Gene detail

Detailed information of FUN_035175-T1 in Siderastrea siderea

Genomic Location: contig_39:1669044...1686359
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_035175-T1

ATGGCACATCAAGACGAACTTGCGACAGCAATTTTGAAGAACAAGTCACGGCCAAACCGTTTGTTGGTGGAAGAGGCTATAAACGATGACAACTCCGTTGTTTCTATGTCTCAGGCCAAAATGGAAGAATTACAGCTTTTTCGTGGTGATACAGTTCTTATAAAGGGGAAGAAGAGAAGGGATACAGTCTGCATCGTGCTGTCCGATGATTCAATCTCCAATGACAAAATACGCATGAATCGTGTTGTAAGGAGGAACCTTCGAGTGAGACTTGGAGACATTGTCAGTGTGCAAGCATGCCCTGATGTCAAGTATGGCAAAAGGATTCATGTCTTGCCAGTTGATGACACAGTAGAAGGATTAACAGGGAGTTTGTTTGATGTCTACTTGAAGCCTTATTTCTTGGAAGCCTATAGACCAATCAGGAAAGGTGACATGTTTCTTGTACGCGGTGGCATGAGAGCTGTGGAGTTCAAAGTCATTGAGACTGATCCGTCACCTTACTGCATAGTAGCACCTGACACCGTGATACACTGTGAAGGAGAACCTGTCAAGAGAGAGGAAGAAGAAGAATCTTTGAATGAAGTTGGCTACGATGACATTGGAGGCTGCAGAAAACAGCTGGCACAGATTAAGGAGATGGTGGAGTTACCACTCAGGCATCCTCAGTTGTTCAGAGCTATTGGTGTTAAGCCTCCCCGTGGAATCCTTCTGTATGGCCCACCAGGAACAGGAAAAACCCTTATGGCAAGAGCTGTTGCTAATGAGACAGGAGCCTTTTTCTTCCTAATTAATGgTCCAGAGATCATGAGTAAACTTGCTGGTGAATCAGAAAGTAACCTTAGAAAAGCTTTTgaagaagcagaaaaaaattcacCAGCCATTATTTTCATTGACGAAATTGACGCAATTGCTCCTAAGAGAGATAAGACCCATGGTGAGGTGGAACGACGAATTGTGTCCCAGCTTTTGACTCTTATGGACGGCCTGAAGCAGAGGTCCCATGTTATTGTGATGGCAGCAACCAACAGACCAAACAGTGTTGATCCAGCCCTTCGCAGATTTGgtcGTTTTGACAGGGAGGTAGACATTGGTATACCTGATGCTACAGGCCGTCTAGAGATCTTACGAATCCACACAAAGAACATGAAATTAGGAGATGATGTTGATCTTGAACAGATTGCTAATGAAACTCATGGTTATGTTGGCTCAGATGTTGCATCTCTCTGCTCAGAGGCTGCCCTTCAACAgATTCGTGAAAAAATGGATTTAATTGACTTGGaagatgaacaaattgatgCAGAGGTCCTGGACTCATTAGCTGTTTCTATGGATAACTTTAGGTATGCCATGGGAGTCTCCAATCCATCAGCACTGCGTGAGACTGTAGTTGAGGTTCCAACAACTACCTGGGACGACATTGGTGGTTTAGAAAATGTCAAGCGAGAACTGCAGGAGTTGGTGCAGTACCCTGTGGAACATCCAGACAAGTTCCTCAAGTTTGGAATGACGCCATCCAAAGGTGTGCTGTTTTATGGTCCTCCTGGTTGTGGTAAGACGCTCCTGGCGAAAGCCATTGCAAATGAGTGCCAAGCCAACTTCATTTCTATCAAAGGTCCTGAGCTTCTTACCATGTGGTTTGGTGAATCTGAGGCCAATGTGCGAGATGTTTTTGACAAGGCTCGCAGTGCTGCTCCTTGTGTGTTGTTCTTTGATGAGTTGGACTCCATTGCTAAAGCTAGAGGAGGAAATGTTGGAGATGGAGGTGGAGCAGCTGATCGTGTGATCAACCAGGTGCTTACTGAAATGGATGGCATGAATgtcaagaaaaatgtttttatcaTTGGTGCCACAAACAGGCCAGACATTATTGATCCAGCCATTTTGCGGCCAGGTCGTTTGGATCAACTGATTTATATTCCTCTTCCAGATGAGCCATCACGTGTCTCCATTCTCAAGGCTTGCTTAAGGAAATCCCCAATTGCCAAGGATGTAGACTTGGATTATATTGCCAAGGTTACTCATGGATTCAGCGGTGCTGACCTTACCGAGATCTGCCAACGGGCATGTAAGTTGGCCATAAGAGAGTCAATTGAGACAGAAATCCGCAGAGAAAGAGAGAGGGTTGATAACCCAGACTTAGACATGGAAGTGGAAGACGAGGATCCTGTCCCAGAGATTACAAGAGCTCACTTTGAGGATGCTATGAGATTTGCTCGCAGGTCTGTCAGTGATAACGACATCCGCAAATATGAGATGTTTGCTCAGACTCTTCAGCAGAGCCGTGGATTTGGTGGAAACTTCAGGTTCCCAAGTCAGGGTAGTGGTGGTGGTTCCCAAGGAGGACAAGGTGGATCTGGTGCTGACAATTCTAACTTATACGATGACGGAGATGATGATCTGTACAGTTAG

Transcript

FUN_035175-T1

Protein

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF02359 all species →	CDC48_N	Cell division protein 48 (CDC48), N-terminal domain	Domain	Interproscan
PF00004 all species →	AAA	ATPase family associated with various cellular activities (AAA)	Domain	Interproscan
PF17862 all species →	AAA_lid_3	AAA+ lid domain	Domain	Interproscan
PF09336 all species →	Vps4_C	Vps4 C terminal oligomerisation domain	Domain	Interproscan
PF02933 all species →	CDC48_2	Cell division protein 48 (CDC48), domain 2	Domain	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR003338 all species →	Domain	CDC48, N-terminal subdomain	Interproscan
IPR029067 all species →	Homologous_superfamily	CDC48 domain 2-like superfamily	Interproscan
IPR003959 all species →	Domain	ATPase, AAA-type, core	Interproscan
IPR027417 all species →	Homologous_superfamily	P-loop containing nucleoside triphosphate hydrolase	Interproscan
IPR003960 all species →	Conserved_site	ATPase, AAA-type, conserved site	Interproscan
IPR004201 all species →	Domain	CDC48, domain 2	Interproscan
IPR003593 all species →	Domain	AAA+ ATPase domain	Interproscan
IPR005938 all species →	Family	AAA ATPase, CDC48 family	Interproscan
IPR009010 all species →	Homologous_superfamily	Aspartate decarboxylase-like domain superfamily	Interproscan
IPR041569 all species →	Domain	AAA ATPase, AAA+ lid domain	Interproscan
IPR015415 all species →	Domain	Spastin/Vps4, C-terminal	Interproscan
IPR050168 all species →	Family	AAA ATPase domain-containing protein	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR23077 all species →	AAA-FAMILY ATPASE	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0005524 all species →	Molecular Function	ATP binding	Interproscan
GO:0016887 all species →	Molecular Function	ATP hydrolysis activity	Interproscan
GO:0016787 all species →	Molecular Function	hydrolase activity	Interproscan
GO:0005634 all species →	Cellular Component	nucleus	Interproscan
GO:0005829 all species →	Cellular Component	cytosol	Interproscan
GO:0030433 all species →	Biological Process	obsolete ubiquitin-dependent ERAD pathway	Interproscan
GO:0030970 all species →	Biological Process	retrograde protein transport, ER to cytosol	Interproscan
GO:0031593 all species →	Molecular Function	polyubiquitin modification-dependent protein binding	Interproscan
GO:0034098 all species →	Cellular Component	VCP-NPL4-UFD1 AAA ATPase complex	Interproscan
GO:0051228 all species →	Biological Process	mitotic spindle disassembly	Interproscan
GO:0071712 all species →	Biological Process	obsolete ER-associated misfolded protein catabolic process	Interproscan
GO:0097352 all species →	Biological Process	autophagosome maturation	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
K13525	VCP, CDC48; transitional endoplasmic reticulum ATPase	-	Exosome	ko04147	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_035175-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

9TPM > 0

7Conditions

234.7Max TPM

9.9Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
holobiont · low.pH_high.temp	20	1	0.38	7.68
holobiont · low.pH Control.temp	20	0	0.00	0.00
holobiont · control.pH_high.temp	20	1	0.14	2.81
holobiont · control.pH Control.temp	19	1	1.39	26.33
Whole organism	4	4	105.22	132.63
unannotated	1	1	234.68	234.68
live coral tissue/skeleton	1	1	151.82	151.82

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

SRA run	Condition	Tissue	Developmental stage	Treatment	Study	TPM
SRR22214408	holobiont · low.pH_high.temp	holobiont	not recorded	low.pH_high.temp	SRP406607	7.68
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
SRR22214405	holobiont · low.pH_high.temp	holobiont	not recorded	low.pH_high.temp	SRP406607	0.00
SRR22214406	holobiont · low.pH_high.temp	holobiont	not recorded	low.pH_high.temp	SRP406607	0.00
SRR22214407	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
SRR22214410	holobiont · low.pH_high.temp	holobiont	not recorded	low.pH_high.temp	SRP406607	0.00
SRR22214412	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
SRR22214419	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
SRR22214424	holobiont · low.pH Control.temp	holobiont	not recorded	low.pH Control.temp	SRP406607	0.00
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
SRR22214427	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
SRR22214430	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
SRR22214436	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
SRR22214438	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
SRR22214463	holobiont · control.pH_high.temp	holobiont	not recorded	control.pH_high.temp	SRP406607	2.81
SRR22214446	holobiont · control.pH_high.temp	holobiont	not recorded	control.pH_high.temp	SRP406607	0.00
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
SRR22214453	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
SRR22214456	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
SRR22214458	holobiont · control.pH_high.temp	holobiont	not recorded	control.pH_high.temp	SRP406607	0.00
SRR22214459	holobiont · control.pH_high.temp	holobiont	not recorded	control.pH_high.temp	SRP406607	0.00
SRR22214460	holobiont · control.pH_high.temp	holobiont	not recorded	control.pH_high.temp	SRP406607	0.00
SRR22214461	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
SRR22214464	holobiont · control.pH_high.temp	holobiont	not recorded	control.pH_high.temp	SRP406607	0.00
SRR22214465	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
SRR22214471	holobiont · control.pH Control.temp	holobiont	not recorded	control.pH Control.temp	SRP406607	26.33
SRR22214400	holobiont · control.pH Control.temp	holobiont	not recorded	control.pH Control.temp	SRP406607	0.00
SRR22214411	holobiont · control.pH Control.temp	holobiont	not recorded	control.pH Control.temp	SRP406607	0.00
SRR22214422	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
SRR22214470	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
SRR22214524	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
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	132.63
SRR14295600	Whole organism	Whole organism	not recorded	not recorded	SRP315757	102.74
SRR14295601	Whole organism	Whole organism	not recorded	not recorded	SRP315757	93.54
SRR14295604	Whole organism	Whole organism	not recorded	not recorded	SRP315757	91.98
ERR12861049	unannotated	not recorded	not recorded	not recorded	ERP159209	234.68
SRR12454619	live coral tissue/skeleton	live coral tissue/skeleton	not recorded	not recorded	SRP277390	151.82

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.