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LOC100254333 transcription elongation factor SPT6 homolog [ Vitis vinifera (wine grape) ]

Gene ID: 100254333, updated on 23-Oct-2023

Summary

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Gene symbol
LOC100254333
Gene description
transcription elongation factor SPT6 homolog
Locus tag
VIT_00012377001
Gene type
protein coding
RefSeq status
MODEL
Organism
Vitis vinifera
Lineage
Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliopsida; eudicotyledons; Gunneridae; Pentapetalae; rosids; Vitales; Vitaceae; Viteae; Vitis
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Genomic context

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See LOC100254333 in Genome Data Viewer
Location:
chromosome: 13
Exon count:
17
Annotation release Status Assembly Chr Location
RS_2023_09 current ASM3070453v1 (GCF_030704535.1) 13 NC_081817.1 (20677801..20689651)
102 previous assembly 12X (GCF_000003745.3) 13 Unlocalized Scaffold NW_003724178.1 (259238..271088, complement)

Chromosome 13 - NC_081817.1Genomic Context describing neighboring genes Neighboring gene transcription elongation factor SPT6-like Neighboring gene phenylacetaldehyde reductase Neighboring gene (-)-alpha-terpineol synthase-like Neighboring gene (-)-alpha-terpineol synthase-like

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Bibliography

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Related articles in PubMed

  1. The high polyphenol content of grapevine cultivar tannat berries is conferred primarily by genes that are not shared with the reference genome. Da Silva C, et al. Plant Cell, 2013 Dec. PMID 24319081, Free PMC Article

GeneRIFs: Gene References Into Functions

General gene information

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Homology

Gene Ontology Provided by RefSeq

Function Evidence Code Pubs
enables histone binding IEA
Inferred from Electronic Annotation
more info
 PubMed 
enables nucleic acid binding IEA
Inferred from Electronic Annotation
more info
 PubMed 
enables nucleosome binding IEA
Inferred from Electronic Annotation
more info
 PubMed 
Process Evidence Code Pubs
involved_in mRNA transcription by RNA polymerase II IEA
Inferred from Electronic Annotation
more info
 PubMed 
involved_in nucleosome organization IEA
Inferred from Electronic Annotation
more info
 PubMed 
involved_in positive regulation of transcription elongation by RNA polymerase II IEA
Inferred from Electronic Annotation
more info
 PubMed 
involved_in transcription elongation by RNA polymerase II IEA
Inferred from Electronic Annotation
more info
 PubMed 
involved_in transcription elongation-coupled chromatin remodeling IEA
Inferred from Electronic Annotation
more info
 PubMed 
Component Evidence Code Pubs
part_of transcription elongation factor complex IEA
Inferred from Electronic Annotation
more info
 PubMed 

General protein information

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Preferred Names
transcription elongation factor SPT6 homolog; transcription elongation factor SPT6-like

NCBI Reference Sequences (RefSeq)

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RefSeqs of Annotated Genomes: GCF_030704535.1-RS_2023_09

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

Reference ASM3070453v1 Primary Assembly

Genomic

  1. NC_081817.1 Reference ASM3070453v1 Primary Assembly

    Range
    20677801..20689651
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_010647112.2 → XP_010645414.1  transcription elongation factor SPT6-like isoform X1

    Conserved Domains (12) summary
    smart00732
    Location:721 → 839
    YqgFc; Likely ribonuclease with RNase H fold
    smart00316
    Location:1109 → 1180
    S1; Ribosomal protein S1-like RNA-binding domain
    cd09918
    Location:1229 → 1317
    SH2_Nterm_SPT6_like; N-terminal Src homology 2 (SH2) domain found in Spt6
    cd09928
    Location:1328 → 1414
    SH2_Cterm_SPT6_like; C-terminal Src homology 2 (SH2) domain found in Spt6
    pfam09371
    Location:338 → 573
    Tex_N; Tex-like protein N-terminal domain
    pfam14632
    Location:56 → 124
    SPT6_acidic; Acidic N-terminal SPT6
    pfam14633
    Location:1201 → 1413
    SH2_2; SH2 domain
    pfam14641
    Location:283 → 407
    HTH_44; Helix-turn-helix DNA-binding domain of SPT6
    pfam14878
    Location:997 → 1102
    DLD; Death-like domain of SPT6
    pfam15847
    Location:1440 → 1605
    Loricrin; Major keratinocyte cell envelope protein
    pfam16210
    Location:1520 → 1610
    Keratin_2_tail; Keratin type II cytoskeletal 1 tail
    cl22429
    Location:881 → 982
    HHH_5; Helix-hairpin-helix domain

  2. XM_010647115.3 → XP_010645417.1  transcription elongation factor SPT6 homolog isoform X2

    Conserved Domains (11) summary
    smart00732
    Location:721 → 839
    YqgFc; Likely ribonuclease with RNase H fold
    smart00316
    Location:1109 → 1180
    S1; Ribosomal protein S1-like RNA-binding domain
    cd09928
    Location:1258 → 1344
    SH2_Cterm_SPT6_like; C-terminal Src homology 2 (SH2) domain found in Spt6
    pfam09371
    Location:338 → 573
    Tex_N; Tex-like protein N-terminal domain
    pfam14632
    Location:56 → 124
    SPT6_acidic; Acidic N-terminal SPT6
    pfam14633
    Location:1201 → 1343
    SH2_2; SH2 domain
    pfam14641
    Location:283 → 407
    HTH_44; Helix-turn-helix DNA-binding domain of SPT6
    pfam14878
    Location:997 → 1102
    DLD; Death-like domain of SPT6
    pfam15847
    Location:1370 → 1535
    Loricrin; Major keratinocyte cell envelope protein
    pfam16210
    Location:1450 → 1540
    Keratin_2_tail; Keratin type II cytoskeletal 1 tail
    cl22429
    Location:881 → 982
    HHH_5; Helix-hairpin-helix domain
Nucleotide Protein
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