Gene detail

Detailed information of FUN_050914-T1 in Siderastrea siderea

Genomic Location: contig_79:2014905...2029583
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_050914-T1

ATGGCAGATCTAGGTTTTGAGGAAGATCCTGCGGCCGATTTTTTGGCGAGAGAACAAGATGATTTGGCTGAACTGGGAGAGGACTTTGACGAAGGACAGCCACAGCCTAACGAACTTGATAGTTTTGATGGTGGGTTAGATACGGATAATGAACCAGTTGTAAATGGATTTGATGAAGAGATTTCAGGTTCCCACCAGCCAGTGGCACCACTTCCTAGAGAATCTGAACCAGAATCTGTAAGAAAATGGAGGGAAGAAAAAGCTGCTCTCCTTAGCAAAATGGATGctgaggaaaaagaagaaatagAAGAATGGCGTGAAAAAGCCAAAAAGGAGCTTCACGACTGGTATGAAAGACGAGATGAACAGTTAGGAAAGACACAGACAAGTAATAGGGCAGACGAGGAGGCCTTTGTGTCAGATCGTGATGACAGTACTGGCGGccacgactgggaacgagtttgcCGCATGTGCGACTTTAATCCCAAGGGAACTAAGAATACTAAGGATGTATCACGTATGCGTTCAATTTTCCTGCAACTTAAGCAGACACCACTTGCAAAAGAATAGAAATTGCATTACTTAGGTCATCTTTTAAAAGGATTGTTTGATATTATACAGTAGTCTCCAGCTGCCGTGATCAGAAACTTTTTGTCTTAGTAATATTTACTTCAGGCTAATTGAACTCCATTTTTTACATGTTTAAATGTTCAAGACAGCAGGACACTACACTGTACTGTGTCAGAAATCTAACTAGAGAGCAAAGGCTCGCAGGACGAAATTTCactctttttaactttccttgTTTCTTATTTCCCTAAAGAGAATTGCATACCAAGAAAATGAAGACAATATCAGTTTGTCTAGCGAGCCTTAAAGTTATGTTAGAGTTTTGATATATCAAATGTGGccttttaataaaaacaaatcaCCTTTCATCTTATTGCCAAATTGCTCCCTCTTAATTCTTTAacccctaacagtgacgaaaatgtaatttctctttacatcgtCACTACTTGTTttaacattcaagtgatgagaataaaggaattgtTCGCCAAGGATAAGACGTCTTGATATTTggacaaattctcccaactagttccaaaagaaatgtatggagaacagtaaggagaatatgcattttcatatcagcacttaaagggttaaagtttACTTCCTTTTCTTAATAGTTTAATGATTTCAAATTCCTTTAACTTGCCTCGAAGCACATTGTGGTCGTTACTGAAAACTACCACAAAAGATCGTGGTtgctgtttttcaaaaatgccaTCAGTTGTCTTGTTTTTGAGAAATTCTTTGGCCAATTACCAGCAACAGCAGGCTTCACTTGTAATAAATCTCTCGAACAGTTGCCCGAATTGGGGAATTGTTCTCAGCAAACCGAACACGTAGTTTGGTCACAGGTTGTTGATCAAAGGCAGATCCTTTAGCCGATTATCTGAGATAACTAAGTCATTTTAATAGAAGCAAGCTCTGAAATTAATCATGTCATTGCCTATCTGTTGTCAGTAATTATTGTTACATGTAAAGCTAGTTGTAGATTAGTAggtgttttttaaatttaccgCCGGAAAAGTCGTACCTAGTACTTCTCAAAAGAAGATGCTAAACGTAACTTGAAAGATGAAATTGTGTTGAATTTACTGCTAACCAAACGTGCAACCCCATACTAGTTAAATATACCCTTCTTCTTCAATACAGTAAAAATAAATGCTGTTTTGGAGTTACCCTTGTTCGTGTCTTTTGTCCCTCTCGACTTGTGTGAAATTGTTTTGTGCGGCCTTTTAAAGCCTTTTATTAGAGAACTACAGTGTTAAGTAGTAAAACTGCAAGACAGGCGCAGAAGGTGGCTTCATCAACAGAAAAACCTGAATGGTGCTGAGAATGATTCTTATGCTATAATCCCTTAGTGCTTTCGGTTCCCTTTGAACTGAGGTGAGTAAGACTGCCAGACAGCGGGAAATGGCATAAACGCGCATTGGGCGCctcctagcctgttccaggctctcggaTATAGTAGGGATGCAAGATTAAGAAAGGGACTGTGTAAGTAAGACGCGAAGGATCTGGGGTAAAGGGGGCGGTAACGGGAAAGAAGGGAGAAAACCTGACCCTCCTCCGCCCACTTTTGGCAAGTGGGCAGTTGAATTTTTGGTGACAAAATTTCCATCTACTTATAGCGTGAACTTTGCTCGGGTTTCACGCGCGCGAGTAGTTCGAGGTATTGATTGTCCAACAGAAGCAGTCTTGTATGCAGGCCTTGAATCGAATCTGCAGTCAAAATGCTGGACTTTTGCTAATGAATGTTTCATGTCAGGGGAAGAAAGACAGCGGGAACATGCGTTTCTTTAGTTACCCTGTGTGTTATGGAAAATAAGGAATTTGTGGgtcaagaaattcgcttggacAATTTTGCCCACACCGTACTTTGGGGCcccaattatttttttttttttaatacctgCTCTGTGTCTCTTTTCGGAGTGAAGTCTAGAGGTTTCTATGAGTGCCTTTGCTAAACAGGCTTTTACCCTGATCCCAAGGGGTTTCTTTCTTCCAAACCTAAATAAACTAAGCCGCGTTGCAGACGACATgggtggaaggggggggggggggggggcAATTTTAATTCAGCATTTTTGTATTGGAGTATCAACTGGGTTTCAGTAGTCAAGGGCACCCCACGGTTCGTCTCGgtgaaatatctgttcggaagacctTAACTGCCTCAAAAATTGGGATTaaattgtgatgaaaaactAGAATTTCCATTTGCGAAATGCCACCCCCAACTTTCTTTatctaagaaaaaaaatccttttatcatcatctattggcaagcactacagtgacaaacactgtattgtcccgaaagaccttgacaaacagtttttcgtCCTAAAGAAGTGTCGGAATAAGTTTAATTGTTTAATGCACGAAATGTTGCTAATTAGAGAATTGACACCATCTCTTAATGTCCAATCGGAC

Protein

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0007272 (this species only) · gene tree & orthology

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF01086 all species →	Clathrin_lg_ch	Clathrin light chain	Family	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR000996 all species →	Family	Clathrin light chain	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR10639 all species →	CLATHRIN LIGHT CHAIN	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0005198 all species →	Molecular Function	structural molecule activity	Interproscan
GO:0006886 all species →	Biological Process	intracellular protein transport	Interproscan
GO:0016192 all species →	Biological Process	vesicle-mediated transport	Interproscan
GO:0030130 all species →	Cellular Component	clathrin coat of trans-Golgi network vesicle	Interproscan
GO:0030132 all species →	Cellular Component	clathrin coat of coated pit	Interproscan
GO:0005886 all species →	Cellular Component	plasma membrane	Interproscan
GO:0030125 all species →	Cellular Component	clathrin vesicle coat	Interproscan
GO:0032050 all species →	Molecular Function	clathrin heavy chain binding	Interproscan
GO:0072583 all species →	Biological Process	clathrin-dependent endocytosis	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
K04644	CLTA, LCA; clathrin light chain A	-	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_050914-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

82TPM > 0

7Conditions

4,159.3Max TPM

812.4Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
holobiont · low.pH_high.temp	20	18	639.14	1,622.25
holobiont · low.pH Control.temp	20	20	1,125.63	3,037.37
holobiont · control.pH_high.temp	20	20	845.03	2,524.85
holobiont · control.pH Control.temp	19	18	830.63	4,159.28
Whole organism	4	4	176.61	199.21
unannotated	1	1	169.21	169.21
live coral tissue/skeleton	1	1	201.16	201.16

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

SRA run	Condition	Tissue	Developmental stage	Treatment	Study	TPM
SRR22214414	holobiont · low.pH_high.temp	holobiont	not recorded	low.pH_high.temp	SRP406607	1,622.25
SRR22214404	holobiont · low.pH_high.temp	holobiont	not recorded	low.pH_high.temp	SRP406607	1,118.23
SRR22214417	holobiont · low.pH_high.temp	holobiont	not recorded	low.pH_high.temp	SRP406607	1,091.24
SRR22214415	holobiont · low.pH_high.temp	holobiont	not recorded	low.pH_high.temp	SRP406607	1,042.75
SRR22214413	holobiont · low.pH_high.temp	holobiont	not recorded	low.pH_high.temp	SRP406607	845.49
SRR22214418	holobiont · low.pH_high.temp	holobiont	not recorded	low.pH_high.temp	SRP406607	799.58
SRR22214423	holobiont · low.pH_high.temp	holobiont	not recorded	low.pH_high.temp	SRP406607	799.10
SRR22214421	holobiont · low.pH_high.temp	holobiont	not recorded	low.pH_high.temp	SRP406607	787.02
SRR22214409	holobiont · low.pH_high.temp	holobiont	not recorded	low.pH_high.temp	SRP406607	760.78
SRR22214410	holobiont · low.pH_high.temp	holobiont	not recorded	low.pH_high.temp	SRP406607	730.06
SRR22214419	holobiont · low.pH_high.temp	holobiont	not recorded	low.pH_high.temp	SRP406607	706.76
SRR22214406	holobiont · low.pH_high.temp	holobiont	not recorded	low.pH_high.temp	SRP406607	590.38
SRR22214407	holobiont · low.pH_high.temp	holobiont	not recorded	low.pH_high.temp	SRP406607	413.97
SRR22214420	holobiont · low.pH_high.temp	holobiont	not recorded	low.pH_high.temp	SRP406607	335.53
SRR22214412	holobiont · low.pH_high.temp	holobiont	not recorded	low.pH_high.temp	SRP406607	322.25
SRR22214403	holobiont · low.pH_high.temp	holobiont	not recorded	low.pH_high.temp	SRP406607	319.73
SRR22214408	holobiont · low.pH_high.temp	holobiont	not recorded	low.pH_high.temp	SRP406607	289.85
SRR22214402	holobiont · low.pH_high.temp	holobiont	not recorded	low.pH_high.temp	SRP406607	207.73
SRR22214405	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
SRR22214440	holobiont · low.pH Control.temp	holobiont	not recorded	low.pH Control.temp	SRP406607	3,037.37
SRR22214435	holobiont · low.pH Control.temp	holobiont	not recorded	low.pH Control.temp	SRP406607	2,411.04
SRR22214426	holobiont · low.pH Control.temp	holobiont	not recorded	low.pH Control.temp	SRP406607	1,762.37
SRR22214434	holobiont · low.pH Control.temp	holobiont	not recorded	low.pH Control.temp	SRP406607	1,578.78
SRR22214432	holobiont · low.pH Control.temp	holobiont	not recorded	low.pH Control.temp	SRP406607	1,430.30
SRR22214430	holobiont · low.pH Control.temp	holobiont	not recorded	low.pH Control.temp	SRP406607	1,356.28
SRR22214428	holobiont · low.pH Control.temp	holobiont	not recorded	low.pH Control.temp	SRP406607	1,203.10
SRR22214425	holobiont · low.pH Control.temp	holobiont	not recorded	low.pH Control.temp	SRP406607	1,164.55
SRR22214424	holobiont · low.pH Control.temp	holobiont	not recorded	low.pH Control.temp	SRP406607	1,119.47
SRR22214443	holobiont · low.pH Control.temp	holobiont	not recorded	low.pH Control.temp	SRP406607	1,089.04
SRR22214427	holobiont · low.pH Control.temp	holobiont	not recorded	low.pH Control.temp	SRP406607	1,059.80
SRR22214431	holobiont · low.pH Control.temp	holobiont	not recorded	low.pH Control.temp	SRP406607	1,024.04
SRR22214442	holobiont · low.pH Control.temp	holobiont	not recorded	low.pH Control.temp	SRP406607	737.31
SRR22214439	holobiont · low.pH Control.temp	holobiont	not recorded	low.pH Control.temp	SRP406607	668.63
SRR22214438	holobiont · low.pH Control.temp	holobiont	not recorded	low.pH Control.temp	SRP406607	602.94
SRR22214445	holobiont · low.pH Control.temp	holobiont	not recorded	low.pH Control.temp	SRP406607	594.69
SRR22214436	holobiont · low.pH Control.temp	holobiont	not recorded	low.pH Control.temp	SRP406607	534.05
SRR22214441	holobiont · low.pH Control.temp	holobiont	not recorded	low.pH Control.temp	SRP406607	406.58
SRR22214437	holobiont · low.pH Control.temp	holobiont	not recorded	low.pH Control.temp	SRP406607	404.16
SRR22214429	holobiont · low.pH Control.temp	holobiont	not recorded	low.pH Control.temp	SRP406607	328.14
SRR22214449	holobiont · control.pH_high.temp	holobiont	not recorded	control.pH_high.temp	SRP406607	2,524.85
SRR22214452	holobiont · control.pH_high.temp	holobiont	not recorded	control.pH_high.temp	SRP406607	2,302.23
SRR22214457	holobiont · control.pH_high.temp	holobiont	not recorded	control.pH_high.temp	SRP406607	1,685.24
SRR22214450	holobiont · control.pH_high.temp	holobiont	not recorded	control.pH_high.temp	SRP406607	1,250.77
SRR22214456	holobiont · control.pH_high.temp	holobiont	not recorded	control.pH_high.temp	SRP406607	1,175.07
SRR22214446	holobiont · control.pH_high.temp	holobiont	not recorded	control.pH_high.temp	SRP406607	1,075.77
SRR22214454	holobiont · control.pH_high.temp	holobiont	not recorded	control.pH_high.temp	SRP406607	1,034.46
SRR22214465	holobiont · control.pH_high.temp	holobiont	not recorded	control.pH_high.temp	SRP406607	888.29
SRR22214448	holobiont · control.pH_high.temp	holobiont	not recorded	control.pH_high.temp	SRP406607	867.39
SRR22214451	holobiont · control.pH_high.temp	holobiont	not recorded	control.pH_high.temp	SRP406607	803.59
SRR22214453	holobiont · control.pH_high.temp	holobiont	not recorded	control.pH_high.temp	SRP406607	737.76
SRR22214447	holobiont · control.pH_high.temp	holobiont	not recorded	control.pH_high.temp	SRP406607	575.15
SRR22214461	holobiont · control.pH_high.temp	holobiont	not recorded	control.pH_high.temp	SRP406607	411.36
SRR22214458	holobiont · control.pH_high.temp	holobiont	not recorded	control.pH_high.temp	SRP406607	361.68
SRR22214464	holobiont · control.pH_high.temp	holobiont	not recorded	control.pH_high.temp	SRP406607	319.12
SRR22214462	holobiont · control.pH_high.temp	holobiont	not recorded	control.pH_high.temp	SRP406607	262.28
SRR22214460	holobiont · control.pH_high.temp	holobiont	not recorded	control.pH_high.temp	SRP406607	254.06
SRR22214467	holobiont · control.pH_high.temp	holobiont	not recorded	control.pH_high.temp	SRP406607	174.18
SRR22214459	holobiont · control.pH_high.temp	holobiont	not recorded	control.pH_high.temp	SRP406607	126.07
SRR22214463	holobiont · control.pH_high.temp	holobiont	not recorded	control.pH_high.temp	SRP406607	71.21
SRR22214546	holobiont · control.pH Control.temp	holobiont	not recorded	control.pH Control.temp	SRP406607	4,159.28
SRR22214433	holobiont · control.pH Control.temp	holobiont	not recorded	control.pH Control.temp	SRP406607	2,108.64
SRR22214492	holobiont · control.pH Control.temp	holobiont	not recorded	control.pH Control.temp	SRP406607	2,023.73
SRR22214524	holobiont · control.pH Control.temp	holobiont	not recorded	control.pH Control.temp	SRP406607	1,146.39
SRR22214455	holobiont · control.pH Control.temp	holobiont	not recorded	control.pH Control.temp	SRP406607	1,098.22
SRR22214535	holobiont · control.pH Control.temp	holobiont	not recorded	control.pH Control.temp	SRP406607	787.35
SRR22214444	holobiont · control.pH Control.temp	holobiont	not recorded	control.pH Control.temp	SRP406607	660.78
SRR22214422	holobiont · control.pH Control.temp	holobiont	not recorded	control.pH Control.temp	SRP406607	526.93
SRR22214469	holobiont · control.pH Control.temp	holobiont	not recorded	control.pH Control.temp	SRP406607	436.53
SRR22214481	holobiont · control.pH Control.temp	holobiont	not recorded	control.pH Control.temp	SRP406607	408.73
SRR22214400	holobiont · control.pH Control.temp	holobiont	not recorded	control.pH Control.temp	SRP406607	375.75
SRR22214548	holobiont · control.pH Control.temp	holobiont	not recorded	control.pH Control.temp	SRP406607	370.26
SRR22214471	holobiont · control.pH Control.temp	holobiont	not recorded	control.pH Control.temp	SRP406607	354.12
SRR22214411	holobiont · control.pH Control.temp	holobiont	not recorded	control.pH Control.temp	SRP406607	305.74
SRR22214506	holobiont · control.pH Control.temp	holobiont	not recorded	control.pH Control.temp	SRP406607	285.06
SRR22214468	holobiont · control.pH Control.temp	holobiont	not recorded	control.pH Control.temp	SRP406607	254.24
SRR22214466	holobiont · control.pH Control.temp	holobiont	not recorded	control.pH Control.temp	SRP406607	241.67
SRR22214547	holobiont · control.pH Control.temp	holobiont	not recorded	control.pH Control.temp	SRP406607	238.62
SRR22214470	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	199.21
SRR14295600	Whole organism	Whole organism	not recorded	not recorded	SRP315757	195.42
SRR14295604	Whole organism	Whole organism	not recorded	not recorded	SRP315757	176.92
SRR14295601	Whole organism	Whole organism	not recorded	not recorded	SRP315757	134.87
ERR12861049	unannotated	not recorded	not recorded	not recorded	ERP159209	169.21
SRR12454619	live coral tissue/skeleton	live coral tissue/skeleton	not recorded	not recorded	SRP277390	201.16

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.