Gene detail

Detailed information of CAB4003396.1 in Paramuricea clavata

Genomic Location: pcla8_s004710:27602...30647
NR annotation: CAB4003396.1, lin-9 homolog isoform X1 [Paramuricea clavata]
Species Paramuricea clavata · all data for this species · gene families

Gene Structure

More details in JBrowse

Sequence

CDS

Transcript

rna-PACLA_8A043930

CTGAAACCGccatctttaaaattttcacaCAAAGGCGTAAAGGCAGTCAAAATTTGGAAGGTTGTATTGTTTTGTATGTCTACTAGTTGAGGAAGAGTGCTTGATGTTTATCTCAGCAACACGATGGAAAATGATGATTCCGTTGCAATGGAATCTTCAGCGCAAGCGTTGGTCAGTTTGAGAGGAAATCAACCTTCGCTACGAAACTCACATGGAAACGATGAAACACAAACAGACGATGTCTTGCTCTTGTCTGACAACGGAATGGCCCAAACATCTTTCGGTTCACCCCGACGGAAAGCTAGAAAACcgataaaattacaaaatacaaCCGTAAAAGGTTCTCCAACTAAAAAAACGGCGATGAGTTTGATGTCTAAATTACGGAATTTGTTGAAGTTACCAAAAGCTTTCAAATGGTGCTATTTCGAATGGTTTTATTCCAGCCTTGATAAATCACTTTTTCTCAGCGATAATGATTTTTGTGTTTGTCTTAAAGAGCATTTCCCAAGCTTAAATGCCAAAAATCTTCGTAGAGTTGAGTGGAGAGAATTGAGAAGATTAATGGGTAAGCCCAGAAGATGTTCACAATCCTTTTTCAGCGAAGAACGAAGTGCTTTAGAAGAGAAAAGGCAGAAAATTCGACTTCTGCAACAGAGGAAAGTTACAGAGTTGGCAAAGTTTAAAGATCTTCCGAAAGAAATCCCTGTACCACTTGTGATTGGTACTAAAGTTTCAGCTCGGTTACATAAACCACAGAGTGGTATATTTACTGGGCAAATTGATGCAGTTGACAGTACAGCATCTACATACAGGGTACGGTTTGATATTCCAGAGCTTGGAACTCATTCTGTTATGGATATCGATGTTCAAAGTAATGAATCCGAAGAGACAATGCCTATTTCTGCATTTGCATTGAAAGAGCGCCCAAAGCTTGCCAATGTTCCCACATTTAATTCGGTTCGGCGAAAGCTGTCTGCCGTTGGGGATCCTTTGCTGAGCAATTCACCCACACGAGTGCAGCTCCAAGAAGTCCTTGACAAGGGAGATCACACTGTCGGTGGGTTTCCTATTAAGTTTCTTGCTCTTGTGACTAGATTGTCGAAAGTATTAACTTTGAAAAGAGAATATGTTGACAAACTGAAACATTTGAATAGTGAAGCTGAGAAGCTCAAGTCGTACCAATTACCGATTGAACGAGATTTTCAGAGGAAATATGCCGAGGTAGTCCTTGAACTGGAGAGACTTAACACAGATTTGAACAATTACTTGAAGGACGTTGAAGAGTATTGTGTAAACATGAATTCCATCCAAGGATCTGATAGTTTGGATCAATCAGATGGATTGCAGAAGTCGTGTGAGAAACATGCTAAGTCAATGGTTGAGCATTTATCTGGTGATGTTGATCATGATGTAGAAAATGGTTCTACTCTTCAATTGATTGCCAGTCTTACAGCTTTGTTGCTTCAAGTGAAGATGCTTGCAGAGAGTGACTTAAATTCATTTGAATTTAAGAGTTTGGTCGACAGTGTGCAAGAGTTAAAGAAGACGGTAGATTCAACTAATGTAAGTTCTTTCCAAAACAATGTAGAAATTCATATTGCACATATTCAATCAGGGCTTAGTCAAATGGGTAACCTTCAAGCATTTTCAACTAACCCATCCTAGGATAGACTGAcattaaaacaaatttattaGTAGTTTTTAGTGAAGCCAGTGAGCAAATATAGCTAGTATATAGTATGTTGTGTGCACAGATTTGTAGACAGCTTCTGTGTGTCTAGTAATGTTACTTGGAAATTGAACTGTCTGGTTATTCCTCAAAACATCCACATCTCCTAAACAGAGGAGATGAAAGATTTCCAGTCCTCAATAAGATTTCCAGTCCTCAATCAGACCTGAttatgtagctcagttggtagagtgTTGGTTGAACTCTGCTAGCATTTCAAATGTCTCGGGTTTGAAAACCCAGCCACGGCAGGCAGAATTTTCTGCATGTGTGGTTTGAACGCATTTACTCGAGAACATTTCATCATATGTGCATGAGGGCCATCCAGTTAGTAAAAACACAAACGTTTTCAAAAATTGTAGCCCCCTCCCCTCGCCCCTTGTTGCATACTAGAGCTGTTCAGTATACCCCATTGAAATTAATAGAACCGGAACGCTACCTCGAACCGGAAATATCCCTATGTCTGAGAAAGATTACTGTATGACATAATAATTCCTTTATTCCAAATATGGTACAAGCaacacttactggcaaaatggtGCATGACCATAAATGGatatttattgtgtgattttgCACATACTTTTGTGTGCCCAGCAAGTAGTTTGCACTATATTTTGGAATCTGTGAGGTGAATAAGTGAGGACACAAGCTTCAAAAGTTACCTATGCCAAGTTAGACATCTGTACAGTCTACTTATTTTGTAGAAGCAGAATCAGTACTTAATTAATGCAACCCTCAACATGGACCTGCTCAAATCTTGGTTATCCAATCAAGTTAGGTGCCCAGGCCCATCTTGGCAGTCCTGATGACCACAGCTAGGTTTCCCTTTCAGCTTCTGTGCTCACATATCCTCTGACATGACTAAGAAaggattttctggggggtgcaGTCTGGGTAAACTGGGTCTCCCCCCTCTAGCTATTACAAGGCAGGTGCTTCAGTAATTTCCTTAAATCCAAGTTTCTCTGCCTCATCAACTCCAACAAAGACCAATGACTATTTTGGGTTGCTTCTCTGATTATTAACGCAACCTTATTTTCAAAAAGTCTCTCTGAAAGGGTTAAAAATCTATTAATCTATGATCTTCCCAGCCTATCACGAGGTTTTTACTTGGAttgttttgaaatttctttgCAAAACACCACCCAGCTTTGATTGAGatgtggatattttctggaaatagccaattaaataaattgttatCATGATTCTTCTTgtgtataattatgtaaaatattttatcatttgAAGTGAGGACTAGCCTCTGTCATCTTTAATAActgtttttaatgaaaaatgaTTTTAACCGCT

Protein

UniProt (Swiss-Prot top hit)

UniProt accession	Description
Q5TKA1	Protein lin-9 homolog OS=Homo sapiens OX=9606 GN=LIN9 PE=1 SV=1
Q4R8N2	Protein lin-9 homolog OS=Macaca fascicularis OX=9541 GN=LIN9 PE=2 SV=1
Q8C735	Protein lin-9 homolog OS=Mus musculus OX=10090 GN=Lin9 PE=1 SV=2

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0005745 (this species only)

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF19438 all species →	LIN9_C	LIN9 C-terminal	Domain	Interproscan
PF06584 all species →	DIRP	DIRP	Family	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR045831 all species →	Domain	LIN-9, C-terminal	Interproscan
IPR033471 all species →	Domain	DIRP domain	Interproscan
IPR010561 all species →	Family	Protein LIN-9/Protein ALWAYS EARLY	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR21689 all species →	LIN-9	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0000003 all species →	Biological Process	obsolete reproduction	Interproscan
GO:0003677 all species →	Molecular Function	DNA binding	Interproscan
GO:0005654 all species →	Cellular Component	nucleoplasm	Interproscan
GO:0006351 all species →	Biological Process	DNA-templated transcription	Interproscan
GO:0006357 all species →	Biological Process	regulation of transcription by RNA polymerase II	Interproscan
GO:0017053 all species →	Cellular Component	transcription repressor complex	Interproscan
GO:0051726 all species →	Biological Process	regulation of cell cycle	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
K21773	LIN9; protein lin-9	-	Cellular senescence	ko04218	deepkoala

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

Expression pattern (RNA-seq)

Transcript abundance of CAB4003396.1 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

17TPM > 0

4Conditions

23.5Max TPM

6.5Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
apical branchlet · Control at T25	6	5	7.44	16.18
apical branchlet · Temperature treatment at T0	6	6	7.87	23.46
apical branchlet · Temperature treatment at T25	5	4	5.85	16.56
apical branchlet · Control at T0	4	2	3.91	13.84

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	16.18
SRR19977433	apical branchlet · Control at T25	apical branchlet	not recorded	Control at T25	SRP384900	10.64
SRR19977441	apical branchlet · Control at T25	apical branchlet	not recorded	Control at T25	SRP384900	8.35
SRR19977455	apical branchlet · Control at T25	apical branchlet	not recorded	Control at T25	SRP384900	5.96
SRR19977440	apical branchlet · Control at T25	apical branchlet	not recorded	Control at T25	SRP384900	3.52
SRR19977439	apical branchlet · Control at T25	apical branchlet	not recorded	Control at T25	SRP384900	0.00
SRR19977426	apical branchlet · Temperature treatment at T0	apical branchlet	not recorded	Temperature treatment at T0	SRP384900	23.46
SRR19977436	apical branchlet · Temperature treatment at T0	apical branchlet	not recorded	Temperature treatment at T0	SRP384900	10.89
SRR19977428	apical branchlet · Temperature treatment at T0	apical branchlet	not recorded	Temperature treatment at T0	SRP384900	6.52
SRR19977437	apical branchlet · Temperature treatment at T0	apical branchlet	not recorded	Temperature treatment at T0	SRP384900	2.79
SRR19977427	apical branchlet · Temperature treatment at T0	apical branchlet	not recorded	Temperature treatment at T0	SRP384900	2.14
SRR19977438	apical branchlet · Temperature treatment at T0	apical branchlet	not recorded	Temperature treatment at T0	SRP384900	1.39
SRR19977463	apical branchlet · Temperature treatment at T25	apical branchlet	not recorded	Temperature treatment at T25	SRP384900	16.56
SRR19977432	apical branchlet · Temperature treatment at T25	apical branchlet	not recorded	Temperature treatment at T25	SRP384900	7.49
SRR19977425	apical branchlet · Temperature treatment at T25	apical branchlet	not recorded	Temperature treatment at T25	SRP384900	3.23
SRR19977435	apical branchlet · Temperature treatment at T25	apical branchlet	not recorded	Temperature treatment at T25	SRP384900	1.99
SRR19977434	apical branchlet · Temperature treatment at T25	apical branchlet	not recorded	Temperature treatment at T25	SRP384900	0.00
SRR19977445	apical branchlet · Control at T0	apical branchlet	not recorded	Control at T0	SRP384900	13.84
SRR19977443	apical branchlet · Control at T0	apical branchlet	not recorded	Control at T0	SRP384900	1.79
SRR19977442	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.