Gene detail

Detailed information of CAB4044898.1 in Paramuricea clavata

Genomic Location: pcla8_s050236:619...1122
NR annotation: CAB4044898.1, high-affinity choline transporter 1-like, partial [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
Q9VE46	High-affinity choline transporter 1 OS=Drosophila melanogaster OX=7227 GN=ChT PE=2 SV=2
O02228	High-affinity choline transporter 1 OS=Caenorhabditis elegans OX=6239 GN=cho-1 PE=2 SV=2
Q9GZV3	High affinity choline transporter 1 OS=Homo sapiens OX=9606 GN=SLC5A7 PE=1 SV=1

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0001039 (this species only)

Pfam domain

No Pfam domain signature was detected for CAB4044898.1. This gene does have a gene model — the search simply returned no hit.

InterPro

InterPro term	Type	Description	Source
IPR038377 all species →	Homologous_superfamily	Sodium/glucose symporter superfamily	Interproscan
IPR052244 all species →	Family	High-affinity choline transporter	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR45897 all species →	HIGH-AFFINITY CHOLINE TRANSPORTER 1	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0005307 all species →	Molecular Function	choline:sodium symporter activity	Interproscan
GO:0005886 all species →	Cellular Component	plasma membrane	Interproscan
GO:0008292 all species →	Biological Process	acetylcholine biosynthetic process	Interproscan
GO:0015871 all species →	Biological Process	choline transport	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 CAB4044898.1.

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

Expression pattern (RNA-seq)

Transcript abundance of CAB4044898.1 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

96.9Max TPM

40.4Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
apical branchlet · Control at T25	6	5	34.52	64.31
apical branchlet · Temperature treatment at T0	6	5	54.35	96.89
apical branchlet · Temperature treatment at T25	5	5	51.65	83.29
apical branchlet · Control at T0	4	2	14.46	36.62

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

SRA run	Condition	Tissue	Developmental stage	Treatment	Study	TPM
SRR19977433	apical branchlet · Control at T25	apical branchlet	not recorded	Control at T25	SRP384900	64.31
SRR19977441	apical branchlet · Control at T25	apical branchlet	not recorded	Control at T25	SRP384900	45.04
SRR19977455	apical branchlet · Control at T25	apical branchlet	not recorded	Control at T25	SRP384900	40.63
SRR19977444	apical branchlet · Control at T25	apical branchlet	not recorded	Control at T25	SRP384900	30.95
SRR19977440	apical branchlet · Control at T25	apical branchlet	not recorded	Control at T25	SRP384900	26.19
SRR19977439	apical branchlet · Control at T25	apical branchlet	not recorded	Control at T25	SRP384900	0.00
SRR19977437	apical branchlet · Temperature treatment at T0	apical branchlet	not recorded	Temperature treatment at T0	SRP384900	96.89
SRR19977436	apical branchlet · Temperature treatment at T0	apical branchlet	not recorded	Temperature treatment at T0	SRP384900	83.33
SRR19977428	apical branchlet · Temperature treatment at T0	apical branchlet	not recorded	Temperature treatment at T0	SRP384900	65.67
SRR19977427	apical branchlet · Temperature treatment at T0	apical branchlet	not recorded	Temperature treatment at T0	SRP384900	47.24
SRR19977438	apical branchlet · Temperature treatment at T0	apical branchlet	not recorded	Temperature treatment at T0	SRP384900	32.94
SRR19977426	apical branchlet · Temperature treatment at T0	apical branchlet	not recorded	Temperature treatment at T0	SRP384900	0.00
SRR19977425	apical branchlet · Temperature treatment at T25	apical branchlet	not recorded	Temperature treatment at T25	SRP384900	83.29
SRR19977434	apical branchlet · Temperature treatment at T25	apical branchlet	not recorded	Temperature treatment at T25	SRP384900	73.82
SRR19977432	apical branchlet · Temperature treatment at T25	apical branchlet	not recorded	Temperature treatment at T25	SRP384900	45.24
SRR19977435	apical branchlet · Temperature treatment at T25	apical branchlet	not recorded	Temperature treatment at T25	SRP384900	40.94
SRR19977463	apical branchlet · Temperature treatment at T25	apical branchlet	not recorded	Temperature treatment at T25	SRP384900	14.96
SRR19977443	apical branchlet · Control at T0	apical branchlet	not recorded	Control at T0	SRP384900	36.62
SRR19977442	apical branchlet · Control at T0	apical branchlet	not recorded	Control at T0	SRP384900	21.22
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.