Gene detail

Detailed information of CAB3986247.1 in Paramuricea clavata

Genomic Location: pcla8_s001014:1377...3818
NR annotation: CAB3986247.1, RNA-binding 15 [Paramuricea clavata]
Species Paramuricea clavata · all data for this species · gene families

Gene Structure

More details in JBrowse

Sequence

CDS

PACLA_8A003893

ATGGTCATGAAGAGAAGTTCAGATATAGACTCACCGAGGAGAAATAAACGAACTAGTGATGGCCTGGAGGTTTTACATATGGTAAATATCGACAGATATTCTTCCGAAAACGAACGTCGTGCTCGAGAGCATTCACCAGACACTCGCATTTTCAACCGAAAAGGCGAGCGTTCTTCACATATTCATACAGTAAAAAGCGCGTTTGGGGCTGATTCGTACAAGGAAAAAAGGACCGAAAGAGTCAACGAAGCTTCAATTCGTGTTACCAACTTTACTCGGAGTGCAGCAGATCATGTTTTGCGAGAAAAACTCAACTACGAATTCAAGAAATTTGGTGAGATTAGTGTACGAATCGTGCGACATGACGACGAGCGTTACGCTGTTGTTTATTTTCAGAATAGCGACGATGCAGTAGAGGCGAAACGTTCAATTGAGAACCGTGGTCGAGCAATTTTCCTGCAAGATCGTGCTTTGAATTTGCAGTTTAGTATTCCTGGCAGTCGGTTGAGGTATTTGACGCCCGATGTGCTCCAGCAGAAAAGCAGATTTTCCCGGGGTTCGCCTACACGCAGTAAACATGATGAACTGGATGTTGTTGGGGAGGAGCGAAGACATCGTATAAAAGGTGAGCGTTTGTTTAGTGGTCAAAGTGCTATTTCTTCGGCTGCATTGGCAGTTGAGGGAGACGACCCGAAGGCGACTCGAACCCTGTTTGTTGGCAACCTTGAGAGCTCTATTTCTCGCCAAGACGTACGTCGTGAGTTTGAGCAGTTTGGCGTGGTTGAGGATGTTGATATAAAACGACCTATCCGTGGACAAGGAAGTACATATGCTTTTGTAAAGTTTATTGATCTTGATGTTGCAACAAAGGCCAAAGTTGCTATGCAAGGTTCCTTCTTTGGAAGGAATCAGGTAAAGATTGGATATGGCAAAAGCATGCCTACAACTCGGTTGTGGATTGGTGGTCTTGGATCTTGGACATCAATTGTAGAGCTTGAGAGAGAATTTGATCGGTTTGGTGCGATTCGTCGGATTGATTACAACAAGGGCCATGATCATGCATTCATACTTTATGACAGCTTGGATGCCGCTTCTGTTGCTGCAAGGGAAATGCGTGGGTTCAAAATGAATGGGCGGCGCTTGAAACTTGACTTTGCAGAACTAACACAAGGTTTAGAGGAGTATCCTGAGACGTTAGGCCATCTGGTTGAAGACAGAGAAAATCAGTTGACAAATCCAAAAAATCAAGATGCATTGACAAGTGGTGAGTCATTTAAAAAATCCCCTGAGAGAAAGGTTTTTAAGAGAGAGAGAAACAACAGTGATGGTAGTGGAAAATGGAGTGATTCAATGAGTAACCTCAGCTTTAATGATGCAAAGCAAAGTGGTGGAAAGCGCGATAGCTGGCAGTGGATTCATGAAAAAGACACAAAGCAAAAATTGGAGGAAAGACCTAAATTCCGTGGCCCTCGTACCCCATCACCACCTGAAAATGAAAAACTGCCTGCAAGGAACCATAGGAGTAAAGATAGAGCAAAAAGCAGAGAAAAAAACAAGTCTGGCAATGGTGTTTCTCGTTCTCGCAGCCCACCTTCTAAACGTCCACGTAAAACCTCTGGACCTCCACCTGCTTTGTCTCCACAAAGATTTGGATCAATATCACCAAAAAGGAAAAGCCGTTCTGCCTCCCCTGTTAGCGAAAGAAACTACAAGCCTGATGACAAGTATCACAAGGAAAAAGATCAAGAAAAGGATAAATATAAAAATCAAGACCGAAAAGAAAAAACACAAGATAATGAAAGCATTGAATCTGAAAAACCTGCATCTGAATCAAAAGAAATTGTTCCAGTGGAAGAACCTGTTTCTAGTACATCTGAAAGCCTTCAAGATATTGCTAAACGGTTTGCTGTTGCATGGCGTGGATCTCTGATACTAAAAAGTAGCTCTTTTCCTGTTCGTCTTCATTTGATTGGTGGAAACCCAGAAATTGTTGAAGTGTTACTCCGTAATGTGCCTGGAAATTCTGCGCCAAATACCGTTTTACGTATTTCACAACGACTGCGACTTGACCAACCAAAATTAGAGGAAGTATCAAAAAGGATGAATACAGCTGGTGCATGTGGCTATTGTATGTTGCTTGCATTACCTGGTGTGCATGGAGGAGAACCACCCTTAGATACTGAAACCAATATGCCAACTCAACAAAGACCACTACGAAACCTTGTTACCTACCTGAAACAAAAACAAGCTGCTGGTGTTGTTAATTTAATCAATACAAATAATCTATCTCCAACAAATATAAAAGATGAAGATGGTGTGCTTCATGCATTCCCGCCTTGTCAATATTCTCATGACCAGCTTTTAAAAATTGCACCTCATCTTGGCCAAGAAGCATTTAATGAAGACCATCTTGTTGTCGTTGTTATTCGTGGACCTGCATAG

Transcript

rna-PACLA_8A003893

ATGGTCATGAAGAGAAGTTCAGATATAGACTCACCGAGGAGAAATAAACGAACTAGTGATGGCCTGGAGGTTTTACATATGGTAAATATCGACAGATATTCTTCCGAAAACGAACGTCGTGCTCGAGAGCATTCACCAGACACTCGCATTTTCAACCGAAAAGGCGAGCGTTCTTCACATATTCATACAGTAAAAAGCGCGTTTGGGGCTGATTCGTACAAGGAAAAAAGGACCGAAAGAGTCAACGAAGCTTCAATTCGTGTTACCAACTTTACTCGGAGTGCAGCAGATCATGTTTTGCGAGAAAAACTCAACTACGAATTCAAGAAATTTGGTGAGATTAGTGTACGAATCGTGCGACATGACGACGAGCGTTACGCTGTTGTTTATTTTCAGAATAGCGACGATGCAGTAGAGGCGAAACGTTCAATTGAGAACCGTGGTCGAGCAATTTTCCTGCAAGATCGTGCTTTGAATTTGCAGTTTAGTATTCCTGGCAGTCGGTTGAGGTATTTGACGCCCGATGTGCTCCAGCAGAAAAGCAGATTTTCCCGGGGTTCGCCTACACGCAGTAAACATGATGAACTGGATGTTGTTGGGGAGGAGCGAAGACATCGTATAAAAGGTGAGCGTTTGTTTAGTGGTCAAAGTGCTATTTCTTCGGCTGCATTGGCAGTTGAGGGAGACGACCCGAAGGCGACTCGAACCCTGTTTGTTGGCAACCTTGAGAGCTCTATTTCTCGCCAAGACGTACGTCGTGAGTTTGAGCAGTTTGGCGTGGTTGAGGATGTTGATATAAAACGACCTATCCGTGGACAAGGAAGTACATATGCTTTTGTAAAGTTTATTGATCTTGATGTTGCAACAAAGGCCAAAGTTGCTATGCAAGGTTCCTTCTTTGGAAGGAATCAGGTAAAGATTGGATATGGCAAAAGCATGCCTACAACTCGGTTGTGGATTGGTGGTCTTGGATCTTGGACATCAATTGTAGAGCTTGAGAGAGAATTTGATCGGTTTGGTGCGATTCGTCGGATTGATTACAACAAGGGCCATGATCATGCATTCATACTTTATGACAGCTTGGATGCCGCTTCTGTTGCTGCAAGGGAAATGCGTGGGTTCAAAATGAATGGGCGGCGCTTGAAACTTGACTTTGCAGAACTAACACAAGGTTTAGAGGAGTATCCTGAGACGTTAGGCCATCTGGTTGAAGACAGAGAAAATCAGTTGACAAATCCAAAAAATCAAGATGCATTGACAAGTGGTGAGTCATTTAAAAAATCCCCTGAGAGAAAGGTTTTTAAGAGAGAGAGAAACAACAGTGATGGTAGTGGAAAATGGAGTGATTCAATGAGTAACCTCAGCTTTAATGATGCAAAGCAAAGTGGTGGAAAGCGCGATAGCTGGCAGTGGATTCATGAAAAAGACACAAAGCAAAAATTGGAGGAAAGACCTAAATTCCGTGGCCCTCGTACCCCATCACCACCTGAAAATGAAAAACTGCCTGCAAGGAACCATAGGAGTAAAGATAGAGCAAAAAGCAGAGAAAAAAACAAGTCTGGCAATGGTGTTTCTCGTTCTCGCAGCCCACCTTCTAAACGTCCACGTAAAACCTCTGGACCTCCACCTGCTTTGTCTCCACAAAGATTTGGATCAATATCACCAAAAAGGAAAAGCCGTTCTGCCTCCCCTGTTAGCGAAAGAAACTACAAGCCTGATGACAAGTATCACAAGGAAAAAGATCAAGAAAaggataaatataaaaatcaagACCGAAAAGAAAAAACACAAGATAATGAAAGCATTGAATCTGAAAAACCTGCATCTGAATCAAAAGAAATTGTTCCAGTGGAAGAACCTGTTTCTAGTACATCTGAAAGCCTTCAAGATATTGCTAAACGGTTTGCTGTTGCATGGCGTGGATCTCTGATACTAAAAAGTAGCTCTTTTCCTGTTCGTCTTCATTTGATTGGTGGAAACCCAGAAATTGTTGAAGTGTTACTCCGTAATGTGCCTGGAAATTCTGCGCCAAATACCGTTTTACGTATTTCACAACGACTGCGACTTGACCAACCAAAATTAGAGGAAGTATCAAAAAGGATGAATACAGCTGGTGCATGTGGCTATTGTATGTTGCTTGCATTACCTGGTGTGCATGGAGGAGAACCACCCTTAGATACTGAAACCAATATGCCAACTCAACAAAGACCACTACGAAACCTTGTTACCTACCTGAAACAAAAACAAGCTGCTGGTGTTGTTAATTTAATCAATACAAATAATCTATCTCCAACAAATATAAAAGATGAAGATGGTGTGCTTCATGCATTCCCGCCTTGTCAATATTCTCATGACCAGCTTTTAAAAATTGCACCTCATCTTGGCCAAGAAGCATTTAATGAAGACCATCTTGTTGTCGTTGTTATTCGTGGACCTGCATAG

Protein

UniProt (Swiss-Prot top hit)

UniProt accession	Description
Q6PHZ5	Putative RNA-binding protein 15B OS=Mus musculus OX=10090 GN=Rbm15b PE=1 SV=2
Q96T37	RNA-binding protein 15 OS=Homo sapiens OX=9606 GN=RBM15 PE=1 SV=2
Q0VBL3	RNA-binding protein 15 OS=Mus musculus OX=10090 GN=Rbm15 PE=1 SV=1

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0008488 (this species only)

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF00076 all species →	RRM_1	RNA recognition motif	Domain	Interproscan
PF07744 all species →	SPOC	SPOC domain	Domain	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR016194 all species →	Homologous_superfamily	SPOC-like, C-terminal domain superfamily	Interproscan
IPR000504 all species →	Domain	RNA recognition motif domain	Interproscan
IPR035979 all species →	Homologous_superfamily	RNA-binding domain superfamily	Interproscan
IPR012677 all species →	Homologous_superfamily	Nucleotide-binding alpha-beta plait domain superfamily	Interproscan
IPR010912 all species →	Domain	Spen paralogue/orthologue C-terminal, metazoa	Interproscan
IPR012921 all species →	Domain	Spen paralogue and orthologue SPOC, C-terminal	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR23189 all species →	RNA RECOGNITION MOTIF-CONTAINING	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0003723 all species →	Molecular Function	RNA binding	Interproscan
GO:0003676 all species →	Molecular Function	nucleic acid binding	Interproscan
GO:0000381 all species →	Biological Process	regulation of alternative mRNA splicing, via spliceosome	Interproscan
GO:0003729 all species →	Molecular Function	mRNA binding	Interproscan
GO:0005634 all species →	Cellular Component	nucleus	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
K13190	RBM15; RNA-binding protein 15	-	Spliceosome	ko03041	deepkoala

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

Expression pattern (RNA-seq)

Transcript abundance of CAB3986247.1 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

20TPM > 0

4Conditions

114.8Max TPM

26.0Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
apical branchlet · Control at T25	6	6	21.82	36.09
apical branchlet · Temperature treatment at T0	6	6	29.04	63.89
apical branchlet · Temperature treatment at T25	5	5	38.94	114.80
apical branchlet · Control at T0	4	3	11.69	25.44

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

SRA run	Condition	Tissue	Developmental stage	Treatment	Study	TPM
SRR19977444	apical branchlet · Control at T25	apical branchlet	not recorded	Control at T25	SRP384900	36.09
SRR19977433	apical branchlet · Control at T25	apical branchlet	not recorded	Control at T25	SRP384900	28.00
SRR19977441	apical branchlet · Control at T25	apical branchlet	not recorded	Control at T25	SRP384900	23.38
SRR19977455	apical branchlet · Control at T25	apical branchlet	not recorded	Control at T25	SRP384900	16.46
SRR19977440	apical branchlet · Control at T25	apical branchlet	not recorded	Control at T25	SRP384900	13.84
SRR19977439	apical branchlet · Control at T25	apical branchlet	not recorded	Control at T25	SRP384900	13.18
SRR19977436	apical branchlet · Temperature treatment at T0	apical branchlet	not recorded	Temperature treatment at T0	SRP384900	63.89
SRR19977426	apical branchlet · Temperature treatment at T0	apical branchlet	not recorded	Temperature treatment at T0	SRP384900	58.53
SRR19977428	apical branchlet · Temperature treatment at T0	apical branchlet	not recorded	Temperature treatment at T0	SRP384900	19.26
SRR19977427	apical branchlet · Temperature treatment at T0	apical branchlet	not recorded	Temperature treatment at T0	SRP384900	19.26
SRR19977438	apical branchlet · Temperature treatment at T0	apical branchlet	not recorded	Temperature treatment at T0	SRP384900	6.94
SRR19977437	apical branchlet · Temperature treatment at T0	apical branchlet	not recorded	Temperature treatment at T0	SRP384900	6.36
SRR19977434	apical branchlet · Temperature treatment at T25	apical branchlet	not recorded	Temperature treatment at T25	SRP384900	114.80
SRR19977463	apical branchlet · Temperature treatment at T25	apical branchlet	not recorded	Temperature treatment at T25	SRP384900	46.54
SRR19977432	apical branchlet · Temperature treatment at T25	apical branchlet	not recorded	Temperature treatment at T25	SRP384900	16.07
SRR19977435	apical branchlet · Temperature treatment at T25	apical branchlet	not recorded	Temperature treatment at T25	SRP384900	11.53
SRR19977425	apical branchlet · Temperature treatment at T25	apical branchlet	not recorded	Temperature treatment at T25	SRP384900	5.78
SRR19977445	apical branchlet · Control at T0	apical branchlet	not recorded	Control at T0	SRP384900	25.44
SRR19977443	apical branchlet · Control at T0	apical branchlet	not recorded	Control at T0	SRP384900	16.20
SRR19977442	apical branchlet · Control at T0	apical branchlet	not recorded	Control at T0	SRP384900	5.10
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.