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SPIN3 spindlin family member 3 [ Homo sapiens (human) ]

Gene ID: 169981, updated on 5-Mar-2024

Summary

Official Symbol
SPIN3provided by HGNC
Official Full Name
spindlin family member 3provided by HGNC
Primary source
HGNC:HGNC:27272
See related
Ensembl:ENSG00000204271 AllianceGenome:HGNC:27272
Gene type
protein coding
RefSeq status
VALIDATED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
SPIN-3; TDRD27; bA445O16.1
Summary
Enables methylated histone binding activity. Predicted to be involved in regulation of transcription, DNA-templated. Predicted to be integral component of membrane. Predicted to be active in cytosol and nucleoplasm. [provided by Alliance of Genome Resources, Apr 2022]
Expression
Ubiquitous expression in brain (RPKM 4.7), prostate (RPKM 3.7) and 24 other tissues See more
Orthologs
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Genomic context

See SPIN3 in Genome Data Viewer
Location:
Xp11.21
Exon count:
5
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) X NC_000023.11 (56975120..56995541, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) X NC_060947.1 (56273946..56294627, complement)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) X NC_000023.10 (57001553..57021974, complement)

Chromosome X - NC_000023.11Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC124905194 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29689 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20869 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29690 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29691 Neighboring gene H3K4me1 hESC enhancer GRCh37_chrX:56790193-56790694 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29693 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29695 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29694 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chrX:56796358-56796874 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chrX:56796875-56797391 Neighboring gene ubiquinol-cytochrome c reductase binding protein pseudogene 1 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chrX:56798078-56798669 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chrX:56798670-56799260 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chrX:56799261-56799852 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chrX:56804396-56805293 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chrX:56805294-56806192 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29696 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29697 Neighboring gene negative regulator of P-body association Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29698 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29699 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29700 Neighboring gene Sharpr-MPRA regulatory region 15663 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29701 Neighboring gene SPIN2 family pseudogene 1 Neighboring gene MED14-independent group 3 enhancer GRCh37_chrX:57143727-57144926 Neighboring gene spindlin family member 2B

Genomic regions, transcripts, and products

Expression

  • 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

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Clone Names

  • FLJ41127, FLJ54952, MGC40395

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables methylated histone binding IBA
Inferred from Biological aspect of Ancestor
more info
 
enables methylated histone binding IDA
Inferred from Direct Assay
more info
PubMed 
enables protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
Process Evidence Code Pubs
involved_in gamete generation IEA
Inferred from Electronic Annotation
more info
 
involved_in regulation of DNA-templated transcription IBA
Inferred from Biological aspect of Ancestor
more info
 
Component Evidence Code Pubs
is_active_in cytosol IBA
Inferred from Biological aspect of Ancestor
more info
 
is_active_in nucleoplasm IBA
Inferred from Biological aspect of Ancestor
more info
 

General protein information

Preferred Names
spindlin-3
Names
bA445O16.1 (DXF34)
spindlin-like protein 3

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.

mRNA and Protein(s)

  1. NM_001010862.3NP_001010862.2  spindlin-3

    See identical proteins and their annotated locations for NP_001010862.2

    Status: VALIDATED

    Description
    Transcript Variant: This variant (1) represents the longer transcript and encodes the functional protein.
    Source sequence(s)
    AJ271379, AL139397, BX403408, DB151976
    Consensus CDS
    CCDS43963.1
    UniProtKB/Swiss-Prot
    B2RUW3, B7Z8W2, Q5JUX0, Q8N5D9
    Related
    ENSP00000364054.3, ENST00000374919.6
    Conserved Domains (1) summary
    pfam02513
    Location:5099
    Spin-Ssty; Spin/Ssty Family

RNA

  1. NR_027139.2 RNA Sequence

    Status: VALIDATED

    Description
    Transcript Variant: This variant (2) includes three alternate exons at its 3' end, compared to variant 1. This variant is represented as non-coding because the use of the supported translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
    Source sequence(s)
    AL139397, BC032490, DB151976
    Related
    ENST00000640131.1

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_000023.11 Reference GRCh38.p14 Primary Assembly

    Range
    56975120..56995541 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_006724578.4XP_006724641.1  spindlin-3 isoform X1

    See identical proteins and their annotated locations for XP_006724641.1

    UniProtKB/Swiss-Prot
    B2RUW3, B7Z8W2, Q5JUX0, Q8N5D9
    Related
    ENSP00000492381.1, ENST00000639007.1
    Conserved Domains (1) summary
    pfam02513
    Location:5099
    Spin-Ssty; Spin/Ssty Family
  2. XM_006724577.4XP_006724640.1  spindlin-3 isoform X1

    See identical proteins and their annotated locations for XP_006724640.1

    UniProtKB/Swiss-Prot
    B2RUW3, B7Z8W2, Q5JUX0, Q8N5D9
    Related
    ENSP00000491624.1, ENST00000638386.1
    Conserved Domains (1) summary
    pfam02513
    Location:5099
    Spin-Ssty; Spin/Ssty Family
  3. XM_017029315.2XP_016884804.1  spindlin-3 isoform X1

    UniProtKB/Swiss-Prot
    B2RUW3, B7Z8W2, Q5JUX0, Q8N5D9
    Related
    ENSP00000492795.1, ENST00000638257.1
    Conserved Domains (1) summary
    pfam02513
    Location:5099
    Spin-Ssty; Spin/Ssty Family

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060947.1 Alternate T2T-CHM13v2.0

    Range
    56273946..56294627 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054326594.1XP_054182569.1  spindlin-3 isoform X1

    UniProtKB/Swiss-Prot
    B2RUW3, B7Z8W2, Q5JUX0, Q8N5D9
  2. XM_054326595.1XP_054182570.1  spindlin-3 isoform X1

    UniProtKB/Swiss-Prot
    B2RUW3, B7Z8W2, Q5JUX0, Q8N5D9
  3. XM_054326593.1XP_054182568.1  spindlin-3 isoform X1

    UniProtKB/Swiss-Prot
    B2RUW3, B7Z8W2, Q5JUX0, Q8N5D9