Gene detail

Detailed information of FUN_036778-T1 in Siderastrea siderea

Genomic Location: contig_42:2638852...2685109
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_036778-T1

cgagattgggaACCATGTCGGAACGATGATGTCTTGTGGTGCCGGTTGTGAACACTACATTAGACGTTGCTCTTTGCTGGCCCCCTGTTGTAATAAATACTACAGCTGCAGGTTATGTCACAATGAAAAAGAGGATCATGAGTTGGACAGAAAAACTGTGGAAGGAATTAAATGTCTCCAATGTGAGAGTTGTCAGTCAgTGGCTTCCCACTGTCAAGATTGTGGTGTAAAGTTTGGACGGTATTACTGCGAGATTTGTCGATTGTTTGATGACGGTGAAAGAGGACAGTTTCATTGTAATGCTTGTGGAATTTGCAGAGTGGGTGGAGAGGAGAATTTCTTTCATTGCAGTAGATGTGACATGTGCCTAGGAGTTCAACTGAAAGATTCACACAAGTGCATAGAGAAGAGTTCACGTTCAGCTTGTCCAATATGTTATGAGGATATTCATACATCAAGAATACCGTCACATGTCCCCCCTTGTGGACACCTGCTACACAGCACTTGTTTCTCGAAGTTACTTGAGTCAGGGGGATATGCTTGCCCGATATGTAACAGGTCCATGGTGGATATGAGTCGTGCATGGCGAATGTTGGATAATGAGGTAGCACGCACACCAATGCCAGCAGAGTATGCTGATTTCAATGTGATGATTCTCTGCCGTGATTGCCGCAAGGAAAGTAAAGTCAGGTTTCATGTTGTTGGCTTGAAGTGTACAGAGTGCGGTTCATACAACACCAgcagagaaggagaagaagggACTCCTGTCATACCAGTCccagcaacagcagcagcagcagcagcagcagcaccTGACGATGAATGGGAAacagaagaggaagaagaaataGTGGGTGGAGAGGAAGGCCAAGAAAATGAGGCGGAAATAGGAGGCCAAGCAGCACATGATGATGGAGTAAACTTGTCAGAAGTTCAATTGAATATTGACGGAGATAGTAGTAATGTTCTTCCTTTGGACTAAACAGAACGTCACTccgaaaaaaaaactggttaaaAGGAAAAGACGAAAATTCATGTTATATTGTGAAAAATCCTTTTACAACTCCATGGAAATCAAAACAAGAAACTGCTGTTTGTGACTGGCCTCTTTATAACTACAATGATGTTGCTAGAgatttaaaacaaagatttcAAAAGAATGTCCAAAATTTAATTCTCTTCAGCCTGACAAGTTTATTCTTCATGTTTAAGCATTTGTTATTCACCAAAGCTTTGTggtattttctttaatttgtttctcTGACATTTCTCCAGTGCTTTTGCGTGTGTTGGAGGGAAGGGGTGGTACTAAATGCAGAGGAAAGGACACCATAACACGTGTCTTGCTCAGTATGACTAAAATACAGCTACTGGAATTAAAGCACAAAACAAATTGAACCATTTCATGATTTACAGTCTACGTGTTTACCAACGAGGAAATTGTATATGTCTATTATTTGAGTCCACATCCCGAACGATACCCGAACGTTGCCTCTCGAAATAGCTCTTGGGTGGACTATTATGTCTTTGGTTTCTTCAGAATGTCGCGATGGTACGGATGGTTTTACGCGGGACTTTGTCGACCTTGCGATCTTTTCTGAGAATTTTTGGAATCAATTGAATGCGCATAGTTATTGTTTTTGATATTTATTCCTTTGGCACCAAGGACGCCATTCATAATTTCTTAGCTGAAGAAGGCGGTACCACCCTGCCGAAAAGTTCTTAGGTAAATAAGCAAATGGGTGTTGGGTGGGTAGATAAGAAAGTGAAGCCttgtttaaggtgattccatcaaaatagaaggaatatttaaaaatttctaagacttggtccaattggtaattatgtttagaacatttcaaaaaaatgcaattaaaaataggggtcaccgagcttcTTTTGGTACGACATGGATAGCCATcgatagcaactatacgacccgcaaggtttgcctgagaaaccctagtaatgagaaatgagaactataattgctttaaaaagtcattgtttgtattgaaatataggagcagttcaacaaaatagacatttatcttgcattgtacactattttagttgaacagggattaaggatatgaaaaaaaaattaaagaatttgccgcgtgctTACACACcttgctgtacctaaagacgtgttcttttcggcttttcgcgcgctaatcacgcaaaaactgatgcgcagaaaggttgcgcaatgcaattgaagggaatcaccttaaaaggCAAACGTTTGCCCAAACATTTGGGAAAAAGTTGATAATATTTGGTACCTTTCTGAAGTTGCAATCCAGTTCCGTTCTGGCTATCCGAAGCCAAAGGCACTTTTTAATTGTATCTGTGCACCAATAAAGCAGCTTTTAACGAACTTGAGCGTTCTTTTCGGTGTCTTGTAGTTTTTGTGTACTGGTAACAGTCAAGTTTCGAGTTCACCAAGATCCACTGAATAAAAACTTTAAAGACGCATTTTTACAGGGCAAGTGTCAAACTAAAGTAAAATATGCACAAATACTAGCAGGAAGTTGCTGAACTCTATAATGAAACAATACGCAGAGTCGTGAATAGTTCGTCCCCCTCCTGGTATTTGTGTATGTTTTTAGATTGAGACCATCGGGGGCAAGGGTACGTTGTCTAAAATTACGACAACGTACCCTTGCACAGTTAAAAAACGCTCCTATACCACCAAGACGACGAAATCAAGTTAATTCTTAAAAGGTAAGCAAAccaaaatatgtttttttgAGTGACTTCC

Protein

Gene family

Family type	Membership / link
Ubiquitin family	E3\|E3 activity RING\|RING · all ubiquitin genes in this species

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF14599 all species →	zinc_ribbon_6	Zinc-ribbon	Domain	Interproscan
PF05495 all species →	zf-CHY	CHY zinc finger	Domain	Interproscan
PF13639 all species →	zf-RING_2	Ring finger domain	Domain	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR039512 all species →	Domain	RCHY1, zinc-ribbon	Interproscan
IPR001841 all species →	Domain	Zinc finger, RING-type	Interproscan
IPR008913 all species →	Domain	Zinc finger, CHY-type	Interproscan
IPR037274 all species →	Homologous_superfamily	Zinc finger, CHY-type superfamily	Interproscan
IPR013083 all species →	Homologous_superfamily	Zinc finger, RING/FYVE/PHD-type	Interproscan
IPR037275 all species →	Homologous_superfamily	Zinc finger, CTCHY-type superfamily	Interproscan
IPR017921 all species →	Domain	Zinc finger, CTCHY-type	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR21319 all species →	RING FINGER AND CHY ZINC FINGER DOMAIN-CONTAINING PROTEIN 1	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0008270 all species →	Molecular Function	zinc ion binding	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
K10144	RCHY1, PIRH2; RING finger and CHY zinc finger domain-containing protein 1	EC:2.3.2.27	Ubiquitin system	ko04121	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_036778-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

477.1Max TPM

133.4Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
holobiont · low.pH_high.temp	20	18	154.31	450.27
holobiont · low.pH Control.temp	20	16	137.81	367.22
holobiont · control.pH_high.temp	20	14	122.36	343.10
holobiont · control.pH Control.temp	19	12	147.13	477.08
Whole organism	4	4	42.42	45.14
unannotated	1	1	29.41	29.41
live coral tissue/skeleton	1	1	54.30	54.30

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	450.27
SRR22214412	holobiont · low.pH_high.temp	holobiont	not recorded	low.pH_high.temp	SRP406607	315.33
SRR22214407	holobiont · low.pH_high.temp	holobiont	not recorded	low.pH_high.temp	SRP406607	301.67
SRR22214417	holobiont · low.pH_high.temp	holobiont	not recorded	low.pH_high.temp	SRP406607	235.18
SRR22214402	holobiont · low.pH_high.temp	holobiont	not recorded	low.pH_high.temp	SRP406607	220.77
SRR22214413	holobiont · low.pH_high.temp	holobiont	not recorded	low.pH_high.temp	SRP406607	177.51
SRR22214423	holobiont · low.pH_high.temp	holobiont	not recorded	low.pH_high.temp	SRP406607	172.55
SRR22214405	holobiont · low.pH_high.temp	holobiont	not recorded	low.pH_high.temp	SRP406607	167.80
SRR22214418	holobiont · low.pH_high.temp	holobiont	not recorded	low.pH_high.temp	SRP406607	154.15
SRR22214404	holobiont · low.pH_high.temp	holobiont	not recorded	low.pH_high.temp	SRP406607	137.41
SRR22214406	holobiont · low.pH_high.temp	holobiont	not recorded	low.pH_high.temp	SRP406607	135.29
SRR22214419	holobiont · low.pH_high.temp	holobiont	not recorded	low.pH_high.temp	SRP406607	129.96
SRR22214403	holobiont · low.pH_high.temp	holobiont	not recorded	low.pH_high.temp	SRP406607	128.39
SRR22214414	holobiont · low.pH_high.temp	holobiont	not recorded	low.pH_high.temp	SRP406607	108.02
SRR22214410	holobiont · low.pH_high.temp	holobiont	not recorded	low.pH_high.temp	SRP406607	94.92
SRR22214420	holobiont · low.pH_high.temp	holobiont	not recorded	low.pH_high.temp	SRP406607	61.05
SRR22214415	holobiont · low.pH_high.temp	holobiont	not recorded	low.pH_high.temp	SRP406607	50.13
SRR22214421	holobiont · low.pH_high.temp	holobiont	not recorded	low.pH_high.temp	SRP406607	45.77
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
SRR22214428	holobiont · low.pH Control.temp	holobiont	not recorded	low.pH Control.temp	SRP406607	367.22
SRR22214443	holobiont · low.pH Control.temp	holobiont	not recorded	low.pH Control.temp	SRP406607	366.07
SRR22214429	holobiont · low.pH Control.temp	holobiont	not recorded	low.pH Control.temp	SRP406607	306.55
SRR22214430	holobiont · low.pH Control.temp	holobiont	not recorded	low.pH Control.temp	SRP406607	261.25
SRR22214445	holobiont · low.pH Control.temp	holobiont	not recorded	low.pH Control.temp	SRP406607	201.82
SRR22214441	holobiont · low.pH Control.temp	holobiont	not recorded	low.pH Control.temp	SRP406607	191.73
SRR22214425	holobiont · low.pH Control.temp	holobiont	not recorded	low.pH Control.temp	SRP406607	154.45
SRR22214427	holobiont · low.pH Control.temp	holobiont	not recorded	low.pH Control.temp	SRP406607	146.98
SRR22214437	holobiont · low.pH Control.temp	holobiont	not recorded	low.pH Control.temp	SRP406607	134.23
SRR22214439	holobiont · low.pH Control.temp	holobiont	not recorded	low.pH Control.temp	SRP406607	127.67
SRR22214431	holobiont · low.pH Control.temp	holobiont	not recorded	low.pH Control.temp	SRP406607	127.54
SRR22214436	holobiont · low.pH Control.temp	holobiont	not recorded	low.pH Control.temp	SRP406607	124.01
SRR22214435	holobiont · low.pH Control.temp	holobiont	not recorded	low.pH Control.temp	SRP406607	76.86
SRR22214434	holobiont · low.pH Control.temp	holobiont	not recorded	low.pH Control.temp	SRP406607	66.85
SRR22214442	holobiont · low.pH Control.temp	holobiont	not recorded	low.pH Control.temp	SRP406607	60.55
SRR22214426	holobiont · low.pH Control.temp	holobiont	not recorded	low.pH Control.temp	SRP406607	42.46
SRR22214424	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
SRR22214438	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
SRR22214461	holobiont · control.pH_high.temp	holobiont	not recorded	control.pH_high.temp	SRP406607	343.10
SRR22214463	holobiont · control.pH_high.temp	holobiont	not recorded	control.pH_high.temp	SRP406607	268.58
SRR22214465	holobiont · control.pH_high.temp	holobiont	not recorded	control.pH_high.temp	SRP406607	221.25
SRR22214450	holobiont · control.pH_high.temp	holobiont	not recorded	control.pH_high.temp	SRP406607	216.73
SRR22214447	holobiont · control.pH_high.temp	holobiont	not recorded	control.pH_high.temp	SRP406607	193.30
SRR22214459	holobiont · control.pH_high.temp	holobiont	not recorded	control.pH_high.temp	SRP406607	181.94
SRR22214453	holobiont · control.pH_high.temp	holobiont	not recorded	control.pH_high.temp	SRP406607	156.32
SRR22214467	holobiont · control.pH_high.temp	holobiont	not recorded	control.pH_high.temp	SRP406607	146.16
SRR22214458	holobiont · control.pH_high.temp	holobiont	not recorded	control.pH_high.temp	SRP406607	142.19
SRR22214456	holobiont · control.pH_high.temp	holobiont	not recorded	control.pH_high.temp	SRP406607	132.87
SRR22214454	holobiont · control.pH_high.temp	holobiont	not recorded	control.pH_high.temp	SRP406607	127.46
SRR22214462	holobiont · control.pH_high.temp	holobiont	not recorded	control.pH_high.temp	SRP406607	118.84
SRR22214449	holobiont · control.pH_high.temp	holobiont	not recorded	control.pH_high.temp	SRP406607	106.14
SRR22214464	holobiont · control.pH_high.temp	holobiont	not recorded	control.pH_high.temp	SRP406607	92.33
SRR22214446	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
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
SRR22214460	holobiont · control.pH_high.temp	holobiont	not recorded	control.pH_high.temp	SRP406607	0.00
SRR22214400	holobiont · control.pH Control.temp	holobiont	not recorded	control.pH Control.temp	SRP406607	477.08
SRR22214411	holobiont · control.pH Control.temp	holobiont	not recorded	control.pH Control.temp	SRP406607	433.26
SRR22214466	holobiont · control.pH Control.temp	holobiont	not recorded	control.pH Control.temp	SRP406607	335.38
SRR22214548	holobiont · control.pH Control.temp	holobiont	not recorded	control.pH Control.temp	SRP406607	293.63
SRR22214481	holobiont · control.pH Control.temp	holobiont	not recorded	control.pH Control.temp	SRP406607	241.67
SRR22214506	holobiont · control.pH Control.temp	holobiont	not recorded	control.pH Control.temp	SRP406607	188.67
SRR22214471	holobiont · control.pH Control.temp	holobiont	not recorded	control.pH Control.temp	SRP406607	174.70
SRR22214469	holobiont · control.pH Control.temp	holobiont	not recorded	control.pH Control.temp	SRP406607	150.03
SRR22214444	holobiont · control.pH Control.temp	holobiont	not recorded	control.pH Control.temp	SRP406607	143.54
SRR22214547	holobiont · control.pH Control.temp	holobiont	not recorded	control.pH Control.temp	SRP406607	140.26
SRR22214524	holobiont · control.pH Control.temp	holobiont	not recorded	control.pH Control.temp	SRP406607	125.10
SRR22214468	holobiont · control.pH Control.temp	holobiont	not recorded	control.pH Control.temp	SRP406607	92.15
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
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
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
SRR14295600	Whole organism	Whole organism	not recorded	not recorded	SRP315757	45.14
SRR14295603	Whole organism	Whole organism	not recorded	not recorded	SRP315757	43.62
SRR14295604	Whole organism	Whole organism	not recorded	not recorded	SRP315757	41.22
SRR14295601	Whole organism	Whole organism	not recorded	not recorded	SRP315757	39.67
ERR12861049	unannotated	not recorded	not recorded	not recorded	ERP159209	29.41
SRR12454619	live coral tissue/skeleton	live coral tissue/skeleton	not recorded	not recorded	SRP277390	54.30

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.