Gene detail

Detailed information of BRAKERKREP00000013487.1 in Hydra viridissima

Genomic Location: QPEY01000072.1:902920...920982
NR annotation: XP_047142254.1, clustered mitochondria protein homolog [Hydra vulgaris]
Species Hydra viridissima · all data for this species · gene families

Gene Structure

More details in JBrowse

Sequence

CDS

BRAKERKRET00000013487

ATGCCTGCTGAACTGTGTCAAGATCACCAATTAAGTGCTCCAGAAagaatttcttcaaaatacttaaatgGAGAGTCTACAAAAAAGGACATTTCTAATCTTAAAAATCCACTCAGCTgtaatgaaaatgtaaaaacacaagaaaaattaaaaactgaaaccCAAAATCAATCTGAAGTTCCTTGCAATGGTGTTGTAGTCTCTAAACTTAACGATCCTGATGGAAAAGAAGTTCCTGTAAAGCTTTTAGacattaaaattcaaataagtgGTGTTGCAGATCCAGTTACTATTCAACTTTCAAATCATGATACTGTGCAGGACATACGCCAAGTAGTACTAGAAAAACCTGAATGCTGCCATCGCACTTGTTTCTCCTTGTATTTAGAAAATACTCGTCTTGATGACTTCATGGAGCTTCATGATATTGCAGGGCTTACTAATGATTCCATTATAAAAGTAGTTGATGAGCCATATAGTGTTCGCGAGTCTCGAATTCACGTTAGAAGGTTACGTGATTTGTTAATTACAATGCTTGAACCTAATGCTTTTAATGCTACTGATAATCTTTCATTGTCGTATTGTTCTGCTATTACTGAAATTGATATTGAAGAAGAAGccttaaagaatttaaaagaaccAAACAGTGCCAAAACAACTACTGATCTGCTCCCCCCTTCTTGGGCAACGTTGCAGGATGGAGAAAGTCCTTTATTAGAACCTCTTgtcattcaaaataaagatgCACAGCCATATAGTGTTCGCGAGTCTCGAATTCACATTAGAAGGTTACGTGATTTGTTAATTACAATGCTTGAACCTAATGCTTTTAATGCTACTGATAATCTTTCATTGTCGTATTGTTCTGCTATTACTGAAATTGATATTGAAGAAGAAGccttaaagaatttaaaagaaccAAACAGTGCCAAAACAACTACTGATCTGCTCCCCCCTTCTTGGGCAACGTTGCAGGATGGAGAAAGTCCTTTATTAGAACCTCTTgtcattcaaaataaagatgCACAGctgCCGGCTTGTTTAGCAGATCTACGTTATTCCTCTTGGAACCCTCCTCCAGGCTATCGTAAGCTTGCAGGTGATTTATTGTACCTCGAAGTTACATTACTGGAAGATATTGAATATACTCATTACATCACATCTTCATCAAGTggtttttatgtaaacaagtCAACAAAATTGGTTTTTGACCCTAAACCAAGTAATGAAACACCAAGATCTCAGACGCTAGCTGGTTTGCTCATgcttttgagtccattgtttaaaaaaaattttgctgttaTTCAAAGGACAAGcatAAAGAAAAATCCATTGGAGCTTGTTGCTTCTCCTCatcaagtttatccTTGGGTGTCACCACAGTTTGCTCATTATCAAGATCCATTCAGAGCTGAAGATTCTGTGACCAATCGTATTGGGTATGAGGAGCAAATTCCTGGGCAACTAAGAGACTGGAATGAAGAACTACAATCAGCTAAAGAACTCCCAAAAAAGACTCTACAccaaagaattttaagagataGAGCTTTGTATAAGATAACAAGTGATTTTGTAGCTGCTGCATCAAGAGGTGCTGTTGCGGTGGTTGATGGAAATGTTATGGCTATAAACCCTggagaagaagaaaaGATGCGTATGTATATCTGGAACAATATATTCTTCAGTTTTGCATGTGACTCTCGTGATCATTATCAAAAGTATGGAGGGGATGCTGCTGCTTATGCTGCTGCTTCACTTGATCTAAAGGGTATTGAAATGTACAACAAACTTGATCTAGATGGATTATATACCTTGGGCACTGTAGTTGTTGACTACCGTGGATACCGCATAATTGCTCAATCAATTATTCCAGGAATCCTTCAGCGAGAACAAGAAAACTCAGTTGTTTATGGAAGTGTTGATGGTGGGAAAACTATATCTACTGAAGCTAAGTTCCTagaaaaactaaaaatagCTGGTTTATCTCTAAGAATTCGGCCTCACAAaGTAGTAAATGAAAAGGGAGATGATGTAGAGCTCTGTTCATCGTTTGAATGCAAGggAATTATTGGAGCTGATGGCAGATATTACATTCTTGACTTATTTCGAACATTCCCTCCTGATATAAACTTTCTTGAAGttgGAAATGTAACAAGAAGTTTAATAGATGGAGAAGCTTTTCCTGACCAAATAcacaatgataaaaataaatttacttaccCGAAGAGTCATGCACACCAGCTTGTTTCAATAAGACCTCCTGTTGTGGAAGCTTTTATTGGATCAAAGTATGTGTCATTTGTCAAAGTTATTGCTGTCCACAAGCTGCatgatgaaaaattgaaaatagataaaaaagtggctgatgatttaaataaagagaaaatgGTGAAAGAggatttagataaaaatgCTGATGCTTCCAAAACAAATGGCATTGTTGAAAATGGCACTTCACATAAAAGTGAATCTGATGAAGAAAGTAAACAGGCTGAGgctgaaaaactaaaagaagaGGAAGATTTATCAGatatagTAGCTATAGAAGCAGCAGCAAAGGCAGTTGGGTCATTAAACCCAAGAGagttTGATATTCGTTTTAATCCAGACGCATATGTAAAAGAAGTCAAGTTAAGTGAATCTGAAgAAGAAGTTGATAAGCTTGATAAAGCATTAATAGAAGATATTGGTTTATTTATGTCTTCAACTGTTATTTCTAAAATGGTAGAAGATTTTACAACATTAAATTCATCACCAATTGATGGAGTTGCATTAACTGACATTTTACATTCTCGTGGAATTAACATGCGTTATCTTGGAAAAATAGCAAGCATGGtttctgaaaaagaaacttcTGCACATGTGTTTAAAATTGTTGTCAAAGAGATGATTATCAGAAGtgcaaaaaaccattttaaagaATGTATTCAAAGTGctaATCAAAAAAGCTTGTCAGCTGCTGTGAGCCACTTCTTAAACTGTTTCTTAAGTTCTTTTCCATCTCCTCAACCACAAGTGCCTTCCGAAGATaatcaaaaaaaaaagaaaaataaaaaacgccAACAGAAATCACCTCATCTTCCGTCTTATAGTAAAGTTGTTTGGATTTCATTATCGCCTGCAATACTGTGGAATTCTATTATTAACTACATGGATAAGcattttggatttaaattaGAATGTTCGAATATGGATCAATTTGTTACAAAGTTTCACCtacaaaagttaagttttctgagagaattttgcaaaaagaCTGGAGTTCAGATATTGCTGCGTGAATATgattttaactcaaaaaaaaacccaacatTTTATGTAGATGATATTATTAACTTGTTTCCTGTTGTTAAATATGCCACTCCCAAAGCTACAGATGCatgtgttatttttgaaactgcTCAAGCAAGACTTCAAGCAGGGTTTTTTGGCGAAGCACATGAGTTGATGATAGAAGCATTGAATATGTTTAATCAAGTATATGGACCTCTGCATGAGGATATTGTAGTTTGCTACCGTGCCATTGCCAGAATACATTACCTTGCAGATGATGCCCCTCAAGCAGTTTCATTCCAAAAAAAAGCTGTAATAGTTGCAGAAAGAATATTTGGAATTGATCATCCTGAAACTTTAGTTGCTTATGTTCATTTGGCACTTTATTGCTATCATGCTGGACTTGCCGGTGCGTCTTTAAAGTTAATGTATCGTTCAAGATATTTGACTTTACTTGCGTTCGGTGATGACCATCCAGATATGGCTGCATTTGATacaaatatTGGTTTAATGCTTCACAACCAAAGAGAATTCTCTGTAGGTTGTAAGTTTCTAGAACGTTCTTGCAATCTTCAGATGAAGTATCATGGACCTAAAAGTATTCATACTGCAACGAGCCATCATCTTGTTGCAAGAGCTTTAACCGCTCTAGGAGAATACAAATCAGCATTGAGCAGTGAAAAGATGACATTCTCAATCTATCAAAAccatTTTGGCGATGGTGACCCAAGGACGAAAGAGAGTTCCGACGCTTTGAAAACAATCCTTAACCAGGCTgttatgttacaaaaaactttaaaagatataaCAGAAAAAGGTTCAATTAACTCTGCACGTCTTCCTCGGCTTGATGATGAAAAAGAGGATAAACTTGTTTTAGCGATGGTAAATAAAATCCAAGAGTTAAGCGAAACCGATCACCCTGTCAAAATTTCGAAATCGGCCAGAACGTGA

Transcript

BRAKERKRET00000013487

Protein

UniProt (Swiss-Prot top hit)

UniProt accession	Description
Q0IHW8	Clustered mitochondria protein homolog OS=Xenopus tropicalis OX=8364 GN=cluh PE=2 SV=1
Q5SW19	Clustered mitochondria protein homolog OS=Mus musculus OX=10090 GN=Cluh PE=1 SV=2
O75153	Clustered mitochondria protein homolog OS=Homo sapiens OX=9606 GN=CLUH PE=1 SV=2

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0004584 (this species only) · gene tree & orthology

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF15044 all species →	CLU_N	Mitochondrial function, CLU-N-term	Family	Interproscan
PF12807 all species →	eIF3_p135	Translation initiation factor eIF3 subunit 135	Family	Interproscan
PF13424 all species →	TPR_12	Tetratricopeptide repeat	Repeat	Interproscan
PF13236 all species →	CLU	Clustered mitochondria	Domain	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR011990 all species →	Homologous_superfamily	Tetratricopeptide-like helical domain superfamily	Interproscan
IPR027523 all species →	Family	CLU domain containing protein	Interproscan
IPR028275 all species →	Domain	Clustered mitochondria protein, N-terminal	Interproscan
IPR033646 all species →	Domain	CLU central domain	Interproscan
IPR023231 all species →	Homologous_superfamily	GSKIP domain superfamily	Interproscan
IPR025697 all species →	Domain	CLU domain	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR12601 all species →	EUKARYOTIC TRANSLATION INITIATION FACTOR 3 SUBUNIT EIF-3	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0005515 all species →	Molecular Function	protein binding	Interproscan
GO:0003729 all species →	Molecular Function	mRNA binding	Interproscan
GO:0005737 all species →	Cellular Component	cytoplasm	Interproscan
GO:0006996 all species →	Biological Process	organelle organization	Interproscan
GO:0048312 all species →	Biological Process	intracellular distribution of mitochondria	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
K03255	TIF31, CLU1; protein TIF31	-	Translation factors	ko03012	deepkoala

Searching by KO or pathway ID across all species is available on the KEGG Pathway page.

Expression pattern (RNA-seq)

Transcript abundance of BRAKERKREP00000013487.1 across 29 RNA-seq samples of Hydra viridissima. 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.

29Samples

17TPM > 0

7Conditions

111.4Max TPM

37.4Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
whole body	18	7	15.75	97.89
Whole	6	6	100.28	111.37
aposymbioic hydra M9 strain · aposymbioic hydra rep1	1	1	49.43	49.43
aposymbioic hydra M9 strain · aposymbioic hydra rep2	1	1	56.05	56.05
symbioic hydra M9 strain · symbioic hydra rep1	1	1	45.75	45.75
symbioic hydra M9 strain · symbioic hydra rep2	1	1	48.31	48.31
unannotated	1	0	0.00	0.00

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

SRA run	Condition	Tissue	Developmental stage	Treatment	Study	TPM
SRR21134060	whole body	whole body	not recorded	not recorded	SRP392977	97.89
SRR21134064	whole body	whole body	not recorded	not recorded	SRP392977	79.43
SRR21134052	whole body	whole body	not recorded	not recorded	SRP392977	44.67
SRR21134059	whole body	whole body	not recorded	not recorded	SRP392977	36.03
SRR21134056	whole body	whole body	not recorded	not recorded	SRP392977	24.81
SRR21134054	whole body	whole body	not recorded	not recorded	SRP392977	0.38
SRR21134057	whole body	whole body	not recorded	not recorded	SRP392977	0.37
SRR21134050	whole body	whole body	not recorded	not recorded	SRP392977	0.00
SRR21134051	whole body	whole body	not recorded	not recorded	SRP392977	0.00
SRR21134053	whole body	whole body	not recorded	not recorded	SRP392977	0.00
SRR21134055	whole body	whole body	not recorded	not recorded	SRP392977	0.00
SRR21134058	whole body	whole body	not recorded	not recorded	SRP392977	0.00
SRR21134061	whole body	whole body	not recorded	not recorded	SRP392977	0.00
SRR21134062	whole body	whole body	not recorded	not recorded	SRP392977	0.00
SRR21134063	whole body	whole body	not recorded	not recorded	SRP392977	0.00
SRR21134065	whole body	whole body	not recorded	not recorded	SRP392977	0.00
SRR21134066	whole body	whole body	not recorded	not recorded	SRP392977	0.00
SRR21134067	whole body	whole body	not recorded	not recorded	SRP392977	0.00
SRR10058804	Whole	Whole	not recorded	not recorded	SRP220397	111.37
SRR10058802	Whole	Whole	not recorded	not recorded	SRP220397	106.94
SRR10058805	Whole	Whole	not recorded	not recorded	SRP220397	101.23
SRR10058807	Whole	Whole	not recorded	not recorded	SRP220397	95.62
SRR10058803	Whole	Whole	not recorded	not recorded	SRP220397	95.20
SRR10058806	Whole	Whole	not recorded	not recorded	SRP220397	91.33
DRR048593	aposymbioic hydra M9 strain · aposymbioic hydra rep1	not recorded	not recorded	aposymbioic hydra rep1	DRP003902	49.43
DRR048594	aposymbioic hydra M9 strain · aposymbioic hydra rep2	not recorded	not recorded	aposymbioic hydra rep2	DRP003902	56.05
DRR048595	symbioic hydra M9 strain · symbioic hydra rep1	not recorded	not recorded	symbioic hydra rep1	DRP003902	45.75
DRR048596	symbioic hydra M9 strain · symbioic hydra rep2	not recorded	not recorded	symbioic hydra rep2	DRP003902	48.31
ERR13389755	unannotated	not recorded	not recorded	not recorded	ERP162636	0.00

Source: CnidoSite RNA-seq expression matrices (HVIRI_TPM, StringTie quantification over 29 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.