Gene detail

Detailed information of evm.model.Ap1.2746 in Astrangia poculata

Genomic Location: Ap1:28136190...28138211
NR annotation: KAJ7339471.1, 5' exonuclease Apollo [Desmophyllum pertusum]
Species Astrangia poculata · all data for this species · gene families

Gene Structure

More details in JBrowse

Sequence

CDS

evm.model.Ap1.2746

atgcacgcggatcacacggctggtttgacatcttcatggaacgcgtacacaatttactgttcagagctaacaaggaggcttgtaatagctaaacttggtgttaaaagtgacctcgtcgttggtctaccattggatgaaagcgtgatcataaacctggacgaagctgggaaggaaaccatgactgtcacacttgttgatgccaaccattgccctggctctgtcatgttcattttcgaaggctactttggaaaaattttctacactggcgactttcgttattgtgaacgtttaacgacacactctgctatccaagggaagatatttgacgtgctttatttggacaacacttactgtgaccccaagtgcgtttttccttcgcgtactcaagcgactgtaaacatattggagataattcgaagtcatccagactgcaaagtggttatcgggcttcacaatcttggcaaagaaatgcttctacatacaattgccgtggtgtgtcaaacgtggataggagtggaccctacgagaaaagaaacactgaaacttctcgaaatgccagatgtgttcacatgtgaggtagataaagttagaataagagtagtgaaaagccttgaagtcaccaagaaaaacgttcagttttggaactctgaagagccaaccattgctatactgccgacttgcctcttcattggctcaacaaacccctatgccaatgtggagaatgttttcgttgttccctattcagatcatagttcttttgaagagttgagaaagtttgttcagaatgtcaagcctagaaaaattattcccatcgtacacaagcacagactgtcaccaggtgaaaccataaacagtagagtgaatatgaatgttttccaagacctgacagattcttccccatcgtcacaatatattgtccctccctctgtacaatgtttcatgactggagcagtacagcaaaggacaaacaagagagtgaaagcaactggaaagctttgctcgaggaaatctgttaagaataagaaacctcgtggagttgtcttccctcccagccaggaagcaacaggaatagaggaagacaaatgtgatgcagaaattaaggaattggatgaaaacttcacagcagtaaggggtgcaagtattaagaaacatagcaagacacaggaaaacacagaagatgacaggaatattggccacatttcctgcaggtgtccatttggtttccattgtagtcattcaggtgaaagagatctcgatgtggcactgcgcacctcgggatatgaaataaatgcagttgcttctttgtcagtcaaatgtggctcggcagacaatgaatcagaagaagattcaaatttggatattgtttctggtgaaatagatcatggtaaagcacaccagattgtcaaggttgattcttcatccattgaacctgtcttggtagatagcaagttggcagggaaattagatgtaaataatatttcagatgataataattttcaagatgaaagcatggtgcaagagatcacaagagatcaaaaagattcagttgctttgtcgtccatcaagccttgcttggcagacagtgaatcaagagaaaagtcaaaggtgcccaactgtgaagattataaacaacctggtgagacaccaaggaggatggaagacaagaaagatgtggttgattcatctatcacaaccaaggatgtgagtgatgagtataaaaactctcccaatagaaatcttcccattagagggcatggagaagatgaagcaaatacaggtgcttctcctcatatcataacaaaagatgtcagcagcaacaatgtgattgatccagcaaagaatctttcagtgaaaagaaagtacagagagttcaatggccacaatgatgagaacaatgtcaatagtgttgtcgagcatagctctggcattaagaaattcaatatttacactggatgctcatgtgattttgcacgtaaagttttggaagacatggtgaaaaacagtgctcttagagacaaatga

Transcript

evm.model.Ap1.2746

ATGCACGCGGATCACACGGCTGGTTTGACATCTTCATGGAACGCGTACACAATTTACTGTTCAGAGCTAACAAGGAGGCTTGTAATAGCTAAACTTGGTGTTAAAAGTGACCTCGTCGTTGGTCTACCATTGGATGAAAGCGTGATCATAAACCTGGACGAAGCTGGGAAGGAAACCATGACTGTCACACTTGTTGATGCCAACCATTGCCCTGGCTCTGTCATGTTCATTTTCGAAGGCTACTTTGGAAAAATTTTCTACACTGGCGACTTTCGTTATTGTGAACGTTTAACGACACACTCTGCTATCCAAGGGAAGATATTTGACGTGCTTTATTTGGACAACACTTACTGTGACCCCAAGTGCGTTTTTCCTTCGCGTACTCAAGCGACTGTAAACATATTGGAGATAATTCGAAGTCATCCAGACTGCAAAGTGGTTATCGGGCTTCACAATCTTGGCAAAGAAATGCTTCTACATACAATTGCCGTGGTGTGTCAAACGTGGATAGGAGTGGACCCTACGAGAAAAGAAACACTGAAACTTCTCGAAATGCCAGATGTGTTCACATGTGAGGTAGATAAAGTTAGAATAAGAGTAGTGAAAAGCCTTGAAGTCACCAAGAAAAACGTTCAGTTTTGGAACTCTGAAGAGCCAACCATTGCTATACTGCCGACTTGCCTCTTCATTGGCTCAACAAACCCCTATGCCAATGTGGAGAATGTTTTCGTTGTTCCCTATTCAGATCATAGTTCTTTTGAAGAGTTGAGAAAGTTTGTTCAGAATGTCAAGCCTAGAAAAATTATTCCCATCGTACACAAGCACAGACTGTCACCAGGTGAAACCATAAACAGTAGAGTGAATATGAATGTTTTCCAAGACCTGACAGATTCTTCCCCATCGTCACAATATATTGTCCCTCCCTCTGTACAATGTTTCATGACTGGAGCAGTACAGCAAAGGACAAACAAGAGAGTGAAAGCAACTGGAAAGCTTTGCTCGAGGAAATCTGTTAAGAATAAGAAACCTCGTGGAGTTGTCTTCCCTCCCAGCCAGGAAGCAACAGGAATAGAGGAAGACAAATGTGATGCAGAAATTAAGGAATTGGATGAAAACTTCACAGCAGTAAGGGGTGCAAGTATTAAGAAACATAGCAAGACACAGGAAAACACAGAAGATGACAGGAATATTGGCCACATTTCCTGCAGGTGTCCATTTGGTTTCCATTGTAGTCATTCAGGTGAAAGAGATCTCGATGTGGCACTGCGCACCTCGGGATATGAAATAAATGCAGTTGCTTCTTTGTCAGTCAAATGTGGCTCGGCAGACAATGAATCAGAAGAAGATTCAAATTTGGATATTGTTTCTGGTGAAATAGATCATGGTAAAGCACACCAGATTGTCAAGGTTGATTCTTCATCCATTGAACCTGTCTTGGTAGATAGCAAGTTGGCAGGGAAATTAGATGTAAATAATATTTCAGATGATAATAATTTTCAAGATGAAAGCATGGTGCAAGAGATCACAAGAGATCAAAAAGATTCAGTTGCTTTGTCGTCCATCAAGCCTTGCTTGGCAGACAGTGAATCAAGAGAAAAGTCAAAGGTGCCCAACTGTGAAGATTATAAACAACCTGGTGAGACACCAAGGAGGATGGAAGACAAGAAAGATGTGGTTGATTCATCTATCACAACCAAGGATGTGAGTGATGAGTATAAAAACTCTCCCAATAGAAATCTTCCCATTAGAGGGCATGGAGAAGATGAAGCAAATACAGGTGCTTCTCCTCATATCATAACAAAAGATGTCAGCAGCAACAATGTGATTGATCCAGCAAAGAATCTTTCAGTGAAAAGAAAGTACAGAGAGTTCAATGGCCACAATGATGAGAACAATGTCAATAGTGTTGTCGAGCATAGCTCTGGCATTAAGAAATTCAATATTTACACTGGATGCTCATGTGATTTTGCACGTAAAGTTTTGGAAGACATGGTGAAAAACAGTGCTCTTAGAGACAAATGA

Protein

UniProt (Swiss-Prot top hit)

UniProt accession	Description
D2H8V8	5' exonuclease Apollo OS=Ailuropoda melanoleuca OX=9646 GN=DCLRE1B PE=3 SV=1
Q9H816	5' exonuclease Apollo OS=Homo sapiens OX=9606 GN=DCLRE1B PE=1 SV=1
B0V2S2	5' exonuclease Apollo OS=Danio rerio OX=7955 GN=dclre1b PE=2 SV=1

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0002228 (this species only) · gene tree & orthology

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF07522 all species →	DRMBL	DNA repair metallo-beta-lactamase	Domain	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR011084 all species →	Domain	DNA repair metallo-beta-lactamase	Interproscan
IPR036866 all species →	Homologous_superfamily	Ribonuclease Z/Hydroxyacylglutathione hydrolase-like	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR23240 all species →	DNA CROSS-LINK REPAIR PROTEIN PSO2/SNM1-RELATED	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0000723 all species →	Biological Process	telomere maintenance	Interproscan
GO:0003684 all species →	Molecular Function	damaged DNA binding	Interproscan
GO:0006303 all species →	Biological Process	double-strand break repair via nonhomologous end joining	Interproscan
GO:0035312 all species →	Molecular Function	5'-3' DNA exonuclease activity	Interproscan
GO:0036297 all species →	Biological Process	interstrand cross-link repair	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
K15341	DCLRE1B, SNM1B; DNA cross-link repair 1B protein	EC:3.1.-.-	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 evm.model.Ap1.2746 across 49 RNA-seq samples of Astrangia poculata. 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.

49Samples

1TPM > 0

4Conditions

207.6Max TPM

4.2Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
whole organism · cold control	14	0	0.00	0.00
whole organism · heat control	12	0	0.00	0.00
whole organism · cold challenge	12	1	17.30	207.57
whole organism · heat challenge	11	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
SRR10674714	whole organism · cold control	whole organism	not recorded	cold control	SRP237293	0.00
SRR10674715	whole organism · cold control	whole organism	not recorded	cold control	SRP237293	0.00
SRR10674724	whole organism · cold control	whole organism	not recorded	cold control	SRP237293	0.00
SRR10674733	whole organism · cold control	whole organism	not recorded	cold control	SRP237293	0.00
SRR10674734	whole organism · cold control	whole organism	not recorded	cold control	SRP237293	0.00
SRR10674735	whole organism · cold control	whole organism	not recorded	cold control	SRP237293	0.00
SRR10674736	whole organism · cold control	whole organism	not recorded	cold control	SRP237293	0.00
SRR10674737	whole organism · cold control	whole organism	not recorded	cold control	SRP237293	0.00
SRR10674739	whole organism · cold control	whole organism	not recorded	cold control	SRP237293	0.00
SRR10674743	whole organism · cold control	whole organism	not recorded	cold control	SRP237293	0.00
SRR10674746	whole organism · cold control	whole organism	not recorded	cold control	SRP237293	0.00
SRR10674747	whole organism · cold control	whole organism	not recorded	cold control	SRP237293	0.00
SRR10674748	whole organism · cold control	whole organism	not recorded	cold control	SRP237293	0.00
SRR10674750	whole organism · cold control	whole organism	not recorded	cold control	SRP237293	0.00
SRR10674706	whole organism · heat control	whole organism	not recorded	heat control	SRP237293	0.00
SRR10674707	whole organism · heat control	whole organism	not recorded	heat control	SRP237293	0.00
SRR10674708	whole organism · heat control	whole organism	not recorded	heat control	SRP237293	0.00
SRR10674717	whole organism · heat control	whole organism	not recorded	heat control	SRP237293	0.00
SRR10674718	whole organism · heat control	whole organism	not recorded	heat control	SRP237293	0.00
SRR10674720	whole organism · heat control	whole organism	not recorded	heat control	SRP237293	0.00
SRR10674721	whole organism · heat control	whole organism	not recorded	heat control	SRP237293	0.00
SRR10674725	whole organism · heat control	whole organism	not recorded	heat control	SRP237293	0.00
SRR10674731	whole organism · heat control	whole organism	not recorded	heat control	SRP237293	0.00
SRR10674741	whole organism · heat control	whole organism	not recorded	heat control	SRP237293	0.00
SRR10674752	whole organism · heat control	whole organism	not recorded	heat control	SRP237293	0.00
SRR10674753	whole organism · heat control	whole organism	not recorded	heat control	SRP237293	0.00
SRR10674744	whole organism · cold challenge	whole organism	not recorded	cold challenge	SRP237293	207.57
SRR10674711	whole organism · cold challenge	whole organism	not recorded	cold challenge	SRP237293	0.00
SRR10674712	whole organism · cold challenge	whole organism	not recorded	cold challenge	SRP237293	0.00
SRR10674713	whole organism · cold challenge	whole organism	not recorded	cold challenge	SRP237293	0.00
SRR10674722	whole organism · cold challenge	whole organism	not recorded	cold challenge	SRP237293	0.00
SRR10674723	whole organism · cold challenge	whole organism	not recorded	cold challenge	SRP237293	0.00
SRR10674730	whole organism · cold challenge	whole organism	not recorded	cold challenge	SRP237293	0.00
SRR10674732	whole organism · cold challenge	whole organism	not recorded	cold challenge	SRP237293	0.00
SRR10674738	whole organism · cold challenge	whole organism	not recorded	cold challenge	SRP237293	0.00
SRR10674740	whole organism · cold challenge	whole organism	not recorded	cold challenge	SRP237293	0.00
SRR10674745	whole organism · cold challenge	whole organism	not recorded	cold challenge	SRP237293	0.00
SRR10674749	whole organism · cold challenge	whole organism	not recorded	cold challenge	SRP237293	0.00
SRR10674709	whole organism · heat challenge	whole organism	not recorded	heat challenge	SRP237293	0.00
SRR10674710	whole organism · heat challenge	whole organism	not recorded	heat challenge	SRP237293	0.00
SRR10674716	whole organism · heat challenge	whole organism	not recorded	heat challenge	SRP237293	0.00
SRR10674719	whole organism · heat challenge	whole organism	not recorded	heat challenge	SRP237293	0.00
SRR10674726	whole organism · heat challenge	whole organism	not recorded	heat challenge	SRP237293	0.00
SRR10674727	whole organism · heat challenge	whole organism	not recorded	heat challenge	SRP237293	0.00
SRR10674728	whole organism · heat challenge	whole organism	not recorded	heat challenge	SRP237293	0.00
SRR10674729	whole organism · heat challenge	whole organism	not recorded	heat challenge	SRP237293	0.00
SRR10674742	whole organism · heat challenge	whole organism	not recorded	heat challenge	SRP237293	0.00
SRR10674751	whole organism · heat challenge	whole organism	not recorded	heat challenge	SRP237293	0.00
SRR10674754	whole organism · heat challenge	whole organism	not recorded	heat challenge	SRP237293	0.00

Source: CnidoSite RNA-seq expression matrices (APOCU_TPM, StringTie quantification over 49 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.