Gene detail

Detailed information of CAB4030858.1 in Paramuricea clavata

Genomic Location: pcla8_s018497:10...2433
NR annotation: CAB4030858.1, ATP-dependent DNA helicase PIF1, partial [Paramuricea clavata]
Species Paramuricea clavata · all data for this species · gene families

Gene Structure

More details in JBrowse

Sequence

CDS

PACLA_8A077445

ATGGCAAATGATGTAGAGGAAAATCCTGGACCCACAATATATGATGTGGTTGATCCAACTAAAACAATATGTGCAGATTTTAGTCAGGGAAATACAAAAAAGTTTCGACAAAATGCTGGTAAACAATGTTTAGCAATGTCTTTGACTGCGATAATATATAATCATATCACAAATGCAAATGCATGGGATTCAACTGTATTAAATTCCATACTGTGTGCTGGAAATAACCTTTATTCTTTTATAAGCAATTCTGTTAAGAAAAGCTATTTGCTTTTAACTGACGTGCCTGAAATGGTTTCGGTTTTTGATGGCATTTATTGTATGCAATATGGTGAACCGTTTGCTGGTGACTTATTCATGGCAAATACTGCTCTACCTTATTATTCTATAGAGAATGCTCTTAATAATCTGTTTATGGAAAATTATCAACATTGTATGTTGACGATTGGTTGTAATACTGTTGCAATTTTTAAGACTTCTGAAGGAACCTTTAAAGTATTTGATTCTCATTCAAGAGATTTATATGGGATCCCACACCCTTTTGGAAAATGCATATTAGCATCCGTTGATAGTATAGAAAGCCTGGTGATATATTTCCAGAGTACCATACCTCCGGGTAATGAAACACCCTTCGAAGTTAAAGGAGTAACTGTTCAGTTAAATTCTGATATAACACAAATAAGTGGACTTGCTTCAAGTGAAAGTGCAAAAGAGCATGTGAAACAAAAGTATTCAGAATTAACTGAGAGTCAGAAACAGACTAGACTTGAAAATGCTAGAAAGTATAAAAAAGCAAAGCAAGCAGCAGAAACTGAAACTGAAAAACAAACTAGACTTGAAAATGCTAGAGAGTATCAAAAAGCAAAACGAGCTTCAGAAACCGAGAATGAGAAACAAACTAGACTTAGAAATGTTAGAAATTATGAAAAAAGAAAACAAGGACAGGAAACTGAGATTGAAAAGCAAGCATGTCTTGCCAGTGCCAATCAGAACAAGAGAAAACGTTTGTGTTCTACTCACATTGTAAGCCAACAGGATTATTTAAACAAATATGACATTGAAAAAGATGGTAGTATTCATGAACAGAGTTGGGCCCAATTTAACATTAATAAATTTTATAAATCTATTCAATTTTTTATTAATCAATGCACTATATGTCATGAAGCATGGCCACTGAACTCTAAACCAAGGTCACCTGATTGTTATATATGCTCTCGATGTGCTCGAGACACAAAATCTCCCAGAAAGTTCTCACTTGAAAATTCAATGATTCCTTCTCCAGTGCCAACTGAGTTACAAAATTTAACTCAAGTAGAGGAGATGTTAGTTGCTCGTGCTCTTCCTATCATGAGAGTTTACATTAAGCCTGGTGGACAACGAGGTTACTCAGGTCATTGTGTTAATTTGCCGCAAAATGTTAAGGAACTTGCAACATCATTGCCAAGATATCCCAAAGATTTGTCCGTGATTATTGTCAAAGTCAAAGGTAAAGATAACTCGTTTAGAGATGTTGCTGTGAGAAGAGAAAAAGTACATAATGCATTATTATGGCTTGTGCAAAATAATCCTCATTATGCTGAATTAGAAATTAATGAAGATGCACTAAACTCTTTACCTGAAAATGGCATTCCAGCAGATCTCATGACAGTTGAGACTGAAAATGAAATAATCTCAAATGATGATGCTATGTCAGATTTGGGGCCACCCACTGATAACCCTTCTGAAGATATAGTGTATAACAACTCGACAGACATGAATAGTTTCTTGCCTGTTGGTGAACAGCAGGAACAAGAAATAGAAGCAGTTAGAAATCAGCTTTCTGCAAATGAACCGATACCATGGCCTGCTATTGAATGTGAGCCATTAAATGAATATCAGATATCACATCTGGCCACTATGGCTTTTCCAACATTATTTCCTGATGGGAAAGGTGATCCCACTAATCAAAGTATCTTGAGGAATGTTCCCCTTCAAGAAAGAATTAAGCATCTTTTGAAATTTTCTGAATTTATTGATGGTAAATGGGTATATCGTTTTGCTAACCACCCTAGATTTTCATACTGGGCATTCAATATGATTCACAGGAAACGTATACTACAACAAAGTGGAATATTCATTAAACAAAATCCAGGTGAAGCACACCTCACTATTGACGAGCTACGTGAAATGGCTGCAAGTGACAACTCAGCTTTATTGATGTCCAAAGTGTCCAGATACATTGGCAATATTGCAGGTACTAATGCTTACTGGAATAAAGTAAGAGAGGAACTCAAAGCTATAATAACTAATGTTGGAGCACCAACATTGTTCTTTACTTTCTCATCAGCAGATATGCACTGGCCTGAATTACATGCTCTCTTTGGAGCAAAGACCGGTAACGCTACCAGTCAGATCAGACGACAAAATGTGATCAACAATCCCCAT

Transcript

rna-PACLA_8A077445

ATGGCAAATGATGTAGAGGAAAATCCTGGACCCACAATATATGATGTGGTTGATCCAACTAAAACAATATGTGCAGATTTTAGTCAGGGAAATACAAAAAAGTTTCGACAAAATGCTGGTAAACAATGTTTAGCAATGTCTTTGACTGCGATAATATATAATCATATCACAAATGCAAATGCATGGGAttcaactgtattaaattccatACTGTGTGCTGGAAATAACCTTTATTCTTTTATAAGCAATTCTGTTAAGAAAAGCTATTTGCTTTTAACTGACGTGCCTGAAATGGTTTCGGTTTTTGATGGCATTTATTGTATGCAATATGGTGAACCGTTTGCTGGTGACTTATTCATGGCAAATACTGCTCTACCTTATTATTCTATAGAGAATGCTCTTAATAATCTGTTTATGGaaaattatcaacattgtaTGTTGACGATTGGTTGTAATACTGTTGCAATTTTTAAGACTTCTGAAGGAACCTTTAAAGTATTTGATTCTCATTCAAGAGATTTATATGGGATCCCACACCCTTTTGGAAAATGCATATTAGCATCCGTTGATAGTATAGAAAGCCTGGTGATATATTTCCAGAGTACCATACCTCCGGGTAATGAAACACCCTTCGAAGTTAAAGGAGTAACTGTTCAGTTAAATTCTGATATAACACAAATAAGTGGACTTGCTTCAAGTGAAAGTGCAAAAGAGCATGTGAAACAAAAGTATTCAGAATTAACTGAGAGTCAGAAACAGACTAGACTTGAAAATGCTAGAAAGTATAAAAAAGCAAAGCAAGCAGCAGAAACTGAAACTGAAAAACAAACTAGACTTGAAAATGCTAGAGAGTATCAAAAAGCAAAACGAGCTTCAGAAACCGAGAATGAGAAACAAACTAGACTTAGAAATGTTAGAAATtatgaaaaaagaaaacaaggACAGGAAACTGAGATTGAAAAGCAAGCATGTCTTGCCAGTGCCAATCAGAACAAGAGAAAACGTTTGTGTTCTACTCACATTGTAAGCCAACAGGATTATTTAAACAAATATGACATTGAAAAAGATGGTAGTATTCATGAACAGAGTTGGGCCCAATTTAAcattaataaattttataaatctattcaattttttattaatcaaTGCACTATATGTCATGAAGCATGGCCACTGAACTCTAAACCAAGGTCACCTGATTGTTATATATGCTCTCGATGTGCTCGAGACACAAAATCTCCCAGAAAGTTCTCACTTGAAAATTCAATGATTCCTTCTCCAGTGCCAACTGAGTTACAAAATTTAACTCAAGTAGAGGAGATGTTAGTTGCTCGTGCTCTTCCTATCATGAGAGTTTACATTAAGCCTGGTGGACAACGAGGTTACTCAGGTCATTGTGTTAATTTGCCGCAAAATGTTAAGGAACTTGCAACATCATTGCCAAGATATCCCAAAGATTTGTCCGTGATTATTGTCAAAGTCAAAGGTAAAGATAACTCGTTTAGAGATGTTGCTGTGAGAAGAGAAAAAGTACATAATGCATTATTATGGCTTGTGCAAAATAATCCTCATTATGCTGAATTAGAAATTAATGAAGATGCACTAAACTCTTTACCTGAAAATGGCATTCCAGCAGATCTCATGACAGTTGAGACTGAAAATGAAATAATCTCAAATGATGATGCTATGTCAGATTTGGGGCCACCCACTGATAACCCTTCTGAAGATATAGTGTATAACAACTCGACAGACATGAATAGTTTCTTGCCTGTTGGTGAACAGCAGGAACAAGAAATAGAAGCAGTTAGAAATCAGCTTTCTGCAAATGAACCGATACCATGGCCTGCTATTGAATGTGAGCCATTAAATGAATATCAGATATCACATCTGGCCACTATGGCTTTTCCAACATTATTTCCTGATGGGAAAGGTGATCCCACTAATCAAAGTATCTTGAGGAATGTTCCCCTTCAAGAAAGAATTAAGcatcttttgaaattttctgAATTTATTGATGGTAAATGGGTATATCGTTTTGCTAACCACCCTAGATTTTCATACTGGGCATTCAATATGATTCACAGGAAACGTATACTACAACAAAGTGGAATATTCATTAAACAAAATCCAGGTGAAGCACACCTCACTATTGACGAGCTACGTGAAATGGCTGCAAGTGACAACTCAGCTTTATTGATGTCCAAAGTGTCCAGATACATTGGCAATATTGCAGGTACTAATGCTTACTGGAATAAAGTAAGAGAGGAACTCAAAGCTATAATAACTAATGTTGGAGCACCAACATTGTTCTTTACTTTCTCATCAGCAGATATGCACTGGCCTGAATTACATGCTCTCTTTGGAGCAAAGACCGGTAACGCTACCAGTCAGATCAGACGACAAAATGTGATCAACAATCCCCAT

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)	OG0000098 (this species only)

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF04843 all species →	Herpes_teg_N	Herpesvirus tegument protein, N-terminal conserved region	Family	Interproscan
PF20209 all species →	DUF6570	Domain of unknown function (DUF6570)	Domain	Interproscan
PF14214 all species →	Helitron_like_N	Helitron helicase-like domain at N-terminus	Family	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR006928 all species →	Domain	Herpesvirus large tegument protein, USP domain	Interproscan
IPR046700 all species →	Domain	Domain of unknown function DUF6570	Interproscan
IPR038765 all species →	Homologous_superfamily	Papain-like cysteine peptidase superfamily	Interproscan
IPR025476 all species →	Domain	Helitron helicase-like domain	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR40552 all species →	AT05186P-RELATED	Interproscan

Gene Ontology

No Gene Ontology signature was detected for CAB4030858.1. This gene does have a gene model — the search simply returned no hit.

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 CAB4030858.1.

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

Expression pattern (RNA-seq)

Transcript abundance of CAB4030858.1 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

6TPM > 0

4Conditions

1.2Max TPM

0.1Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
apical branchlet · Control at T25	6	3	0.06	0.26
apical branchlet · Temperature treatment at T0	6	1	0.06	0.37
apical branchlet · Temperature treatment at T25	5	1	0.25	1.24
apical branchlet · Control at T0	4	1	0.12	0.49

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	0.26
SRR19977444	apical branchlet · Control at T25	apical branchlet	not recorded	Control at T25	SRP384900	0.08
SRR19977441	apical branchlet · Control at T25	apical branchlet	not recorded	Control at T25	SRP384900	0.05
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
SRR19977455	apical branchlet · Control at T25	apical branchlet	not recorded	Control at T25	SRP384900	0.00
SRR19977438	apical branchlet · Temperature treatment at T0	apical branchlet	not recorded	Temperature treatment at T0	SRP384900	0.37
SRR19977426	apical branchlet · Temperature treatment at T0	apical branchlet	not recorded	Temperature treatment at T0	SRP384900	0.00
SRR19977427	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	1.24
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	0.49
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.