Gene detail

Detailed information of CAB4025406.1 in Paramuricea clavata

Genomic Location: pcla8_s014304:1...6097
NR annotation: CAB4025406.1, Usher syndrome type-1G, partial [Paramuricea clavata]
Species Paramuricea clavata · all data for this species · gene families

Gene Structure

More details in JBrowse

Sequence

CDS

Transcript

rna-PACLA_8A020136

ATACTTTGTGCGAAAGGGTAAGATAGCAACATTTCTAGCTTTTATTTCTAGGTTTTAAAACATATATGTTTCTGCTTATTTCCATACAAATTACAAGAGGAAAATTGCTATGTAAATTTCGAAGTGTGTAAATAACTCGCTAACTTAGTCCGACGGCGGCTGCGAATAAATTTTAcataaaagttttttaaaagtttttaaattgGACGAATAGATTTCGGGGGAATTTGGGAAGCCATTTGAGTGCTTGAGGACATTTTTTAGTGGTTCTAAAACGCTTTCGGAAACGGTTTGAGAGGTTTTTCCCCTGTAGATCCCACGATTTACCCCTGTAGATCCCACGATTTTAGTGGAATATTTTTATTCGCTTCATTGCGTTTTTATAGATTATTCTTCAGCTTGCCGTCTGTAATTAAAGTATCGTTAGACTTGATAGATAGCtttgtcaaaagcttttttttgtttaaaaGATTGTATTTTCTATATATGTATTTTCTGCGGCTTATACTCTGGTGGGCAACTGAAGTCTACTGTACTTGTTCAGTGTTCACACAGCGGATCGTACAAATTTAAGCATTATTTTGAAGTGTGAACGGATAATTAAAAGAACTGAATAGTTGCAATTATAAATAACACGAACGAATATACTGAATTATTAGCAACATTTTTTCGTCTACTgtaatagttttaaaaattcTGACGCGATTTTGTGGGATTAGTTTGTGGTTTTTCGATACCTGCAGCCAGGAATAGATTAATAACAAAGTTTTGCATTGCTAATAGCAActttataatattttcaaaatattttgaagcgtTTTTAGAGTGCTTTTGTCTTGATGCCACGAAACTAGCTGTATTATTGCGCAAGCCAGAAATCAGAATATTCTGTTATAAGCCTATCTGAGTGAATAGTTTATCATTTTTGTCATAAGGAAGGTCTTAAACAATACTAGTTGCTAATCTCTTAGCAAACAGAACGTGTAtgtatacatttttaaaatttttatatcaCGTAATTTTTATCTTTTCCCCTACAAGCCGCAGATATATTGTATTACTGACGTAGATCCCAAGCAATTACGTGAACGCATTGTTCATAAATAAAGTAAAACTAGACATAGTTTGCCAGCATAAAATTGCATGAATGAGTAGTGTTGCCTATGAGATCAATGGTGTTGCCATATTTACATAGATTAGTGAATTATTGCGTTGATGAGATAAATATAGTTTAGTGCACAAGTTTTGCAATTCTTTAGTATAGTTTCTATTGCTCAGGCAGATCTAGCctcggtgggggggggggttaatttTTCTAGGGGTAATGCCTTCTTCCTTAACTACTGCAAATGTCATAAAAAATGACACAGAAAGCATAGAGTTTCGACATCTTATTGGTACTAACCTATCCCGGTtaaatattaacccattaagctgcaatgcacccTAGTATGTCATACTTACTTTACTCTGTATAATGCCACACAATTCCAGTGCTGAAAAAAAATTCGACAGCACCAGCAGCAACACTGCCAGAGAATTTTTAATAGCAAGAAATTTTCTTACATTCAGCAGGAAATGTTTCCCATCATATATATTCAAATGCCATAtcaggcacagattttctggggggtgcgcacctccccccagaaatgatttgcacacacccccagaggcatttggcaccgcccccaaaagtttttgcacccccacaaattatatatattttgatttgattgtttcatatttgattattcttactactaaatttgtaaaattaccaatattatggtctcagatcttgccatgccggcctagaaaacaaattttgttaaactttttccttggcctttccgggtgctgccaccaggccccggccaaagcaagcagcagcactccccccagatatttatccacccccgaacgaaaatatgaaaatccgtctctgtgCCATATAATTTGCTTCTTGATATAAAATTCCAAATGtatttttgaaatgaaattgtcAGGTGTGGAGAAATTATTTTACTTCAGACACACAACAGTACACCCCCGGCTGAAAATCTACAAGCACCTGTGCCAGGTGACAGCATCACTCTGGATGCCCCTTCAATGTAAATTCTTTAATGAGCTCCCCATCTTTAATATGACCCGTCTTTAGGGGGGGAGGGATTCATTAACCTGCACGACTCTCTATTAAGCTTAATTCCAACCCACCAGCTGAGAAACACATGTCTAGTCAttagattattattatttctgAATATCAAAGCCTCTGTCACttgcaaaaaatattacaaaatatttacaaaaatatgatGCAGAAACTGCTATCCTTACTTCTGTAAAAACCTCTATCCCATAATATATGGCAATTagtaaaaactagtaaaaaTCTATAAATATGATGCTATCCTTATACTTGTGTACAAACCTCTATCCCATAATATATGGCAATTagtaaaaactagtaaaaaTCTATAAATATGAAGCAATATAAAAGtttattaaaggtgatctacagtccgatctgagcatgtgcacaaatgagcccactttttatgataaaaacagtttaactatgttttgagttcttgaaaagcctgattgttgtttcttgatcaattattatactctagaagcttgaaaatataattagttgtcgaataaagctcaatattttggacacaaaaatgtaaacaaaggctttgtttacatacggactgtagatcacctttaaaaaaCTCTTTCAAGCATTCCTTAGATTTATCAATTTGCCTGGTGCCCTGGatgttcctaacttcctgttagTTTACTGCATTCTTTCATTTCTTCTATTTCCATGTTTTGGCTAAATTAGTAAGCCCCCTCTCCACTTAGCTCCCCTCCCCACTAAGTCCCCCTCTCCACTAAGTCCCCCTCTCCACTAAGTCCCCCTCTCCACTAAGTCCCCCTCTCCACTAAGTCCCCTTTCCACTAAGTCCCCTCTCAACTAAGTCCCCTCTCCACTAAGTCCCCTCTCCACTAAGTCCCCTCTCCACTAAGTCCATGAAATGGGCTAAAATAAATAAGCCCCGCTGGAGACAACTTTGCATTCTTGTGCTATCAACCAAATTTATGAAAGGTGGGAGGTGTCACCCCTAACCTCCCCCCTTCTTAGACCCCCTAATAACATGACATTTTATTTCTTACTAGTGGTGATCCAGACAAACCATGCTACGATGGATCAACCAGTGTCCATCTTGCAGCGGCGTGCGGTCAATTCCACTGCTTAGTTTTCCTCACAAAATTTGGCTCGAACATCTGGTCTCTGGATAACCAGTACCACACTCCCCTGGAAGAGGCAGCCGCGCGCGGACAACTGGACTGCGTGCAATACCTGGACCGCGTTGTGGCGGAGCAGATGCTGCACCATCGGGCACGTGCGAACAAGCAGAAAAAAGACGCGGAAAAAATTGCCAGAAAACGGATGAAAAAAGTCGAGCGACACCAGAAAAAGCGCGACAAGGAATACGCCAAGCGAGTGaggaaacaaaatggcgtcattGTTAATGATAGCAAGGAGAATGTCCCGAACGAGCAATGGACTGCGGAGAAGAATCGTCGGAATAGCAACAGCAGTAGCGCCGCAAACAGCAGTGGTTTTGAGAGTATGAGGCGCGCGCAAAGTTTGGAGCATTTTACGCAAATCACCGGAATGAAAGGTGGGAAAAGTTCTGCCCGCTCCGCCCAGAACAATCGACCCAACAGCGTCCAAGGGTCCTTGCGCAAGACCTTCCTTGGACCGCGGACCAGGTCTGCAAGCGCGTCCTCGATGAACGGTGGCAAGTCCCGCAGCCTGACTAGTCTGGACAGCGCGAATATCATCCTCCAACCACGGGCCGTCCGGTCTGGGAACGGCAATTTTGTGGGACGTCCAAAAGACCAGTACCTGGTCCGCTCTTCGGACGGACGAGGGAACAGCTTCACCTCCATCGAAAACATGCAGAAATTCGGAAGTCTGTCCAGTTATAATAGTCGTACGTCGACCGCACCAAGTTCGAGGTATAGCTGGAGCTCAAGCAGGTCGATGGATTCCGACGTCGACACGGACAACGACGACGAACTTCAAACGAACGATCCAAAATTAGCACCGCTCATGacttttttggcttcacttAATTTAGAACAGTTTACAGTGACGATGAAACGCGAGAGCATTGATATGAAAGCGTTAGCCTTATGTACTGACAATGATTTAAAGTCCGCGGGGATACCGTTAGGACCTCGAAGGAAGATTTTGGAGGCGATAGAACGAAGGCAGAAAGCGTGTGCTGAACCAGGGGCCATGATGGACACGCATTTGTAAGGTGCACACGAACTGTTCTAACATGAAACACCGCGGTTGGACAGAGTTGGGGGTGCAAACCACGCTACCCCAACATTCGTGTGCTTTTGGTGGGAGCTATGTTTAaagccaggggccggttgtataaaactcttaatcactattttgtagttaaatagtgattaactctcaaataggcgcttcttattggatgacgtttgcacttaaccatagttaactttaatcacttttttatacaaccagcccctggtttagtatcaaagtttctgtgatcacagtaggaagtgtgcataggtaaattttaagttttgaagattttgactcacactacacaacttttgcctaaaactgtcgcatgcaacctgcttataactcgagttgtactgtgtaaatcaagcacacaactcgtcTACGTTGTCGTGGGtcagttgtgtgcttgatttacacagtacaactcgacttataagcaggttgcatgcgacacgCCGACATTTTTAGGGAAgttttcaaaacatagaatttacctatgcaaaattcctactgtgatcacagaaactttgatagtgtaaggggcggaccattagaaatcccgggagggggggtgaaaattcccaaaaaaaaattcgtgcaaagaaaaatgcctggaaaaaaaattcgtgcagccattacgtcagagaaaaaaaaattcgtgcaagcaaacagcaaagtcATGGGCGTACCGTGCAGTTGGCAGTCGGGtaatattcgctgaacagtcgggcaattttagtttattaaaaaaaaaaaatttgacaaattctgtcaattttgtggtaaCTTTTGGTATGTGGTatgtctggaaaaaatttttgacccctaaaatggtacactgaccgaaattttttttggcgacggggggggggtcgccatgAGCAAAGTACaagtagtcttgaaaaaaaattcgtgcagatgTTAAGTGCATTCCTGCAGAcacatgagactgaaaaaaaaattcgtgccgcaaaaattttataccccccctcccgggatttctaatggtccgcccctaaactATAGCTTTATGACGTGTTAAGTAAACACTGAGGACTGTTTTTTTTCACCATGCCAAACACACGAACGTTGGGACAATATGCATACCCGACTACTGCATGTGTCTACCGTATGACGACTCTTATAAAGAAACATCAAGAAACGAGACGGGTGTATCATATAATGTATCATAGATTACATCTAAGGGTGAATAGAACAGTCGctcaaaaaaatattgtcatacCACCATGTTTGAAACTCTCATGTTTGGAAAGAGCATTTTACATTATGATCTAACCAGCCAATCACGTTGAACTAGCTGATTGGTTGAACATTGAGTTTCAAATGTGCTGAATATAAACAATGTCTTTTTCTGTGATTGTACGTTTTTAGATGCATGCAAGATATACAAACATTTTTAGATATATTCGTCTAAtttatcatattatatataacatTCAAGCGACGTTTAACCCGCTCTTTATAATAGACTGTACATAGTATTCATTCTGGAGTTTTTAGAAGACTTTTTAACACGCACGAGCCAATATTCTGCACGTTTTACGTGTTAGCCTGTTTAATTGACACAATGAAATTTGGAAACGAACGCTTTAATTGCTATACTGGCAAAGTTGAGCAAATTATTTTAACGCTTTCTATTAATAAAAGCAATatgtattgtaattatatatagaatatataataaaggtTTTATAAACC

Protein

UniProt (Swiss-Prot top hit)

UniProt accession	Description
Q495M9	pre-mRNA splicing regulator USH1G OS=Homo sapiens OX=9606 GN=USH1G PE=1 SV=1
Q80T11	pre-mRNA splicing regulator USH1G OS=Mus musculus OX=10090 GN=Ush1g PE=1 SV=1
Q8N8V4	Ankyrin repeat and SAM domain-containing protein 4B OS=Homo sapiens OX=9606 GN=ANKS4B PE=1 SV=2

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0008639 (this species only)

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF12796 all species →	Ank_2	Ankyrin repeats (3 copies)	Repeat	Interproscan
PF00536 all species →	SAM_1	SAM domain (Sterile alpha motif)	Domain	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR002110 all species →	Repeat	Ankyrin repeat	Interproscan
IPR013761 all species →	Homologous_superfamily	Sterile alpha motif/pointed domain superfamily	Interproscan
IPR001660 all species →	Domain	Sterile alpha motif domain	Interproscan
IPR036770 all species →	Homologous_superfamily	Ankyrin repeat-containing domain superfamily	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR10627 all species →	SCP160	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0005515 all species →	Molecular Function	protein 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

KO	Enzyme	Enzyme ID	Pathway	Map ID	Source
K21878	USH1G; Usher syndrome type-1G protein	-	Cilium and associated proteins	ko03037	deepkoala

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

Expression pattern (RNA-seq)

Transcript abundance of CAB4025406.1 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

52.0Max TPM

7.7Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
apical branchlet · Control at T25	6	4	17.21	52.03
apical branchlet · Temperature treatment at T0	6	2	6.69	27.71
apical branchlet · Temperature treatment at T25	5	1	0.01	0.03
apical branchlet · Control at T0	4	1	4.82	19.26

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	52.03
SRR19977455	apical branchlet · Control at T25	apical branchlet	not recorded	Control at T25	SRP384900	28.67
SRR19977440	apical branchlet · Control at T25	apical branchlet	not recorded	Control at T25	SRP384900	12.22
SRR19977444	apical branchlet · Control at T25	apical branchlet	not recorded	Control at T25	SRP384900	10.33
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
SRR19977428	apical branchlet · Temperature treatment at T0	apical branchlet	not recorded	Temperature treatment at T0	SRP384900	27.71
SRR19977427	apical branchlet · Temperature treatment at T0	apical branchlet	not recorded	Temperature treatment at T0	SRP384900	12.43
SRR19977426	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
SRR19977438	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	0.03
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	19.26
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.