Gene detail

Detailed information of CAB3978212.1 in Paramuricea clavata

Genomic Location: pcla8_s000109:67916...70735
NR annotation: CAB3978212.1, Transposon Ty3-G Gag-Pol poly [Paramuricea clavata]
Species Paramuricea clavata · all data for this species · gene families

Gene Structure

More details in JBrowse

Sequence

CDS

PACLA_8A085958

ATGGAAACGAATCAAAATTCGGAAAATATTCAAGCAGGTGAATCGAGTGGAGCTGTTGTTTTAAATACGAATGCAAAAGTACTCGAAGTTGGTGGTTTTCCTTGCTTCGACCCCAAGGGAGATCCAAATACACTATCAATTCGCTGGAGAAGATGGAAACGCGCTTTCAACCTGTATATGGTGTCAAAAGGAGTTACAAATGAACAGCAAAAAGTTGCTTTGCTATTACACTCCGGAGGAATGGAATTACAAGAACTGTATTATACTTTAAAGCCAGATAGTGAAGATAACAATCTTCAGGAATGTTTGAACGCTTTAGATGCATATTTTACACCTAAAGTAAATGTGGCTTTTGAAAGACATATGTTTCGACAAATGCAGCAAAAAGAGAATGAAACCATAGATCAGTTTGTTTGTCGACTTCGACAAAAGTCTATTTCATGCGAGTTTACCAATGTAGATGAAGCAATTCGTGATCAAATTATTGAAAAATGCAGAGACCCAAAGCTTCGTCGAAAGTTTCTTGAAAAGACAGGTACAGTAACTTTATCTGTGCTTCAAGACACGGCTAGAGTTCACGAAACTGTAAACACACAAATGCAATCTATGGATAGATTAGGTACAAATCAAGTACATGGAATATTCCAAGGTAATCGAAGGGAGAAAGGAAAGTATGGTGCCAAATCTGATGACCGTGCATCTGATGGAAAACATAAAGAGGGTAGGAAATGTTATCGATGCAATATGACAGGACACATCGGACGAGATAAAAGCTGTCCTGCAATAAGTAAAACATGTAAAAAGTGTGGATTGGTGGGTCATTTTGCAGTTTGTTGTCGTACTAAAGCCCCAAAGAAACCCTCAAATGGAAAACAACGTCAAGATGGAGCTTATCAAGTAGAGGAAGAGAAACAGAAACCAGAAACGGACAATTATGCTTTTGTAGTTAAACCTGCTGGTGAAAAGACAGGTGGAGTTGTTGATCTTATCATTGGAGGTGTGGAGTTAAATAATGTCCTTATCGATTCTGGAGCTTCCTGCAATATAATGGATCGAGCAACATGGGAAAATCTGAAACAAAAAGGTGTGAAGTGTGAATCTCAGAAAAGCGAAAAGAAATTGTTCGCATATGGACAAACGGATTCAATTGAGGTTTTGGGAACATTCAAAAGCGATATTTTCTGTAAAGATTCAAGGGTAAGCTGTGTCGATGAGTTTACCGTAGTTGAAGGTCCAGGAAAAGTTTTACTTGGAAAGAATACAGCTGAGAAATTAAATGTTCTTAGAGTGGGACCTCCACGTTCTCCACAAGTCTACTCGGTTGCATATGAAGGCAGTGATAAAGATATTATGAATGATTTTAAAGAAATTTTCTCAGGAGTGGGAAAACTAAAGGATTTCCAGATGAAATTGCACATTAAAGATGATGTGAAACCAGTAGCACAACCAGTAAGAAGATTACCGTTTGGTCTCAGAGCAAAAGTGGACAAAAAGCTTAATGAGTTATTAGAAGAAGATATTATTGAAGAAGTACCAACTGGCCCTACCGGTTGGATATCACCTCTTGTTGTCGTACCAAAACCGGACGGTGATATTCGTATTTGTGTCGATATGAGGCGAGCGAACGAAGCTATTGAAAGGGAGCGTCATCCAATCCCCACTATAGAGGAAGTCTTATACGAGTTAAATGGATCAACAGTCTACAGTAAATTAGATTTGAAATGGGGATTTCATCAAGTCGAGCTTGAAGAGTCATCGCGTCGTATCACCACATTTGTAACGCATAGTGGACTATATAGATACAAGAGGTTGATGTTTGGAATAACCTCAGCACCCGAGATGTACCAGAAGATAGTCAAGGATGTATTGATTGGTTGCAAAGGAGTTGCCAACATTGCGGATGACTTGATCATCCATGGACGGGGAATTGAAGAGCACGACAAGAATTTGGTAGCTGTACTTAATCGTTTACGGGAGTGCGGATTAACCCTAAATGCAAACAAGTGTCAGTTTCGACTTCCAAAGTTGACATTTTTTGGTCATGATCTTAGTTGTGATGGTGTTTCGCCAAATGAAGAGAAGGTGGCAGCAGTAAGAGATGCCAAACCCCCAAAGAATGCTGCAGAAGTTAGATCTTTCCTAGGCCTAGTGCAGTACTGTGCCAAGTTCCTACCTGATTTTGCACAAGTGGCAGAGCCAATCAGAAAATTAACTAGAAAGAATCAACAATTTGAATGGGGAAAAGCTCAACAACAGTCTTTTTCAACATTGAAAGATCTTTTAACTCAGGCCGAAACGCTTGCTTACTTCAAGAACGATTGTGAAACACGCATTATTGCTGATGCTGGTCCTACAGGGATTGGAGCGGTTCTCACACAGTTACAGGGTGATTCATGGAGAGTAATTTCGTATGCATCTAGGAACCTCACTGACGTCGAAAGGAGGTATTCCCAAACGGAGAAAGAAGGTCTTGCGTTGGTGTGGGCATGTGAGAGATTCAAGTTGTATGTTTATGGTCGTAAATTTGAGCTAGAGACGGACCACAAGCCTTTACAGTATATATACAACACATCGTCTAAGCCGTCTGCGCGACTCGAAAGATGGGTTCTTCGGCTACAAGGTTATCACTTCAAGGTTGTCTATCGGCCGGGAAAAACTAACATAGCTGATGCTTTGTCTAGGTTAAATTCGAAAGTTCCTAAAGATCACAGTGGCGAAACTGTGGATGTTGTTCGAATTATCGCGCAAGAAAGTACACCGGTGGCATTCAAACAGCTAAAGAAGTTGAAAGAGAATCGGAGAAGGATCCTGAACTTGTAA

Transcript

rna-PACLA_8A085958

ATGGAAACGAATCAAAATTCGGAAAATATTCAAGCAGGTGAATCGAGTGGAGCTGTTGTTTTAAATACGAATGCAAAAGTACTCGAAGTTGGTGGTTTTCCTTGCTTCGACCCCAAGGGAGATCCAAATACACTATCAATTCGCTGGAGAAGATGGAAACGCGCTTTCAACCTGTATATGGTGTCAAAAGGAGTTACAAATGAACAGCAAAAAGTTGCTTTGCTATTACACTCCGGAGGAATGGAATTACAAGAACTGTATTATACTTTAAAGCCAGATAGTGAAGATAACAATCTTCAGGAATGTTTGAACGCTTTAGATGCATATTTTACACCTAAAGTAAATGTGGCTTTTGAAAGACATATGTTTCGACAAATGCAGCAAAAAGAGAATGAAACCATAGATCAGTTTGTTTGTCGACTTCGACAAAAGTCTATTTCATGCGAGTTTACCAATGTAGATGAAGCAATTCGTGATcaaattattgaaaaatgcaGAGACCCAAAGCTTCGTCGAAAGTTTCTTGAAAAGACAGGTACAGTAACTTTATCTGTGCTTCAAGACACGGCTAGAGTTCACGAAACTGTAAACACACAAATGCAATCTATGGATAGATTAGGTACAAATCAAGTACATGGAATATTCCAAGGTAATCGAAGGGAGAAAGGAAAGTATGGTGCCAAATCTGATGACCGTGCATCTGATGGAAAACATAAAGAGGGTAGGAAATGTTATCGATGCAATATGACAGGACACATCGGACGAGATAAAAGCTGTCCTGCAATAAGTAAAACATGTAAAAAGTGTGGATTGGTGGGTCATTTTGCAGTTTGTTGTCGTACTAAAGCCCCAAAGAAACCCTCAAATGGAAAACAACGTCAAGATGGAGCTTATCAAGTAGAGGAAGAGAAACAGAAACCAGAAACGGACAATTATGCTTTTGTAGTTAAACCTGCTGGTGAAAAGACAGGTGGAGTTGTTGATCTTATCATTGGAGGTGTGGAGTTAAATAATGTCCTTATCGATTCTGGAGCTTCCTGCAATATAATGGATCGAGCAACATGGGAAAATCTGAAACAAAAAGGTGTGAAGTGTGAATCTCAGAAAAGCGAAAAGAAATTGTTCGCATATGGACAAACGGATTCAATTGAGGTTTTGGGAACATTCAAAAGCGATATTTTCTGTAAAGATTCAAGGGTAAGCTGTGTCGATGAGTTTACCGTAGTTGAAGGTCCAGGAAAAGTTTTACTTGGAAAGAATACAGCTGAGAAATTAAATGTTCTTAGAGTGGGACCTCCACGTTCTCCACAAGTCTACTCGGTTGCATATGAAGGCAGTGATAAAGATATTATGAatgattttaaagaaattttctcAGGAGTGGGAAAACTAAAGGATTTCCAGATGAAATTGCACATTAAAGATGATGTGAAACCAGTAGCACAACCAGTAAGAAGATTACCGTTTGGTCTCAGAGCAAAAGTGGACAAAAAGCTTAATGAGTTATTAGAAGAAGATATTATTGAAGAAGTACCAACTGGCCCTACCGGTTGGATATCACCTCTTGTTGTCGTACCAAAACCGGACGGTGATATTCGTATTTGTGTCGATATGAGGCGAGCGAACGAAGCTATTGAAAGGGAGCGTCATCCAATCCCCACTATAGAGGAAGTCTTATACGAGTTAAATGGATCAACAGTCTACAGTAAATTAGATTTGAAATGGGGATTTCATCAAGTCGAGCTTGAAGAGTCATCGCGTCGTATCACCACATTTGTAACGCATAGTGGACTATATAGATACAAGAGGTTGATGTTTGGAATAACCTCAGCACCCGAGATGTACCAGAAGATAGTCAAGGATGTATTGATTGGTTGCAAAGGAGTTGCCAACATTGCGGATGACTTGATCATCCATGGACGGGGAATTGAAGAGCACGACAAGAATTTGGTAGCTGTACTTAATCGTTTACGGGAGTGCGGATTAACCCTAAATGCAAACAAGTGTCAGTTTCGACTTCCAAAGTTGACATTTTTTGGTCATGATCTTAGTTGTGATGGTGTTTCGCCAAATGAAGAGAAGGTGGCAGCAGTAAGAGATGCCAAACCCCCAAAGAATGCTGCAGAAGTTAGATCTTTCCTAGGCCTAGTGCAGTACTGTGCCAAGTTCCTACCTGATTTTGCACAAGTGGCAGAGCCAATCAGAAAATTAACTAGAAAGAATCAACAATTTGAATGGGGAAAAGCTCAACAACAGTCTTTTTCAACATTGAAAGATCTTTTAACTCAGGCCGAAACGCTTGCTTACTTCAAGAACGATTGTGAAACACGCATTATTGCTGATGCTGGTCCTACAGGGATTGGAGCGGTTCTCACACAGTTACAGGGTGATTCATGGAGAGTAATTTCGTATGCATCTAGGAACCTCACTGACGTCGAAAGGAGGTATTCCCAAACGGAGAAAGAAGGTCTTGCGTTGGTGTGGGCATGTGAGAGATTCAAGTTGTATGTTTATGGTCGTAAATTTGAGCTAGAGACGGACCACAAGcctttacagtatatatacaacACATCGTCTAAGCCGTCTGCGCGACTCGAAAGATGGGTTCTTCGGCTACAAGGTTATCACTTCAAGGTTGTCTATCGGCCGGGAAAAACTAACATAGCTGATGCTTTGTCTAGGTTAAATTCGAAAGTTCCTAAAGATCACAGTGGCGAAACTGTGGATGTTGTTCGAATTATCGCGCAAGAAAGTACACCGGTGGCATTCAAACAGCTAAAGAAGTTGAAAGAGAATCGGAGAAGGATCCTGAACTTGTAA

Protein

UniProt (Swiss-Prot top hit)

UniProt accession	Description
P10394	Retrovirus-related Pol polyprotein from transposon 412 OS=Drosophila melanogaster OX=7227 GN=POL PE=4 SV=1
P0CT41	Transposon Tf2-12 polyprotein OS=Schizosaccharomyces pombe (strain 972 / ATCC 24843) OX=284812 GN=Tf2-12 PE=3 SV=1
P0CT34	Transposon Tf2-1 polyprotein OS=Schizosaccharomyces pombe (strain 972 / ATCC 24843) OX=284812 GN=Tf2-1 PE=3 SV=1

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0000003 (this species only)

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF00078 all species →	RVT_1	Reverse transcriptase (RNA-dependent DNA polymerase)	Domain	Interproscan
PF17917 all species →	RT_RNaseH	RNase H-like domain found in reverse transcriptase	Domain	Interproscan
PF14893 all species →	PNMA	PNMA	Family	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR000477 all species →	Domain	Reverse transcriptase domain	Interproscan
IPR043128 all species →	Homologous_superfamily	Reverse transcriptase/Diguanylate cyclase domain	Interproscan
IPR001878 all species →	Domain	Zinc finger, CCHC-type	Interproscan
IPR050951 all species →	Family	Retrovirus-related Pol polyprotein	Interproscan
IPR041373 all species →	Domain	Reverse transcriptase, RNase H-like domain	Interproscan
IPR021109 all species →	Homologous_superfamily	Aspartic peptidase domain superfamily	Interproscan
IPR036875 all species →	Homologous_superfamily	Zinc finger, CCHC-type superfamily	Interproscan
IPR048270 all species →	Domain	Paraneoplastic antigen Ma-like, C-terminal domain	Interproscan
IPR043502 all species →	Homologous_superfamily	DNA/RNA polymerase superfamily	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR37984 all species →	PROTEIN CBG26694	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

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 CAB3978212.1.

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

Expression pattern (RNA-seq)

Transcript abundance of CAB3978212.1 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

3TPM > 0

4Conditions

0.1Max TPM

0.0Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
apical branchlet · Control at T25	6	2	0.02	0.08
apical branchlet · Temperature treatment at T0	6	0	0.00	0.00
apical branchlet · Temperature treatment at T25	5	1	0.02	0.08
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
SRR19977455	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
SRR19977440	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
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
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	0.08
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
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.