Gene detail

Detailed information of FUN_021286-T1 in Siderastrea siderea

Genomic Location: contig_19:4827968...4848842
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_021286-T1

atggcgagTTCTAGCGACGATGAAGAGACGAATAGCTCTGAGCGATTCGAAAATCTTTGCCGTGATCTTAACATGGATGAAGAGACTAGTCAAGAAGCATGGTCTTCGTATCAGAAGATAAGCACGAACTACACTTTAGAGGCAAGCTTACCTTTTGTGTGTGAATGTTTGCGTTCGTTACATGTTTGCTTCGAATCGCAGTTTCATAGAACGGGGGACAGTCTACATTGGCTGGCATGTGCTTTGTACGTTGCTTGCCGCAAAAGCGTTGTTCCAACCGTTGATAGTTCGGGAACGGTCGAGGGAAATTGCGTCTCGCTAACCCGATTGCTGAGAGCAGCCAAATTAAGTCTGATTCAGTTCTTTAGCAAGATGAAGAAGTGGCTGGACATGTCGACCGTGTCCGGCGACTTTCGAAAGAAAATCGAGTTATTGGAAAGGAACTTCCACGTTTCCACAGTCATTTTCAAGAAGTACGAGCCTATTTTTATGGAAATCTTTAAGGATCCCCGAGAGGAAAACACAAAGACTCAGAGAGGCCGAAAATCAAGAAAACAGCCTTGCTCCGTCGGCGACGTCTTCGCGTTCTGTTGGACTTTGTATATTCAAGCAAAAGGCCATTTTCCAGCAATCAGTGATGACTTGGTGAACTCTTACCATTTGCTGTTGTGTTGCTTGGATTTGCTGTATTCAAATGCATTGTATACAAAGAATCGCCAGGGTTTGCTGAATCCAAACTTCGAAGGTCTACCTCCAGATTTTGGTAACAGAGATTTCAGACCTCCAGCTGATGTGCCTTGTGTTGTTGAACGGCTTTGTTACAAGCATCAAGGAATAGTGTTGGAAGCTAAAGGAATCAAAGAACATCATTGGAAGCCATTCATAAAGCAACTATTTGAAAAGAAGACATTAAAGGGAAACGAAGAGAACTTGACAGGCATTCTTGATCCAGGAAATTTTGAGCAAAACTGCAAATCTGTCAATAAAGAATATGAAGAGTATGTATTATCTGTTGGAGATTTTGATGAAAGAATCTTCTTAGATGACGAAGCCCACATTGAAATAGGTACTCCAGCCAAGAATTACAGTTTTACAGAAGTGGATGAACAACAGAGGGAAATTTTGTATGATTCTGAAACATTCACTTGGCAGCTGTATAAACCTGTCAAAGACAAAGAGATGGCAAGATTAGTGTCTCAAAATGAGTTTATTGTCATGGTGTTTCTACAGACTAGAAGTCTTGCACCTTCAACACCATTGACTGGCAGAAGATATCTCAAGgagaaagatccaaaGATAACCCCCGTATCCACAGCCACACAGTCAGTGAGTAGACTACAAGCCCTCCTGTCAGGATTGAAAGCAGGACCCAGTGATCGCCTCATTAAGATATTTTCCGAGTGCAGTAGAAATCCTCAGGAAGCGATTGAGAGACGAGTTGAAACTCTTGGAGAAACTTTCCTCCGGGAGTATGTACAGCCATCGCCTGATAGACCCAAGTCTCCCTGCTCAACAAGAGAGTTTGCCTCAAAGAGACTGAAACTTGCAGAAGTTCTGTATTACAAGGTGCTGGAAAGTATTACTTTGTTAGAGCAGAGAAGACTGCAAGGTCATCTTGATTTGACAAGTTTGTTGGAACAAGAGTCTTTTCACTGTTCTCTGATGGCCTGCTGTCtggaaattgttattttctcTTACAACTCTCAAAGGACCTTTCCATGGATAATTGACATCTTTGACATCAGTCCGTACCACTTTCTCAAAGTCATTGAAGTTTTCATCAAAGCTGAGGATGGACTGTCGAGAGATGTTGTCAAACATCTTAATCATATTGAGGAACAGATTCTTGAGTGCCTTGCCTGGAGCCACGATTCCCCTCTGTGGTCATCAATTCAACAGGCTGGTTCAGTTCCATCATGTGAAGAGGTATCCATACCATTTCAATTAGAAGCAGCTCACAGCACACAGAACCTCCTGGCCTCGCCAATCATCCACCCTCGTGTCCAGAGAATCTGCGGTGAGGAGGGTGCTGCCAGACGAGtccTTCAGTTGCAAAGCTCTCCAACAGCACATGAAGTATTTAGTTCACCAATCACTCCCAGCAGTGGTGCCAGGCGTAATTTGTTGGTCAACTTTGGCAGCTCTTCCCCTGCTCAGAATCCTCAACCCGTAACTCTGTCCCCAACAACAAGACAAACTACAGCAAGGAATGCTCCCACATTGATAATTACGCCAGCACCTGCCAGTGGTGGCTATATTGTGAATGGAGTCACTCAAGCTGTGGTATTGCCAAGCACTTCAAACACAGTGCAAGTGACATCGCCACAGGCTGGCAGTGTTTTGGCTCCTAGTGTGGCAACAGCATCACCAACCTCGAGTCCAGTGAGGCCATCATCAGTACCGACCACACCCAAACCTAAGAGTGCAACTCCAAGCAAACCAAGGAAGACTGGTTCTTTGGCACTGTTCTTCAGGAAGCTTTACCATCTGGCCAGTGTTCGGCTCAGAGATCTCTGCACAAAACTGGATGTCCATGAGGATCTTCGTGTAAAGATGTGGACTTGTTTTGAACACACACTGATGCATATGACAGAGCTAATGAAAGATAGACACATTGATCAGATACTGATGTGCTCCATTTACGTCATGGGAAAGgttacaAATGCAGACTTGTCATTCCAGAACATTATGAAGTGTTACCGCACTCAACCTCAAGCTGTCAGCCATGTTTACAGAAGTGTGCTTCTCAGAGGAAGAAGACGGGCTCCCATTGGAAGCAGTGGTAGTGATGGTGGAGCTAAAGGTGTCAAAAGCGAGCCTGGAAGTAGTGGGCCTGCCAGCCCAGTTCAGGGCGCTAGCAGTGCAAGGGCTAGTCCAGTGAGAAGCGCAAGCGCAGTGCCTTCTACACCCCCTCCATCCAGTGCTCATACCTCAGGATCCAGCAGTACCGAAAACAGTCCAAACATTGATGGGGAACGAGGAGATCTTATAGAGTTCTACAACAagGTGTTCATCAAAAGGGTGAAGAACTTTGCTCTCAAGTTCTCTCCTGGCGACAGAGCATTGGATTCCCCTCCACTTTCTCCTCTGCCAGTGATGAAAAATCAGGCTCATTCTCCACGACGCAAAGTGTCCACACGACATTCTGTGTATATTTCTCCTCACAAGAATGGAGTGTCAATGACACCAACAACAAGGCTGTTGTACTGCTTCAAAGAAAGCCCGGCTGAGAAACTTCGAGATATCAACCAAATGTTGAAGCAGGGTGCAGGAGAGATGAGCCGTAAGCGAGCCCTCCTGCAGGATGACAAGAGTAGTCAGCCACCAACCAAACGAACACCGTCAGAGGAGGTTCTTCAGCGTAAGCTAACAAGCATGATTGAAGAACGGCAAGCTTCAGCCTCAAGATAA

Transcript

FUN_021286-T1

Protein

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF01857 all species →	RB_B	Retinoblastoma-associated protein B domain	Domain	Interproscan
PF11934 all species →	DUF3452	Domain of unknown function (DUF3452)	Family	Interproscan
PF01858 all species →	RB_A	Retinoblastoma-associated protein A domain	Domain	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR028309 all species →	Family	Retinoblastoma protein family	Interproscan
IPR036915 all species →	Homologous_superfamily	Cyclin-like superfamily	Interproscan
IPR002719 all species →	Domain	Retinoblastoma-associated protein, B-box	Interproscan
IPR024599 all species →	Domain	Retinoblastoma-associated protein, N-terminal	Interproscan
IPR002720 all species →	Domain	Retinoblastoma-associated protein, A-box	Interproscan
IPR015030 all species →	Domain	Retinoblastoma-associated protein, C-terminal	Interproscan
IPR013763 all species →	Domain	Cyclin-like domain	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR13742 all species →	RETINOBLASTOMA-ASSOCIATED PROTEIN RB -RELATED	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0000785 all species →	Cellular Component	chromatin	Interproscan
GO:0000977 all species →	Molecular Function	RNA polymerase II transcription regulatory region sequence-specific DNA binding	Interproscan
GO:0005667 all species →	Cellular Component	transcription regulator complex	Interproscan
GO:0006357 all species →	Biological Process	regulation of transcription by RNA polymerase II	Interproscan
GO:0030154 all species →	Biological Process	cell differentiation	Interproscan
GO:0051726 all species →	Biological Process	regulation of cell cycle	Interproscan
GO:2000134 all species →	Biological Process	negative regulation of G1/S transition of mitotic cell cycle	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
K04681	RBL1; retinoblastoma-like protein 1	-	Transcription factors	ko03000	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_021286-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

15TPM > 0

7Conditions

37.1Max TPM

3.2Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
holobiont · low.pH_high.temp	20	0	0.00	0.00
holobiont · low.pH Control.temp	20	1	0.88	17.58
holobiont · control.pH_high.temp	20	2	0.57	7.06
holobiont · control.pH Control.temp	19	6	7.60	37.14
Whole organism	4	4	16.85	23.69
unannotated	1	1	13.84	13.84
live coral tissue/skeleton	1	1	19.93	19.93

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	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
SRR22214408	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
SRR22214426	holobiont · low.pH Control.temp	holobiont	not recorded	low.pH Control.temp	SRP406607	17.58
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
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
SRR22214462	holobiont · control.pH_high.temp	holobiont	not recorded	control.pH_high.temp	SRP406607	7.06
SRR22214463	holobiont · control.pH_high.temp	holobiont	not recorded	control.pH_high.temp	SRP406607	4.30
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
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
SRR22214524	holobiont · control.pH Control.temp	holobiont	not recorded	control.pH Control.temp	SRP406607	37.14
SRR22214492	holobiont · control.pH Control.temp	holobiont	not recorded	control.pH Control.temp	SRP406607	35.13
SRR22214455	holobiont · control.pH Control.temp	holobiont	not recorded	control.pH Control.temp	SRP406607	23.67
SRR22214548	holobiont · control.pH Control.temp	holobiont	not recorded	control.pH Control.temp	SRP406607	21.27
SRR22214466	holobiont · control.pH Control.temp	holobiont	not recorded	control.pH Control.temp	SRP406607	14.83
SRR22214506	holobiont · control.pH Control.temp	holobiont	not recorded	control.pH Control.temp	SRP406607	12.33
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
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
SRR22214471	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
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
SRR14295604	Whole organism	Whole organism	not recorded	not recorded	SRP315757	23.69
SRR14295603	Whole organism	Whole organism	not recorded	not recorded	SRP315757	15.90
SRR14295601	Whole organism	Whole organism	not recorded	not recorded	SRP315757	15.14
SRR14295600	Whole organism	Whole organism	not recorded	not recorded	SRP315757	12.69
ERR12861049	unannotated	not recorded	not recorded	not recorded	ERP159209	13.84
SRR12454619	live coral tissue/skeleton	live coral tissue/skeleton	not recorded	not recorded	SRP277390	19.93

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.