Gene detail

Detailed information of CAB4007247.1 in Paramuricea clavata

Genomic Location: not available for this species
NR annotation: CAB4007247.1, Collagen alpha-1(IV) chain [Paramuricea clavata]
Species Paramuricea clavata · all data for this species · gene families

Sequence

No sequence record for CAB4007247.1 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
Q7SIB3	Collagen alpha-2(IV) chain (Fragment) OS=Bos taurus OX=9913 GN=COL4A2 PE=1 SV=1
P27393	Collagen alpha-2(IV) chain OS=Ascaris suum OX=6253 PE=2 SV=1
P02463	Collagen alpha-1(IV) chain OS=Mus musculus OX=10090 GN=Col4a1 PE=1 SV=4

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0001899 (this species only)

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF01413 all species →	C4	C-terminal tandem repeated domain in type 4 procollagen	Domain	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR019326 all species →	Family	Protein NDNF	Interproscan
IPR001442 all species →	Domain	Collagen IV, non-collagenous	Interproscan
IPR036954 all species →	Homologous_superfamily	Collagen IV, non-collagenous domain superfamily	Interproscan
IPR016187 all species →	Homologous_superfamily	C-type lectin fold	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR14619 all species →	NEURON-DERIVED NEUROTROPHIC FACTOR	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0005201 all species →	Molecular Function	extracellular matrix structural constituent	Interproscan
GO:0005581 all species →	Cellular Component	collagen trimer	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 CAB4007247.1.

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

Expression pattern (RNA-seq)

Transcript abundance of CAB4007247.1 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

309.0Max TPM

105.9Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
apical branchlet · Control at T25	6	4	111.24	280.81
apical branchlet · Temperature treatment at T0	6	5	152.15	309.01
apical branchlet · Temperature treatment at T25	5	3	97.33	211.80
apical branchlet · Control at T0	4	1	39.13	156.53

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	280.81
SRR19977440	apical branchlet · Control at T25	apical branchlet	not recorded	Control at T25	SRP384900	182.56
SRR19977455	apical branchlet · Control at T25	apical branchlet	not recorded	Control at T25	SRP384900	119.21
SRR19977444	apical branchlet · Control at T25	apical branchlet	not recorded	Control at T25	SRP384900	84.84
SRR19977433	apical branchlet · Control at T25	apical branchlet	not recorded	Control at T25	SRP384900	0.00
SRR19977439	apical branchlet · Control at T25	apical branchlet	not recorded	Control at T25	SRP384900	0.00
SRR19977427	apical branchlet · Temperature treatment at T0	apical branchlet	not recorded	Temperature treatment at T0	SRP384900	309.01
SRR19977436	apical branchlet · Temperature treatment at T0	apical branchlet	not recorded	Temperature treatment at T0	SRP384900	246.13
SRR19977437	apical branchlet · Temperature treatment at T0	apical branchlet	not recorded	Temperature treatment at T0	SRP384900	143.23
SRR19977438	apical branchlet · Temperature treatment at T0	apical branchlet	not recorded	Temperature treatment at T0	SRP384900	115.15
SRR19977428	apical branchlet · Temperature treatment at T0	apical branchlet	not recorded	Temperature treatment at T0	SRP384900	99.38
SRR19977426	apical branchlet · Temperature treatment at T0	apical branchlet	not recorded	Temperature treatment at T0	SRP384900	0.00
SRR19977434	apical branchlet · Temperature treatment at T25	apical branchlet	not recorded	Temperature treatment at T25	SRP384900	211.80
SRR19977435	apical branchlet · Temperature treatment at T25	apical branchlet	not recorded	Temperature treatment at T25	SRP384900	199.03
SRR19977425	apical branchlet · Temperature treatment at T25	apical branchlet	not recorded	Temperature treatment at T25	SRP384900	75.81
SRR19977432	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	156.53
SRR19977442	apical branchlet · Control at T0	apical branchlet	not recorded	Control at T0	SRP384900	0.00
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.