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

Gene ID: 303281, updated on 28-Oct-2024

Summary

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, Oct 2024]
Expression
Biased expression in Adrenal (RPKM 237.3), Spleen (RPKM 159.6) and 9 other tissues See more
Orthologs
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Genomic context

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

Expression

  • Project title: A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages 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

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

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
 
Component Evidence Code Pubs
part_of transcription elongation factor complex IBA
Inferred from Biological aspect of Ancestor
more info
 

General protein information

Preferred Names
transcription elongation factor SPT6

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_001191820.2NP_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:12271282
    S1; Ribosomal protein S1-like RNA-binding domain
    cd09918
    Location:13311415
    SH2_Nterm_SPT6_like; N-terminal Src homology 2 (SH2) domain found in Spt6
    cd09928
    Location:14241515
    SH2_Cterm_SPT6_like; C-terminal Src homology 2 (SH2) domain found in Spt6
    COG2183
    Location:3721353
    Tex; Transcriptional accessory protein Tex/SPT6 [Transcription]
    pfam14639
    Location:775931
    YqgF; Holliday-junction resolvase-like of SPT6
    pfam09371
    Location:565623
    Tex_N; Tex-like protein N-terminal domain
    pfam14633
    Location:13041514
    SH2_2; SH2 domain
    pfam14635
    Location:9351038
    HHH_7; Helix-hairpin-helix motif
    pfam14641
    Location:348422
    HTH_44; Helix-turn-helix DNA-binding domain of SPT6
    pfam14878
    Location:10531157
    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_039085998.2XP_038941926.1  transcription elongation factor SPT6 isoform X2

    UniProtKB/TrEMBL
    A0A8I6AFN6
    Conserved Domains (2) summary
    COG2183
    Location:3701351
    Tex; Transcriptional accessory protein Tex/SPT6 [Transcription]
    pfam14633
    Location:13061510
    SH2_2; SH2 domain
  2. XM_008768006.4XP_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:12261281
    S1; Ribosomal protein S1-like RNA-binding domain
    cd09918
    Location:13301414
    SH2_Nterm_SPT6_like; N-terminal Src homology 2 (SH2) domain found in Spt6
    cd09928
    Location:14231514
    SH2_Cterm_SPT6_like; C-terminal Src homology 2 (SH2) domain found in Spt6
    COG2183
    Location:3711352
    Tex; Transcriptional accessory protein Tex/SPT6 [Transcription]
    pfam14639
    Location:774930
    YqgF; Holliday-junction resolvase-like of SPT6
    pfam09371
    Location:564622
    Tex_N; Tex-like protein N-terminal domain
    pfam14633
    Location:13031513
    SH2_2; SH2 domain
    pfam14635
    Location:9341037
    HHH_7; Helix-hairpin-helix motif
    pfam14641
    Location:347421
    HTH_44; Helix-turn-helix DNA-binding domain of SPT6
    pfam14878
    Location:10521156
    DLD; Death-like domain of SPT6
  3. XM_008768008.4XP_008766230.1  transcription elongation factor SPT6 isoform X3

    UniProtKB/TrEMBL
    A0A8I6AFN6, F1LR36
    Conserved Domains (10) summary
    smart00316
    Location:11041159
    S1; Ribosomal protein S1-like RNA-binding domain
    cd09918
    Location:12081292
    SH2_Nterm_SPT6_like; N-terminal Src homology 2 (SH2) domain found in Spt6
    cd09928
    Location:13011392
    SH2_Cterm_SPT6_like; C-terminal Src homology 2 (SH2) domain found in Spt6
    COG2183
    Location:2491230
    Tex; Transcriptional accessory protein Tex/SPT6 [Transcription]
    pfam14639
    Location:652808
    YqgF; Holliday-junction resolvase-like of SPT6
    pfam09371
    Location:442500
    Tex_N; Tex-like protein N-terminal domain
    pfam14633
    Location:11811391
    SH2_2; SH2 domain
    pfam14635
    Location:812915
    HHH_7; Helix-hairpin-helix motif
    pfam14641
    Location:225299
    HTH_44; Helix-turn-helix DNA-binding domain of SPT6
    pfam14878
    Location:9301034
    DLD; Death-like domain of SPT6
  4. XM_063269048.1XP_063125118.1  transcription elongation factor SPT6 isoform X2

  5. XM_008768007.4XP_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:12261281
    S1; Ribosomal protein S1-like RNA-binding domain
    cd09918
    Location:13301414
    SH2_Nterm_SPT6_like; N-terminal Src homology 2 (SH2) domain found in Spt6
    cd09928
    Location:14231514
    SH2_Cterm_SPT6_like; C-terminal Src homology 2 (SH2) domain found in Spt6
    COG2183
    Location:3711352
    Tex; Transcriptional accessory protein Tex/SPT6 [Transcription]
    pfam14639
    Location:774930
    YqgF; Holliday-junction resolvase-like of SPT6
    pfam09371
    Location:564622
    Tex_N; Tex-like protein N-terminal domain
    pfam14633
    Location:13031513
    SH2_2; SH2 domain
    pfam14635
    Location:9341037
    HHH_7; Helix-hairpin-helix motif
    pfam14641
    Location:347421
    HTH_44; Helix-turn-helix DNA-binding domain of SPT6
    pfam14878
    Location:10521156
    DLD; Death-like domain of SPT6
  6. XM_063269049.1XP_063125119.1  transcription elongation factor SPT6 isoform X3

    UniProtKB/TrEMBL
    F1LR36
  7. XM_063269047.1XP_063125117.1  transcription elongation factor SPT6 isoform X1

    UniProtKB/TrEMBL
    A0A0G2K0J0
  8. XM_063269045.1XP_063125115.1  transcription elongation factor SPT6 isoform X1

    UniProtKB/TrEMBL
    A0A0G2K0J0
  9. XM_063269046.1XP_063125116.1  transcription elongation factor SPT6 isoform X1

    UniProtKB/TrEMBL
    A0A0G2K0J0

RNA

  1. XR_005489830.2 RNA Sequence