U.S. flag

An official website of the United States government

Format

Send to:

Choose Destination

Links from GEO Profiles

    • Showing Current items.

    Supt6h SPT6 homolog, histone chaperone and transcription elongation factor [ Rattus norvegicus (Norway rat) ]

    Gene ID: 303281, updated on 9-Dec-2024

    Summary

    Go to the top of the page Help
    Official Symbol
    Supt6hprovided by RGD
    Official Full Name
    SPT6 homolog, histone chaperone and transcription elongation factorprovided by RGD
    Primary source
    RGD:1309290
    See related
    EnsemblRapid:ENSRNOG00000012240 AllianceGenome:RGD:1309290
    Gene type
    protein coding
    RefSeq status
    PROVISIONAL
    Organism
    Rattus norvegicus
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
    Summary
    Predicted to enable histone binding activity and nucleosome binding activity. Predicted to be involved in several processes, including chromatin remodeling; regulation of mRNA export from nucleus; and regulation of nucleobase-containing compound metabolic process. Predicted to act upstream of or within blastocyst formation. Predicted to be part of transcription elongation factor complex. Orthologous to human SUPT6H (SPT6 homolog, histone chaperone and transcription elongation factor). [provided by Alliance of Genome Resources, Dec 2024]
    Expression
    Biased expression in Adrenal (RPKM 237.3), Spleen (RPKM 159.6) and 9 other tissues See more
    Orthologs
    human mouse all
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    Go to the top of the page Help
    See Supt6h in Genome Data Viewer
    Location:
    10q25
    Exon count:
    41
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCr8 (GCF_036323735.1) 10 NC_086028.1 (63601990..63638851, complement)
    RS_2023_06 previous assembly mRatBN7.2 (GCF_015227675.2) 10 NC_051345.1 (63103920..63140780, complement)
    106 previous assembly Rnor_6.0 (GCF_000001895.5) 10 NC_005109.4 (65470470..65507581, complement)

    Chromosome 10 - NC_086028.1Genomic Context describing neighboring genes Neighboring gene RAB34, member RAS oncogene family Neighboring gene protein interacting with cyclin A1 Neighboring gene stromal cell derived factor 2 Neighboring gene bridge-like lipid transfer protein family member 2 Neighboring gene uncharacterized LOC120095269 Neighboring gene U6 spliceosomal RNA Neighboring gene ribosomal protein L37A, pseudogene 13 Neighboring gene ribosomal protein S6 kinase related

    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: A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages
    • Description: 320 RNA samples isolated from 11 organs (adrenal gland, brain, heart, kidney, liver, lung, muscle, spleen, thymus, and testes or uterus) from both sexes of Fischer 344 rats across four developmental stages (2-, 6-, 21-, and 104-weeks-old)
    • BioProject: PRJNA238328
    • Publication: PMID 24510058
    • Analysis date: Mon Jun 6 17:44:12 2016

    Bibliography

    Go to the top of the pageHelp

    Related articles in PubMed

    1. Functional interaction between pleiotropic transactivator pUL69 of human cytomegalovirus and the human homolog of yeast chromatin regulatory protein SPT6. Winkler M, et al. J Virol, 2000 Sep. PMID 10933715, Free PMC Article
    2. The histone chaperone Spt6 coordinates histone H3K27 demethylation and myogenesis. Wang AH, et al. EMBO J, 2013 Apr 17. PMID 23503590, Free PMC Article
    3. Histone chaperone Spt6 is required for class switch recombination but not somatic hypermutation. Okazaki IM, et al. Proc Natl Acad Sci U S A, 2011 May 10. PMID 21518874, Free PMC Article
    4. The Spt6 SH2 domain binds Ser2-P RNAPII to direct Iws1-dependent mRNA splicing and export. Yoh SM, et al. Genes Dev, 2007 Jan 15. PMID 17234882, Free PMC Article
    5. JUNB-FBXO21-ERK axis promotes cartilage degeneration in osteoarthritis by inhibiting autophagy. Lin Z, et al. Aging Cell, 2021 Feb. PMID 33450132, Free PMC Article

    See all (10) citations in PubMed

    GeneRIFs: Gene References Into Functions

    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

    Gene Ontology Provided by RGD

    Function Evidence Code Pubs
    enables DNA binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables histone binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables histone binding ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables nucleosome binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    Process Evidence Code Pubs
    acts_upstream_of_or_within blastocyst formation ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in nucleosome organization IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in positive regulation of transcription elongation by RNA polymerase II ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in regulation of isotype switching ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in regulation of mRNA export from nucleus ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in regulation of mRNA processing ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in regulation of muscle cell differentiation ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in transcription elongation by RNA polymerase II IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in transcription elongation-coupled chromatin remodeling ISO
    Inferred from Sequence Orthology
    more info
    		  
    Component Evidence Code Pubs
    part_of transcription elongation factor complex IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  

    General protein information

    Go to the top of the page Help
    Preferred Names
    transcription elongation factor SPT6

    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_001191820.2 → NP_001178749.1  transcription elongation factor SPT6

      Status: PROVISIONAL

      Source sequence(s)
      JAXUCZ010000010
      UniProtKB/TrEMBL
      A0A8I6AFN6
      Related
      ENSRNOP00000016759.6, ENSRNOT00000016759.8
      Conserved Domains (10) summary
      smart00316
      Location:1227 → 1282
      S1; Ribosomal protein S1-like RNA-binding domain
      cd09918
      Location:1331 → 1415
      SH2_Nterm_SPT6_like; N-terminal Src homology 2 (SH2) domain found in Spt6
      cd09928
      Location:1424 → 1515
      SH2_Cterm_SPT6_like; C-terminal Src homology 2 (SH2) domain found in Spt6
      COG2183
      Location:372 → 1353
      Tex; Transcriptional accessory protein Tex/SPT6 [Transcription]
      pfam14639
      Location:775 → 931
      YqgF; Holliday-junction resolvase-like of SPT6
      pfam09371
      Location:565 → 623
      Tex_N; Tex-like protein N-terminal domain
      pfam14633
      Location:1304 → 1514
      SH2_2; SH2 domain
      pfam14635
      Location:935 → 1038
      HHH_7; Helix-hairpin-helix motif
      pfam14641
      Location:348 → 422
      HTH_44; Helix-turn-helix DNA-binding domain of SPT6
      pfam14878
      Location:1053 → 1157
      DLD; Death-like domain of SPT6

    RefSeqs of Annotated Genomes: GCF_036323735.1-RS_2024_02

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

    Reference GRCr8

    Genomic

    1. NC_086028.1 Reference GRCr8

      Range
      63601990..63638851 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_039085998.2 → XP_038941926.1  transcription elongation factor SPT6 isoform X2

      UniProtKB/TrEMBL
      A0A8I6AFN6
      Conserved Domains (2) summary
      COG2183
      Location:370 → 1351
      Tex; Transcriptional accessory protein Tex/SPT6 [Transcription]
      pfam14633
      Location:1306 → 1510
      SH2_2; SH2 domain

    2. XM_008768006.4 → XP_008766228.1  transcription elongation factor SPT6 isoform X1

      See identical proteins and their annotated locations for XP_008766228.1

      UniProtKB/TrEMBL
      A0A0G2K0J0, A0A8I6AFN6
      Conserved Domains (10) summary
      smart00316
      Location:1226 → 1281
      S1; Ribosomal protein S1-like RNA-binding domain
      cd09918
      Location:1330 → 1414
      SH2_Nterm_SPT6_like; N-terminal Src homology 2 (SH2) domain found in Spt6
      cd09928
      Location:1423 → 1514
      SH2_Cterm_SPT6_like; C-terminal Src homology 2 (SH2) domain found in Spt6
      COG2183
      Location:371 → 1352
      Tex; Transcriptional accessory protein Tex/SPT6 [Transcription]
      pfam14639
      Location:774 → 930
      YqgF; Holliday-junction resolvase-like of SPT6
      pfam09371
      Location:564 → 622
      Tex_N; Tex-like protein N-terminal domain
      pfam14633
      Location:1303 → 1513
      SH2_2; SH2 domain
      pfam14635
      Location:934 → 1037
      HHH_7; Helix-hairpin-helix motif
      pfam14641
      Location:347 → 421
      HTH_44; Helix-turn-helix DNA-binding domain of SPT6
      pfam14878
      Location:1052 → 1156
      DLD; Death-like domain of SPT6

    3. XM_008768008.4 → XP_008766230.1  transcription elongation factor SPT6 isoform X3

      UniProtKB/TrEMBL
      A0A8I6AFN6, F1LR36
      Conserved Domains (10) summary
      smart00316
      Location:1104 → 1159
      S1; Ribosomal protein S1-like RNA-binding domain
      cd09918
      Location:1208 → 1292
      SH2_Nterm_SPT6_like; N-terminal Src homology 2 (SH2) domain found in Spt6
      cd09928
      Location:1301 → 1392
      SH2_Cterm_SPT6_like; C-terminal Src homology 2 (SH2) domain found in Spt6
      COG2183
      Location:249 → 1230
      Tex; Transcriptional accessory protein Tex/SPT6 [Transcription]
      pfam14639
      Location:652 → 808
      YqgF; Holliday-junction resolvase-like of SPT6
      pfam09371
      Location:442 → 500
      Tex_N; Tex-like protein N-terminal domain
      pfam14633
      Location:1181 → 1391
      SH2_2; SH2 domain
      pfam14635
      Location:812 → 915
      HHH_7; Helix-hairpin-helix motif
      pfam14641
      Location:225 → 299
      HTH_44; Helix-turn-helix DNA-binding domain of SPT6
      pfam14878
      Location:930 → 1034
      DLD; Death-like domain of SPT6

    4. XM_063269048.1 → XP_063125118.1  transcription elongation factor SPT6 isoform X2

      UniProtKB/TrEMBL
      A0A8I6AFN6

    5. XM_008768007.4 → XP_008766229.1  transcription elongation factor SPT6 isoform X1

      See identical proteins and their annotated locations for XP_008766229.1

      UniProtKB/TrEMBL
      A0A0G2K0J0, A0A8I6AFN6
      Related
      ENSRNOP00000071467.1, ENSRNOT00000089615.3
      Conserved Domains (10) summary
      smart00316
      Location:1226 → 1281
      S1; Ribosomal protein S1-like RNA-binding domain
      cd09918
      Location:1330 → 1414
      SH2_Nterm_SPT6_like; N-terminal Src homology 2 (SH2) domain found in Spt6
      cd09928
      Location:1423 → 1514
      SH2_Cterm_SPT6_like; C-terminal Src homology 2 (SH2) domain found in Spt6
      COG2183
      Location:371 → 1352
      Tex; Transcriptional accessory protein Tex/SPT6 [Transcription]
      pfam14639
      Location:774 → 930
      YqgF; Holliday-junction resolvase-like of SPT6
      pfam09371
      Location:564 → 622
      Tex_N; Tex-like protein N-terminal domain
      pfam14633
      Location:1303 → 1513
      SH2_2; SH2 domain
      pfam14635
      Location:934 → 1037
      HHH_7; Helix-hairpin-helix motif
      pfam14641
      Location:347 → 421
      HTH_44; Helix-turn-helix DNA-binding domain of SPT6
      pfam14878
      Location:1052 → 1156
      DLD; Death-like domain of SPT6

    6. XM_063269049.1 → XP_063125119.1  transcription elongation factor SPT6 isoform X3

      UniProtKB/TrEMBL
      A0A8I6AFN6, F1LR36

    7. XM_063269047.1 → XP_063125117.1  transcription elongation factor SPT6 isoform X1

      UniProtKB/TrEMBL
      A0A0G2K0J0, A0A8I6AFN6

    8. XM_063269045.1 → XP_063125115.1  transcription elongation factor SPT6 isoform X1

      UniProtKB/TrEMBL
      A0A0G2K0J0, A0A8I6AFN6

    9. XM_063269046.1 → XP_063125116.1  transcription elongation factor SPT6 isoform X1

      UniProtKB/TrEMBL
      A0A0G2K0J0, A0A8I6AFN6

    RNA

    1. XR_005489830.2 RNA Sequence

    Nucleotide Protein Strain
    Heading Accession and Version

    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