Gene detail

Detailed information of CAB3983573.1 in Paramuricea clavata

Genomic Location: pcla8_s000654:29240...31412
NR annotation: CAB3983573.1, transcription factor SOX-9 [Paramuricea clavata]
Species Paramuricea clavata · all data for this species · gene families

Gene Structure

More details in JBrowse

Sequence

CDS

Transcript

rna-PACLA_8A071340

CGAACATTCTGATATGCTAGTTGGCCACGCTATACCCTCTCAGTGGTGTATATTATGCCTTGTCTCTTAATTGTATACTTTTATTCCGACACAAAGTTTTCTTAGAGCGAGCTTCACAAAGGAATTATTATACTCGAAGATTGAAAACTCTTTATTGAAAGCAATGGGTAGCAAAGCGGTTGACTTTCAAAAAGGAATAAAACAAGAACCACAACAATTCGAAAGGGGTGACTCTGCGAAGCAAGACGACCAAAGCGAACTTAGTTTGGCGATCGCGAAAGCAGTGACTCAAGTTTTAGAAAGTTCAGACTGGCGTGCTCTATCCTTCCCGCTCCAGGCAAACGCTGCCAAACACTCCAAAGCAAAAAATGCCGTGAAAAGACCCATGAATCCGTTTATGCTCTATGCACAAGCAGCCAGGAAGAAACTTTCAAACCTTTATCCCGATCTAAGCTATGCAAAGTTGAGTAAGACGTTGGGACGCATTTGGAAATCCTTGGATCAAGTGGAGAAACAACCGTTTATAGACGAAGCCGAAAGATTACGGCAGAAACATAAAATCGAGCATCCCGATTATAAGTTTCAACCGAAACGTCGCGAGAAGAAGAGAGTGCATTCACCGAATAGGGAATCGTTCGAGGATAGTAAAATCAGCACAGGTGATGTTTTAAAGGCCCTAAGCTCAGGTGTGAGCGCCAAACACCACCACGAATCACAGAGCCACTGGGCACAAACGATTCATAACAGTATCTCGGTTCGAGGTGGTATCGTACAACAAAATGGTGTGAGTCCACAATCCAATGGTATTTCCCCTCCTCCGCCATACTCTGGTACTCCTAGGAGTTGCCCAAGTCCAATAATCCCTAAGATGAGTGCAAATACAGTGTACGAAATTAACCCTGCTCCACATCCCGCCACGAGCAATAATCTAACACCTTTCACGTCCAGATACATCACCCCACCGCCACCACTGCAACGAGCTCCCACGACAGCGAGTCTTTTCTCACCTTCGTCCTACCGTATACCCAAATCACAACTGCCAAATCCACCTCCATTCCACGAAATGCACGGTTTCCAACCTCCAACTACGATTCAAAATTACCCCAGCGATCTGCCGTTGGCAATTGGGAACTCGTTCATGAAATGTTCGCCTCAACTGGCACGACCGCCTCATTTGACTCCGAGCGAAGACCAGTCGACTAATTTGTTGACGGGAGTTAATCAAATCTTGAGAGATATGTTTGGGAATGAGAAAAGCAGTGTTATGTAATTGACACATTGCGCTTGTATTTGAATAAAGACTTTGGTGTTGTAATGTATAAACAACACTTGAGCCAGAGAACGCTAATTTTTAGAGAGGCTGTCTTGAGCAAAATGCATACACTGACGAATTAACTAACTCCAAATGTACACTTGCTTTTCGCTTCTTCTATCACATAATACCATtcctattttaatattttattccgAATTCTGGGCTATATCAATACAGTGTAGCACAGTAGGCTGTTGAAATTGTTATATAAACATGTTTAACAACTGAACAAAAACTCTTTCAAATTTCGCAAATTAAACTGTTAGCGAATCATTGTTGCATTAAACATGGCGCGCGATGTAAAATGGTATTGTAATAGGTTGTCAATTCATATCGAAATTAATATGGCGTACTTCTGAAGTTGATGTCTATAGAAGCTGTTTATTTTAAGTGTATATAGACATACAGTATCAGAGATATTGGCCTACATCCATGCAGTTAGCCGTGTCTGATTGttatacataaatatttttactacaTAGTTCAATGTCAGTGATAGGAGTCGTTACTTGTTAGATTGAAAAATAGGCATCTAAAGTTTAGTTACAATATATTTGTTTAGAACACTAGTCTAAGAAAATTGTTCAATTGCATAagaatttaataatatttaatatttagcTTCAAAATGAATTTTTCATCTGAAGCGAATTAAGTGAGCTTTTGACTTGCTTAAATTTTATGGTGGTTTGTTTTATAACACTTTGTTATAAATTCCATTCACCGTTATTGAATACATACGTTAAAGATATCACTTTAGCAAGGTTTTTACTTTCATAAATttgttatttaaataattattttacctTGTACATAAATATACGTATCATAAATTTCCATTAAAgataaatttgatat

Protein

UniProt (Swiss-Prot top hit)

UniProt accession	Description
P48434	Transcription factor SOX-9 OS=Gallus gallus OX=9031 GN=SOX9 PE=1 SV=3
Q04887	Transcription factor SOX-9 OS=Mus musculus OX=10090 GN=Sox9 PE=1 SV=2
F1LYL9	Transcription factor SOX-9 OS=Rattus norvegicus OX=10116 GN=Sox9 PE=1 SV=2

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0005988 (this species only) · gene tree & orthology

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
IPR009071 all species →	Domain	High mobility group box domain	Interproscan
IPR036910 all species →	Homologous_superfamily	High mobility group box domain superfamily	Interproscan
IPR050917 all species →	Family	SOX Transcription Factors	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR45803 all species →	SOX100B	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:0005634 all species →	Cellular Component	nucleus	Interproscan
GO:0006357 all species →	Biological Process	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

KO	Enzyme	Enzyme ID	Pathway	Map ID	Source
K18435	SOX9; transcription factor SOX9 (SOX group E)	-	Transcription factors	ko03000	deepkoala

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

Expression pattern (RNA-seq)

Transcript abundance of CAB3983573.1 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

18TPM > 0

4Conditions

31.2Max TPM

15.1Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
apical branchlet · Control at T25	6	5	16.99	31.24
apical branchlet · Temperature treatment at T0	6	5	10.52	17.69
apical branchlet · Temperature treatment at T25	5	5	21.05	27.18
apical branchlet · Control at T0	4	3	11.83	19.40

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

SRA run	Condition	Tissue	Developmental stage	Treatment	Study	TPM
SRR19977441	apical branchlet · Control at T25	apical branchlet	not recorded	Control at T25	SRP384900	31.24
SRR19977440	apical branchlet · Control at T25	apical branchlet	not recorded	Control at T25	SRP384900	30.66
SRR19977433	apical branchlet · Control at T25	apical branchlet	not recorded	Control at T25	SRP384900	17.46
SRR19977455	apical branchlet · Control at T25	apical branchlet	not recorded	Control at T25	SRP384900	15.81
SRR19977444	apical branchlet · Control at T25	apical branchlet	not recorded	Control at T25	SRP384900	6.75
SRR19977439	apical branchlet · Control at T25	apical branchlet	not recorded	Control at T25	SRP384900	0.00
SRR19977436	apical branchlet · Temperature treatment at T0	apical branchlet	not recorded	Temperature treatment at T0	SRP384900	17.69
SRR19977428	apical branchlet · Temperature treatment at T0	apical branchlet	not recorded	Temperature treatment at T0	SRP384900	13.11
SRR19977438	apical branchlet · Temperature treatment at T0	apical branchlet	not recorded	Temperature treatment at T0	SRP384900	11.98
SRR19977437	apical branchlet · Temperature treatment at T0	apical branchlet	not recorded	Temperature treatment at T0	SRP384900	10.77
SRR19977427	apical branchlet · Temperature treatment at T0	apical branchlet	not recorded	Temperature treatment at T0	SRP384900	9.54
SRR19977426	apical branchlet · Temperature treatment at T0	apical branchlet	not recorded	Temperature treatment at T0	SRP384900	0.00
SRR19977463	apical branchlet · Temperature treatment at T25	apical branchlet	not recorded	Temperature treatment at T25	SRP384900	27.18
SRR19977434	apical branchlet · Temperature treatment at T25	apical branchlet	not recorded	Temperature treatment at T25	SRP384900	26.06
SRR19977425	apical branchlet · Temperature treatment at T25	apical branchlet	not recorded	Temperature treatment at T25	SRP384900	25.13
SRR19977435	apical branchlet · Temperature treatment at T25	apical branchlet	not recorded	Temperature treatment at T25	SRP384900	16.36
SRR19977432	apical branchlet · Temperature treatment at T25	apical branchlet	not recorded	Temperature treatment at T25	SRP384900	10.49
SRR19977445	apical branchlet · Control at T0	apical branchlet	not recorded	Control at T0	SRP384900	19.40
SRR19977443	apical branchlet · Control at T0	apical branchlet	not recorded	Control at T0	SRP384900	18.07
SRR19977442	apical branchlet · Control at T0	apical branchlet	not recorded	Control at T0	SRP384900	9.85
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.