Gene detail

Detailed information of CAB4020352.1 in Paramuricea clavata

Genomic Location: pcla8_s011344:2065...4563
NR annotation: CAB4020352.1, DNA topoisomerase 3-beta-1 [Paramuricea clavata]
Species Paramuricea clavata · all data for this species · gene families

Gene Structure

More details in JBrowse

Sequence

CDS

PACLA_8A043134

ATGACAACGCGAAAAGGTTTGAACGGCGCTTGCTCTGTTCACGAATACAATGGTACCTTTCAAGGCACGACAGTGAAATTTAAAGTGACTTCTGTTTGTGGTCATGTCATGGCGCTGGATTTCCACCATAAGTACAACAATTGGGATGCGGTCAATCCGGTCGAACTCTTCCAAGCAGAAACGCTGAAAAAAGAGGCTAACCCAAAACTGAATATGGTGAAATTTTTACAACAAGAGGCAAAAGGGGTTGACATTGTTGTGTTGTGGTTAGATTGTGACAAAGAAGGGGAGAATATTTGTTTCGAAGTTTTGGATTGTGTCGAACCGGTCATGAATACAACACGGTCCAACCAGCAAACAGTATTTCGAGCAAAGTTTTCTGCCATTACAGAATCTGATATCAAGCTTGCTATGAATACTCTTATCGAACCCGATGAAAACCAAGCCCGCTCAGTCGACGCCCGACAAGAACTTGACCTGAGAATCGGCTGTGCATTTACAAGGTTTCAGACAAAGTATTTTCAAGGAAAGTACGGGGACCTTGATAGTAGTTTGATTTCATATGGCCCTTGTCAGACTCCCACCCTGGGTTTCTGTGTTCAGCGGCATGATGCCATTACTTCATTTAAGCCAGAACCATTTTGGGTTCTGCAATTGAAAGTGGAAAGTTCGCTTGGACGAACGTTTGCATTAGATTGGGAAAGAGTTCGAGTTTTCGATAAGGAAGTGGCGACGGTTTACTACAGTAAAGTTCAAGAAGTGCAAGAAGTCATCGTCGAGAGTATCTCAAAGAAGGAAAAAGCAAAGCAACGGCCACAAGCATTGCATACGGTTGAAATGCTTCGTGTTGGTTCATCAGCATTAGGCATGGGACCACAGCATACAATGCAGATTGCAGAAAGCCTGTATACCCAGGGATACATCAGTTACCCAAGAACGGAAACCACCCAATATCCCGAAAAGTTTGATCTTCGCGGAACCCTGCAGCAACTTCAAGGAGGAGCAGCATGGGGTGCTACTGTCCGAGAGCTATTGCACACAGCGATGAACAAGCCTAGGAAAGGTCATGATGTTGGCGACCACCCCCCTATCACACCAATGAGGCTTGCAAGGGAGGGTGAGTTGAGTGGAGATGCTTGGAGGTTGTATGACTACATCACCAGACATTTTATTGCAACTTTGAGTCCCGATTGCAAGTACCTCCAAACGACGATTTCTTTTACAGCTGGTGAAGAATCGTTTAGTTTCAGCGGTAAGACCCCAATTGATCCTGGGTTTACATCCATCATGCCTTGGGCGGCCATTCCTGTTGAGGAAACCATCCCTCCTCTCGAGAAAGGTGCGACATGCAAGGTGTCTGAATTGAAAGTTGCCGAGCGACAAACGTCCCCACCGGACTACCTCACAGAAAGCGAGTTGATCACCCTGATGGAGAAACACGGCATTGGGACAGATGCCAGTATTCCAGTCCATATCAATAATATTACCCAGCGAAACTACGTCCAACTGCACAGCGGTCGTCGGCTTGTCCCAACTTCACTTGGCATCGTGCTGGTTCATGGTTATCAGAAAATAGACCAGGAATTAGTTTTGCCTACAATGAGATCATCTGTTGAAGGAACACTAAATCTTATTGCAGTTGGCAAAGCAAATTTTGATGCAGTACTGTCACACACAATTGATATTTTCTGCCGAAAATATTTGTATTTCGAGAAGTGTATAACCAACATGGATGAACTGTTTGAGGTTTCATTCACCAAGCTAGCAGACACAGGCAAGGCCTTGTCTCGTTGTGGCAAATGTGTTCGTTACATGAAGTTAGTGAGTGCTAAGCCAATTAGACTGCACTGCTCTCATTGTGATGAAACATACAGTCTGCCTCAGAATGGAACTATTAAGTTATACAAAGAGTTAAAATGCCCTTTAGATGATTTCGAGCTGGTAGTTTGCTCGACAGGCAGTCAAGGCAAGACGACCCCAATTTGCCCGTACTGCTACAATAATCCACCCTTCCCCAGCATGAAGAAAGGTATGGGCTGTCCCGAATGTCGTCATCCCAGTTGCAAATTCTCACCCGCCACCCTCAGTGTCTGCCCGTGTCTGACATGTGAAGAGGGTATGGTCGTCATGGACACCATGTCTGGCCCAAAATGGAAAATGGCTTGCAATAAATGCAACATGGTGCTTCACGTATTTGAGGATGCCTTTAAGGTGTCTTTATCAGAAGACGGTTGTGACGAATGTGGTGCATCGCTCATCGACGTCACATTCCATCGGAACAAGTCTCCCCTCCCAGGTGACAAAACAGAACACACCGGTTGTGCATTCTGTGACCCTGTTCTTGTGCCGATGGTGAAGTTTGATATGGCAAAAGGACGGCATCCAATGTTTCGTCGTGGCCGAGGGGGCAAACGAGGGCGTGGACGGGGCAGGCGTGGCAGAAGGGGACGAGGCAAACCCAAGGACAAAATGGCACAGCTTGATGCGTTTTTCTTGTGA

Transcript

rna-PACLA_8A043134-2

ATGACAACGCGAAAAGGTTTGAACGGCGCTTGCTCTGTTCACGAATACAATGGTACCTTTCAAGGCACGACAGTGAAATTTAAAGTGACTTCTGTTTGTGGTCATGTCATGGCGCTGGATTTCCACCATAAGTACAACAATTGGGATGCGGTCAATCCGGTCGAACTCTTCCAAGCAGAAACGCTGAAAAAAGAGGCTAACCCAAAACTGAATATGGTGAAATTTTTACAACAAGAGGCAAAAGGGGTTGACATTGTTGTGTTGTGGTTAGATTGTGACAAAGAAGGGGAGAATATTTGTTTCGAAGTTTTGGATTGTGTCGAACCGGTCATGAATACAACACGGTCCAACCAGCAAACAGTATTTCGAGCAAAGTTTTCTGCCATTACAGAATCTGATATCAAGCTTGCTATGAATACTCTTATCGAACCCGATGAAAACCAAGCCCGCTCAGTCGACGCCCGACAAGAACTTGACCTGAGAATCGGCTGTGCATTTACAAGGTTTCAGACAAAGTATTTTCAAGGAAAGTACGGGGACCTTGATAGTAGTTTGATTTCATATGGCCCTTGTCAGACTCCCACCCTGGGTTTCTGTGTTCAGCGGCATGATGCCATTACTTCATTTAAGCCAGAACCATTTTGGGTTCTGCAATTGAAAGTGGAAAGTTCGCTTGGACGAACGTTTGCATTAGATTGGGAAAGAGTTCGAGTTTTCGATAAGGAAGTGGCGACGGTTTACTACAGTAAAGTTCAAGAAGTGCAAGAAGTCATCGTCGAGAGTATCTCAAAGAAGGAAAAAGCAAAGCAACGGCCACAAGCATTGCATACGGTTGAAATGCTTCGTGTTGGTTCATCAGCATTAGGCATGGGACCACAGCATACAATGCAGATTGCAGAAAGCCTGTATACCCAGGGATACATCAGTTACCCAAGAACGGAAACCACCCAATATCCCGAAAAGTTTGATCTTCGCGGAACCCTGCAGCAACTTCAAGGAGGAGCAGCATGGGGTGCTACTGTCCGAGAGCTATTGCACACAGCGATGAACAAGCCTAGGAAAGGTCATGATGTTGGCGACCACCCCCCTATCACACCAATGAGGCTTGCAAGGGAGGGTGAGTTGAGTGGAGATGCTTGGAGGTTGTATGACTACATCACCAGACATTTTATTGCAACTTTGAGTCCCGATTGCAAGTACCTCCAAACGACGATTTCTTTTACAGCTGGTGAAGAATCGTTTAGTTTCAGCGGTAAGACCCCAATTGATCCTGGGTTTACATCCATCATGCCTTGGGCGGCCATTCCTGTTGAGGAAACCATCCCTCCTCTCGAGAAAGGTGCGACATGCAAGGTGTCTGAATTGAAAGTTGCCGAGCGACAAACGTCCCCACCGGACTACCTCACAGAAAGCGAGTTGATCACCCTGATGGAGAAACACGGCATTGGGACAGATGCCAGTATTCCAGtccatatcaataatattaccCAGCGAAACTACGTCCAACTGCACAGCGGTCGTCGGCTTGTCCCAACTTCACTTGGCATCGTGCTGGTTCATGGTTATCAGAAAATAGACCAGGAATTAGTTTTGCCTACAATGAGATCATCTGTTGAAGGAACACTAAATCTTATTGCAGTTGGCAAAGCAAATTTTGATGCAGTACTGTCACACACAATTGATATTTTCTGccgaaaatatttgtatttcgaGAAGTGTATAACCAACATGGATGAACTGTTTGAGGTTTCATTCACCAAGCTAGCAGACACAGGCAAGGCCTTGTCTCGTTGTGGCAAATGTGTTCGTTACATGAAGTTAGTGAGTGCTAAGCCAATTAGACTGCACTGCTCTCATTGTGATGAAACATACAGTCTGCCTCAGAATGGAACTATTAAGTTATACAAAGAGTTAAAATGCCCTTTAGATGATTTCGAGCTGGTAGTTTGCTCGACAGGCAGTCAAGGCAAGACGACCCCAATTTGCCCGTACTGCTACAATAATCCACCCTTCCCCAGCATGAAGAAAGGTATGGGCTGTCCCGAATGTCGTCATCCCAGTTGCAAATTCTCACCCGCCACCCTCAGTGTCTGCCCGTGTCTGACATGTGAAGAGGGTATGGTCGTCATGGACACCATGTCTGGCCCAAAATGGAAAATGGCTTGCAATAAATGCAACATGGTGCTTCACGTATTTGAGGATGCCTTTAAGGTGTCTTTATCAGAAGACGGTTGTGACGAATGTGGTGCATCGCTCATCGACGTCACATTCCATCGGAACAAGTCTCCCCTCCCAGGTGACAAAACAGAACACACCGGTTGTGCATTCTGTGACCCTGTTCTTGTGCCGATGGTGAAGTTTGATATGGCAAAAGGACGGCATCCAATGTTTCGTCGTGGCCGAGGGGGCAAACGAGGGCGTGGACGGGGCAGGCGTGGCAGAAGGGGACGAGGCAAACCCAAGGACAAAATGGCACAGCTTGATGCGTTTTTCTTGTGA

Protein

UniProt (Swiss-Prot top hit)

UniProt accession	Description
O95985	DNA topoisomerase 3-beta-1 OS=Homo sapiens OX=9606 GN=TOP3B PE=1 SV=1
Q9Z321	DNA topoisomerase 3-beta-1 OS=Mus musculus OX=10090 GN=Top3b PE=1 SV=1
O96651	DNA topoisomerase 3-beta OS=Drosophila melanogaster OX=7227 GN=Top3beta PE=2 SV=2

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0007997 (this species only)

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF01131 all species →	Topoisom_bac	DNA topoisomerase	Family	Interproscan
PF01751 all species →	Toprim	Toprim domain	Family	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR006171 all species →	Domain	TOPRIM domain	Interproscan
IPR003601 all species →	Domain	DNA topoisomerase, type IA, domain 2	Interproscan
IPR023406 all species →	Active_site	DNA topoisomerase, type IA, active site	Interproscan
IPR003602 all species →	Domain	DNA topoisomerase, type IA, DNA-binding domain	Interproscan
IPR013497 all species →	Domain	DNA topoisomerase, type IA, central	Interproscan
IPR023405 all species →	Homologous_superfamily	DNA topoisomerase, type IA, core domain	Interproscan
IPR000380 all species →	Family	DNA topoisomerase, type IA	Interproscan
IPR013824 all species →	Homologous_superfamily	DNA topoisomerase, type IA, central region, subdomain 1	Interproscan
IPR034144 all species →	Domain	DNA topoisomerase 3-like, TOPRIM domain	Interproscan
IPR013825 all species →	Homologous_superfamily	DNA topoisomerase, type IA, central region, subdomain 2	Interproscan
IPR013826 all species →	Homologous_superfamily	DNA topoisomerase, type IA, central region, subdomain 3	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR11390 all species →	PROKARYOTIC DNA TOPOISOMERASE	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0003677 all species →	Molecular Function	DNA binding	Interproscan
GO:0003916 all species →	Molecular Function	DNA topoisomerase activity	Interproscan
GO:0006265 all species →	Biological Process	DNA topological change	Interproscan
GO:0003917 all species →	Molecular Function	DNA topoisomerase type I (single strand cut, ATP-independent) activity	Interproscan
GO:0005634 all species →	Cellular Component	nucleus	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
K03165	TOP3; DNA topoisomerase III	EC:5.6.2.1	DNA repair and recombination proteins	ko03400	deepkoala

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

Expression pattern (RNA-seq)

Transcript abundance of CAB4020352.1 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

10TPM > 0

4Conditions

15.2Max TPM

2.1Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
apical branchlet · Control at T25	6	4	2.23	7.16
apical branchlet · Temperature treatment at T0	6	3	2.41	13.75
apical branchlet · Temperature treatment at T25	5	2	3.07	15.17
apical branchlet · Control at T0	4	1	0.22	0.89

Per sample · hover a bar for the full sample record · show / hide the sample table

SRA run	Condition	Tissue	Developmental stage	Treatment	Study	TPM
SRR19977444	apical branchlet · Control at T25	apical branchlet	not recorded	Control at T25	SRP384900	7.16
SRR19977441	apical branchlet · Control at T25	apical branchlet	not recorded	Control at T25	SRP384900	3.76
SRR19977455	apical branchlet · Control at T25	apical branchlet	not recorded	Control at T25	SRP384900	1.99
SRR19977440	apical branchlet · Control at T25	apical branchlet	not recorded	Control at T25	SRP384900	0.45
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	13.75
SRR19977427	apical branchlet · Temperature treatment at T0	apical branchlet	not recorded	Temperature treatment at T0	SRP384900	0.44
SRR19977438	apical branchlet · Temperature treatment at T0	apical branchlet	not recorded	Temperature treatment at T0	SRP384900	0.30
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
SRR19977463	apical branchlet · Temperature treatment at T25	apical branchlet	not recorded	Temperature treatment at T25	SRP384900	15.17
SRR19977435	apical branchlet · Temperature treatment at T25	apical branchlet	not recorded	Temperature treatment at T25	SRP384900	0.19
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
SRR19977443	apical branchlet · Control at T0	apical branchlet	not recorded	Control at T0	SRP384900	0.89
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.