Gene detail

Detailed information of FUN_042457-T1 in Siderastrea siderea

Genomic Location: contig_55:120552...133009
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_042457-T1

atATTTAAATGAAATCAAGCTTTACCAAGATTGATTTTCTGGTCTGAGCGTGGTCAAGTCGTCTATAGCCTTTCCTTCCTTTTCATTCTTTTTAGTCTGAATCACTGAACTCTTATCTGATTGTATTTGATTATTGCGAGGTAAAAAAGACAAGTGGAGGGTTTATTTCGTTTTCTCCTCCTGCTTTgctctttctttcaaaattttctttcctGTCCGGGAGGGAACTGGGTTGGAGGTGAAACCGAAAAGCACATGTTGCAACCTCAACTCGATGTTTTCCGATAACGAAGTTAACACTTCCGGAGATCCATATTAGGTAAGACTCGTAGTGTTTAGGTCTATTTATTAGACAGGCGCAACGAAATTTTCTTAGCGGATGTTGCTCACGAAGGGGGAAGGAGTTTAGTTAGGTTTCGGGGGAAGAAAATGCGATGGCCATTGTTTTAGAACCAAAAAGTTCTTACAACCTTATCTCTCAGACAGATTCAAGCAATAACAGGCTTCTTGTACATGTAAAATTGACGGATTCGTGTTTACGAGCGCTTGAAGAGTATCAGTCACTGGAGGTCTTGTCAAGGCGGAGGCCCACCATTAGATTTTCAGGATTTCAAGGGGCAATATCAATACCACTGGGTAAAACCAATTCAGAAGATGAAAACACTGCAAAATTTCAACTGGATTGCTCCATGTTACAATCAGGTGGACAGCAGGGTGGTATGGACTGCATCCAGCAGTCTGTTGGTAATAACGACATCAGAACTGTTGGAGTGGTCACACACAAGATCAATGTTAAGGCTACCGATGATAGTTATCAGATGACACAGCAAAGAATGAAAGAGGTTgaggaagaaagaaaaggagTTAGCACGAAGGTGATTAATATGCCAAAGAAAGGTAGTAAAAAGATTTCCAAGGTTGGATCAGTGTACAAGCAACAAAACAGTGTACTTTCAGCTGTAAAGAGACAAATTAAATCTGGTGTAGTAGGAGCCAAAGTGTCAAGTAGTCCTAGTAAATCATTCAGGGAAAGGGTTATTCATTTATTAGCAGTTAGACCTTACAAGAAACCAGAATTAATATCTAAACTCACTAAAGATGGAGTGAATTTAAAAGACAGGAATTCATTGACAGGGATTTTACAACAGGTCGCTGTTCTGACTGATAATCAGTACCGATTACATAAGCATTTGTATTCAGAAGTTCAGGTAGAAACATGGCCAAACTATAGTGAAGCTGAAAAACAGATGTTGCGTAGaaaaacaaaattagaaatgaatgaTAGCCCTTTAGTAACATCTTCATCTTCTCCAACAAAAAATTCTGAGacaaacagacaaccaaacaaaaggaTCTGTCCCAGTGAATctgaaagatcttcaaagagACAACGCATTGCTcacataaacaaaaacaacaacataatAGTGAAAGATTCTGTAAATAAAAGTTCCAAAGTTGATAAACCATCCAAGACCAGCCCCAGTGATAGCAAGGAAGTTTCACCTCTAGCAGAGAAAGAAGAAGTAGAATCAAGTACAACAGGAAATATTGAAAACTCAATTAATGGAGTAAACAGCTTGGATTCTCCAGAATATATGAGGAAATACAAACCTATCACAACGCGTGAACAGCGTTGCTTGTATAAGACAGACTTTCAAGCAGAGTATGAGGTTTACAAagtcctgaaagaaaaggtggACTCTGTTTCTACAAAGTTCACAGAGCTTGAAAATAAACGACAGCAGTTTCCAGAAGAAAGCGTAGAAAGAAAGGCCACAGATGCGGAAATTCTAGAACTCTATGGGAAGATACAGAAGGACTCTTTGTGGCAACAGACGAAGAAACAGTGTAAAGAGCTGCACACTAAACTGTCGTACATCAAAGGACTTATAACTGCGTATGACAAGCGTGTGACAAACACGTGACACTCGGTTGATTGGTACGTAAACACAGAACAAGCATTCCGTGCTGCTTTCCTCCTTGGTGCccagacaacaacaacaaccgcAAATGTGCGTGGAGCAACGACGTCACCCAAGATGTCTGGAACTGAGAGACCCCTTTGCCCATGAGCAGTAACAAGCAGTGAAGACCTGACTGCTGGTCAGAAAGAATGCATGCTCTGGTTAGGTACCCAAAATCAAAGATGTCGTATTTGATGCGTCTGTGCACGCGCACTGGAGGAAAAGCAACCAATCACTGGACATGAATTCAAGGAGATTTCCTTTAAATGGAAATTCAGTAGTAATGATCCCTGGCTGTGGGGAATAAACAACAAATGTAGtataaattaaatttaattatCTTGTAAATTGCTGCAATTGCAGGCTAGGTAAATTTTATCGAATTTCTTTACTTCTACTAAAGATTCAGTAACACTTGTGAGATGTGTGAGGCCTGAGCATGTTGTGGAATCAAATTCTGAAATAGAAGGCCTGCCTTTCTAGGATATTCTTTCActtgctgttttttctgatagagACTTTTAGAAGGTCATATTAAATAAAAGCTTAGAATTCCTGTGACAGTGCAATCTGTTGCAGAGTTATGTGCCAAATGCAACCCCGATCAGGATTGCGAGTAGTCtctgtattttttctttcatggATCATAGCCTGCAtgcatccccctcccccccccccccccattattTCCTTCTACCGCGGGCTAGTGGATCATAACACATGTAAATACGAGAAGCTCAACATTTTCTCCTGTTGTGTGGGAGGATGATAATCTACTTTTTTCCCCACATTTCTGCGCtatgtagcctgcgtgcagacgtcttcTTGAAATAGGAAGTATCCGCACGCAGGCTCCTGCTCAAATTTTCCTAGAATCGTCGAGCCAAGGCTGTGTCCTTCTTTGCTGACATGAAGAGAAACCAGTGTGGAACCGATCATTGTACACACTGCTTGTAGAAAAAGGCGTGGTCGTACTCGGGCCACTaggggaccgttcatttttgatgaggtaggggggctggtgggatttgagggggggccatgcAAACAAATATGGCTTCAAGGGGGGCAGCCAGAAAAATATGGTGtgtgaaggggggggggtcaccaaaaaaaaatttcctttaagtttagtattggcagcatctgtaataatgtgtcagaaggccaaaaatagctaTTCTTAGGTTCTGAAAAAATTTtgccgggggagaatgcccccagACCCACCGgctttattatacacccaacggtAACTCTACctcaccaactgtttcattacaaaatacagccaggggaatgtcaactcttttttggccTATGCTGGTCTGTTTCTTAAACAAATGATAACATTGTCCAAAATACATCAATATGTGCTTTAAACTGGCcttaattgtctgtttatgtacttcagaatgcaccaaattgcattagagcatctccagattttcaaacatttccaggggaagatactaCCTTGAGTGCCTGTCAATAAAGACACTGTTCAATTTAAGCtggataagttttagatttactttatcactttttcctctttttgtaaggatagcaaacaacttTACATTTATATCAACACCAtgtgtttcatgaactttattcagttagttcgctgttatgtattgctcaaaatgttcggttcgaaatcccatacaaagtctcatattttgaaacg

Protein

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF07303 all species →	Occludin_ELL	Occludin homology domain	Domain	Interproscan
PF10390 all species →	ELL	RNA polymerase II elongation factor ELL	Family	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR010844 all species →	Domain	Occludin homology domain	Interproscan
IPR031176 all species →	Family	ELL/occludin family	Interproscan
IPR019464 all species →	Domain	RNA polymerase II elongation factor ELL, N-terminal	Interproscan
IPR036390 all species →	Homologous_superfamily	Winged helix DNA-binding domain superfamily	Interproscan
IPR042065 all species →	Homologous_superfamily	E3 ubiquitin-protein ligase ELL-like	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR23288 all species →	OCCLUDIN AND RNA POLYMERASE II ELONGATION FACTOR ELL	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0000987 all species →	Molecular Function	cis-regulatory region sequence-specific DNA binding	Interproscan
GO:0008023 all species →	Cellular Component	transcription elongation factor complex	Interproscan
GO:0032968 all species →	Biological Process	positive regulation of transcription elongation by RNA polymerase II	Interproscan
GO:0042795 all species →	Biological Process	snRNA transcription by RNA polymerase II	Interproscan
GO:0006368 all species →	Biological Process	transcription elongation by RNA polymerase II	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
K15183	ELL; RNA polymerase II elongation factor ELL	-	Transcription machinery	ko03021	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_042457-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

50TPM > 0

7Conditions

356.0Max TPM

77.7Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
holobiont · low.pH_high.temp	20	12	87.06	285.98
holobiont · low.pH Control.temp	20	9	76.76	318.93
holobiont · control.pH_high.temp	20	12	69.66	279.76
holobiont · control.pH Control.temp	19	11	91.05	356.01
Whole organism	4	4	35.08	39.00
unannotated	1	1	26.26	26.26
live coral tissue/skeleton	1	1	34.47	34.47

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

SRA run	Condition	Tissue	Developmental stage	Treatment	Study	TPM
SRR22214402	holobiont · low.pH_high.temp	holobiont	not recorded	low.pH_high.temp	SRP406607	285.98
SRR22214419	holobiont · low.pH_high.temp	holobiont	not recorded	low.pH_high.temp	SRP406607	284.94
SRR22214410	holobiont · low.pH_high.temp	holobiont	not recorded	low.pH_high.temp	SRP406607	263.57
SRR22214409	holobiont · low.pH_high.temp	holobiont	not recorded	low.pH_high.temp	SRP406607	247.74
SRR22214420	holobiont · low.pH_high.temp	holobiont	not recorded	low.pH_high.temp	SRP406607	185.01
SRR22214413	holobiont · low.pH_high.temp	holobiont	not recorded	low.pH_high.temp	SRP406607	183.09
SRR22214405	holobiont · low.pH_high.temp	holobiont	not recorded	low.pH_high.temp	SRP406607	89.63
SRR22214412	holobiont · low.pH_high.temp	holobiont	not recorded	low.pH_high.temp	SRP406607	59.18
SRR22214406	holobiont · low.pH_high.temp	holobiont	not recorded	low.pH_high.temp	SRP406607	51.71
SRR22214423	holobiont · low.pH_high.temp	holobiont	not recorded	low.pH_high.temp	SRP406607	42.21
SRR22214404	holobiont · low.pH_high.temp	holobiont	not recorded	low.pH_high.temp	SRP406607	30.62
SRR22214408	holobiont · low.pH_high.temp	holobiont	not recorded	low.pH_high.temp	SRP406607	17.42
SRR22214403	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
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
SRR22214421	holobiont · low.pH_high.temp	holobiont	not recorded	low.pH_high.temp	SRP406607	0.00
SRR22214431	holobiont · low.pH Control.temp	holobiont	not recorded	low.pH Control.temp	SRP406607	318.93
SRR22214442	holobiont · low.pH Control.temp	holobiont	not recorded	low.pH Control.temp	SRP406607	280.16
SRR22214443	holobiont · low.pH Control.temp	holobiont	not recorded	low.pH Control.temp	SRP406607	265.14
SRR22214435	holobiont · low.pH Control.temp	holobiont	not recorded	low.pH Control.temp	SRP406607	163.09
SRR22214424	holobiont · low.pH Control.temp	holobiont	not recorded	low.pH Control.temp	SRP406607	130.49
SRR22214438	holobiont · low.pH Control.temp	holobiont	not recorded	low.pH Control.temp	SRP406607	114.30
SRR22214430	holobiont · low.pH Control.temp	holobiont	not recorded	low.pH Control.temp	SRP406607	106.18
SRR22214436	holobiont · low.pH Control.temp	holobiont	not recorded	low.pH Control.temp	SRP406607	93.98
SRR22214429	holobiont · low.pH Control.temp	holobiont	not recorded	low.pH Control.temp	SRP406607	62.91
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
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
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
SRR22214445	holobiont · low.pH Control.temp	holobiont	not recorded	low.pH Control.temp	SRP406607	0.00
SRR22214454	holobiont · control.pH_high.temp	holobiont	not recorded	control.pH_high.temp	SRP406607	279.76
SRR22214453	holobiont · control.pH_high.temp	holobiont	not recorded	control.pH_high.temp	SRP406607	266.08
SRR22214446	holobiont · control.pH_high.temp	holobiont	not recorded	control.pH_high.temp	SRP406607	177.32
SRR22214464	holobiont · control.pH_high.temp	holobiont	not recorded	control.pH_high.temp	SRP406607	135.21
SRR22214463	holobiont · control.pH_high.temp	holobiont	not recorded	control.pH_high.temp	SRP406607	127.67
SRR22214465	holobiont · control.pH_high.temp	holobiont	not recorded	control.pH_high.temp	SRP406607	113.82
SRR22214460	holobiont · control.pH_high.temp	holobiont	not recorded	control.pH_high.temp	SRP406607	92.68
SRR22214462	holobiont · control.pH_high.temp	holobiont	not recorded	control.pH_high.temp	SRP406607	54.84
SRR22214467	holobiont · control.pH_high.temp	holobiont	not recorded	control.pH_high.temp	SRP406607	50.00
SRR22214458	holobiont · control.pH_high.temp	holobiont	not recorded	control.pH_high.temp	SRP406607	36.95
SRR22214456	holobiont · control.pH_high.temp	holobiont	not recorded	control.pH_high.temp	SRP406607	34.74
SRR22214459	holobiont · control.pH_high.temp	holobiont	not recorded	control.pH_high.temp	SRP406607	24.23
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
SRR22214457	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
SRR22214535	holobiont · control.pH Control.temp	holobiont	not recorded	control.pH Control.temp	SRP406607	356.01
SRR22214524	holobiont · control.pH Control.temp	holobiont	not recorded	control.pH Control.temp	SRP406607	336.76
SRR22214468	holobiont · control.pH Control.temp	holobiont	not recorded	control.pH Control.temp	SRP406607	248.51
SRR22214422	holobiont · control.pH Control.temp	holobiont	not recorded	control.pH Control.temp	SRP406607	192.85
SRR22214466	holobiont · control.pH Control.temp	holobiont	not recorded	control.pH Control.temp	SRP406607	151.31
SRR22214506	holobiont · control.pH Control.temp	holobiont	not recorded	control.pH Control.temp	SRP406607	135.33
SRR22214548	holobiont · control.pH Control.temp	holobiont	not recorded	control.pH Control.temp	SRP406607	95.28
SRR22214471	holobiont · control.pH Control.temp	holobiont	not recorded	control.pH Control.temp	SRP406607	72.31
SRR22214547	holobiont · control.pH Control.temp	holobiont	not recorded	control.pH Control.temp	SRP406607	70.59
SRR22214469	holobiont · control.pH Control.temp	holobiont	not recorded	control.pH Control.temp	SRP406607	46.23
SRR22214400	holobiont · control.pH Control.temp	holobiont	not recorded	control.pH Control.temp	SRP406607	24.69
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
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
SRR22214546	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	39.00
SRR14295600	Whole organism	Whole organism	not recorded	not recorded	SRP315757	35.57
SRR14295604	Whole organism	Whole organism	not recorded	not recorded	SRP315757	33.58
SRR14295601	Whole organism	Whole organism	not recorded	not recorded	SRP315757	32.16
ERR12861049	unannotated	not recorded	not recorded	not recorded	ERP159209	26.26
SRR12454619	live coral tissue/skeleton	live coral tissue/skeleton	not recorded	not recorded	SRP277390	34.47

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.