Gene detail

Detailed information of CAB4035006.1 in Paramuricea clavata

Genomic Location: pcla8_s022897:532...3367
NR annotation: CAB4035006.1, Retrovirus-related Pol poly from transposon TNT 1-94 [Paramuricea clavata]
Species Paramuricea clavata · all data for this species · gene families

Gene Structure

More details in JBrowse

Sequence

CDS

PACLA_8A016273

ATGGAGGAAAAATGGTCAATCGACAAGTTAGACGGGAGCAATTGGAGTACTTGGAAGTTTCAAATGAAGCATTTGCTGTTGGCGAAAGGGCTGTGGGGTTTCGTAGACGGTTCGGTAGAGCTAGCAGGGTCAGCTTCGGGAGAAACGGCGGCACAATTTCGTTCGAAAGCGCAAAGGGCGTTCTCAACAATTGTTTTAGCAATTAAATCAGCTCAGCTATATTTGGTTAGCTCATGTGAAAATCCGAAGCAAGCGTGGGATGCACTAAAGAATCATTTTGAGCGAGATACGTTGGCGAACAAACTGTTTTTAAAGAAAAAGTATTTCCGAACGGAGATGATAGAAGGAACTTCTATGGAGAAACATTTGAAACACATGAAGGACATCGCATCTGAAGAGGATCAAGTTGTGACTTTATTAGGAAGTTTGCCTAGAAGTTATGCAACTCTCGTAACTGCTTTAGAAGCCAGAGTTGATGATGTGAAAATGGACTTCGTTCAACAAGCTTTTATGCATGAAGAATCGAAGCAAGGACCTAAGAACGAGTCAGTTAAGAATGAGTCTGCCTTAATGGGAAACCGAAATAAAAATTTTCAGGAAAGTCGGACGTGTTTTAAGTGTGGAACTGTTGGCCATATTCGTCGAAATTGCCCTCAGGAAAAAGCGAGATATACAAAGCCAGTGTATAAATCAAGACATGGAGCAAAAGTCGGAAAGACCCAAAACTCTGATAGTGAATCTGAAAGTAGTGCTTGTGTATTTACAGTTTCCGAGGGAAATGCAAAGCTTTCTGATTGTCATTGGTTGATCGATTCTGGAGCTTCAAGTCATATGACGAAGGAAAAAAGTGTTCTGGTGAATTATCAACAGTTTGGGGAACCCGAAAGCGTTGCCTTGGGAGATGGTCGTGTTGTACAAGCGTTGGGATCTGGTAACGTGCATATGGATATGTTGTTCTCTGGGAGCAAGTCGAAGCGAGGTGTACTGTGTAATGTGTTGTATGTTCCAAAGCTTACCTCTAACCTGTTTTCCGTTCGAGCTGCCGTTGCGAAAGGTAACGTGGTGAAGTTTCGTGGTGATAAATGCTGGATAAGTGATGCCAGTGGGAGACTACGAGGAATGGGATCATTAGCCAACAAGTTGTACAAGTTGGATTGCGAAGACGTCTCAAACGGACACGCTACGTTAGCTTCACAGGAAAGTAGTGATCTTTGGCATCAACGGTTGGGACACGTACACGAGCAACGACTAAATAGCTGCATTAAGAATAATATTGTGAAAGGAATTTGTTGTGAAAACGTTGACAAACTTTCGTTCTGCGAAGCATGTTTGGCTGGAAAAATGCATCGAAAGCCATTTCTTGCTCGGGAAGAAATTCGTTCATCTCACAAGCTACAGCTAGTACATAGCGATGTGTGTGGTCCAATGCAAACAGAGTCATTTGGCGGAGCAAGATATTTCGTGACGTTCACTGATGATTACTCTCGATGTTGTGCAGTGTACTTTATGAAGCAGAAGTTAGAAGTTCTGGAGAAATTTAAAGAGTTTGAGGCTGCAGCAACGAACGAGGCTGGAAGATCGATAGGAATATTGCGAACTGATAATGGTGGCGAGTATCTTTCCACAGAATTTCAAGATTATCTCAAAGCGAAAGGTATTAAGCATGAATTAACTGTTCCATATTCTCCTCAGCAAAATGGTGTCGCTGAACGTATGAATAGAACGTTGGTCGAGTCTGCTCGGTCGATGATCGCACAAGCAAGATTACCTAAGATGTACTGGGCTGAAGCCATTTCCACGGCTGTTTATGTGAGAAATCGAATGCCTACGACAGCAATCAAAGGGAATACAACGCCGTACGAGCGATGGTATGAAAGAAAACCGAACGTCAGTCATTTCCGTGTGTTTGGGTGTATGGCCTTCGCCCATGTTCCAGACAGCAAACGACAAAAATTGGACAAGAAAGCGGAAAGACTACGCTTTGTTGGTTATTGTCGTACGTCAAAAGGATACCGTTTGTTCGATGAAATCAAGCGAAAGATGGTCGTCCGAAGGGATGTCGAGTTCAATGAAAACGATTTTGGCGACAAGGACGAAATGATGACGACAAAATCTCAAGATCAAACGACAGAAGACGTGAAAGACGAAACGGTGGAATTCGAAGAAGAAAAAGTGGGAGAAGAAGTATCCACAGAACCAAGGACTTCTGGTAGAACACGGAAAGCACCTGTCAGATTATTGGATTTGAATATTTATTCGAACAGTCACATTTTTGTGATAAAATATGACCATTTAATGAGTAAAATATATCGAGATACAACTTGA

Transcript

rna-PACLA_8A016273

attttctgataaatttcaaagttctcattgtttacagggctcattgttcttcccaagcaatacaatcacaataattgtgatgaatttactctgtacaagttgtagctgagttgactcgagtcatttacggcaaaatcagcaagtcgagtccgagtcgagtcatttggggctgttgagtcgagtcgagtcatttttcgtattggactcgagtcgagtcgagtcgctgaaaatagcgactcgagttgactcgagtcagagtcaatgactcgactcgttacaacactgcatataacatgttgttgttgtaaaaGTTTTTTAGTTAGAAATACATTTATCGCAAAACAACACTCGGATTGTGAGTTTGTctacaggttatgggcccagaaCATGCTGTTAGGATCGTTTAACAATCCTACGTCGCCGGTTTTTCGATAGAACTTCAGTTTGCTGAACAAATAACCGCTTGTAATAATAACTCGTGCTGGTCTGTTGACGACTAATGGAGGAAAAATGGTCAATCGACAAGTTAGACGGGAGCAATTGGAGTACTTGGAAGTTTCAAATGAAGCATTTGCTGTTGGCGAAAGGGCTGTGGGGTTTCGTAGACGGTTCGGTAGAGCTAGCAGGGTCAGCTTCGGGAGAAACGGCGGCACAATTTCGTTCGAAAGCGCAAAGGGCGTTCTCAACAATTGTTTTAGCAATTAAATCAGCTCAGCTATATTTGGTTAGCTCATGTGAAAATCCGAAGCAAGCGTGGGATGCACTAAAGAATCATTTTGAGCGAGATACGTTGGCGAACAAACTGTTTTTAAAGAAAAAGTATTTCCGAACGGAGATGATAGAAGGAACTTCTATGGAGAAACATTTGAAACACATGAAGGACATCGCATCTGAAGAGGATCAAGTTGTGACTTTATTAGGAAGTTTGCCTAGAAGTTATGCAACTCTCGTAACTGCTTTAGAAGCCAGAGTTGATGATGTGAAAATGGACTTCGTTCAACAAGCTTTTATGCATGAAGAATCGAAGCAAGGACCTAAGAACGAGTCAGTTAAGAATGAGTCTGCCTTAATGGGAAAccgaaataaaaattttcaggaAAGTCGGACGTGTTTTAAGTGTGGAACTGTTGGCCATATTCGTCGAAATTGCCCTCAGGAAAAAGCGAGATATACAAAGCCAGTGTATAAATCAAGACATGGAGCAAAAGTCGGAAAGACCCAAAACTCTGATAGTGAATCTGAAAGTAGTGCTTGTGTATTTACAGTTTCCGAGGGAAATGCAAAGCTTTCTGATTGTCATTGGTTGATCGATTCTGGAGCTTCAAGTCATATGACGAAGGAAAAAAGTGTTCTGGTGAATTATCAACAGTTTGGGGAACCCGAAAGCGTTGCCTTGGGAGATGGTCGTGTTGTACAAGCGTTGGGATCTGGTAACGTGCATATGGATATGTTGTTCTCTGGGAGCAAGTCGAAGCGAGGTGTACTGTGTAATGTGTTGTATGTTCCAAAGCTTACCTCTAACCTGTTTTCCGTTCGAGCTGCCGTTGCGAAAGGTAACGTGGTGAAGTTTCGTGGTGATAAATGCTGGATAAGTGATGCCAGTGGGAGACTACGAGGAATGGGATCATTAGCCAACAAGTTGTACAAGTTGGATTGCGAAGACGTCTCAAACGGACACGCTACGTTAGCTTCACAGGAAAGTAGTGATCTTTGGCATCAACGGTTGGGACACGTACACGAGCAACGACTAAATAGCTGCAttaagaataatattgtgaaagGAATTTGTTGTGAAAACGTTGACAAACTTTCGTTCTGCGAAGCATGTTTGGCTGGAAAAATGCATCGAAAGCCATTTCTTGCTCGGGAAGAAATTCGTTCATCTCACAAGCTACAGCTAGTACATAGCGATGTGTGTGGTCCAATGCAAACAGAGTCATTTGGCGGAGCAAGATATTTCGTGACGTTCACTGATGATTACTCTCGATGTTGTGCAGTGTACTTTATGAAGCAGAAGTTAGAAGTTCTGGAGAAATTTAAAGAGTTTGAGGCTGCAGCAACGAACGAGGCTGGAAGATCGATAGGAATATTGCGAACTGATAATGGTGGCGAGTATCTTTCCACAGAATTTCAAGATTATCTCAAAGCGAAAGGTATTAAGCATGAATTAACTGTTCCATATTCTCCTCAGCAAAATGGTGTCGCTGAACGTATGAATAGAACGTTGGTCGAGTCTGCTCGGTCGATGATCGCACAAGCAAGATTACCTAAGATGTACTGGGCTGAAGCCATTTCCACGGCTGTTTATGTGAGAAATCGAATGCCTACGACAGCAATCAAAGGGAATACAACGCCGTACGAGCGATGGTATGAAAGAAAACCGAACGTCAGTCATTTCCGTGTGTTTGGGTGTATGGCCTTCGCCCATGTTCCAGACAGCAAACGACAAAAATTGGACAAGAAAGCGGAAAGACTACGCTTTGTTGGTTATTGTCGTACGTCAAAAGGATACCGTTTGTTCGATGAAATCAAGCGAAAGATGGTCGTCCGAAGGGATGTCGAGTTCAATGAAAACGATTTTGGCGACAAGGACGAAATGATGACGACAAAATCTCAAGATCAAACGACAGAAGACGTGAAAGACGAAACGGTGGAATTCGAAGAAGAAAAAGTGGGAGAAGAAGTATCCACAGAACCAAGGACTTCTGGTAGAACACGGAAAGCACCTGTCAGATTATTGGATTTGAATATTTATTCGAACAGTCACATTTTTGTGATAAAATATGACCATTTAATGAGTAAAATATATCGAGatacaacttgaacaagaactgCA

Protein

UniProt (Swiss-Prot top hit)

UniProt accession	Description
P10978	Retrovirus-related Pol polyprotein from transposon TNT 1-94 OS=Nicotiana tabacum OX=4097 PE=2 SV=1
P04146	Copia protein OS=Drosophila melanogaster OX=7227 GN=GIP PE=1 SV=3
Q9ZT94	Retrovirus-related Pol polyprotein from transposon RE2 OS=Arabidopsis thaliana OX=3702 GN=RE2 PE=4 SV=1

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0000038 (this species only)

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF00098 all species →	zf-CCHC	Zinc knuckle	Domain	Interproscan
PF13976 all species →	gag_pre-integrs	GAG-pre-integrase domain	Domain	Interproscan
PF14223 all species →	Retrotran_gag_2	gag-polypeptide of LTR copia-type	Family	Interproscan
PF13961 all species →	DUF4219	Domain of unknown function (DUF4219)	Domain	Interproscan
PF00665 all species →	rve	Integrase core domain	Domain	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR001878 all species →	Domain	Zinc finger, CCHC-type	Interproscan
IPR025724 all species →	Domain	GAG-pre-integrase domain	Interproscan
IPR036397 all species →	Homologous_superfamily	Ribonuclease H superfamily	Interproscan
IPR036875 all species →	Homologous_superfamily	Zinc finger, CCHC-type superfamily	Interproscan
IPR001584 all species →	Domain	Integrase, catalytic core	Interproscan
IPR012337 all species →	Homologous_superfamily	Ribonuclease H-like superfamily	Interproscan
IPR025314 all species →	Domain	Domain of unknown function DUF4219	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR42648 all species →	TRANSPOSASE, PUTATIVE-RELATED	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0003676 all species →	Molecular Function	nucleic acid binding	Interproscan
GO:0008270 all species →	Molecular Function	zinc ion binding	Interproscan
GO:0015074 all species →	Biological Process	DNA integration	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 CAB4035006.1.

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

Expression pattern (RNA-seq)

Transcript abundance of CAB4035006.1 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

12TPM > 0

4Conditions

10.9Max TPM

1.0Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
apical branchlet · Control at T25	6	4	0.41	1.55
apical branchlet · Temperature treatment at T0	6	3	0.47	2.17
apical branchlet · Temperature treatment at T25	5	3	0.83	2.68
apical branchlet · Control at T0	4	2	2.87	10.86

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	1.55
SRR19977455	apical branchlet · Control at T25	apical branchlet	not recorded	Control at T25	SRP384900	0.42
SRR19977441	apical branchlet · Control at T25	apical branchlet	not recorded	Control at T25	SRP384900	0.34
SRR19977444	apical branchlet · Control at T25	apical branchlet	not recorded	Control at T25	SRP384900	0.14
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
SRR19977437	apical branchlet · Temperature treatment at T0	apical branchlet	not recorded	Temperature treatment at T0	SRP384900	2.17
SRR19977438	apical branchlet · Temperature treatment at T0	apical branchlet	not recorded	Temperature treatment at T0	SRP384900	0.61
SRR19977427	apical branchlet · Temperature treatment at T0	apical branchlet	not recorded	Temperature treatment at T0	SRP384900	0.06
SRR19977426	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
SRR19977432	apical branchlet · Temperature treatment at T25	apical branchlet	not recorded	Temperature treatment at T25	SRP384900	2.68
SRR19977425	apical branchlet · Temperature treatment at T25	apical branchlet	not recorded	Temperature treatment at T25	SRP384900	0.99
SRR19977435	apical branchlet · Temperature treatment at T25	apical branchlet	not recorded	Temperature treatment at T25	SRP384900	0.49
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
SRR19977446	apical branchlet · Control at T0	apical branchlet	not recorded	Control at T0	SRP384900	10.86
SRR19977443	apical branchlet · Control at T0	apical branchlet	not recorded	Control at T0	SRP384900	0.62
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

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.