Format

Send to:

Choose Destination

Links from GEO Profiles

    • Showing Current items.

    SWT1 SWT1 RNA endoribonuclease homolog [ Homo sapiens (human) ]

    Gene ID: 54823, updated on 3-Apr-2024

    Summary

    Go to the top of the page Help
    Official Symbol
    SWT1provided by HGNC
    Official Full Name
    SWT1 RNA endoribonuclease homologprovided by HGNC
    Primary source
    HGNC:HGNC:16785
    See related
    Ensembl:ENSG00000116668 MIM:619513; AllianceGenome:HGNC:16785
    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
    HsSwt1; C1orf26
    Summary
    Predicted to be active in nucleus. [provided by Alliance of Genome Resources, Apr 2022]
    Expression
    Broad expression in testis (RPKM 13.8), bone marrow (RPKM 2.1) and 20 other tissues See more
    Orthologs
    mouse all
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    Go to the top of the page Help
    Location:
    1q25.3
    Exon count:
    25
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (185157060..185291781)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (184513970..184648685)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (185126192..185260913)

    Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr1:184985922-184987121 Neighboring gene RNA, 5S ribosomal pseudogene 72 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1643 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr1:185034115-185035314 Neighboring gene ReSE screen-validated silencer GRCh37_chr1:185041955-185042087 Neighboring gene ring finger protein 2 Neighboring gene ferritin heavy chain 1 pseudogene 25 Neighboring gene tRNA methyltransferase 1 like Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:185125173-185126078 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1645 Neighboring gene ribosomal protein L22 pseudogene 24 Neighboring gene ribosomal protein L5 pseudogene 5 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:185226026-185226636 Neighboring gene uncharacterized LOC105371651 Neighboring gene proteasome (prosome, macropain) 26S subunit, non-ATPase, 7 pseudogene Neighboring gene influenza virus NS1A binding protein Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:185285701-185286314 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1647 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2242 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2243 Neighboring gene microtubule associated protein 1 light chain 3 beta pseudogene Neighboring gene CBS mRNA stabilizing lncRNA

    Genomic regions, transcripts, and products

    Go to the top of the page Help

    Go to nucleotide: Graphics FASTA GenBank

    Expression

    Go to the top of the page Help
    • 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

    Go to the top of the pageHelp

    Related articles in PubMed

    1. Cloning and characterization of 13 novel transcripts and the human RGS8 gene from the 1q25 region encompassing the hereditary prostate cancer (HPC1) locus. Sood R, et al. Genomics, 2001 Apr 15. PMID 11318611
    2. An endoribonuclease functionally linked to perinuclear mRNP quality control associates with the nuclear pore complexes. Skruzný M, et al. PLoS Biol, 2009 Jan 6. PMID 19127978, Free PMC Article
    3. Aurora kinase A regulates Survivin stability through targeting FBXL7 in gastric cancer drug resistance and prognosis. Kamran M, et al. Oncogenesis, 2017 Feb 20. PMID 28218735, Free PMC Article
    4. Replication of previous genome-wide association studies of bone mineral density in premenopausal American women. Ichikawa S, et al. J Bone Miner Res, 2010 Aug. PMID 20200978, Free PMC Article
    5. Coeliac disease-associated risk variants in TNFAIP3 and REL implicate altered NF-kappaB signalling. Trynka G, et al. Gut, 2009 Aug. PMID 19240061

    See all (16) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Observational study of gene-disease association. (HuGE Navigator)
      Title: New genetic associations detected in a host response study to hepatitis B vaccine.
    Submit: New GeneRIF Correction

    Phenotypes

    Go to the top of the page Help

    Find tests for this gene in the NIH Genetic Testing Registry (GTR)

    Review eQTL and phenotype association data in this region using PheGenI

    Variation

    Go to the top of the page Help

    See variants in ClinVar

    See studies and variants in dbVar

    See Variation Viewer (GRCh37.p13)

    See Variation Viewer (GRCh38)

    Genotypes

    Interactions

    Go to the top of the page Help
    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Go to the top of the page Help

    Markers

    Homology

    Clone Names

    • FLJ20121, FLJ35944

    Gene Ontology Provided by GOA

    Component Evidence Code Pubs
    is_active_in nucleus IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  

    General protein information

    Go to the top of the page Help
    Preferred Names
    transcriptional protein SWT1

    NCBI Reference Sequences (RefSeq)

    Go to the top of the page Help

    NEW Try the new Transcript table

    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_001105518.2 → NP_001098988.1  transcriptional protein SWT1

      See identical proteins and their annotated locations for NP_001098988.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) differs in the 5' UTR compared to variant 1. Both variants 1 and 2 encode the same protein.
      Source sequence(s)
      AF288392, AK000128, AK127980, BI756018, DB453411, DB518900
      Consensus CDS
      CCDS1367.1
      UniProtKB/Swiss-Prot
      Q5T5J6, Q8NEK9, Q9BZQ7, Q9NXQ0
      UniProtKB/TrEMBL
      A8K5X8
      Related
      ENSP00000356471.3, ENST00000367501.7
      Conserved Domains (1) summary
      cd18727
      Location:391 → 532
      PIN_Swt1-like; VapC-like PIN domain of Saccharomyces cerevisiae Swt1p, human SWT1 and related proteins

    2. NM_017673.7 → NP_060143.4  transcriptional protein SWT1

      See identical proteins and their annotated locations for NP_060143.4

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) represents the longer transcript. Both variants 1 and 2 encode the same protein.
      Source sequence(s)
      AF288392, AK000128, BC030781, BI756018, DB518900
      Consensus CDS
      CCDS1367.1
      UniProtKB/Swiss-Prot
      Q5T5J6, Q8NEK9, Q9BZQ7, Q9NXQ0
      UniProtKB/TrEMBL
      A8K5X8
      Related
      ENSP00000356470.4, ENST00000367500.9
      Conserved Domains (1) summary
      cd18727
      Location:391 → 532
      PIN_Swt1-like; VapC-like PIN domain of Saccharomyces cerevisiae Swt1p, human SWT1 and related proteins

    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_000001.11 Reference GRCh38.p14 Primary Assembly

      Range
      185157060..185291781
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_005245271.3 → XP_005245328.1  transcriptional protein SWT1 isoform X1

      See identical proteins and their annotated locations for XP_005245328.1

      UniProtKB/TrEMBL
      A8K5X8
      Conserved Domains (1) summary
      cd09880
      Location:396 → 537
      PIN_Smg5-Smg6-like; PIN domain

    2. XM_047423246.1 → XP_047279202.1  transcriptional protein SWT1 isoform X3

    3. XM_017001528.3 → XP_016857017.1  transcriptional protein SWT1 isoform X3

      UniProtKB/TrEMBL
      A8K5X8

    4. XM_017001530.3 → XP_016857019.1  transcriptional protein SWT1 isoform X5

      UniProtKB/TrEMBL
      A8K5X8

    5. XM_011509657.2 → XP_011507959.1  transcriptional protein SWT1 isoform X1

      See identical proteins and their annotated locations for XP_011507959.1

      UniProtKB/TrEMBL
      A8K5X8
      Conserved Domains (1) summary
      cd09880
      Location:396 → 537
      PIN_Smg5-Smg6-like; PIN domain

    6. XM_005245273.2 → XP_005245330.1  transcriptional protein SWT1 isoform X1

      See identical proteins and their annotated locations for XP_005245330.1

      UniProtKB/TrEMBL
      A8K5X8
      Conserved Domains (1) summary
      cd09880
      Location:396 → 537
      PIN_Smg5-Smg6-like; PIN domain

    7. XM_017001527.2 → XP_016857016.1  transcriptional protein SWT1 isoform X2

      UniProtKB/Swiss-Prot
      Q5T5J6, Q8NEK9, Q9BZQ7, Q9NXQ0
      UniProtKB/TrEMBL
      A8K5X8
      Conserved Domains (1) summary
      cd18727
      Location:391 → 532
      PIN_Swt1-like; VapC-like PIN domain of Saccharomyces cerevisiae Swt1p, human SWT1 and related proteins

    8. XM_047423249.1 → XP_047279205.1  transcriptional protein SWT1 isoform X6

    9. XM_047423243.1 → XP_047279199.1  transcriptional protein SWT1 isoform X2

      UniProtKB/Swiss-Prot
      Q5T5J6, Q8NEK9, Q9BZQ7, Q9NXQ0

    10. XM_024447752.2 → XP_024303520.1  transcriptional protein SWT1 isoform X1

      UniProtKB/TrEMBL
      A8K5X8
      Conserved Domains (1) summary
      cd09880
      Location:396 → 537
      PIN_Smg5-Smg6-like; PIN domain

    11. XM_024447754.2 → XP_024303522.1  transcriptional protein SWT1 isoform X2

      UniProtKB/Swiss-Prot
      Q5T5J6, Q8NEK9, Q9BZQ7, Q9NXQ0
      UniProtKB/TrEMBL
      A8K5X8
      Conserved Domains (1) summary
      cd18727
      Location:391 → 532
      PIN_Swt1-like; VapC-like PIN domain of Saccharomyces cerevisiae Swt1p, human SWT1 and related proteins

    12. XM_024447753.2 → XP_024303521.1  transcriptional protein SWT1 isoform X1

      UniProtKB/TrEMBL
      A8K5X8
      Conserved Domains (1) summary
      cd09880
      Location:396 → 537
      PIN_Smg5-Smg6-like; PIN domain

    13. XM_047423248.1 → XP_047279204.1  transcriptional protein SWT1 isoform X4

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060925.1 Alternate T2T-CHM13v2.0

      Range
      184513970..184648685
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054337210.1 → XP_054193185.1  transcriptional protein SWT1 isoform X1

    2. XM_054337215.1 → XP_054193190.1  transcriptional protein SWT1 isoform X3

    3. XM_054337216.1 → XP_054193191.1  transcriptional protein SWT1 isoform X3

    4. XM_054337218.1 → XP_054193193.1  transcriptional protein SWT1 isoform X5

    5. XM_054337207.1 → XP_054193182.1  transcriptional protein SWT1 isoform X1

    6. XM_054337214.1 → XP_054193189.1  transcriptional protein SWT1 isoform X2

      UniProtKB/Swiss-Prot
      Q5T5J6, Q8NEK9, Q9BZQ7, Q9NXQ0

    7. XM_054337209.1 → XP_054193184.1  transcriptional protein SWT1 isoform X1

    8. XM_054337219.1 → XP_054193194.1  transcriptional protein SWT1 isoform X6

    9. XM_054337212.1 → XP_054193187.1  transcriptional protein SWT1 isoform X2

      UniProtKB/Swiss-Prot
      Q5T5J6, Q8NEK9, Q9BZQ7, Q9NXQ0

    10. XM_054337208.1 → XP_054193183.1  transcriptional protein SWT1 isoform X1

    11. XM_054337213.1 → XP_054193188.1  transcriptional protein SWT1 isoform X2

      UniProtKB/Swiss-Prot
      Q5T5J6, Q8NEK9, Q9BZQ7, Q9NXQ0

    12. XM_054337211.1 → XP_054193186.1  transcriptional protein SWT1 isoform X1

    13. XM_054337217.1 → XP_054193192.1  transcriptional protein SWT1 isoform X4

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q5T5J6.1 GenPept UniProtKB/Swiss-Prot:Q5T5J6

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

    Chemical Information
    Molecular Biology Databases
    Research Materials
    Tools
    Miscellaneous