Gene detail

Detailed information of BRAKERKREP00000023707.1 in Hydra viridissima

Genomic Location: not available for this species
NR annotation: WP_066356259.1, TonB-dependent receptor [Bordetella bronchialis]
Species Hydra viridissima · all data for this species · gene families

Sequence

CDS

BRAKERKRET00000023707

ATGCGTGTATCTTGTATTTGCTGGCAGGTCGCCTTGGCCTGTGGCGCGCCCGCGTTAACGACTGCGCAACCAGCGCCGCCGCCCATTTCGCAGCAGGACGCCATCGTCGTCACTGCTAACCGTGTGGCCCAACCCTATAAGAAGGTGTTGGGCGATGTGACGGTACTCGACCGCGACGTGCTAGCCGAGGCCGGGCAAAGCACGTTGGCCGAAGTGCTCGCGCGCAGCCATGGTATCGAATACGTTAACAATGGCAATCCGCAAGGCATGACAAGTCTTTTTATGCGTGGCGCCAATAGCAACCAGACCCTGGTATTGCTGGATGGGCAGCGCATCAATAACGCTACCAATGGCCTGCCAGCGCTCAACGCCCTGGCGCCGGCCAACATCGAACGAGTGGAAATCGTCCGCGGAGCGCTCAGTAGTTTGTATGGTGCCGATGCGATGGGGGGCGTTATCAATATCATCACTCAACCCGCCTCTACTCAGCCATTTTCAGCTTGGACCAACGCGGGCGTAGGCACCTATGCCACCGGTAGCTATAGCGCCGGACTAGCGGGCACGACGGACGGCTGGCGCTATAGCTTAGCGGCCGGTTACGGCCAAAGCAGCGGCTATAACGCCAGCAACCGCAAGAACATCTTTAACTACAACCCGGATAAAGATAGCTACTACCAAAACAATGTGGCCACCTCTTTAGGCTACACATGGCAGCCAGAGCAAACCCTGGCTGCGCGCTACTATCGAAGTCGCGTCAACAGCGGCTATGACAACGGTCTGCCCTACTTTAACGATCGGGCTATTCAAACTGTGGCAGCCTATACGCTAGCCAGCACTAACCGCCTAACCGATTTCTGGTTAAGCATGCTGCGCGTGGGCAGCACGGTAGATAACAATCGTTCCGAGAATGCACCCGGCGACGTCAAGCCTGGAGACACGCCCGACGGTATAAGCACCTTCCGCACCCACCAGACCCAGTATGTCTGGCAAAACGATTTAACGCTGGCGCCACAACACAAGCTAACGCTGGCCTACGAATATCTACGCCAGAGCGTGGCTGGCGATATTGCCGACTTCCATACTTACCCGCCCACCTTTACTGATTATCGACAGACGCACCGTCACACCAACTCGTACACTGGTGTTTACCTAGGTGACTTCGGACGCCACCATGTGCAGGCCAGTCTACGCAACGACCGCAACTCGCAGTTTGGCAGTCACACCACGGGCGGTCTGACCTATGGGTGGGACATAACGCCGAATCTCCGAGCGATAGGCGCTGGCAACACGGGTTTTCGCGCGCCTGGTTTCAATGAGCTGTATTGGCCGGATGACAGCGGGTTTCGCGGCAATCCCAACTTAAAACCGGAAAAATCTCGCAACGCCGAAATGGGACTGCGCTATGAAGACGGTACGAGCGAACTAGGCGCCACTTATTATCACAACCGCATCCATAACTTGATTGTTAATGAACAGCTCAATGATCCCCAGCCGGTCTACCAACCGTACAACGTTGGCAAGGCAACGCTGGCAGGCTTTACTTTCACCGGCGCCCGTCGATTCGGCCATACCCGTTTGCGCGCCGAGGTGGATTTGACCGATCCGCGCAACGACGATACCGGCCGCCAGCTACCACAACGTGCACGGCAGCGACCAACGCTACGACGCCCTCACCGGCGACCGACTGGCCGGCTATGGGTTGTGCAACCTAACAGCAACATACGATTTGACCAGCAATATACAAATACAGGTGCGATGGAACAACGTATTCGATCACCGCTATACCTTGCTGCAGGGCTACAACACGCCCGGCTCGAACGCGTTTATCAACCTGCGCTGGCACATGTGAAAGCGATAGGTGCTGGGCTACTGATCACACTAGCGCTATGCGCGCATGCAGCCTGGGCAGAACTTTGGGTCGCGGATGACCGCGGCAACAGGGTAATGTTGGTCGCCCCAGCCCGGCGCGCCATCATACTTGCGCCGCACGCCGCCGAACTTGCGTATGCGGCGGGCGCCGGCAACCACATCATCGGCACGGTACGCGGCAGTGACTACCCCCCTACGCTGCGGGCTGTGCCGTCAGTCGGCGATGGCACTATGCCTGACGCCGAGCGTATCGTCGCTTTGCATCCCGATCTGGTTATCGCCTGGCAGACGGCCGCAGTCGCACCATTGGCACCTATCTTGCAGCGCTTGAATGTGCCGCTCTACTATAGCGATCCCCAAACCCTGGCCGCTATACCGGCAGCCATTGTACGAATGGGTCAGCTGTTTGGCACCCAGGCCCAAGCTGAAGCAGCGGCCGCAGCCATGCAGCACCGCCTAGAGGTTTTGCAAAGCCAGTATAGCCAACGCCAACCAATCAAAGTCTTTATACAGACTGGCTTGGCGCCCTTGTACACCTTGAACCGCACCAGCATTATTAGCGACGCCGTGGCGATATGCGGCGGCGTCAATGTATTTGGCAACGCCGCCGTCGTGGCGCCGCAAGTTACATGGGAAGCCGTCCTAGCGGCGCAGCCGCAAGCCGTACTGGCCGGCGTATCGAACCCTAGCGACAATAAAGCAAACTTGCATACCTGGCGAGCCATGGGCTTACCGGCTGCCGCGGCCGGCCATGTTTTTGGCATTGACGCCGACATGCTTTATCGACCCGCGCCACGACTCATCGACGCCACCGAACAACTCTGCAAAATGCTAGATAGTCTGCGTCACTAA

Transcript

BRAKERKRET00000023707

Protein

UniProt (Swiss-Prot top hit)

UniProt accession	Description
Q6LLU3	Vitamin B12 transporter BtuB OS=Photobacterium profundum (strain SS9) OX=298386 GN=btuB PE=3 SV=1
A7FD14	Vitamin B12 transporter BtuB OS=Yersinia pseudotuberculosis serotype O:1b (strain IP 31758) OX=349747 GN=btuB PE=3 SV=1
Q66G57	Vitamin B12 transporter BtuB OS=Yersinia pseudotuberculosis serotype I (strain IP32953) OX=273123 GN=btuB PE=3 SV=1

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0016188 (this species only)

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF01497 all species →	Peripla_BP_2	Periplasmic binding protein	Domain	Interproscan
PF07715 all species →	Plug	TonB-dependent Receptor Plug Domain	Domain	Interproscan
PF00593 all species →	TonB_dep_Rec	TonB dependent receptor	Family	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR002491 all species →	Domain	ABC transporter periplasmic binding domain	Interproscan
IPR036942 all species →	Homologous_superfamily	TonB-dependent receptor-like, beta-barrel domain superfamily	Interproscan
IPR039426 all species →	Family	TonB-dependent receptor-like	Interproscan
IPR012910 all species →	Domain	TonB-dependent receptor, plug domain	Interproscan
IPR000531 all species →	Domain	TonB-dependent receptor-like, beta-barrel	Interproscan
IPR037066 all species →	Homologous_superfamily	TonB-dependent receptor, plug domain superfamily	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR30069 all species →	TONB-DEPENDENT OUTER MEMBRANE RECEPTOR	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0015889 all species →	Biological Process	cobalamin transport	Interproscan
GO:0031230 all species →	Cellular Component	obsolete intrinsic component of cell outer membrane	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

No KEGG orthology assignment for BRAKERKREP00000023707.1.

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

Expression pattern (RNA-seq)

Transcript abundance of BRAKERKREP00000023707.1 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

11TPM > 0

7Conditions

37.1Max TPM

10.1Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
whole body	18	2	3.98	37.09
Whole	6	5	23.05	34.09
aposymbioic hydra M9 strain · aposymbioic hydra rep1	1	1	26.66	26.66
aposymbioic hydra M9 strain · aposymbioic hydra rep2	1	1	23.22	23.22
symbioic hydra M9 strain · symbioic hydra rep1	1	1	17.52	17.52
symbioic hydra M9 strain · symbioic hydra rep2	1	1	16.30	16.30
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
SRR21134064	whole body	whole body	not recorded	not recorded	SRP392977	37.09
SRR21134060	whole body	whole body	not recorded	not recorded	SRP392977	34.62
SRR21134050	whole body	whole body	not recorded	not recorded	SRP392977	0.00
SRR21134051	whole body	whole body	not recorded	not recorded	SRP392977	0.00
SRR21134052	whole body	whole body	not recorded	not recorded	SRP392977	0.00
SRR21134053	whole body	whole body	not recorded	not recorded	SRP392977	0.00
SRR21134054	whole body	whole body	not recorded	not recorded	SRP392977	0.00
SRR21134055	whole body	whole body	not recorded	not recorded	SRP392977	0.00
SRR21134056	whole body	whole body	not recorded	not recorded	SRP392977	0.00
SRR21134057	whole body	whole body	not recorded	not recorded	SRP392977	0.00
SRR21134058	whole body	whole body	not recorded	not recorded	SRP392977	0.00
SRR21134059	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
SRR10058806	Whole	Whole	not recorded	not recorded	SRP220397	34.09
SRR10058803	Whole	Whole	not recorded	not recorded	SRP220397	30.52
SRR10058804	Whole	Whole	not recorded	not recorded	SRP220397	28.13
SRR10058807	Whole	Whole	not recorded	not recorded	SRP220397	24.89
SRR10058805	Whole	Whole	not recorded	not recorded	SRP220397	20.66
SRR10058802	Whole	Whole	not recorded	not recorded	SRP220397	0.00
DRR048593	aposymbioic hydra M9 strain · aposymbioic hydra rep1	not recorded	not recorded	aposymbioic hydra rep1	DRP003902	26.66
DRR048594	aposymbioic hydra M9 strain · aposymbioic hydra rep2	not recorded	not recorded	aposymbioic hydra rep2	DRP003902	23.22
DRR048595	symbioic hydra M9 strain · symbioic hydra rep1	not recorded	not recorded	symbioic hydra rep1	DRP003902	17.52
DRR048596	symbioic hydra M9 strain · symbioic hydra rep2	not recorded	not recorded	symbioic hydra rep2	DRP003902	16.30
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.