Gene detail

Detailed information of CAB3978315.1 in Paramuricea clavata

Genomic Location: not available for this species
NR annotation: CAB3978315.1, 40S ribosomal S4, X isoform, partial [Paramuricea clavata]
Species Paramuricea clavata · all data for this species · gene families

Sequence

No sequence record for CAB3978315.1 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
P47961	Small ribosomal subunit protein eS4 OS=Cricetulus griseus OX=10029 GN=RPS4 PE=2 SV=2
Q90YS0	Small ribosomal subunit protein eS4 OS=Ictalurus punctatus OX=7998 GN=rps4 PE=2 SV=3
Q76N24	Small ribosomal subunit protein eS4 OS=Chlorocebus aethiops OX=9534 GN=RPS4X PE=1 SV=3

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0006633 (this species only)

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF00046 all species →	Homeodomain	Homeodomain	Domain	Interproscan
PF00900 all species →	Ribosomal_S4e	Ribosomal family S4e	Family	Interproscan
PF00157 all species →	Pou	Pou domain - N-terminal to homeobox domain	Domain	Interproscan
PF16121 all species →	40S_S4_C	40S ribosomal protein S4 C-terminus	Family	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR001356 all species →	Domain	Homeobox domain	Interproscan
IPR000876 all species →	Family	Small ribosomal subunit protein eS4	Interproscan
IPR009057 all species →	Homologous_superfamily	Homeobox-like domain superfamily	Interproscan
IPR010982 all species →	Homologous_superfamily	Lambda repressor-like, DNA-binding domain superfamily	Interproscan
IPR036986 all species →	Homologous_superfamily	RNA-binding S4 domain superfamily	Interproscan
IPR013845 all species →	Domain	Small ribosomal subunit protein eS4, central region	Interproscan
IPR000327 all species →	Domain	POU-specific domain	Interproscan
IPR038237 all species →	Homologous_superfamily	Small ribosomal subunit protein eS4, central domain superfamily	Interproscan
IPR017970 all species →	Conserved_site	Homeobox, conserved site	Interproscan
IPR013847 all species →	Domain	POU domain	Interproscan
IPR002942 all species →	Domain	RNA-binding S4 domain	Interproscan
IPR014722 all species →	Homologous_superfamily	Large ribosomal subunit protein uL2, domain 2	Interproscan
IPR041982 all species →	Domain	Small ribosomal subunit protein eS4, KOW domain	Interproscan
IPR032277 all species →	Domain	Small ribosomal subunit protein eS4, C-terminal domain	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR11581 all species →	30S/40S RIBOSOMAL PROTEIN S4	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0003677 all species →	Molecular Function	DNA binding	Interproscan
GO:0003735 all species →	Molecular Function	structural constituent of ribosome	Interproscan
GO:0005840 all species →	Cellular Component	ribosome	Interproscan
GO:0006412 all species →	Biological Process	translation	Interproscan
GO:0003723 all species →	Molecular Function	RNA binding	Interproscan
GO:0003700 all species →	Molecular Function	DNA-binding transcription factor activity	Interproscan
GO:0006355 all species →	Biological Process	regulation of DNA-templated transcription	Interproscan
GO:0000981 all species →	Molecular Function	DNA-binding transcription factor activity, RNA polymerase II-specific	Interproscan
GO:0022627 all species →	Cellular Component	cytosolic small ribosomal subunit	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

KO	Enzyme	Enzyme ID	Pathway	Map ID	Source
K08840	TNIK; TRAF2 and NCK interacting kinase	EC:2.7.11.1	Protein kinases	ko01001	deepkoala

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

Expression pattern (RNA-seq)

Transcript abundance of CAB3978315.1 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

21TPM > 0

4Conditions

1,213.8Max TPM

565.8Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
apical branchlet · Control at T25	6	6	683.89	1,213.84
apical branchlet · Temperature treatment at T0	6	6	536.66	927.13
apical branchlet · Temperature treatment at T25	5	5	434.75	721.31
apical branchlet · Control at T0	4	4	596.35	1,098.39

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	1,213.84
SRR19977441	apical branchlet · Control at T25	apical branchlet	not recorded	Control at T25	SRP384900	837.28
SRR19977440	apical branchlet · Control at T25	apical branchlet	not recorded	Control at T25	SRP384900	661.89
SRR19977455	apical branchlet · Control at T25	apical branchlet	not recorded	Control at T25	SRP384900	624.67
SRR19977444	apical branchlet · Control at T25	apical branchlet	not recorded	Control at T25	SRP384900	454.06
SRR19977433	apical branchlet · Control at T25	apical branchlet	not recorded	Control at T25	SRP384900	311.61
SRR19977427	apical branchlet · Temperature treatment at T0	apical branchlet	not recorded	Temperature treatment at T0	SRP384900	927.13
SRR19977436	apical branchlet · Temperature treatment at T0	apical branchlet	not recorded	Temperature treatment at T0	SRP384900	610.06
SRR19977428	apical branchlet · Temperature treatment at T0	apical branchlet	not recorded	Temperature treatment at T0	SRP384900	596.63
SRR19977437	apical branchlet · Temperature treatment at T0	apical branchlet	not recorded	Temperature treatment at T0	SRP384900	504.69
SRR19977438	apical branchlet · Temperature treatment at T0	apical branchlet	not recorded	Temperature treatment at T0	SRP384900	387.90
SRR19977426	apical branchlet · Temperature treatment at T0	apical branchlet	not recorded	Temperature treatment at T0	SRP384900	193.53
SRR19977435	apical branchlet · Temperature treatment at T25	apical branchlet	not recorded	Temperature treatment at T25	SRP384900	721.31
SRR19977432	apical branchlet · Temperature treatment at T25	apical branchlet	not recorded	Temperature treatment at T25	SRP384900	623.46
SRR19977434	apical branchlet · Temperature treatment at T25	apical branchlet	not recorded	Temperature treatment at T25	SRP384900	360.18
SRR19977425	apical branchlet · Temperature treatment at T25	apical branchlet	not recorded	Temperature treatment at T25	SRP384900	269.11
SRR19977463	apical branchlet · Temperature treatment at T25	apical branchlet	not recorded	Temperature treatment at T25	SRP384900	199.67
SRR19977445	apical branchlet · Control at T0	apical branchlet	not recorded	Control at T0	SRP384900	1,098.39
SRR19977443	apical branchlet · Control at T0	apical branchlet	not recorded	Control at T0	SRP384900	697.16
SRR19977442	apical branchlet · Control at T0	apical branchlet	not recorded	Control at T0	SRP384900	416.39
SRR19977446	apical branchlet · Control at T0	apical branchlet	not recorded	Control at T0	SRP384900	173.47

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.