Gene detail

Detailed information of CAB3983401.1 in Paramuricea clavata

Genomic Location: pcla8_s000632:38484...39521
NR annotation: CAB3983401.1, transcription factor SOX-7 [Paramuricea clavata]
Species Paramuricea clavata · all data for this species · gene families

Gene Structure

More details in JBrowse

Sequence

CDS

Transcript

Protein

UniProt (Swiss-Prot top hit)

UniProt accession	Description
Q28GD5	Transcription factor Sox-7 OS=Xenopus tropicalis OX=8364 GN=sox7 PE=2 SV=1
O42342	Transcription factor Sox-7 OS=Xenopus laevis OX=8355 GN=sox7 PE=2 SV=1
P40646	Transcription factor SOX-7 OS=Mus musculus OX=10090 GN=Sox7 PE=1 SV=2

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0000488 (this species only)

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF00505 all species →	HMG_box	HMG (high mobility group) box	Domain	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR036910 all species →	Homologous_superfamily	High mobility group box domain superfamily	Interproscan
IPR050140 all species →	Family	SRY-related HMG-box transcription factors	Interproscan
IPR009071 all species →	Domain	High mobility group box domain	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR10270 all species →	SOX TRANSCRIPTION FACTOR	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0000978 all species →	Molecular Function	RNA polymerase II cis-regulatory region sequence-specific DNA binding	Interproscan
GO:0000981 all species →	Molecular Function	DNA-binding transcription factor activity, RNA polymerase II-specific	Interproscan
GO:0001228 all species →	Molecular Function	DNA-binding transcription activator activity, RNA polymerase II-specific	Interproscan
GO:0001525 all species →	Biological Process	angiogenesis	Interproscan
GO:0001570 all species →	Biological Process	vasculogenesis	Interproscan
GO:0006355 all species →	Biological Process	regulation of DNA-templated transcription	Interproscan
GO:0007507 all species →	Biological Process	heart development	Interproscan
GO:0009653 all species →	Biological Process	anatomical structure morphogenesis	Interproscan
GO:0030154 all species →	Biological Process	cell differentiation	Interproscan
GO:0045944 all species →	Biological Process	positive regulation of transcription 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

No KEGG orthology assignment for CAB3983401.1.

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

Expression pattern (RNA-seq)

Transcript abundance of CAB3983401.1 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

19TPM > 0

4Conditions

39.5Max TPM

10.5Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
apical branchlet · Control at T25	6	6	8.37	17.35
apical branchlet · Temperature treatment at T0	6	4	5.39	12.82
apical branchlet · Temperature treatment at T25	5	5	21.01	39.51
apical branchlet · Control at T0	4	4	8.16	16.47

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

SRA run	Condition	Tissue	Developmental stage	Treatment	Study	TPM
SRR19977439	apical branchlet · Control at T25	apical branchlet	not recorded	Control at T25	SRP384900	17.35
SRR19977440	apical branchlet · Control at T25	apical branchlet	not recorded	Control at T25	SRP384900	13.14
SRR19977433	apical branchlet · Control at T25	apical branchlet	not recorded	Control at T25	SRP384900	8.81
SRR19977455	apical branchlet · Control at T25	apical branchlet	not recorded	Control at T25	SRP384900	7.70
SRR19977444	apical branchlet · Control at T25	apical branchlet	not recorded	Control at T25	SRP384900	2.06
SRR19977441	apical branchlet · Control at T25	apical branchlet	not recorded	Control at T25	SRP384900	1.19
SRR19977437	apical branchlet · Temperature treatment at T0	apical branchlet	not recorded	Temperature treatment at T0	SRP384900	12.82
SRR19977427	apical branchlet · Temperature treatment at T0	apical branchlet	not recorded	Temperature treatment at T0	SRP384900	10.58
SRR19977436	apical branchlet · Temperature treatment at T0	apical branchlet	not recorded	Temperature treatment at T0	SRP384900	7.57
SRR19977438	apical branchlet · Temperature treatment at T0	apical branchlet	not recorded	Temperature treatment at T0	SRP384900	1.34
SRR19977426	apical branchlet · Temperature treatment at T0	apical branchlet	not recorded	Temperature treatment at T0	SRP384900	0.00
SRR19977428	apical branchlet · Temperature treatment at T0	apical branchlet	not recorded	Temperature treatment at T0	SRP384900	0.00
SRR19977425	apical branchlet · Temperature treatment at T25	apical branchlet	not recorded	Temperature treatment at T25	SRP384900	39.51
SRR19977432	apical branchlet · Temperature treatment at T25	apical branchlet	not recorded	Temperature treatment at T25	SRP384900	31.45
SRR19977463	apical branchlet · Temperature treatment at T25	apical branchlet	not recorded	Temperature treatment at T25	SRP384900	23.15
SRR19977434	apical branchlet · Temperature treatment at T25	apical branchlet	not recorded	Temperature treatment at T25	SRP384900	8.20
SRR19977435	apical branchlet · Temperature treatment at T25	apical branchlet	not recorded	Temperature treatment at T25	SRP384900	2.75
SRR19977443	apical branchlet · Control at T0	apical branchlet	not recorded	Control at T0	SRP384900	16.47
SRR19977446	apical branchlet · Control at T0	apical branchlet	not recorded	Control at T0	SRP384900	9.37
SRR19977445	apical branchlet · Control at T0	apical branchlet	not recorded	Control at T0	SRP384900	4.20
SRR19977442	apical branchlet · Control at T0	apical branchlet	not recorded	Control at T0	SRP384900	2.58

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.