct-2023

Summary

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Official Symbol
SPATA41provided by HGNC
Official Full Name
spermatogenesis associated 41provided by HGNC
Primary source
HGNC:HGNC:48613
See related
Ensembl:ENSG00000189419 AllianceGenome:HGNC:48613
Gene type
ncRNA
RefSeq status
VALIDATED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
HSD47
Expression
Biased expression in testis (RPKM 2.7), liver (RPKM 0.6) and 11 other tissues See more
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Genomic context

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See SPATA41 in Genome Data Viewer
Location:
15q26.3
Exon count:
2
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 15 NC_000015.10 (100344457..100350718, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 15 NC_060939.1 (98101463..98107725, complement)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 15 NC_000015.9 (100884662..100890923, complement)

Chromosome 15 - NC_000015.10Genomic Context describing neighboring genes Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr15:100515897-100516492 Neighboring gene uncharacterized LOC105371022 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr15:100516493-100517088 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr15:100521898-100522876 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr15:100523855-100524832 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:100532449-100532963 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:100532964-100533477 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr15:100537785-100538412 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:100538413-100539040 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:100539041-100539668 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:100542118-100542966 Neighboring gene ADAM metallopeptidase with thrombospondin type 1 motif 17 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr15:100556815-100558014 Neighboring gene Sharpr-MPRA regulatory region 8829 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:100624491-100624991 Neighboring gene RNA, 5S ribosomal pseudogene 402 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:100648765-100649612 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr15:100651166-100652365 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr15:100663469-100664668 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10166 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10165 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6876 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:100739855-100740621 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:100740622-100741387 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:100742159-100742696 Neighboring gene Sharpr-MPRA regulatory region 9518 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr15:100781303-100782502 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:100805303-100805804 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr15:100819145-100819835 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:100849823-100850322 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr15:100880514-100881032 Neighboring gene uncharacterized LOC105371021 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10167 Neighboring gene CERS3 antisense RNA 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10168 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10169 Neighboring gene ceramide synthase 3 Neighboring gene MPRA-validated peak2453 silencer Neighboring gene RNA, U6 small nuclear 322, pseudogene Neighboring gene PRKX pseudogene 1

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • Project title: HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

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Related articles in PubMed

  1. Identification of a 5-lncRNA-Based Signature for Immune Characteristics and Prognosis of Lung Squamous Cell Carcinoma and Verification of the Function of lncRNA SPATA41. Huan S, et al. Front Genet, 2022. PMID 36105081, Free PMC Article
  2. Diversification of transcriptional modulation: large-scale identification and characterization of putative alternative promoters of human genes. Kimura K, et al. Genome Res, 2006 Jan. PMID 16344560, Free PMC Article
  3. Complete sequencing and characterization of 21,243 full-length human cDNAs. Ota T, et al. Nat Genet, 2004 Jan. PMID 14702039
  4. Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. Strausberg RL, et al. Proc Natl Acad Sci U S A, 2002 Dec 24. PMID 12477932, Free PMC Article

GeneRIFs: Gene References Into Functions

Phenotypes

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Review eQTL and phenotype association data in this region using PheGenI

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Genotypes

General gene information

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Other Names

  • spermatogenesis associated 41 (non-protein coding)

Clone Names

  • FLJ32974, FLJ42289

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

RNA

  1. NR_028139.1 RNA Sequence

    Status: VALIDATED

    Description
    Transcript Variant: This variant (1) represents the longer transcript.
    Source sequence(s)
    AC015723, AK057536, AK124283, BC028144, DB060272
    Related
    ENST00000662214.1

  2. NR_028140.1 RNA Sequence

    Status: VALIDATED

    Description
    Transcript Variant: This variant (2) lacks three alternate segments, compared to variant 1.
    Source sequence(s)
    AC015723, AK057536, BC028144, DB060272
    Related
    ENST00000558307.1

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000015.10 Reference GRCh38.p14 Primary Assembly

    Range
    100344457..100350718 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060939.1 Alternate T2T-CHM13v2.0

    Range
    98101463..98107725 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Suppressed Reference Sequence(s)

The following Reference Sequences have been suppressed. Explain

  1. NM_207383.2: Suppressed sequence

    Description
    NM_207383.2: This RefSeq was permanently suppressed because currently there is support for the transcript but not for the protein.
Nucleotide Protein
Heading Accession and Version

Gene LinkOut

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