Gene detail

Detailed information of ENSCIQP00000008941.1 in Millepora alcicornis

Genomic Location: chr15:97604338...97661197
NR annotation: XP_047124039.1, transcription elongation factor SPT5 [Hydra vulgaris]
Species Millepora alcicornis · all data for this species · gene families

Gene Structure

More details in JBrowse

Sequence

CDS

ENSCIQT00000010450

atgattcctaatTTTACTTCTGATTTCGCTGAGGTATCTCACTTGTTCATTGGATTGTTTCATTCTTTCAGAGACCCGAATCTATGGATGGTGCGTTGCAGAATGGGAGAAGAGAAGCAAGTCGTATTTGCATTAATGAGAAAATTTCTAACTTTGGAAAACTCGGAAACGCCATTGCAGATTAAATCAGCAATTGCAGTGGAGGGTTTGAAAGGTTACATATACGTGGAAGCATACAAGCAGACACACGTGAAAGCGGCTATCGAAGGATTTGGTGCACTGCGTTATGGTCTTTGGTCTCAACAATTGGTGCCATTGAATGAAATGGTCGATGTGTTGAAGGTTGTAAAGGACATAGTTCAAGTTAAGCCAAAATCTTGGGTTCGTATCAAACGCGGAATATATAAAGATGACCTCGCTCAGGTACGGGTGACACTGAAAATAGTCCCACGTATAGATTACAACCAACCGAGAGGTGTGATGCGTTCAGTTAGCGTAAGTACAGTTCGATATGTTGtTTTCGGATTTTTTGTCATCTTATTTACTAGGAGTATTGGAGGAGAAATAACACAGGATGGAGATTTCTACATGTTTGAGAACAATCGCTACCGTGCTGGTTTTCTCTACAAAACTATGGTCATGTCAGCTATAATTACCGAAGGTGTTAAACCCACTTTAGCCGAGCTTGAGAAGTTCGAAGCAAGTATAGATGATGCTGAATTGGATCTTGGTCGAAGCAAAGCAAAAGAAGAGACAGAACATTCATTAGCACCGGGAGACGTAGTCCGTGTTGCCGAGGGTGAGTTGATCAACCTACAAGGAAAAGTTATCAGCGTGGATGGGAATACTATCACTATAATGCCCAAACATGAAGATTTGAAGGACCCTCTTGAGTTTCCAGCTTATGAattgcagaagttcttcaaagttggtgatcatgtgaaaGTGATGCGTGGAAAGTTTGAGGGAGACACTGGCTTGATTGTCCGTGTAGAAGAAAACGTGATTGTGCTATTCTCGGATCTTACATTTCACGAGTTGAAAGTGAAACCAGACGACTTGCAGCTCTGTAGTGATATGAGTACTGGAGTAGATTCAATGGGACAGCATCAGTGGGGTGATATGGTAGCCCTAGATCCGCAAACAGTTGGTGTTATTGTGCGATTGGAGCGAGAGACATTTTCTATACTTAATCAGCATGGAAAGGTAAGGTTGCATTCCCTGGAGATGTTTTTGTATCACTTTACACGAAATTATCTGCGTGATATAGTCAAAGTGGTGGACGGACCTCATGAGGGCTTGCAGGGCGAGATCAAACATCTCTATCGTGGCTTTGCATTTATTCAGTCAAAAATGGTATTGGATAATGGTGGTATCATGGTGCTAAGGAGTAAAATGCTTCTGCAGGCTGGAGGCTCTAAAGTAAGTTGGATCAGGATCCTTTTGGAAATCATAAGGTGTGATGTCACAGGTATAATCTATAATTTAGGTGGAGGTGCTGGTGGTGCAACCAGAGGCCGCGGTCGCGGACGTGGAAGAGGTGCTAGAGATAATTCTCTTATTGGACAGACAGTGCGCATTGCACAAGGACCGTTTAAAGGTTATATTggtattataaaagatgcgacAGAATCACTGGCACGTGTCGAACTGCATACCAACTGTAAAACAATATCAGTCGATCGTTCGAGATTAGCGCTTGTGTCAGGACAAAACAAAGGTGGCGGTGTTACAGTTTATGGGCATACTCCAATGTATGCTTCTGGACAAACTCCAATGCACGGTAACCAGACCCCAATGTATGGTAGCAGGACGCCGAACTACGGCTCCCGAACCCCGTCCCATGATCCTTCACGCACACCTAGTCATGATCCAGCTAGAACTCCCAGCCATGTTGGACATGGGGGAGCTTGGGATCCAACACAACCGAATACTCCTGCGCGACCCTCGGACGAATTTGATAACTATAGTTTTGATGGACCAGGACCATCTCCAgtgttccgaaaatatgcaacaaatttacaTCCGCAAACGCCCTCTCATGGTGGTTTCAATGCGCCGTTTACACCTGGTACACCTGGCACACCCATGTCAAATGTATTTGGTGGAGATTCTTCCTATTCACCCATGCATACCCCCAGCCCAATGCATGGAAATCCGCTAACTCCAGGTTCTGGTTTGGGACCTATGTCACCGGCATATACACCGCAAACTCCATTGACCCAGTTTGACGAGGGTATgttttttaCGATAGATGGCGAAAATGCAACCGTTCATTTTTACGATTCCAAAGATACGTTAATCCTGTCAACATCGTCGTTAGAAATTGTCACACCAGCCAAAAAGGATAGGGTGAAATTCATTGCGGGAAGTGACAAAGATGATACCGGTGTCTTGATCAATATTGATGGGTTGGATGGTATTATTAAAATGGACCGGGCAGATTCACTGAAAATTTTACAGTTAGATTTCTTAGCAAAATACGTACCAAATGAATAA

Transcript

ENSCIQT00000010450

Protein

UniProt (Swiss-Prot top hit)

UniProt accession	Description
Q5ZI08	Transcription elongation factor SPT5 OS=Gallus gallus OX=9031 GN=SUPT5H PE=2 SV=1
O55201	Transcription elongation factor SPT5 OS=Mus musculus OX=10090 GN=Supt5h PE=1 SV=1
O00267	Transcription elongation factor SPT5 OS=Homo sapiens OX=9606 GN=SUPT5H PE=1 SV=1

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0005121 (this species only) · gene tree & orthology

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF03439 all species →	Spt5-NGN	Early transcription elongation factor of RNA pol II, NGN section	Family	Interproscan
PF00467 all species →	KOW	KOW motif	Family	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR014722 all species →	Homologous_superfamily	Large ribosomal subunit protein uL2, domain 2	Interproscan
IPR039659 all species →	Family	Transcription elongation factor SPT5	Interproscan
IPR041978 all species →	Domain	Spt5, KOW domain repeat 5	Interproscan
IPR041973 all species →	Domain	Spt5, KOW domain repeat 1	Interproscan
IPR005100 all species →	Domain	NGN domain	Interproscan
IPR039385 all species →	Domain	NGN domain, eukaryotic	Interproscan
IPR008991 all species →	Homologous_superfamily	Translation protein SH3-like domain superfamily	Interproscan
IPR041977 all species →	Domain	Spt5, KOW domain repeat 4	Interproscan
IPR041980 all species →	Domain	Spt5, KOW domain repeat 6	Interproscan
IPR036735 all species →	Homologous_superfamily	NusG, N-terminal domain superfamily	Interproscan
IPR041976 all species →	Domain	Spt5, KOW domain repeat 3	Interproscan
IPR005824 all species →	Domain	KOW	Interproscan
IPR041975 all species →	Domain	Spt5, KOW domain repeat 2	Interproscan
IPR024945 all species →	Domain	Spt5 C-terminal domain	Interproscan
IPR006645 all species →	Domain	NusG-like, N-terminal	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR11125 all species →	SUPPRESSOR OF TY 5	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0003729 all species →	Molecular Function	mRNA binding	Interproscan
GO:0006357 all species →	Biological Process	regulation of transcription by RNA polymerase II	Interproscan
GO:0006368 all species →	Biological Process	transcription elongation by RNA polymerase II	Interproscan
GO:0032044 all species →	Cellular Component	DSIF complex	Interproscan
GO:0032784 all species →	Biological Process	regulation of DNA-templated transcription elongation	Interproscan
GO:0006354 all species →	Biological Process	DNA-templated transcription elongation	Interproscan
GO:0005515 all species →	Molecular Function	protein binding	Interproscan
GO:0140673 all species →	Biological Process	transcription elongation-coupled chromatin remodeling	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
K15172	SUPT5H, SPT5; transcription elongation factor SPT5	-	Messenger RNA biogenesis	ko03019	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 Millepora alcicornis 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 Millepora alcicornis, 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 →