Gene detail

Detailed information of CAB3983589.1 in Paramuricea clavata

Genomic Location: not available for this species
NR annotation: CAB3983589.1, Transcription elongation factor SPT4 [Paramuricea clavata]
Species Paramuricea clavata · all data for this species · gene families

Sequence

No sequence record for CAB3983589.1 in PCLAV (the gene ID may belong to a different isoform naming scheme). Try the gene search.

UniProt (Swiss-Prot top hit)

UniProt accession	Description
Q5HZ97	Transcription elongation factor SPT4 OS=Xenopus laevis OX=8355 GN=supt4h1 PE=3 SV=1
P63271	Transcription elongation factor SPT4-A OS=Mus musculus OX=10090 GN=Supt4h1a PE=2 SV=1
Q3SYX6	Transcription elongation factor SPT4 OS=Bos taurus OX=9913 GN=SUPT4H1 PE=3 SV=1

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0009629 (this species only)

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF06093 all species →	Spt4	Spt4/RpoE2 zinc finger	Domain	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR009287 all species →	Family	Transcription initiation Spt4	Interproscan
IPR029040 all species →	Homologous_superfamily	RNA polymerase subunit RPABC4/transcription elongation factor Spt4	Interproscan
IPR022800 all species →	Domain	Spt4/RpoE2 zinc finger	Interproscan
IPR038510 all species →	Homologous_superfamily	Spt4 superfamily	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR12882 all species →	SUPPRESSOR OF TY 4	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0005634 all species →	Cellular Component	nucleus	Interproscan
GO:0006355 all species →	Biological Process	regulation of DNA-templated transcription	Interproscan
GO:0008270 all species →	Molecular Function	zinc ion binding	Interproscan
GO:0140673 all species →	Biological Process	transcription elongation-coupled chromatin remodeling	Interproscan
GO:0000993 all species →	Molecular Function	RNA polymerase II complex binding	Interproscan
GO:0006325 all species →	Biological Process	chromatin organization	Interproscan
GO:0032044 all species →	Cellular Component	DSIF complex	Interproscan
GO:0034243 all species →	Biological Process	regulation of transcription elongation by RNA polymerase II	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
K15171	SUPT4H1, SPT4; transcription elongation factor SPT4	-	Messenger RNA biogenesis	ko03019	deepkoala

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

Expression pattern (RNA-seq)

Transcript abundance of CAB3983589.1 across 21 RNA-seq samples of Paramuricea clavata. Values are TPM (transcripts per million) from the StringTie quantification; one bar is one sample, grouped and coloured by condition, sorted by expression within each group.

21Samples

13TPM > 0

4Conditions

78.1Max TPM

21.1Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
apical branchlet · Control at T25	6	5	37.80	78.12
apical branchlet · Temperature treatment at T0	6	4	22.96	62.84
apical branchlet · Temperature treatment at T25	5	2	8.69	23.67
apical branchlet · Control at T0	4	2	8.91	20.00

Per sample · hover a bar for the full sample record · show / hide the sample table

SRA run	Condition	Tissue	Developmental stage	Treatment	Study	TPM
SRR19977444	apical branchlet · Control at T25	apical branchlet	not recorded	Control at T25	SRP384900	78.12
SRR19977455	apical branchlet · Control at T25	apical branchlet	not recorded	Control at T25	SRP384900	46.09
SRR19977439	apical branchlet · Control at T25	apical branchlet	not recorded	Control at T25	SRP384900	39.77
SRR19977441	apical branchlet · Control at T25	apical branchlet	not recorded	Control at T25	SRP384900	38.89
SRR19977440	apical branchlet · Control at T25	apical branchlet	not recorded	Control at T25	SRP384900	23.94
SRR19977433	apical branchlet · Control at T25	apical branchlet	not recorded	Control at T25	SRP384900	0.00
SRR19977428	apical branchlet · Temperature treatment at T0	apical branchlet	not recorded	Temperature treatment at T0	SRP384900	62.84
SRR19977436	apical branchlet · Temperature treatment at T0	apical branchlet	not recorded	Temperature treatment at T0	SRP384900	45.39
SRR19977427	apical branchlet · Temperature treatment at T0	apical branchlet	not recorded	Temperature treatment at T0	SRP384900	19.37
SRR19977438	apical branchlet · Temperature treatment at T0	apical branchlet	not recorded	Temperature treatment at T0	SRP384900	10.17
SRR19977426	apical branchlet · Temperature treatment at T0	apical branchlet	not recorded	Temperature treatment at T0	SRP384900	0.00
SRR19977437	apical branchlet · Temperature treatment at T0	apical branchlet	not recorded	Temperature treatment at T0	SRP384900	0.00
SRR19977435	apical branchlet · Temperature treatment at T25	apical branchlet	not recorded	Temperature treatment at T25	SRP384900	23.67
SRR19977425	apical branchlet · Temperature treatment at T25	apical branchlet	not recorded	Temperature treatment at T25	SRP384900	19.80
SRR19977432	apical branchlet · Temperature treatment at T25	apical branchlet	not recorded	Temperature treatment at T25	SRP384900	0.00
SRR19977434	apical branchlet · Temperature treatment at T25	apical branchlet	not recorded	Temperature treatment at T25	SRP384900	0.00
SRR19977463	apical branchlet · Temperature treatment at T25	apical branchlet	not recorded	Temperature treatment at T25	SRP384900	0.00
SRR19977443	apical branchlet · Control at T0	apical branchlet	not recorded	Control at T0	SRP384900	20.00
SRR19977442	apical branchlet · Control at T0	apical branchlet	not recorded	Control at T0	SRP384900	15.66
SRR19977445	apical branchlet · Control at T0	apical branchlet	not recorded	Control at T0	SRP384900	0.00
SRR19977446	apical branchlet · Control at T0	apical branchlet	not recorded	Control at T0	SRP384900	0.00

Source: CnidoSite RNA-seq expression matrices (PCLAV_TPM, StringTie quantification over 21 runs), joined to SRA sample metadata. Samples whose tissue/treatment is not recorded in the source metadata are grouped by the descriptor carried in the expression matrix itself.