supt6h SPT6 homolog, histone chaperone and transcription elongation factor [Danio rerio (zebrafish)] - Gene

Summary

Official Symbol: supt6hprovided by ZNC
Official Full Name: SPT6 homolog, histone chaperone and transcription elongation factorprovided by ZNC
Primary source: ZFIN:ZDB-GENE-030131-7949
See related: Ensembl:ENSDARG00000006524 AllianceGenome:ZFIN:ZDB-GENE-030131-7949
Gene type: protein coding
RefSeq status: PROVISIONAL
Organism: Danio rerio
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Actinopterygii; Neopterygii; Teleostei; Ostariophysi; Cypriniformes; Danionidae; Danioninae; Danio
Also known as: Spt6; wu:fj42h11
Summary: Predicted to enable histone binding activity and nucleosome binding activity. Involved in negative regulation of histone H3-K27 methylation. Acts upstream of or within embryonic heart tube development; otic vesicle development; and somitogenesis. Predicted to be located in nucleus. Predicted to be part of transcription elongation factor complex. Predicted to be active in transcriptionally active chromatin. Orthologous to human SUPT6H (SPT6 homolog, histone chaperone and transcription elongation factor). [provided by Alliance of Genome Resources, Apr 2022]
Orthologs: human mouse all
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Genomic context

Location:: chromosome: 21

Exon count:: 38

Annotation release	Status	Assembly	Chr	Location
106	current	GRCz11 (GCF_000002035.6)	21	NC_007132.7 (26028939..26058547)
105	previous assembly	GRCz10 (GCF_000002035.5)	21	NC_007132.6 (25992248..26021852)

Chromosome 21 - NC_007132.7 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: Sequencing the Zebrafish transcriptome from a range of tissues and developmental stages
Description: Sequencing the Zebrafish transcriptome from a range of tissues and developmental stages
BioProject: PRJEB1986
Analysis date: Fri Dec 8 19:48:10 2017

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Spt6 is essential for the transcriptional response to activation of the Notch pathway.
Title: The role of the SPT6 chromatin remodeling factor in zebrafish embryogenesis.

Submit: New GeneRIF Correction

General gene information

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Gene Ontology Provided by ZFIN

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	ISS Inferred from Sequence or Structural Similarity more info
enables nucleic acid binding	IEA Inferred from Electronic Annotation more info
enables nucleosome binding	IBA Inferred from Biological aspect of Ancestor more info
enables translation elongation factor activity	IEA Inferred from Electronic Annotation more info

Process	Evidence Code	Pubs
acts_upstream_of_or_within embryonic heart tube development	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within heart development	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within nucleobase-containing compound metabolic process	IEA Inferred from Electronic Annotation more info
involved_in nucleosome organization	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of_or_within otic vesicle development	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in positive regulation of transcription elongation by RNA polymerase II	ISS Inferred from Sequence or Structural Similarity more info
acts_upstream_of_or_within somitogenesis	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in transcription elongation by RNA polymerase II	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of_or_within transcription elongation-coupled chromatin remodeling	IEA Inferred from Electronic Annotation more info
involved_in transcription elongation-coupled chromatin remodeling	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within translation	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within translational elongation	IEA Inferred from Electronic Annotation more info

Component	Evidence Code	Pubs
located_in nucleus	IEA Inferred from Electronic Annotation more info
part_of transcription elongation factor complex	IBA Inferred from Biological aspect of Ancestor more info

General protein information

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Preferred Names: transcription elongation factor SPT6

Names: pan; pandora; protein pandora; suppressor of Ty 6 homolog

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)

NM_145118.1 → NP_660094.1 transcription elongation factor SPT6

See identical proteins and their annotated locations for NP_660094.1

Status: PROVISIONAL

Source sequence(s)

AF421378

UniProtKB/Swiss-Prot

Q4V961, Q6P4U2, Q8UVK2

Related

ENSDARP00000013353.6, ENSDART00000028007.7

Conserved Domains (10) summary

smart00316
Location:1218 → 1273

S1; Ribosomal protein S1-like RNA-binding domain

cd09918
Location:1322 → 1406

SH2_Nterm_SPT6_like; N-terminal Src homology 2 (SH2) domain found in Spt6

cd09928
Location:1415 → 1506

SH2_Cterm_SPT6_like; C-terminal Src homology 2 (SH2) domain found in Spt6

COG2183
Location:360 → 1344

Tex; Transcriptional accessory protein Tex/SPT6 [Transcription]

pfam14639
Location:766 → 922

YqgF; Holliday-junction resolvase-like of SPT6

pfam09371
Location:557 → 618

Tex_N; Tex-like protein N-terminal domain

pfam14633
Location:1295 → 1505

SH2_2; SH2 domain

pfam14635
Location:926 → 1029

HHH_7; Helix-hairpin-helix motif

pfam14641
Location:336 → 410

HTH_44; Helix-turn-helix DNA-binding domain of SPT6

pfam14878
Location:1044 → 1148

DLD; Death-like domain of SPT6

RefSeqs of Annotated Genomes: Danio rerio Annotation Release 106 details...

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

Reference GRCz11 Primary Assembly

Genomic

NC_007132.7 Reference GRCz11 Primary Assembly

Range

26028939..26058547

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_009295470.3 → XP_009293745.1 transcription elongation factor SPT6 isoform X1

UniProtKB/TrEMBL

A0A8M3AWY8

Conserved Domains (10) summary

smart00316
Location:1220 → 1275

S1; Ribosomal protein S1-like RNA-binding domain

cd09918
Location:1324 → 1408

SH2_Nterm_SPT6_like; N-terminal Src homology 2 (SH2) domain found in Spt6

cd09928
Location:1417 → 1508

SH2_Cterm_SPT6_like; C-terminal Src homology 2 (SH2) domain found in Spt6

COG2183
Location:360 → 1346

Tex; Transcriptional accessory protein Tex/SPT6 [Transcription]

pfam14639
Location:768 → 924

YqgF; Holliday-junction resolvase-like of SPT6

pfam09371
Location:557 → 618

Tex_N; Tex-like protein N-terminal domain

pfam14633
Location:1297 → 1507

SH2_2; SH2 domain

pfam14635
Location:928 → 1031

HHH_7; Helix-hairpin-helix motif

pfam14641
Location:336 → 410

HTH_44; Helix-turn-helix DNA-binding domain of SPT6

pfam14878
Location:1046 → 1150

DLD; Death-like domain of SPT6