Gene detail

Detailed information of FUN_007479-T1 in Siderastrea siderea

Genomic Location: contig_5:14294003...14322375
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

FUN_007479-T1

ATGCAGGTCAGTTCATGGATGGTACACATGGAGTCAACTTTGAGCAAAGGAGGTTCTTTGGTTGATGACCTCAATCTGCGCTGTGTCCTATTCATTAAGGGCATTCTTATTGCTCACACTGTCAGTCATTTGGTCCGCACCGTTATGAACATGCATCTTGTGTTGTCTAAACCACTGACCAAAGCTGCTGTGCTGGCCTTGTGCAGGCTCACAGAACTTCTGAAGGCTATTGAACACACATTTCACCGACGCAGTATGCTGATCGCAGAAAGTGTGAATCACATGCTACAGCACTTGACATTTATGGCTTTAGCTTGCATCGACACTGCTAAGAAACGTATTGCAGCAGATAAGAAGTATACAGACAAGCGTCTTGATGTGTTAGCAGCGCTTGTTTTGGTGCAGAATGCCCTTAATGGACCAGCCACAAAGGAACGCAGACTTATCACACAACTGGGTATTCACGTTGGAACACAGTTTAAATCACTTCGTGACGAAGAGATGACAAGTTTAACTAGCGTAATGAAGAGGATTAATCTCGTCAGTGATTTAAGAGCAAGAGTCAAGAAAGCGTGTGACTGTGGCTTTCTACACTGGCACAGGGTTGTATTTCCAATTTATTTGGATGACTTGTACGAGGGTGCAACAGACGTTCATCGGGTTCACTACATGATCAGCGCTCTGAGAGACTGTGTCCCAGTCCTTCAGCAGGTCAAACACGAGTCGTCCCCTCAGGTCATGTTGGACTCGTTTGAGAAGGAGATTAGTGACACATTACATGAACACTTGCTTCAGCCTCTGTGTCGTGGCATTGAAACTGATCTACGTCTTCACATACATCAGCATTTGCAGCTAGATGACAGAAATCCTTTCAAGGTCGGGATGAGGGACCTTTCTCAGTTTTTGAAGATACGACCCATCCGGTTCTTCAACCAGTTCGTCAACATCAAACAACACGTGACCCATTACCTGGACACAACATTTTATAATCTGACCACAGTGGCTCTTCATGATTGGAGGACTTACGGTGAAATGAGGAACCAGGCCAGCCAGAAATATGGACTGGAGATGACTGAAGCTCACCTGCCTAGTCAGACACTGGAACAGGGTCTGGATGTGTTGGAGATCATGCGAAACATTCACGTGTTTGTTTCGCGATATCTGTACAACCTCAACAATCAGATTTTTGTTGAAACAGCATCGAACAACAAACATTTGAACACGATCAACATCCGCCATATTGCCAACTCCATCCGCACGCATGGCTCAGGAATCATgaacacgacggtgaatttcaCCTATCAGTTTCTGCGCAAGAAATTCTTCatcttttcacagtttttgTATGACGAACACATCAAGGCGAGGCTCATCAAGGATATTCGCTTCTTCAAAGAAACGAAGGCGCAAAGTGATCAGAAATACCCGTTTGAACGAGCTGAGAAGTTCAACAAAGGAATCCGTAAACTTGGTTTGACACCTGACGGTCAAACCTACTTGGACCAGTTCAGAATTCTCATCAGCCAGATAGGAAATGCCATGGGTTACATCCGAATGATTCGTTCCGGAGGTCTTCACTGCTGCAGCAACGCCATCAGATTCGTTCCTGATCTTGAGGACATTGTGTCTTTTGAGGAACTCGTAAAGGAAGAGAATCTGTCAGAAGAAGCAGAGCAGGCCTCCAAGAACTTAGATGCTGCGATTGACAACTTGGCAAAAAACTTCGCTGGTGCAACGGAATATTTCAAGCTTCTCGTTGATGTGTTTGCACCTGAGTTTAGGGACAGCAAGAACATGCATCTTAGGAACTTCTACGTCATCGTACCTCCTTTGACGCTCAACTTTGTGGAATACATGTTAAGCTGCAAGGAAAAGttgaacaagaaaaacaaagttgGAGCGGCATTCACTGATGATGGCTTTGTTATGGGTGTAGCGTATATTTTGAAGCTATTGGATCAGTATCACGAGTTTGACTCGCTTCACTGGTTCCAGTCAGTGCAGGACAAGTACGCCAAGGAGAAGGCTGAGGTGAAGGCATCTCTCAATCGTGGGACTGCGCGAGATGAAAAGTTACAACAGACGATGAATTTAACCTTAAAACGCCTGAACACTTATCAACAGGAATTTGAGCTGGTGTACTTCTCGCTAAACAGTGCAAGGATCTTCTTCCGAGCTGACAAAACCGCGGAcgaagaaaaagaggaaaaagaaagcaaagaaaactCAGAAGGTGCCCCCTCAAATGAAGAGTCTGGCACCCCTCCCCCGTCAGCGGAGGCCGCAGCAAGCTGA

Transcript

FUN_007479-T1

tgcagttatagacgcaacttctgcagttgcgaaaagaagcCTAAAAAAAACTTCAGGCTTGTATGGGATgtgaacccttgacctctgcaaTACTGGAGCAGCACTCTAagcaattgagctaacaagccaactgggagctggtcattaattTTAGTCGGTTTTTTATACACCTgtgaaggatgaagatgaaatgatCATCAATATTATATATTAGTactgcgggatgaagaattgaatgtaaagaagatcattgCAGTTATATGTAGCTAACTGAGCTATTGAACAAATTGCACACACAACTGCTGACTTGAATGTCTTTTGTGCAGGGATGCTCAGCTTTACCAGATGCAGGTCAGTTCATGGATGGTACACATGGAGTCAACTTTGAGCAAAGGAGGTTCTTTGGTTGATGACCTCAATCTGCGCTGTGTCCTATTCATTAAGGGCATTCTTATTGCTCACACTGTCAGTCATTTGGTCCGCACCGTTATGAACATGCATCTTGTGTTGTCTAAACCACTGACCAAAGCTGCTGTGCTGGCCTTGTGCAGGCTCACAGAACTTCTGAAGGCTATTGAACACACATTTCACCGACGCAGTATGCTGATCGCAGAAAGTGTGAATCACATGCTACAGCACTTGACATTTATGGCTTTAGCTTGCATCGACACTGCTAAGAAACGTATTGCAGCAGATAAGAAGTATACAGACAAGCGTCTTGATGTGTTAGCAGCGCTTGTTTTGGTGCAGAATGCCCTTAATGGACCAGCCACAAAGGAACGCAGACTTATCACACAACTGGGTATTCACGTTGGAACACAGTTTAAATCACTTCGTGACGAAGAGATGACAAGTTTAACTAGCGTAATGAAGAGGATTAATCTCGTCAGTGATTTAAGAGCAAGAGTCAAGAAAGCGTGTGACTGTGGCTTTCTACACTGGCACAGGGTTGTATTTCCAATTTATTTGGATGACTTGTACGAGGGTGCAACAGACGTTCATCGGGTTCACTACATGATCAGCGCTCTGAGAGACTGTGTCCCAGTCCTTCAGCAGGTCAAACACGAGTCGTCCCCTCAGGTCATGTTGGACTCGTTTGAGAAGGAGATTAGTGACACATTACATGAACACTTGCTTCAGCCTCTGTGTCGTGGCATTGAAACTGATCTACGTCTTCACATACATCAGCATTTGCAGCTAGATGACAGAAATCCTTTCAAGGTCGGGATGAGGGACCTTTCTCAGTTTTTGAAGATACGACCCATCCGGTTCTTCAACCAGTTCGTCAACATCAAACAACACGTGACCCATTACCTGGACACAACATTTTATAATCTGACCACAGTGGCTCTTCATGATTGGAGGACTTACGGTGAAATGAGGAACCAGGCCAGCCAGAAATATGGACTGGAGATGACTGAAGCTCACCTGCCTAGTCAGACACTGGAACAGGGTCTGGATGTGTTGGAGATCATGCGAAACATTCACGTGTTTGTTTCGCGATATCTGTACAACCTCAACAATCAGATTTTTGTTGAAACAGCATCGAACAACAAACATTTGAACACGATCAACATCCGCCATATTGCCAACTCCATCCGCACGCATGGCTCAGGAATCATgaacacgacggtgaatttcaCCTATCAGTTTCTGCGCAAGAAATTCTTCatcttttcacagtttttgTATGACGAACACATCAAGGCGAGGCTCATCAAGGATATTCGCTTCTTCAAAGAAACGAAGGCGCAAAGTGATCAGAAATACCCGTTTGAACGAGCTGAGAAGTTCAACAAAGGAATCCGTAAACTTGGTTTGACACCTGACGGTCAAACCTACTTGGACCAGTTCAGAATTCTCATCAGCCAGATAGGAAATGCCATGGGTTACATCCGAATGATTCGTTCCGGAGGTCTTCACTGCTGCAGCAACGCCATCAGATTCGTTCCTGATCTTGAGGACATTGTGTCTTTTGAGGAACTCGTAAAGGAAGAGAATCTGTCAGAAGAAGCAGAGCAGGCCTCCAAGAACTTAGATGCTGCGATTGACAACTTGGCAAAAAACTTCGCTGGTGCAACGGAATATTTCAAGCTTCTCGTTGATGTGTTTGCACCTGAGTTTAGGGACAGCAAGAACATGCATCTTAGGAACTTCTACGTCATCGTACCTCCTTTGACGCTCAACTTTGTGGAATACATGTTAAGCTGCAAGGAAAAGttgaacaagaaaaacaaagttgGAGCGGCATTCACTGATGATGGCTTTGTTATGGGTGTAGCGTATATTTTGAAGCTATTGGATCAGTATCACGAGTTTGACTCGCTTCACTGGTTCCAGTCAGTGCAGGACAAGTACGCCAAGGAGAAGGCTGAGGTGAAGGCATCTCTCAATCGTGGGACTGCGCGAGATGAAAAGTTACAACAGACGATGAATTTAACCTTAAAACGCCTGAACACTTATCAACAGGAATTTGAGCTGGTGTACTTCTCGCTAAACAGTGCAAGGATCTTCTTCCGAGCTGACAAAACCGCGGAcgaagaaaaagaggaaaaagaaagcaaagaaaactCAGAAGGTGCCCCCTCAAATGAAGAGTCTGGCACCCCTCCCCCGTCAGCGGAGGCCGCAGCAAGCTGA

Protein

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF14744 all species →	WASH-7_mid	WASH complex subunit 7	Family	Interproscan
PF14746 all species →	WASH-7_C	WASH complex subunit 7, C-terminal	Family	Interproscan
PF14745 all species →	WASH-4_N	WASH complex subunit 4, N-terminal	Domain	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR027307 all species →	Family	WASH complex subunit 7	Interproscan
IPR028282 all species →	Domain	WASH complex subunit 7, central domain	Interproscan
IPR028283 all species →	Domain	WASH complex subunit 7, C-terminal	Interproscan
IPR028191 all species →	Domain	WASH complex subunit 4, N-terminal	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR31409 all species →	WASH COMPLEX SUBUNIT 4	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0005768 all species →	Cellular Component	endosome	Interproscan
GO:0007032 all species →	Biological Process	endosome organization	Interproscan
GO:0016197 all species →	Biological Process	endosomal transport	Interproscan
GO:0071203 all species →	Cellular Component	WASH complex	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
K18465	MRT43, SWIP; WASH complex subunit 7	-	Membrane trafficking	ko04131	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_007479-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

66TPM > 0

7Conditions

340.3Max TPM

91.9Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
holobiont · low.pH_high.temp	20	17	133.45	340.30
holobiont · low.pH Control.temp	20	12	74.40	295.06
holobiont · control.pH_high.temp	20	17	118.91	304.18
holobiont · control.pH Control.temp	19	14	57.42	146.33
Whole organism	4	4	30.54	54.30
unannotated	1	1	33.74	33.74
live coral tissue/skeleton	1	1	29.72	29.72

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	340.30
SRR22214412	holobiont · low.pH_high.temp	holobiont	not recorded	low.pH_high.temp	SRP406607	283.41
SRR22214413	holobiont · low.pH_high.temp	holobiont	not recorded	low.pH_high.temp	SRP406607	240.18
SRR22214404	holobiont · low.pH_high.temp	holobiont	not recorded	low.pH_high.temp	SRP406607	234.42
SRR22214403	holobiont · low.pH_high.temp	holobiont	not recorded	low.pH_high.temp	SRP406607	197.32
SRR22214410	holobiont · low.pH_high.temp	holobiont	not recorded	low.pH_high.temp	SRP406607	194.06
SRR22214419	holobiont · low.pH_high.temp	holobiont	not recorded	low.pH_high.temp	SRP406607	183.95
SRR22214423	holobiont · low.pH_high.temp	holobiont	not recorded	low.pH_high.temp	SRP406607	151.88
SRR22214408	holobiont · low.pH_high.temp	holobiont	not recorded	low.pH_high.temp	SRP406607	140.43
SRR22214406	holobiont · low.pH_high.temp	holobiont	not recorded	low.pH_high.temp	SRP406607	125.21
SRR22214402	holobiont · low.pH_high.temp	holobiont	not recorded	low.pH_high.temp	SRP406607	120.09
SRR22214407	holobiont · low.pH_high.temp	holobiont	not recorded	low.pH_high.temp	SRP406607	117.26
SRR22214418	holobiont · low.pH_high.temp	holobiont	not recorded	low.pH_high.temp	SRP406607	103.70
SRR22214417	holobiont · low.pH_high.temp	holobiont	not recorded	low.pH_high.temp	SRP406607	82.67
SRR22214420	holobiont · low.pH_high.temp	holobiont	not recorded	low.pH_high.temp	SRP406607	71.51
SRR22214414	holobiont · low.pH_high.temp	holobiont	not recorded	low.pH_high.temp	SRP406607	61.92
SRR22214415	holobiont · low.pH_high.temp	holobiont	not recorded	low.pH_high.temp	SRP406607	20.72
SRR22214409	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
SRR22214421	holobiont · low.pH_high.temp	holobiont	not recorded	low.pH_high.temp	SRP406607	0.00
SRR22214443	holobiont · low.pH Control.temp	holobiont	not recorded	low.pH Control.temp	SRP406607	295.06
SRR22214429	holobiont · low.pH Control.temp	holobiont	not recorded	low.pH Control.temp	SRP406607	253.61
SRR22214428	holobiont · low.pH Control.temp	holobiont	not recorded	low.pH Control.temp	SRP406607	159.37
SRR22214430	holobiont · low.pH Control.temp	holobiont	not recorded	low.pH Control.temp	SRP406607	135.84
SRR22214438	holobiont · low.pH Control.temp	holobiont	not recorded	low.pH Control.temp	SRP406607	133.74
SRR22214431	holobiont · low.pH Control.temp	holobiont	not recorded	low.pH Control.temp	SRP406607	119.67
SRR22214445	holobiont · low.pH Control.temp	holobiont	not recorded	low.pH Control.temp	SRP406607	119.28
SRR22214441	holobiont · low.pH Control.temp	holobiont	not recorded	low.pH Control.temp	SRP406607	94.81
SRR22214436	holobiont · low.pH Control.temp	holobiont	not recorded	low.pH Control.temp	SRP406607	79.87
SRR22214426	holobiont · low.pH Control.temp	holobiont	not recorded	low.pH Control.temp	SRP406607	51.08
SRR22214425	holobiont · low.pH Control.temp	holobiont	not recorded	low.pH Control.temp	SRP406607	24.26
SRR22214442	holobiont · low.pH Control.temp	holobiont	not recorded	low.pH Control.temp	SRP406607	21.44
SRR22214424	holobiont · low.pH Control.temp	holobiont	not recorded	low.pH Control.temp	SRP406607	0.00
SRR22214427	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
SRR22214456	holobiont · control.pH_high.temp	holobiont	not recorded	control.pH_high.temp	SRP406607	304.18
SRR22214457	holobiont · control.pH_high.temp	holobiont	not recorded	control.pH_high.temp	SRP406607	268.70
SRR22214463	holobiont · control.pH_high.temp	holobiont	not recorded	control.pH_high.temp	SRP406607	198.09
SRR22214453	holobiont · control.pH_high.temp	holobiont	not recorded	control.pH_high.temp	SRP406607	192.87
SRR22214467	holobiont · control.pH_high.temp	holobiont	not recorded	control.pH_high.temp	SRP406607	172.82
SRR22214462	holobiont · control.pH_high.temp	holobiont	not recorded	control.pH_high.temp	SRP406607	160.94
SRR22214464	holobiont · control.pH_high.temp	holobiont	not recorded	control.pH_high.temp	SRP406607	155.49
SRR22214460	holobiont · control.pH_high.temp	holobiont	not recorded	control.pH_high.temp	SRP406607	147.80
SRR22214461	holobiont · control.pH_high.temp	holobiont	not recorded	control.pH_high.temp	SRP406607	141.96
SRR22214448	holobiont · control.pH_high.temp	holobiont	not recorded	control.pH_high.temp	SRP406607	126.82
SRR22214459	holobiont · control.pH_high.temp	holobiont	not recorded	control.pH_high.temp	SRP406607	117.29
SRR22214447	holobiont · control.pH_high.temp	holobiont	not recorded	control.pH_high.temp	SRP406607	105.19
SRR22214458	holobiont · control.pH_high.temp	holobiont	not recorded	control.pH_high.temp	SRP406607	67.04
SRR22214449	holobiont · control.pH_high.temp	holobiont	not recorded	control.pH_high.temp	SRP406607	63.38
SRR22214454	holobiont · control.pH_high.temp	holobiont	not recorded	control.pH_high.temp	SRP406607	61.91
SRR22214446	holobiont · control.pH_high.temp	holobiont	not recorded	control.pH_high.temp	SRP406607	47.58
SRR22214465	holobiont · control.pH_high.temp	holobiont	not recorded	control.pH_high.temp	SRP406607	46.08
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
SRR22214466	holobiont · control.pH Control.temp	holobiont	not recorded	control.pH Control.temp	SRP406607	146.33
SRR22214548	holobiont · control.pH Control.temp	holobiont	not recorded	control.pH Control.temp	SRP406607	131.23
SRR22214506	holobiont · control.pH Control.temp	holobiont	not recorded	control.pH Control.temp	SRP406607	116.75
SRR22214455	holobiont · control.pH Control.temp	holobiont	not recorded	control.pH Control.temp	SRP406607	91.77
SRR22214400	holobiont · control.pH Control.temp	holobiont	not recorded	control.pH Control.temp	SRP406607	84.00
SRR22214469	holobiont · control.pH Control.temp	holobiont	not recorded	control.pH Control.temp	SRP406607	82.34
SRR22214471	holobiont · control.pH Control.temp	holobiont	not recorded	control.pH Control.temp	SRP406607	72.64
SRR22214422	holobiont · control.pH Control.temp	holobiont	not recorded	control.pH Control.temp	SRP406607	71.17
SRR22214444	holobiont · control.pH Control.temp	holobiont	not recorded	control.pH Control.temp	SRP406607	69.16
SRR22214411	holobiont · control.pH Control.temp	holobiont	not recorded	control.pH Control.temp	SRP406607	59.85
SRR22214547	holobiont · control.pH Control.temp	holobiont	not recorded	control.pH Control.temp	SRP406607	49.67
SRR22214468	holobiont · control.pH Control.temp	holobiont	not recorded	control.pH Control.temp	SRP406607	46.78
SRR22214524	holobiont · control.pH Control.temp	holobiont	not recorded	control.pH Control.temp	SRP406607	35.83
SRR22214481	holobiont · control.pH Control.temp	holobiont	not recorded	control.pH Control.temp	SRP406607	33.50
SRR22214433	holobiont · control.pH Control.temp	holobiont	not recorded	control.pH Control.temp	SRP406607	0.00
SRR22214470	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
SRR22214535	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
SRR14295601	Whole organism	Whole organism	not recorded	not recorded	SRP315757	54.30
SRR14295600	Whole organism	Whole organism	not recorded	not recorded	SRP315757	24.28
SRR14295604	Whole organism	Whole organism	not recorded	not recorded	SRP315757	23.56
SRR14295603	Whole organism	Whole organism	not recorded	not recorded	SRP315757	20.00
ERR12861049	unannotated	not recorded	not recorded	not recorded	ERP159209	33.74
SRR12454619	live coral tissue/skeleton	live coral tissue/skeleton	not recorded	not recorded	SRP277390	29.72

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.