Gene detail

Detailed information of CAB3999231.1 in Paramuricea clavata

Genomic Location: pcla8_s003605:17725...20721
NR annotation: CAB3999231.1, Gastrula zinc finger [Paramuricea clavata]
Species Paramuricea clavata · all data for this species · gene families

Gene Structure

More details in JBrowse

Sequence

CDS

PACLA_8A038779

ATGGCGGGTAACTTTAACATGAACGAATTCAGTGTAGAACAACTTTTGGCTCTCAACAGTATCATAGACAGTGATGAGGATATGGATACAAGAGTAGAAGGCATCCTGGAGGATAGAAACTATAGAATCACCCCTGATGACAAGGGTGAAAGTCCATTCCAAGGAAAAAGACAATTCGTAGATGAAGTTGACCGTGATACGGAAACAAAGAAACCAAGACGTATTCCTAAAAACTATAAGGGTAGAAGAGGAATTATGCCAACATGGAAGTACTCTGACAGACAAGAGGCCAAGGCGCTACTTGTAGAGGAGGCATACCAGAGTTTACTGTTTAAGGGAGTTCAGGGGTTACCACCAACAATGGGAGGTAGATGGCGTACAGACGATGTTCTTGTTAATGAGGAAATTAAGAGAATCGAAAACGAAAGGAATCCTAAGGTAAAGCGTCCCAGAGGTAGACCACCAAAGGCAAAGGTTGATGCCGAAGTGAAGGTGCCAAAGAAGAGGGGCAGACCACCAAAGGCAAAGACAGAGGCTGAAGTGAAAGTGCCAAAGAAGAGAGGTAGACCACCAAAGGTAAAGACTGATGTTAAGGTTAGGAAGCAAACTGTAGCAGAAAGATTCCTGAATCAGAGGAAGGTAAAACTCTCAGTACCAGCAGATAGTGTCATAACTCCAACAGGTCCAGGTAAGTTCACAGTTCGCGTGGATCTTAATAAGAGACCTGTGAGGAAAGCTCCTGAGGTACCTAAGGGTGTAGCTCCATGGAGACCGATACCTAAGCCTAGAACGGTACTTCCTAGGGAAAGACCTGTACCGAAACATAGAACTAAGCTTCTTAAGGAAAGACCTGTACCGAAACCTAGGACTATGAAACCAGTGTCTCCTCCTAAGGTCCGTAAGCCTGTAAGGATGTCGAGGGAAGTCAAGGAGCAGCCTATAGTCGTTACACCAGAGGAACAAGAAATCGATCCATTTGGAACAGACCTTGAAAAGCCATTCCACAGGAAAATTGAAACAGCCGCAAATGGAGCCGCCGTGACTTACTCGATAACTCCTCATTATATGGACCCTCTGGACCAGATGACTGCAAGTAGACAGGTAGTGAGAGGAATACTTGTGAACGAGTTGAAAAGAATGGGCGGGTTGAAGTACACAGAGACTCTGAAGGTGAGAATGTCAAAGGAAATCGATGACGGGAAAACCAAGAAGGACTCAGTCTACTTCAAATCTAAAACTGGTACTGCGACTAACTTCGAGGACATTGAAAGTACTGCTGCTCAAAACCAACTGACAATATTGTCTAGAATTGAAACCTTCCAAAACCTAGGTTCAAACTGGATTATACTCAATATTGACAGTCATTATGTGAACATTGCAATGTACAAACCACTAGCTGGGAGTTCATACATGGAACTTCCTAAGGACATTAGTAATTCAATGTGTGGACTCATCAATATGAAGAATGATGACGACATGTGCTTTATGTGGCGTCATGTGAGACATCTAAATCCTAGGGCTAGGAGGGCAACCACTATTACCCAAAAGGACAGGGAATTCAAAATGAACCTGGATTATGAAGGTATTGACTTCCCTGTGAAGATAAGCGATATTGATAAGATTGAGAGGAAAAATAGTATCAACATATCAGTGTTCGGTTATAAGGGTAAAAAGCAGTTCTACCCCATAAGGATTTCAAAGGCTAAATATGATGAGCATTTGGAGCTTCTACTCCTGGGTGATGGTGAACGTGGTAGACATTACGTGCTTATAAAGGATGTAAACAGAATGGTGTGTAGTGTGAGTAAACATGGACACAAGCAACACTTCTGCTTACACTGTCTTCATAGTTGCGTTAGCGAGGAGGTACTGGAGAAGCATAAGGAAACATGTCTGGAGGTAAATGGAACTCAGGCTGTAAAGCTTCCCAAGGAAGGGACAAAAATAAAGTTCAAAAATCATAGGAACTCAATGCCTGTGCCGTTTGTGATATATGCTGATTTTGAGTCCATACTGGTGCCTGAGGAGAGAAAAGAGAAGTCAGAGAACCCTGAGGATGAAAGTAGTACGGACCTTTACCAGACACACAAGGCTTGTAGTTTTGGTTTGAAGACTGTCTGCCACTATGATGATAAGTACTCCGGTGAGTATAAGAGTTATGTTGGAAGTGACGCTGCATTGGTCTTCCTAAAGACGGTAGTAAAAGAGTCCTTCAGATGTAGGGAAATGATTGACAAAATATTCAGGAAGAAAATGGTAATTACGCCCAAAGAGGAAGCAGAATTCCTGGTTACAAGAAACTGCCATATATGTGGTAACGACCTATGTGAGGACCGTGTGAGAGACCATGACCATGTAACAGGTAAGTACCGCGGAGCTGCTCACAATATATGCAATCTTAAGTATAGAATTACATGGAAAGTACCTGTGGTCTTCCACAACCTGAGAGGTTATGATGGTCATCTGATTATGCAGGAAATTGGCAAGTTCAAGATGGATGTTAATGTGATCCCAAATAATATGGAAAAATACATCTCATTCTCACTGGGTAAGAATCTGGTCTTCATAGACTCTATACAGTTCATGGCTTCTTCACTGGAAGCACTGGTAAGTAACTTTTCACCTGAGGACTTCAGGATAGTAGGTAAGAGGTGGAAGGGTGAGGACTTCAATCTAGTGACACAAAAAGGAGTGTTCCCATATGAGTTCCTAGATAATATTAGCAAACTCAATACAGAAGGTCTTCCGAGCAAGGATAATTTCTACTCGTCACTGTATGAGTCAGAGGTGAAGGAGGAAGATTACCAGAGAGCTCAGAAAGTATGGGATCACTTCAAGATGAAAACCATGAGAGATTACCATGATCTCTACTTAGAGACTGACGTTCTTCTGCTGGCTGATGTGTTTGAGAACTTCAGGAGAACATGTCTGGAAAGTTACAAACTTGACCCCGCACATTACGTGTCAGCACCTAGTCTGAGTTGGGACGCTTCCTGA

Transcript

rna-PACLA_8A038779

atggcgGGTAACTTTAACATGAACGAATTCAGTGTAGAACAACTTTTGGCTCTCAACAGTATCATAGACAGTGATGAGGATATGGATACAAGAGTAGAAGGCATCCTGGAGGATAGAAACTATAGAATCACCCCTGATGACAAGGGTGAAAGTCCATTCCAAGGAAAAAGACAATTCGTAGATGAAGTTGACCGTGATACGGAAACAAAGAAACCAAGACGTATTCCTAAAAACTATAAGGGTAGAAGAGGAATTATGCCAACATGGAAGTACTCTGACAGACAAGAGGCCAAGGCGCTACTTGTAGAGGAGGCATACCAGAGTTTACTGTTTAAGGGAGTTCAGGGGTTACCACCAACAATGGGAGGTAGATGGCGTACAGACGATGTTCTTGTTAATGAGGAAATTAAGAGAATCGAAAACGAAAGGAATCCTAAGGTAAAGCGTCccagaggtagaccaccaaaggcaaAGGTTGATGCCGAAGTGAAGGTGCCAAAGAAGAGGGGCAGACCACCAAAGGCAAAGACAGAGGCTGAAGTGAAAGTGCCAAAGaagagaggtagaccaccaaaggtaAAGACTGATGTTAAGGTTAGGAAGCAAACTGTAGCAGAAAGATTCCTGAATCAGAGGAAGGTAAAACTCTCAGTACCAGCAGATAGTGTCATAACTCCAACAGGTCCAGGTAAGTTCACAGTTCGCGTGGATCTTAATAAGAGACCTGTGAGGAAAGCTCCTGAGGTACCTAAGGGTGTAGCTCCATGGAGACCGATACCTAAGCCTAGAACGGTACTTCCTAGGGAAAGACCTGTACCGAAACATAGAACTAAGCTTCTTAAGGAAAGACCTGTACCGAAACCTAGGACTATGAAACCAGTGTCTCCTCCTAAGGTCCGTAAGCCTGTAAGGATGTCGAGGGAAGTCAAGGAGCAGCCTATAGTCGTTACACCAGAGGAACAAGAAATCGATCCATTTGGAACAGACCTTGAAAAGCCATTccacaggaaaattgaaacagCCGCAAATGGAGCCGCCGTGACTTACTCGATAACTCCTCATTATATGGACCCTCTGGACCAGATGACTGCAAGTAGACAGGTAGTGAGAGGAATACTTGTGAACGAGTTGAAAAGAATGGGCGGGTTGAAGTACACAGAGACTCTGAAGGTGAGAATGTCAAAGGAAATCGATGACGGGAAAACCAAGAAGGACTCAGTCTACTTCAAATCTAAAACTGGTACTGCGACTAACTTCGAGGACATTGAAAGTACTGCTGCTCAAAACCAACTGACAATATTGTCTAGAATTGAAACCTTCCAAAACCTAGGTTCAAACTGGATTATACTCAATATTGACAGTCATTATGTGAACATTGCAATGTACAAACCACTAGCTGGGAGTTCATACATGGAACTTCCTAAGGACATTAGTAATTCAATGTGTGGACTCATCAATATGAAGAATGATGACGACATGTGCTTTATGTGGCGTCATGTGAGACATCTAAATCCTAGGGCTAGGAGGGCAACCACTATTACCCAAAAGGACAGGGAATTCAAAATGAACCTGGATTATGAAGGTATTGACTTCCCTGTGAAGATAAGCGATATTGATAAGATTGAGAGGAAAAATAGTATCAACATATCAGTGTTCGGTTATAAGGGTAAAAAGCAGTTCTACCCCATAAGGATTTCAAAGGCTAAATATGATGAGCATTTGGAGCTTCTACTCCTGGGTGATGGTGAACGTGGTAGACATTACGTGCTTATAAAGGATGTAAACAGAATGGTGTGTAGTGTGAGTAAACATGGACACAAGCAACACTTCTGCTTACACTGTCTTCATAGTTGCGTTAGCGAGGAGGTACTGGAGAAGCATAAGGAAACATGTCTGGAGGTAAATGGAACTCAGGCTGTAAAGCTTCCCAAGGAAGGGAcaaaaataaagttcaaaaatcaTAGGAACTCAATGCCTGTGCCGTTTGTGATATATGCTGATTTTGAGTCCATACTGGTGCCTGAGGAGAGAAAAGAGAAGTCAGAGAACCCTGAGGATGAAAGTAGTACGGACCTTTACCAGACACACAAGGCTTGTAGTTTTGGTTTGAAGACTGTCTGCCACTATGATGATAAGTACTCCGGTGAGTATAAGAGTTATGTTGGAAGTGACGCTGCATTGGTCTTCCTAAAGACGGTAGTAAAAGAGTCCTTCAGATGTAGGGAAATGATTGACAAAATATTCAGGAAGAAAATGGTAATTACGCCCAAAGAGGAAGCAGAATTCCTGGTTACAAGAAACTGCCATATATGTGGTAACGACCTATGTGAGGACCGTGTGAGAGACCATGACCATGTAACAGGTAAGTACCGCGGAGCTGCTCACAATATATGCAATCTTAAGTATAGAATTACATGGAAAGTACCTGTGGTCTTCCACAACCTGAGAGGTTATGATGGTCATCTGATTATGCAGGAAATTGGCAAGTTCAAGATGGATGTTAATGTGATCCcaaataatatggaaaaataCATCTCATTCTCACTGGGTAAGAATCTGGTCTTCATAGACTCTATACAGTTCATGGCTTCTTCACTGGAAGCACTGGTAAGTAACTTTTCACCTGAGGACTTCAGGATAGTAGGTAAGAGGTGGAAGGGTGAGGACTTCAATCTAGTGACACAAAAAGGAGTGTTCCCATATGAGTTCCTAGATAATATTAGCAAACTCAATACAGAAGGTCTTCCGAGCAAGGATAATTTCTACTCGTCACTGTATGAGTCAGAGGTGAAGGAGGAAGATTACCAGAGAGCTCAGAAAGTATGGGATCACTTCAAGATGAAAACCATGAGAGATTACCATGATCTCTACTTAGAGACTGACGTTCTTCTGCTGGCTGATGTGTTTGAGAACTTCAGGAGAACATGTCTGGAAAGTTACAAACTTGACCCCGCACATTACGTGTCAGCACCTAGTCTGAGTTGGGACGCTTCCTGA

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)	OG0000017 (this species only)

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF03175 all species →	DNA_pol_B_2	DNA polymerase type B, organellar and viral	Family	Interproscan
PF02178 all species →	AT_hook	AT hook motif	Motif	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR017956 all species →	Conserved_site	AT hook, DNA-binding motif	Interproscan
IPR004868 all species →	Domain	DNA-directed DNA polymerase, family B, mitochondria/virus	Interproscan
IPR012337 all species →	Homologous_superfamily	Ribonuclease H-like superfamily	Interproscan
IPR036397 all species →	Homologous_superfamily	Ribonuclease H superfamily	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR31511 all species →	PROTEIN CBG23764	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0003677 all species →	Molecular Function	DNA binding	Interproscan
GO:0000166 all species →	Molecular Function	nucleotide binding	Interproscan
GO:0003887 all species →	Molecular Function	DNA-directed DNA polymerase activity	Interproscan
GO:0006260 all species →	Biological Process	DNA replication	Interproscan
GO:0003676 all species →	Molecular Function	nucleic acid 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

No KEGG orthology assignment for CAB3999231.1.

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

Expression pattern (RNA-seq)

Transcript abundance of CAB3999231.1 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

2TPM > 0

4Conditions

0.1Max TPM

0.0Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
apical branchlet · Control at T25	6	1	0.01	0.09
apical branchlet · Temperature treatment at T0	6	1	0.00	0.03
apical branchlet · Temperature treatment at T25	5	0	0.00	0.00
apical branchlet · Control at T0	4	0	0.00	0.00

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	0.09
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
SRR19977441	apical branchlet · Control at T25	apical branchlet	not recorded	Control at T25	SRP384900	0.00
SRR19977444	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	0.03
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
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
SRR19977435	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
SRR19977442	apical branchlet · Control at T0	apical branchlet	not recorded	Control at T0	SRP384900	0.00
SRR19977443	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.