Gene detail

Detailed information of CAB4010674.1 in Paramuricea clavata

Genomic Location: pcla8_s007043:6814...8649
NR annotation: CAB4010674.1, collagen alpha-1(XIV) chain-like [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
A2AX52	Collagen alpha-4(VI) chain OS=Mus musculus OX=10090 GN=Col6a4 PE=1 SV=2
P13944	Collagen alpha-1(XII) chain OS=Gallus gallus OX=9031 GN=COL12A1 PE=1 SV=3
P15989	Collagen alpha-3(VI) chain OS=Gallus gallus OX=9031 GN=COL6A3 PE=2 SV=2

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0007916 (this species only)

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF00092 all species →	VWA	von Willebrand factor type A domain	Domain	Interproscan
PF16754 all species →	Pesticin	Bacterial toxin homologue of phage lysozyme, C-term	Domain	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR002035 all species →	Domain	von Willebrand factor, type A	Interproscan
IPR031922 all species →	Domain	Pesticin, C-terminal	Interproscan
IPR050525 all species →	Family	Extracellular Matrix Assembly and Organization	Interproscan
IPR023347 all species →	Homologous_superfamily	Lysozyme domain superfamily	Interproscan
IPR023346 all species →	Homologous_superfamily	Lysozyme-like domain superfamily	Interproscan
IPR036465 all species →	Homologous_superfamily	von Willebrand factor A-like domain superfamily	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR24020 all species →	COLLAGEN ALPHA	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0003796 all species →	Molecular Function	lysozyme activity	Interproscan
GO:0062023 all species →	Cellular Component	collagen-containing extracellular matrix	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 CAB4010674.1.

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

Expression pattern (RNA-seq)

Transcript abundance of CAB4010674.1 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

15TPM > 0

4Conditions

35.9Max TPM

4.4Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
apical branchlet · Control at T25	6	6	4.98	14.75
apical branchlet · Temperature treatment at T0	6	4	7.55	35.86
apical branchlet · Temperature treatment at T25	5	3	1.59	4.14
apical branchlet · Control at T0	4	2	2.53	7.93

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	14.75
SRR19977433	apical branchlet · Control at T25	apical branchlet	not recorded	Control at T25	SRP384900	8.83
SRR19977440	apical branchlet · Control at T25	apical branchlet	not recorded	Control at T25	SRP384900	4.16
SRR19977441	apical branchlet · Control at T25	apical branchlet	not recorded	Control at T25	SRP384900	1.15
SRR19977444	apical branchlet · Control at T25	apical branchlet	not recorded	Control at T25	SRP384900	0.55
SRR19977455	apical branchlet · Control at T25	apical branchlet	not recorded	Control at T25	SRP384900	0.43
SRR19977436	apical branchlet · Temperature treatment at T0	apical branchlet	not recorded	Temperature treatment at T0	SRP384900	35.86
SRR19977428	apical branchlet · Temperature treatment at T0	apical branchlet	not recorded	Temperature treatment at T0	SRP384900	4.79
SRR19977438	apical branchlet · Temperature treatment at T0	apical branchlet	not recorded	Temperature treatment at T0	SRP384900	3.55
SRR19977427	apical branchlet · Temperature treatment at T0	apical branchlet	not recorded	Temperature treatment at T0	SRP384900	1.12
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
SRR19977432	apical branchlet · Temperature treatment at T25	apical branchlet	not recorded	Temperature treatment at T25	SRP384900	4.14
SRR19977425	apical branchlet · Temperature treatment at T25	apical branchlet	not recorded	Temperature treatment at T25	SRP384900	2.29
SRR19977435	apical branchlet · Temperature treatment at T25	apical branchlet	not recorded	Temperature treatment at T25	SRP384900	1.53
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	7.93
SRR19977442	apical branchlet · Control at T0	apical branchlet	not recorded	Control at T0	SRP384900	2.17
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.