Gene detail

Detailed information of CAB4026087.1 in Paramuricea clavata

Genomic Location: pcla8_s014776:617...2598
NR annotation: CAB4026087.1, PREDICTED: chitobiase-like, partial [Paramuricea clavata]
Species Paramuricea clavata · all data for this species · gene families

Gene Structure

More details in JBrowse

Sequence

CDS

Transcript

rna-PACLA_8A041556-2

ATGGGTTGGCATATATCGCCAACAACCTTGATATACATTATGAAGTTCTTGACAACTTGGAAAGTGCGGAAACCTATAGATCTAGACTGACTCTCACCAACAGAGGAACTAAAGAGATACGACACGGACCTTGGGCTATATATTTCAACTTTATTCGTTTGATTGAACCTAAACATTTACTGGAAAATCCAAGtcgatatattataccgaatgTTGGGATGAAATTTGTTCATATTACTGGGTCACTTTTTAAACTGGAACCTGTACAAGGTCAGTATTTCATTTCGTATTTGCACAAATGCTGAAACTTGTTTGCGAAAGGAGTGGCAAGTATTATATGGCTCATTAAAGCTCACTGTATATGTAGTAAGGAATAGTCAGATTAGGGCTGTGCTCTGTCTGCCCACCTATCATCTGTAATTGAGTGATAAAgtcattaaaacaaaacaaacaaaacgaaAAAGTCAGCGAGTCCTACACATCGAAGCTGCAtgcaatttaaatatatttattaaaataatttgcattttggTCTTTAGATTTTGGTCTTTGAATTTAGATATTGTTAGCGACTTCGTTCCTAGGAAATTTAGGCGTGCAGAATCCAAAATGTTTAGAACAAAAATTTCGTCGTGTAAACACAATCGACCGACCAAAAAGCCTCCCAAAATGACTGTCGTATAAACGAGCcttatatatttgtaatattatATTCTTTACCGCCCCACTTGGAAAGAAGCTTCAGTTGAAGGACTTGAAGGGGCCAGCACAGTCAAATAAAGTGTTATCATATCATATCCTATCCTATCCTGTTCTATCCTATCGTCtattaaggaggctccctacagttttaatTAACGTTATAGCGCACAACTTTGCTTTTAGGCCCATTGTTTCCGTAGTTTGCAAAATATGATTGACTGCGGATGTAAAAGAATGAGTCACTGGTGATTACCGTTAcagatatatctatatatttctacgcaatacaccctttcgataattacgtcatttggtcttggagcctcgctctaatgaatcgtgagccaatcaccttgcgtaaatTACTAATGAGAGcaaggctccaagaccaaaaagtatgtgtgacgtaattatcgaaagggtgtattatcaTATAAGAGGATAGTTATACACTTTAATTATAGACGTGTCACTTTTCTGTTTTTTTTGCTTTGTTTTTGTGGACTGAAACATTTTGCGAAATAATCGTGATGAAAAGCAAAGAATAACATTGATCGCCAAACAACTCGGAACATGatctgtttttattatatatcttGCATTTATTTGTTTTCCAAGGTTTCCGAGCACTCTCATTTGGTAAAAATCTGTCTTTCGATTTCGACTCTCAATACTTCTCTGTTGCAAGGACGGATGTAATGGCTAACTGGTATATTGCGTCTGAGGGTCTCAAGGCTGTGAATGTTAAAATGACGTCTGGCGAAGATCTGAAATTTGTCGGGAAGTTTGATACGAAGGAAAAATGGAAGCGAACTAAAGACGATAAGTATAATCCATTTACACCAGCAGAGCGTTTGAAACAAATTGAGGTGGAAACAAAGAAACCTGAACCTGGGTCAATAATACCAACTCCTGTTGAAATGAAGGTAGAAAGTGGAAAATATGTGAACATTAATGACTGGGTGATTGCTACATCAGCAGAATATGAGAATGAAGCCAAGTATCTTGGGAACAAACTAAAGCTCTCTATAGGAATTAACACTGCTGTAaccaatactaaaatattgcgtcttttacaagaaaatgttgATGTGAAAATTGACGGACGAAGCAGTACTAGTAAGGAGAGATACCAAGTTGATGTGAAAGAAAATACAATCACAATTTCAGCGCCTGAATCAAGCGGGATTTTCTATGGAATTCAGTCACTCTTGGCTGTTACAAATGTTGAAAGAAAACAAGTTCTTATGGTGAGCTTATTTTGTCATATCGTAGTCTGA

Protein

UniProt (Swiss-Prot top hit)

No Swiss-Prot hit above the reporting threshold for this gene.

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0000952 (this species only)

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF02838 all species →	Glyco_hydro_20b	Glycosyl hydrolase family 20, domain 2	Domain	Interproscan
PF03173 all species →	CHB_HEX	Putative carbohydrate binding domain	Domain	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR015882 all species →	Domain	Beta-hexosaminidase, bacterial type, N-terminal	Interproscan
IPR029018 all species →	Homologous_superfamily	Beta-hexosaminidase-like, domain 2	Interproscan
IPR012291 all species →	Homologous_superfamily	CBM2, carbohydrate-binding domain superfamily	Interproscan
IPR008965 all species →	Homologous_superfamily	CBM2/CBM3, carbohydrate-binding domain superfamily	Interproscan
IPR004866 all species →	Domain	Chitobiase/beta-hexosaminidases, N-terminal domain	Interproscan

PANTHER

No PANTHER signature was detected for CAB4026087.1. This gene does have a gene model — the search simply returned no hit.

Gene Ontology

GO term	Category	Description	Source
GO:0004553 all species →	Molecular Function	hydrolase activity, hydrolyzing O-glycosyl compounds	Interproscan
GO:0030247 all species →	Molecular Function	polysaccharide binding	Interproscan
GO:0030246 all species →	Molecular Function	carbohydrate binding	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 CAB4026087.1.

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

Expression pattern (RNA-seq)

Transcript abundance of CAB4026087.1 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

8TPM > 0

4Conditions

0.6Max TPM

0.2Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
apical branchlet · Control at T25	6	4	0.23	0.58
apical branchlet · Temperature treatment at T0	6	2	0.19	0.62
apical branchlet · Temperature treatment at T25	5	1	0.09	0.45
apical branchlet · Control at T0	4	1	0.13	0.53

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

SRA run	Condition	Tissue	Developmental stage	Treatment	Study	TPM
SRR19977440	apical branchlet · Control at T25	apical branchlet	not recorded	Control at T25	SRP384900	0.58
SRR19977444	apical branchlet · Control at T25	apical branchlet	not recorded	Control at T25	SRP384900	0.45
SRR19977455	apical branchlet · Control at T25	apical branchlet	not recorded	Control at T25	SRP384900	0.34
SRR19977441	apical branchlet · Control at T25	apical branchlet	not recorded	Control at T25	SRP384900	0.01
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	0.62
SRR19977438	apical branchlet · Temperature treatment at T0	apical branchlet	not recorded	Temperature treatment at T0	SRP384900	0.52
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
SRR19977435	apical branchlet · Temperature treatment at T25	apical branchlet	not recorded	Temperature treatment at T25	SRP384900	0.45
SRR19977425	apical branchlet · Temperature treatment at T25	apical branchlet	not recorded	Temperature treatment at T25	SRP384900	0.00
SRR19977432	apical branchlet · Temperature treatment at T25	apical branchlet	not recorded	Temperature treatment at T25	SRP384900	0.00
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	0.53
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.