Gene detail

Detailed information of ANN27092-RA in Montipora grisea

Genomic Location: Scaffold_3670__1_contigs__length_35145:4857...15418
NR annotation: XP_019848744.1, PREDICTED: transcription elongation factor SPT6-like [Amphimedon queenslandica]
Species Montipora grisea · all data for this species · gene families

Gene Structure

More details in JBrowse

Sequence

CDS

ANN27092-RA

ATGTCAAGTCTGGGGACGATATCACAACGATTACGTAAACGTCACCACCTAGACATGGACGAGGAAGATTTTGTTGAGAGTGAGGCTGAAGAGTCTGGTGAGGAGGAAGATTCGTCTTCTGAAGAGGAAGAGGAGGAACAAGGAGACATAGATGATCTGATTGACGATAACGTTGAGGAGGAGGGGGAGGAAGAAGGAGATGGAGAAGATTCAGACACGGACTCAATCAGTCGGAAGAAAACTAGAAAGAGAAAGTTGACTGATGACAGACTGGAGGAGGAGGACTATGAACTCATAAAAGAGAACATTGGCATCGAGCTCCCAAGGGTTAAGTATCGCCGTGTGCGTCAGTTTGACAGTGACGATGAGGAGGGGGAGGACAAGGGAAGTGTGGTGATGGAGAGGGGACGAGATGAAGACAAATCCTTATCCACTGCAGAGACAGAGGACCTAACTCAAGAGAAAGATGTGTTTGGAGACAGCGATGAAGAAGAGTTTCCCGATAGTCAACTCACAGACAAAAGACAAAAGACTCAGGTGGAGGCGAGAAGGCTGGAGGAGCAGGAAGGAGAGATAGGATCTGACTCAGAGGATGCACAAGACATCTTTGGCTTGGACTTTGACCCCACTGAGCTTGAGCAGATGGCAGAGGAAGAGTATGCTAGTGAGGAAGAAGATGACACTGGGGAGCTGAGAACCAAGAAACGAAAAAAGCTCCGCAAAGCCAAAAAGACAATGAGCATTTACAATATCTATGAACCCAGCGAACTGGAGAGGAGACACTTCACAGAGAGGGATGCAGAGATACGTGTCACAGATATGCCAGAGCGGTTTCAGGTGCGCTCAATTCCCGTACAGGCCACGGAGGAGGGGGAACTGGATGAAGAGGCAGAGTGGATCTACCAGCAGGCTTTCTGTAAACCTCCCATTTCCAAACAGCCTTACTACTACACTGACAAGCATCGCAGTGCCTCCCAGCGAGGCGGTTATGGGGCCACGGTCCCAAAGATCAAAGAGGCACTAAACTTTATGAGAAACCATTTCTTTGAAGTCCCGTTCATAGCCAACTACCGGAAGGAGTATGTGGAGCCCGAACTGGACAACCACGACCTCTGGAAGATATGGCTGTGGGACGAAAAGTGGATGCAGCTGCGTCAGCGTAAGAGGAACATGCAGAGGTTGTTTGAACGGATGCAGAGTTACCAGTATGACAAGATCAAGGAACAGCCGGACAAGGCCCTCACCGAGGACACACGCCCACTCACCGAGGAGGACATTAGGAGGTTAGAAGGGATAAAGACCAACGAGGAGCTCCAGGACGTCTACGCACACTTCCTGCTCTACTATGGCCGGGACCTCGTGGCCATGCAGAACAAAAACTCCCACAGGCGAGATGTCCGTGATCTTGACACTGACCTTTCCATGGATGGGGATGTGGAGAAGAAGAAAGGACAGACCTCTGTGAAACAGGCTCACCGGAGGGACTTCTATGCCATCTGCCAGGAGAACGGGCTGGGGTCTCTGGCAGGGAAGTTTGGGCTCACTCCAGAGCAGTTTGGGGAGAACTTAAGAGATAACTACCAGAGACATGAGACAGAGCAGCACACCATTGAACCTGAAGAAGCTGCGGAAGACTACAGACAGGCAACCGGGTATTTCTCCACAATACGTGCTGTGCTTCAGGGGGCGTGTCACATGGTGGCCATGCAGATTGCCTGCGAGCCACTTGTGAGACAGACCCTCAGGCTAGTATTTCAAACTCGGGCTGTCCTCTCCGTCAAACCCACCAAGAAAGGGAAGAAGATGATTGACGACACTCACCCCTGCTTCTCCATGAAGTACCTGCTTAACAAGCCGGTGAGAGAGCTAAAAGGAGACGAGTTTCTGAAGCTGGTTCAGGCGGAGGAAGACAGGCTTATTGAGATGAAGCTGAGCATCGATCTTGAGCGCGGCCAAGAGAAGAGGACTGTGGATCATCATCAGACCTACTTTGAAGAGATACGACAACTGTTCTATCGAGACGAGTTCAGCCTGCTGGTAGAGAAGTGGAATGCCCAGCGAGCTCAGGCTGTAGCCCATGCCCTCCTCAAGGTCCTGTACCCTCTGATGGAGAAAGAGCTCAAAACCAAGTTGCTGAATGAGGCTAAAGATCATGTGTTGCAGAGCTGTGTGCACAAGTTCCGTAGGTGGATTGACATTGCTCCTTTTCCAGTGAAACGGGATGATGAGAGTCTCGTCCCTGAGGAAGGCTCGTATCCCAGGGTCTTGGCTTGTGCTTACACTCCTGATAAAACTGTCCCAGCATTCTGCTGTTTCCTGGATGGCAGTGGTGATGTGGTAGACTTCCTGAGACTCAACCATCTTCTCAAGAGAAGGACGAGTCCCATGGAACGGGAGAGGGAGGAGAAGGAGAATGATCTACAGTCGTTCAAAAAATTTGTGACACAGAAGAGACCCGAACTCATTGTGGTAGCAGCAGAGTCAAGGGAGGCAGTAAGCGTAGTGGAGGATTTCAGGCAGTGTATAGCTGAGCTGGAACAGGAGGAAGACCTGCCACTCATTCCCGTGGAGTTCATAGACCCTAGTGTTTCCAAGATATACTCCAAAGCCAGACGAGGGAGGGAAGAGTTTGCAGACTACCCCGAGCTGCTGCGTATGGCTGTGTCTCTGGGACGACAGATGCAAGAACCACTGATGGAGTTTTCCTCTCTCCTCCTCTCGGAGGACGAGGAAATTTTCTCACTTGGCATGCATCCTTTGCAGAGCTCACTGGCCAAAGACCGGCTTTACCAGGCAATGGAGATTGAACTAGTGTCAAAAGTGAATGAGGTTGGCGTGGATGTCAATTTCTGTCTCGAGCATCCTCACGCTGCTGACATGCTTCCCTTCGTGTGTGGTCTGGGGTCGAGAAAGTCAGCAGCTCTCTTCAAGATTCTGAAGCAGGAGAATGCACAGTTGCAGAATCGTTCTCAGCTGGTGACACAGTGCTCAATAGGACCACACGTCTTCATCAACTGTTCAGGCTTCATCAAGATCGACACTTCTAGATTCACTGACGTTGACAGTATATACATTGAAGTTCTGGACAGTACCAGAGTGCACCCAGAGACCTATGAGTGGGCACGTAAGATGGCTGTTGATGCTCTGGAGTACGATGAGACTGGTGATGAACAGAACCCCAGTGCAGCGGTGGAGGACATTCTTTCCACACCTGACAAGCTGAGGGATTTGGACCTCGATGCCTTTGCAGAGGAGCTGGAGAGACAAGACTATGGCAACAAGAGAACAACACTGTACGATATTCGAGATGAGCTCTTTGGCCCCTACAAGGAACGTCGGACTCCATACGCTCCTCTCTCAAGTGAAGAGAAGTTCATTCTAATGACGGGAGAGACCCCAGAGAGTCTGTACGAGGGTAGATTGATCACGTGTACTGTAGTGGGCATTGTCCGCAAGAAGCAGGTGAGAGAGGTGCTCGACCGAGCCAACCCCATCACCAACGAAAGGACAGGATTCTGGCAGTGTCCCTTTTGTCTCAAATCCGATTTCCGAAACATAAGCTTGGTTTGGCAACACTTTGATGATGGTAGCTGTCCCGGCCAGGGCATAGGGGTGAGGACGAGGCTGGAGAATGGTCTGAGTGGCTTCATACACACGAAGAACCTCAGTGACAGAGCCGTCAGTGCACCAGAGGAGAGAGTACATATTGGAATGACAATTCACTGTCGTATTCTCCGGGTGAACCTGGACAGGTTTTCTGTGGACCTCACCTGTCGATCCTCTGATCTCAGTGACAAGGAGGGCAGGTTTAGTCTACCAAAGGATACATTCTATGACCATGCATTGGCTGAGAGTGAAGAGAAAAAAGAAGAGAATGCGCAGAATAAACCAGCACAAAGATATGTGAAGCGGGTGATTGTTCACCCTTCGTTCATGAACATATCGTTCAAAGATGCGGAGAAGGCGCTGGCAAAGCTGGATCAAGGAGAAGCCATATTCAGACCTAGCAGTAAGGGTCCAGATCATCTTACTATCACCTGGAAGGTGGATGAAGATATACACCAGCACGTTGACATTAAGGAACACGGAAAACCTAACCCGTACAGCTTGGGAAAGTCACTCATGATCGGAAAGGACGAATTCGAGGACCTGGACGAGATTCTTGCCCGCTTTGTTCAGCCAATGGCTGCATATGCTCGTGACCTCCTCACCCACAAATGCTACAGGGCGGCCAACGGCGGGGACAAGAAAACACTTGAGAAACTACTTGCAGAAGAAAAGGCAAAGAACCCTAAACGTATCCCATACTTCTTCAGTGCTTCCAAACAGTACCCAGGCAAGTTCATGCTAGCTTACCAGCCAGCAGGCAAACCAAGGACAGAGCTCATTACTGTCACTCCCGATGGCTTTCGATACCGTGCCCGCGTTCACAACGGAATCAATGAACTCATAAAATGGTTCAAAGAGCACTACCGGGATCCCATGCCTCGCCCTATACCCTCGACCACCTCTCAGGTGCCATCCAATGTCATGGCCACATCTCAGCAAGTGGATCCTAGTATATTGCACCATCTCCAAGCTGCAGTGCACACTGTCCACCACCAACGAGGAGGAAGCAGCACAGGGACCCCCTATACTCCGTCTCAGTGGTCCAATACCACTCCAACCCCTCAGTATGGTCAATCAGCCTACCAGTACAGTAGCTACGGTCACTATCAGGGCCAGTTTGCTGGAGATGGATCACAGTATCGGCAACCAGCCCACTACCTCCCTGGGGCCGCCGGTGGAGGATATGCCAGGGAAAGGTGGAATCCCCCTCCAAATTGGACGCCAACACAACCCATCACACATACACCCTCCCATGCCCATACTCCTGCCTACACACCCACCCAAACTCCACGGTCATTCATTGGCAGTGTCCACAGCACTCCCCAGCAACAGGGAAGAGGCCCGCCATATTACCGGCATCGACCTGGCTCTCCCAGCAGTACCCCATTACAGGACGAGTAA

Transcript

ANN27092-RA

Protein

UniProt (Swiss-Prot top hit)

UniProt accession	Description
Q62383	Transcription elongation factor SPT6 OS=Mus musculus OX=10090 GN=Supt6h PE=1 SV=2
Q8UVK2	Transcription elongation factor SPT6 OS=Danio rerio OX=7955 GN=supt6h PE=1 SV=1
Q7KZ85	Transcription elongation factor SPT6 OS=Homo sapiens OX=9606 GN=SUPT6H PE=1 SV=2

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0003315 (this species only) · gene tree & orthology

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF14633 all species →	SH2_2	SH2 domain	Domain	Interproscan
PF14641 all species →	HTH_44	Helix-turn-helix DNA-binding domain of SPT6	Domain	Interproscan
PF14635 all species →	HHH_7	Helix-hairpin-helix motif	Domain	Interproscan
PF17674 all species →	HHH_9	HHH domain	Domain	Interproscan
PF14639 all species →	YqgF	Holliday-junction resolvase-like of SPT6	Domain	Interproscan
PF14632 all species →	SPT6_acidic	Acidic N-terminal SPT6	Family	Interproscan
PF00575 all species →	S1	S1 RNA binding domain	Domain	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR006641 all species →	Domain	YqgF/RNase H-like domain	Interproscan
IPR035420 all species →	Domain	Spt6, SH2 domain	Interproscan
IPR036860 all species →	Homologous_superfamily	SH2 domain superfamily	Interproscan
IPR017072 all species →	Family	Transcription elongation factor Spt6	Interproscan
IPR028088 all species →	Domain	Helix-turn-helix DNA-binding domain of Spt6	Interproscan
IPR023319 all species →	Homologous_superfamily	Tex-like protein, HTH domain superfamily	Interproscan
IPR035018 all species →	Domain	Spt6, SH2 domain, C terminus	Interproscan
IPR010994 all species →	Homologous_superfamily	RuvA domain 2-like	Interproscan
IPR032706 all species →	Domain	Transcription elongation factor Spt6, helix-hairpin-helix motif	Interproscan
IPR012340 all species →	Homologous_superfamily	Nucleic acid-binding, OB-fold	Interproscan
IPR041692 all species →	Domain	HHH domain 9	Interproscan
IPR023323 all species →	Homologous_superfamily	Tex-like domain superfamily	Interproscan
IPR028231 all species →	Domain	Transcription elongation factor Spt6, YqgF domain	Interproscan
IPR000980 all species →	Domain	SH2 domain	Interproscan
IPR028083 all species →	Domain	Spt6 acidic, N-terminal domain	Interproscan
IPR042066 all species →	Homologous_superfamily	Spt6, Death-like domain	Interproscan
IPR003029 all species →	Domain	S1 domain	Interproscan
IPR037027 all species →	Homologous_superfamily	YqgF/RNase H-like domain superfamily	Interproscan
IPR035019 all species →	Domain	Spt6, SH2 domain, N terminus	Interproscan
IPR012337 all species →	Homologous_superfamily	Ribonuclease H-like superfamily	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR10145 all species →	TRANSCRIPTION ELONGATION FACTOR SPT6	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0006139 all species →	Biological Process	nucleobase-containing compound metabolic process	Interproscan
GO:0006368 all species →	Biological Process	transcription elongation by RNA polymerase II	Interproscan
GO:0008023 all species →	Cellular Component	transcription elongation factor complex	Interproscan
GO:0031491 all species →	Molecular Function	nucleosome binding	Interproscan
GO:0034728 all species →	Biological Process	nucleosome organization	Interproscan
GO:0042393 all species →	Molecular Function	histone binding	Interproscan
GO:0140673 all species →	Biological Process	transcription elongation-coupled chromatin remodeling	Interproscan
GO:0003677 all species →	Molecular Function	DNA binding	Interproscan
GO:0003676 all species →	Molecular Function	nucleic acid binding	Interproscan

Search by domain instead of by gene. Any accession above (InterPro, Pfam, PANTHER, GO, KEGG) can be used as a query on the Functional Domain Search page, which searches all 148 annotated genomes at once.

KEGG pathway

KO	Enzyme	Enzyme ID	Pathway	Map ID	Source
K11292	SUPT6H, SPT6; transcription elongation factor SPT6	-	Chromosome and associated proteins	ko03036	deepkoala

Searching by KO or pathway ID across all species is available on the KEGG Pathway page.

Co-expression network

Genes whose expression across the transcriptome samples of Montipora grisea tracks this one. Counts are over the whole network; the network view itself draws at most 100 partners per query gene (CNIDO_NET_TOP_K), so a hub gene can show fewer edges than the number below.

No co-expression network has been built for this species, so this gene has no partners to show. Networks are available for the species listed on the Network Analysis page.

Single-cell expression

Whether this gene can be visualised in the single-cell atlases of Montipora grisea, and in which cell types it is a marker. Expression is stored per cell, so the violin plot and the cell-type means are computed in the viewer — open a dataset to see them.

No single-cell dataset has been published for this species. The atlases that do exist are listed in the Cell Atlas.

Epigenetic marks

Chromatin and DNA-methylation data covering this gene. Peak calls are listed per sample with the genomic region the peak falls in; DNA methylation is listed as sample availability only, because those tables are queried by the DNA Methylation page itself.

No epigenomic data has been deposited for this species. The assays that exist across the site are described in the Epigenomic Data module.

What you can do with this gene

Every tool below opens with this gene already entered, so you land on the analysis rather than on an empty form. Links open in a new tab.

Analysis	What it does	Status
Primer design	Design PCR / qPCR primers on this gene’s sequence with the published primer3 settings. Opens with the primers already computed.	template found	open →
BLAST	Search this gene’s sequence against the CnidoSite BLAST databases. The query is filled in and the species’ database is preselected — press Run to start.	template found	open →
Expression heatmap	Draw this gene’s expression as a heatmap across all RNA-seq samples, and compare it with the genes you add next to it.	no expression matrix	–
Gene family / orthogroup	Look this gene up in the single-copy orthogroups built from the high-quality cnidarian genomes, and see which other species carry an orthologue.		open →
Gene set analysis	Start a gene-set enrichment analysis with this gene as the seed list. Add more genes on that page before running it.		open →