Gene detail

Detailed information of CAB3993096.1 in Paramuricea clavata

Genomic Location: not available for this species
NR annotation: CAB3993096.1, Protocadherin Fat 4, partial [Paramuricea clavata]
Species Paramuricea clavata · all data for this species · gene families

Sequence

No sequence record for CAB3993096.1 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
Q2PZL6	Protocadherin Fat 4 OS=Mus musculus OX=10090 GN=Fat4 PE=1 SV=2
Q6V0I7	Protocadherin Fat 4 OS=Homo sapiens OX=9606 GN=FAT4 PE=1 SV=2
Q99PF4	Cadherin-23 OS=Mus musculus OX=10090 GN=Cdh23 PE=1 SV=2

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0000235 (this species only)

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF00092 all species →	VWA	von Willebrand factor type A domain	Domain	Interproscan
PF07679 all species →	I-set	Immunoglobulin I-set domain	Domain	Interproscan
PF01085 all species →	HH_signal	Hedgehog amino-terminal signalling domain	Domain	Interproscan
PF13927 all species →	Ig_3	Immunoglobulin domain	Domain	Interproscan
PF00008 all species →	EGF	EGF-like domain	Domain	Interproscan
PF00028 all species →	Cadherin	Cadherin domain	Domain	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR009045 all species →	Homologous_superfamily	Hedgehog signalling/DD-peptidase zinc-binding domain superfamily	Interproscan
IPR007110 all species →	Domain	Immunoglobulin-like domain	Interproscan
IPR036179 all species →	Homologous_superfamily	Immunoglobulin-like domain superfamily	Interproscan
IPR002126 all species →	Domain	Cadherin-like	Interproscan
IPR015919 all species →	Homologous_superfamily	Cadherin-like superfamily	Interproscan
IPR039808 all species →	Family	Cadherin	Interproscan
IPR020894 all species →	Conserved_site	Cadherin conserved site	Interproscan
IPR000742 all species →	Domain	EGF-like domain	Interproscan
IPR000152 all species →	PTM	EGF-type aspartate/asparagine hydroxylation site	Interproscan
IPR001881 all species →	Domain	EGF-like calcium-binding domain	Interproscan
IPR003599 all species →	Domain	Immunoglobulin subtype	Interproscan
IPR002035 all species →	Domain	von Willebrand factor, type A	Interproscan
IPR013098 all species →	Domain	Immunoglobulin I-set	Interproscan
IPR036465 all species →	Homologous_superfamily	von Willebrand factor A-like domain superfamily	Interproscan
IPR000320 all species →	Domain	Hedgehog, N-terminal signalling domain	Interproscan
IPR013783 all species →	Homologous_superfamily	Immunoglobulin-like fold	Interproscan
IPR003598 all species →	Domain	Immunoglobulin subtype 2	Interproscan
IPR018097 all species →	Conserved_site	EGF-like calcium-binding, conserved site	Interproscan
IPR001657 all species →	Family	Hedgehog protein	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR24027 all species →	CADHERIN-23	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0005509 all species →	Molecular Function	calcium ion binding	Interproscan
GO:0007156 all species →	Biological Process	homophilic cell adhesion via plasma membrane adhesion molecules	Interproscan
GO:0016020 all species →	Cellular Component	membrane	Interproscan
GO:0016342 all species →	Cellular Component	catenin complex	Interproscan
GO:0045296 all species →	Molecular Function	cadherin binding	Interproscan
GO:0098609 all species →	Biological Process	cell-cell adhesion	Interproscan
GO:0098742 all species →	Biological Process	cell-cell adhesion via plasma-membrane adhesion molecules	Interproscan
GO:0005886 all species →	Cellular Component	plasma membrane	Interproscan
GO:0007155 all species →	Biological Process	cell adhesion	Interproscan
GO:0007267 all species →	Biological Process	cell-cell signaling	Interproscan
GO:0007275 all species →	Biological Process	multicellular organism development	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 CAB3993096.1.

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

Expression pattern (RNA-seq)

Transcript abundance of CAB3993096.1 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

11TPM > 0

4Conditions

9.8Max TPM

1.6Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
apical branchlet · Control at T25	6	4	1.09	2.51
apical branchlet · Temperature treatment at T0	6	2	0.29	1.10
apical branchlet · Temperature treatment at T25	5	4	4.51	9.78
apical branchlet · Control at T0	4	1	0.62	2.48

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	2.51
SRR19977455	apical branchlet · Control at T25	apical branchlet	not recorded	Control at T25	SRP384900	1.67
SRR19977444	apical branchlet · Control at T25	apical branchlet	not recorded	Control at T25	SRP384900	1.45
SRR19977440	apical branchlet · Control at T25	apical branchlet	not recorded	Control at T25	SRP384900	0.90
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	1.10
SRR19977438	apical branchlet · Temperature treatment at T0	apical branchlet	not recorded	Temperature treatment at T0	SRP384900	0.63
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
SRR19977436	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
SRR19977434	apical branchlet · Temperature treatment at T25	apical branchlet	not recorded	Temperature treatment at T25	SRP384900	9.78
SRR19977432	apical branchlet · Temperature treatment at T25	apical branchlet	not recorded	Temperature treatment at T25	SRP384900	7.90
SRR19977435	apical branchlet · Temperature treatment at T25	apical branchlet	not recorded	Temperature treatment at T25	SRP384900	3.34
SRR19977425	apical branchlet · Temperature treatment at T25	apical branchlet	not recorded	Temperature treatment at T25	SRP384900	1.50
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	2.48
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.