Gene detail

Detailed information of FUN_003073-T1 in Siderastrea siderea

Genomic Location: contig_2:18763199...18781538
NR annotation: no NCBI-NR hit recorded
Species Siderastrea siderea · all data for this species · gene families

Gene Structure

More details in JBrowse

Sequence

CDS

Transcript

FUN_003073-T1

catcacttacgccctttttccaccgggcccttcaaatgtTATCAATTTCTAGGTACTTCTTGTTGCTTCCTCTTTCATGAGCCCAGCTGAAAGCAAATCATTTACTAACATCAGCAGAGTTCGGATGTTTGGTCCTGACAAACTCTCCAAGCCAGTAGCAGCTCAGAAGTGGGACAGAATCAAGTTGGTCTGCACCCAGCCATTTAATAAGAGTGAACAATATGGGCTGTCATTTGTAAACCTCCATTCTCCTCCTGAAGATACTGATGGTGACTCAGATAAAGCTGTTGCAAGCCCCTCTTTGCCAGGTCATTCTAAGAGACTTGGACGCTTCACTTTAAAGGACGACAGTGACAGTGAAGAGAAGAAAGTCGTTACATCTGGAAGTTTATTCTTtaaaaaactgcaaaagaaatcTTCGCCACCCCCCATGTCTACGGCTGCTGAAGTCCGAGCAGCATCAACAGCTGCCAGTTCATcagatgacagaaaagcaggtGCTACCAGCACTGTGCAGGAAGTGAGATACTCAGTAGCTAAGGACAGACACCCAGTAGCCATGGGTGGACAGTCGCCAGCTTCTGATAGACACCCAGTCGCAAATGACAAATTAGGGAAAGTTGGCGAAGAGACCTCTCCAAAAACTGATGTAACACATGTGCAAAGAAGAACTAGTGAGaGCACAAAACGGAAGTATGAAGATGTACCAAAGGAAAACAACAAAGGGAAATCGCCTCCACCGACGAAGAAGAAACGAGGATCTCCAAGTCGTGTTGATGATGACTCGCTCGCATTTGAAGAAATTATGAAAGACgtggtgtttgttttgagtgGTTTTGTGAATCCTGAGCGCGGTAATCTCCGTGACAAAGCCTTGCAGATGGGAGCGCAATATAAACAAGACTGGGGCAGAGGATGTACACATCTAATTTGTGCCTTCGCTAACACTCCCAAGTTCAATCAAGTCAAAGgaaaaggaaaaatagtCACAAAGAAATGGATAAGTGATTGcttcaagaagaagaagcgTTTGCCTACTCGAAACTACCATTTACCAGGTGATAGCAGTTCATCTGAAGAAAGCAGCGAGGAAGAAGAAGTAAAACCTAAAAGGCCTCCGGTTAGGAAAACAGATACAGATACAGGCAGTCGAGATCGCAAGAACGCTGGAGATGAGGAGGACACATCCTCAGTAAGCGATAAACGTCCCATAGGAAAAACCGCTCATGCTTCAGACTCCGTGGGAGAGAAAGATGAGTGCAAGAAAACAGAAGACGCAGATGACGTATATGGCGGCTCTACTGATGATGAGACGCAAGAACAACCTAAAAACGAAAATAGAAAGAACGTTTCAACGCCAAGTCCACAAGAGACTTCATCCAGTGACCGCGACACGGAGGACGAATTGAAGAGagttcaagaggaagaagaaaaaggaaaagaacaacaacaagaagatATTTATGACGGTACAACTGATGACGAACAAGAAGAGACGGCAAATAAAGATGAGGCAGAACCCGCTGACGACGTTTCCTCGGGCTCAGAAGACCTTCCCTCGTTACCAGACTTCTTCTCACACAAGCACTTCCTTTTGTATGGTGAAATTGAGAGCACGACCAGGAGGCTTTTAATCAGATACATCACAGCATATAATGGAACCGTTGAAGAGTACATGAGTGACAATGTGGACTTTGTTATTACCAACGAAGACTGGGATCGGAACTTTGACGAGGCTCTCAACGAAAACGCGTCCTTGGCTTTTGTGCGCCCCAAGTGGATCATGGTTTGTCACGAGAAAGGTGCTCTTGTTCCTTTTCAGCCATACATCATAGTTCCTACGTAGTCTTATCATTAGATCACGTGATCAATTCGTTATCAAAGGACGGAATCACAGAACGATAGTTAGACTGTAACCTTCAAATGTTAAGAAAATGAGAGTATTATTCGAACTATAACCAAGAAGAGAAAAGCTCGGAGAAATATCGGAGATTAGAGATTGCTTCGCTAGAGACAGTTTACTCGCGTTCTGAACTTGCGAGAGACTTTTTGCTGCCATAGTGTAACTATGCATTATATAAAAAGACGGAACTCCACCCGGCTATCCGAGAAACAACGTAACATTTTACAAAGATTGTAACCAAACTGCGCGACGAATGTCAAAGATGGATCATTAATGGCATGGCGACAGCTTGGAAACAGGTTCCCAGTTCCTCTCGGAGATGTTGTCCTCAATTTGTGATAAACTTTGCCGTCACAGTCTGAGTATGTATTACGAAAAACATCGAACTTCACTCGGGTATCCAACGAGCATCGTAGTTGTAGATGGGTGAAGATTATCCGAAAGCTTGTCGAGGAAAGCCGAGTAGAGATCGATCGCGGACAGCATATTTTGGGATCTGTTCAAAGTTTGCTGGCTGGGGACCTTTCATTCGCGTTGTAACTTGGTGGCGTCAACGGATCTCTTCGTGTCTGAAGTAAACCCTTTCTAGTAGAGCTGTAAGATCTTGTAAAGCTCAGTTGAAAAGAACTCTCACGATCACGTGTCGAGGGATAATTTCACATGCAATCGCTCATGCGCAAAATGTACGCTTACGATTAAAAACTCCAGTCATCACTTACGGAAGCTGACTTGAAGAACTACGCGTGTTTTAAAAGCTTGTGTTAGCTACCACATATAGTCGGTACATACTGTATTTGGGAGAGGGGGAATATTTAAAGCCTGGCGATGATCCTATCGTAGAAAGAGAACGAGATCATATTTGATAACAAAATAGTACAGAAAAGAAACAGATTAAAAAATTTTTCACGATTACTGTCCGGCATTTACCCAATGTATAAATAAAATCACACGTAGTGATTTCATTTATATATTCACTATCACATCCTGAGGATTAATTCGAAACTACATTAGGGTTGAGTAAGAACGCTCGCCTTTTACCACTGTTACCCGGGTTCGAGTCCCGCCCTTCGTCTTTAGTTGCGGgttcagtttgttgttgttgttttttttttgtttgtgttttgttttagtgGTTCCCTTTTCTCTGCTACAACCAACATTTCTATCAGTGAATTCCAACTAGATCCGGAAACAGTGAACGGAAGAGCCATACTGTGAATTGCCATTGCAcattccgtttttttttttgctcgtAAAATTTGAGGTTTCGTAGCTCAGTTAGCGAGTAGAAAATTACATTGgggaaaaattcaaaatgtcttTGAAACCCTAGAGGCGCGGTGATGTAGttgttagcgcgttggactttgGAACGGACTTACGATCGCTGGTTCTTGCATTGTCCGCGTCTTGTTTCCTAAGACAAAGAGCTTTTCCCtctgtcattaaagatgtgtttattgttcatcgtggtgtaagataggcaagatgaacgtttattcgtttgtctcacgatgg

Protein

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0001788 (this species only) · gene tree & orthology

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF01834 all species →	XRCC1_N	XRCC1 N terminal domain	Domain	Interproscan
PF00533 all species →	BRCT	BRCA1 C Terminus (BRCT) domain	Family	Interproscan
PF16589 all species →	BRCT_2	BRCT domain, a BRCA1 C-terminus domain	Family	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR036420 all species →	Homologous_superfamily	BRCT domain superfamily	Interproscan
IPR045080 all species →	Domain	XRCC1, first (central) BRCT domain	Interproscan
IPR001357 all species →	Domain	BRCT domain	Interproscan
IPR002706 all species →	Domain	DNA-repair protein Xrcc1, N-terminal	Interproscan
IPR008979 all species →	Homologous_superfamily	Galactose-binding-like domain superfamily	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR11370 all species →	DNA-REPAIR PROTEIN XRCC1	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0000012 all species →	Biological Process	single strand break repair	Interproscan
GO:0003684 all species →	Molecular Function	damaged DNA binding	Interproscan
GO:0006284 all species →	Biological Process	base-excision repair	Interproscan
GO:0006303 all species →	Biological Process	double-strand break repair via nonhomologous end joining	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
K10803	XRCC1; DNA-repair protein XRCC1	-	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 FUN_003073-T1 across 85 RNA-seq samples of Siderastrea siderea. 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.

85Samples

32TPM > 0

7Conditions

868.0Max TPM

48.9Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
holobiont · low.pH_high.temp	20	7	73.68	867.98
holobiont · low.pH Control.temp	20	5	52.81	638.21
holobiont · control.pH_high.temp	20	8	40.18	197.42
holobiont · control.pH Control.temp	19	6	40.22	226.22
Whole organism	4	4	10.35	15.78
unannotated	1	1	8.73	8.73
live coral tissue/skeleton	1	1	9.44	9.44

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

SRA run	Condition	Tissue	Developmental stage	Treatment	Study	TPM
SRR22214405	holobiont · low.pH_high.temp	holobiont	not recorded	low.pH_high.temp	SRP406607	867.98
SRR22214412	holobiont · low.pH_high.temp	holobiont	not recorded	low.pH_high.temp	SRP406607	248.32
SRR22214410	holobiont · low.pH_high.temp	holobiont	not recorded	low.pH_high.temp	SRP406607	156.88
SRR22214408	holobiont · low.pH_high.temp	holobiont	not recorded	low.pH_high.temp	SRP406607	108.74
SRR22214406	holobiont · low.pH_high.temp	holobiont	not recorded	low.pH_high.temp	SRP406607	43.13
SRR22214407	holobiont · low.pH_high.temp	holobiont	not recorded	low.pH_high.temp	SRP406607	27.27
SRR22214419	holobiont · low.pH_high.temp	holobiont	not recorded	low.pH_high.temp	SRP406607	21.20
SRR22214402	holobiont · low.pH_high.temp	holobiont	not recorded	low.pH_high.temp	SRP406607	0.00
SRR22214403	holobiont · low.pH_high.temp	holobiont	not recorded	low.pH_high.temp	SRP406607	0.00
SRR22214404	holobiont · low.pH_high.temp	holobiont	not recorded	low.pH_high.temp	SRP406607	0.00
SRR22214409	holobiont · low.pH_high.temp	holobiont	not recorded	low.pH_high.temp	SRP406607	0.00
SRR22214413	holobiont · low.pH_high.temp	holobiont	not recorded	low.pH_high.temp	SRP406607	0.00
SRR22214414	holobiont · low.pH_high.temp	holobiont	not recorded	low.pH_high.temp	SRP406607	0.00
SRR22214415	holobiont · low.pH_high.temp	holobiont	not recorded	low.pH_high.temp	SRP406607	0.00
SRR22214416	holobiont · low.pH_high.temp	holobiont	not recorded	low.pH_high.temp	SRP406607	0.00
SRR22214417	holobiont · low.pH_high.temp	holobiont	not recorded	low.pH_high.temp	SRP406607	0.00
SRR22214418	holobiont · low.pH_high.temp	holobiont	not recorded	low.pH_high.temp	SRP406607	0.00
SRR22214420	holobiont · low.pH_high.temp	holobiont	not recorded	low.pH_high.temp	SRP406607	0.00
SRR22214421	holobiont · low.pH_high.temp	holobiont	not recorded	low.pH_high.temp	SRP406607	0.00
SRR22214423	holobiont · low.pH_high.temp	holobiont	not recorded	low.pH_high.temp	SRP406607	0.00
SRR22214427	holobiont · low.pH Control.temp	holobiont	not recorded	low.pH Control.temp	SRP406607	638.21
SRR22214436	holobiont · low.pH Control.temp	holobiont	not recorded	low.pH Control.temp	SRP406607	187.79
SRR22214438	holobiont · low.pH Control.temp	holobiont	not recorded	low.pH Control.temp	SRP406607	146.32
SRR22214430	holobiont · low.pH Control.temp	holobiont	not recorded	low.pH Control.temp	SRP406607	59.59
SRR22214424	holobiont · low.pH Control.temp	holobiont	not recorded	low.pH Control.temp	SRP406607	24.38
SRR22214425	holobiont · low.pH Control.temp	holobiont	not recorded	low.pH Control.temp	SRP406607	0.00
SRR22214426	holobiont · low.pH Control.temp	holobiont	not recorded	low.pH Control.temp	SRP406607	0.00
SRR22214428	holobiont · low.pH Control.temp	holobiont	not recorded	low.pH Control.temp	SRP406607	0.00
SRR22214429	holobiont · low.pH Control.temp	holobiont	not recorded	low.pH Control.temp	SRP406607	0.00
SRR22214431	holobiont · low.pH Control.temp	holobiont	not recorded	low.pH Control.temp	SRP406607	0.00
SRR22214432	holobiont · low.pH Control.temp	holobiont	not recorded	low.pH Control.temp	SRP406607	0.00
SRR22214434	holobiont · low.pH Control.temp	holobiont	not recorded	low.pH Control.temp	SRP406607	0.00
SRR22214435	holobiont · low.pH Control.temp	holobiont	not recorded	low.pH Control.temp	SRP406607	0.00
SRR22214437	holobiont · low.pH Control.temp	holobiont	not recorded	low.pH Control.temp	SRP406607	0.00
SRR22214439	holobiont · low.pH Control.temp	holobiont	not recorded	low.pH Control.temp	SRP406607	0.00
SRR22214440	holobiont · low.pH Control.temp	holobiont	not recorded	low.pH Control.temp	SRP406607	0.00
SRR22214441	holobiont · low.pH Control.temp	holobiont	not recorded	low.pH Control.temp	SRP406607	0.00
SRR22214442	holobiont · low.pH Control.temp	holobiont	not recorded	low.pH Control.temp	SRP406607	0.00
SRR22214443	holobiont · low.pH Control.temp	holobiont	not recorded	low.pH Control.temp	SRP406607	0.00
SRR22214445	holobiont · low.pH Control.temp	holobiont	not recorded	low.pH Control.temp	SRP406607	0.00
SRR22214460	holobiont · control.pH_high.temp	holobiont	not recorded	control.pH_high.temp	SRP406607	197.42
SRR22214458	holobiont · control.pH_high.temp	holobiont	not recorded	control.pH_high.temp	SRP406607	191.65
SRR22214453	holobiont · control.pH_high.temp	holobiont	not recorded	control.pH_high.temp	SRP406607	157.30
SRR22214456	holobiont · control.pH_high.temp	holobiont	not recorded	control.pH_high.temp	SRP406607	116.68
SRR22214465	holobiont · control.pH_high.temp	holobiont	not recorded	control.pH_high.temp	SRP406607	62.85
SRR22214461	holobiont · control.pH_high.temp	holobiont	not recorded	control.pH_high.temp	SRP406607	53.32
SRR22214446	holobiont · control.pH_high.temp	holobiont	not recorded	control.pH_high.temp	SRP406607	19.85
SRR22214459	holobiont · control.pH_high.temp	holobiont	not recorded	control.pH_high.temp	SRP406607	4.52
SRR22214447	holobiont · control.pH_high.temp	holobiont	not recorded	control.pH_high.temp	SRP406607	0.00
SRR22214448	holobiont · control.pH_high.temp	holobiont	not recorded	control.pH_high.temp	SRP406607	0.00
SRR22214449	holobiont · control.pH_high.temp	holobiont	not recorded	control.pH_high.temp	SRP406607	0.00
SRR22214450	holobiont · control.pH_high.temp	holobiont	not recorded	control.pH_high.temp	SRP406607	0.00
SRR22214451	holobiont · control.pH_high.temp	holobiont	not recorded	control.pH_high.temp	SRP406607	0.00
SRR22214452	holobiont · control.pH_high.temp	holobiont	not recorded	control.pH_high.temp	SRP406607	0.00
SRR22214454	holobiont · control.pH_high.temp	holobiont	not recorded	control.pH_high.temp	SRP406607	0.00
SRR22214457	holobiont · control.pH_high.temp	holobiont	not recorded	control.pH_high.temp	SRP406607	0.00
SRR22214462	holobiont · control.pH_high.temp	holobiont	not recorded	control.pH_high.temp	SRP406607	0.00
SRR22214463	holobiont · control.pH_high.temp	holobiont	not recorded	control.pH_high.temp	SRP406607	0.00
SRR22214464	holobiont · control.pH_high.temp	holobiont	not recorded	control.pH_high.temp	SRP406607	0.00
SRR22214467	holobiont · control.pH_high.temp	holobiont	not recorded	control.pH_high.temp	SRP406607	0.00
SRR22214422	holobiont · control.pH Control.temp	holobiont	not recorded	control.pH Control.temp	SRP406607	226.22
SRR22214470	holobiont · control.pH Control.temp	holobiont	not recorded	control.pH Control.temp	SRP406607	202.85
SRR22214524	holobiont · control.pH Control.temp	holobiont	not recorded	control.pH Control.temp	SRP406607	172.02
SRR22214400	holobiont · control.pH Control.temp	holobiont	not recorded	control.pH Control.temp	SRP406607	100.95
SRR22214535	holobiont · control.pH Control.temp	holobiont	not recorded	control.pH Control.temp	SRP406607	54.16
SRR22214471	holobiont · control.pH Control.temp	holobiont	not recorded	control.pH Control.temp	SRP406607	7.89
SRR22214411	holobiont · control.pH Control.temp	holobiont	not recorded	control.pH Control.temp	SRP406607	0.00
SRR22214433	holobiont · control.pH Control.temp	holobiont	not recorded	control.pH Control.temp	SRP406607	0.00
SRR22214444	holobiont · control.pH Control.temp	holobiont	not recorded	control.pH Control.temp	SRP406607	0.00
SRR22214455	holobiont · control.pH Control.temp	holobiont	not recorded	control.pH Control.temp	SRP406607	0.00
SRR22214466	holobiont · control.pH Control.temp	holobiont	not recorded	control.pH Control.temp	SRP406607	0.00
SRR22214468	holobiont · control.pH Control.temp	holobiont	not recorded	control.pH Control.temp	SRP406607	0.00
SRR22214469	holobiont · control.pH Control.temp	holobiont	not recorded	control.pH Control.temp	SRP406607	0.00
SRR22214481	holobiont · control.pH Control.temp	holobiont	not recorded	control.pH Control.temp	SRP406607	0.00
SRR22214492	holobiont · control.pH Control.temp	holobiont	not recorded	control.pH Control.temp	SRP406607	0.00
SRR22214506	holobiont · control.pH Control.temp	holobiont	not recorded	control.pH Control.temp	SRP406607	0.00
SRR22214546	holobiont · control.pH Control.temp	holobiont	not recorded	control.pH Control.temp	SRP406607	0.00
SRR22214547	holobiont · control.pH Control.temp	holobiont	not recorded	control.pH Control.temp	SRP406607	0.00
SRR22214548	holobiont · control.pH Control.temp	holobiont	not recorded	control.pH Control.temp	SRP406607	0.00
SRR14295603	Whole organism	Whole organism	not recorded	not recorded	SRP315757	15.78
SRR14295604	Whole organism	Whole organism	not recorded	not recorded	SRP315757	13.06
SRR14295601	Whole organism	Whole organism	not recorded	not recorded	SRP315757	6.95
SRR14295600	Whole organism	Whole organism	not recorded	not recorded	SRP315757	5.60
ERR12861049	unannotated	not recorded	not recorded	not recorded	ERP159209	8.73
SRR12454619	live coral tissue/skeleton	live coral tissue/skeleton	not recorded	not recorded	SRP277390	9.44

Source: CnidoSite RNA-seq expression matrices (SSIDE_TPM, StringTie quantification over 85 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.