Gene detail

Detailed information of XP_001640384.2 in Nematostella vectensis

Genomic Location: NC_064045.1:11614229...11621089
NR annotation: XP_001640384.2, glycine betaine transporter 1 [Nematostella vectensis]
Species Nematostella vectensis · all data for this species · gene families

Gene Structure

More details in JBrowse

Sequence

CDS

LOC5520560

ATGGTTGAACTTCATCACGGAGACCAGTCTCACATTGAAAAATGTCGTACCGTCAAATTCAACATCGGAAAGCTTCGAGTAAACTTTAATCCCGTAGTAACAGCAGGTTCTGCTTTCCTTATCTGGGGGCTCGTGGTGTTTTGTCTCGTTGAGACCAAAGTCGCGGCTGCCCATTTGCCCACATGGACAAGATGGGTTACCGATAAGTGGACCTGGCTCTACATCGGGACCCAAGACTCCTGGGCCGTGTTCATTATCGTTCTGTTCTTCTCAAAGTATTCACATCTCAAGCTTGCTAAATCAGACGACGAAGAGCCGGAGTTTAGCGATGGTTCATACTTCAGTATGCTGTTCGCTGCTGGGATAGGTGTTGGGTTATTTTACTTTGGAATAGCTGAACCTGTGCAACACTATCAGCCCGGTACTCCCGGCGATCCTAGTGGCGTCTGGGGAAACCGCTTTCAAGGGAGGTATTCTGACAACCAGCGCGTCCAGGACGCCATCAACGTGACCTTGTTTCACTGGGGAATCCACGGCTGGATCGTCTACACCATGATTGGTTTGTTGTTGGGCTTCCTGTCTTATCGCTACAACATGCCCATGACCATGCGCACGTGCTTCTACCCGTTGCTAGGCGACAAGATCTACGGCACCTTCGGCGACCTGATCGATATCCTGTCGGTGGTGTGCACCATGTTCGGCGTTTGCACGAGTCTCGGCGCTGGAGCGATCCAACTCAACGACGGACTCAACCGGTTGAATAATAACATTCCAAAGTCACGTGAGAGTCAGGTGATTATCATCTGGGGAATAACAGCGATAGCCACCGCATCTGTGATCAGCGGCATAAAGATTGGTATCCGTCGCCTGAGCGAGATCTGTTTTGCCCTTGGGATGTTTATATTCTTTGTGGTGTTTTATTTTGATGATACCTGGTTCTTGCTGAACGTGTTCGTCCAGAGCATCGGCTACTACCTGCAGTGGATCGTGCAGATTGGCTTCCACACCGACGCCTTCGCTCAACTTGGGAACGCCCCTGACGGCAAGCAAGCCCCAAATTGGATGAATGACTGGACCATTTTCTACTGGGGTTGGTGGATCGCGTGGGCTCCCTTTGTTGGCGTGTTCATCGCGCGCATCTCGCGTGGACGGACCATCAGGCAGTTCATCACCTACACCCTGACCGTCTCCATTATCTATTGCATCATGTGGTTCTCTATTTTCGGCGCTATCGGGATCAAGATGGAGCGCGAGGCGGAACTCGCGGGAATCCAGTGCAACTCTACTTACGGTGGCGCTACTTCCAAGCAGTCTTCCGATGGTCTGTTCCGTCTGTCCTGCCGCCCCTCTACGAGCATGTGGTTTGACGTCATGGATCAATACGGAGGAATCGGACCTTTTCTCTCAGGAATTTCCATCGTCGGCCTCGTCCTCTACTTCGTTACCAGCTCCGACAGTGGCTCTCTCGTGATTGACAGCCTCTCAGCCAATGGCCACCCAGATCCACCGGTGCTGCAGCGAGTGTTCTGGGCTCTGACGGAAGGCGCTTGTGCCACGGGCTTGCTGTGGACGGGCGGATCAAAGGCGTTGAGCGCTCTTCAGGCAGCGTCTGTATCATCAGGTCTCTTGTACACCGTCATCCTCAACTTCGTTTGTATCGCTACATGGCGAGCTGTCAAGTACGACACGGGGGACCTCGATTTTGACGGACCGCGGTTTACTATGGGAATCTTCGATATCTTCTATGCTCCTTCTGTCGGCCGGTTTAAAAGGCTTGCTATTGCTGTTGTCGCCCCCTGGTGGCCTATGGCATACGCTGCTCATAAGGTGGACGGATCACGTCGCTGGCTCGTCATGCTCACCATCGCTGTCCCATTCTACGGATGGCTTCTCCTGCTGGCGTTACATCCCCTTGAGGCCGGCTTAGCTTACATCGGATGGTCTATTCTGATGGGCTTTGTCGTCCTTGGCGCTGGCATTCGTGGGAAGATACGAGAGAGGTACTTCATCATCGGCAACATGGCGGAAGACTTCTTCGCGGTTCTTCTCCTGTACCCTTTCGCAGCTATACAAATGCAGGAACACATGATGTTCTCTAAGAACCCGCACGCTGACCCAGGTCAAAGCCATCCATCTACAGCCAATGGCGGGATCGATGCCAAAGTCAACGTGACCGTAGATATGAATGGGCTGAACGGAAGCAATAACGTGTTCTCAAGACCATCTAAGCTGACAAGAGACAATTTTTCAATGACGTCATATCTTTAA

Transcript

rna-XM_001640334.3

TGACAATTTTTCGCACGCTATTCATAAGCCTAATGGTATTGTCTTttaaatacagaaaaatatttgctcCTTGGGGTAGTTCATACTTGATTGCACCCGTCGCCAGTCGGATCGGTCGCTCATCTTCGAAAGTTCCTTGCAGCGTTTGGATGATTTAGAATGGTTGAACTTCATCACGGAGACCAGTCTCACATTGAAAAATGTCGTACCGTCAAATTCAACATCGGAAAGCTTCGAGTAAACTTTAATCCCGTAGTAACAGCAGGTTCTGCTTTCCTTATCTGGGGGCTCGTGGTGTTTTGTCTCGTTGAGACCAAAGTCGCGGCTGCCCATTTGCCCACATGGACAAGATGGGTTACCGATAAGTGGACCTGGCTCTACATCGGGACCCAAGACTCCTGGGCCGTGTTCATTATCGTTCTGTTCTTCTCAAAGTATTCACATCTCAAGCTTGCTAAATCAGACGACGAAGAGCCGGAGTTTAGCGATGGTTCATACTTCAGTATGCTGTTCGCTGCTGGGATAGGTGTTGGGTTATTTTACTTTGGAATAGCTGAACCTGTGCAACACTATCAGCCCGGTACTCCCGGCGATCCTAGTGGCGTCTGGGGAAACCGCTTTCAAGGGAGGTATTCTGACAACCAGCGCGTCCAGGACGccatcaacgtgaccttgttTCACTGGGGAATCCACGGCTGGATCGTCTACACCATGATTGGTTTGTTGTTGGGCTTCCTGTCTTATCGCTACAACATGCCCATGACCATGCGCACGTGCTTCTACCCGTTGCTAGGCGACAAGATCTACGGCACCTTCGGCGACCTGATCGATATCCTGTCGGTGGTGTGCACCATGTTCGGCGTTTGCACGAGTCTCGGCGCTGGAGCGATCCAACTCAACGACGGACTCAACCGGTTGAATAATAACATTCCAAAGTCACGTGAGAGTCAGGTGATTATCATCTGGGGAATAACAGCGATAGCCACCGCATCTGTGATCAGCGGCATAAAGATTGGTATCCGTCGCCTGAGCGAGATCTGTTTTGCCCTTGGGATGTTTATATTCTTTGTggtgttttattttgatgataCCTGGTTCTTGCTGAACGTGTTCGTCCAGAGCATCGGCTACTACCTGCAGTGGATCGTGCAGATTGGCTTCCACACCGACGCCTTCGCTCAACTTGGGAACGCCCCTGACGGCAAGCAAGCCCCAAATTGGATGAATGACTGGACCATTTTCTACTGGGGTTGGTGGATCGCGTGGGCTCCCTTTGTTGGCGTGTTCATCGCGCGCATCTCGCGTGGACGGACCATCAGGCAGTTCATCACCTACACCCTGACCGTCTCCATTATCTATTGCATCATGTGGTTCTCTATTTTCGGCGCTATCGGGATCAAGATGGAGCGCGAGGCGGAACTCGCGGGAATCCAGTGCAACTCTACTTACGGTGGCGCTACTTCCAAGCAGTCTTCCGATGGTCTGTTCCGTCTGTCCTGCCGCCCCTCTACGAGCATGTGGTTTGACGTCATGGATCAATACGGAGGAATCGGACCTTTTCTCTCAGGAATTTCCATCGTCGGCCTCGTCCTCTACTTCGTTACCAGCTCCGACAGTGGCTCTCTCGTGATTGACAGCCTCTCAGCCAATGGCCACCCAGATCCACCGGTGCTGCAGCGAGTGTTCTGGGCTCTGACGGAAGGCGCTTGTGCCACGGGCTTGCTGTGGACGGGCGGATCAAAGGCGTTGAGCGCTCTTCAGGCAGCGTCTGTATCATCAGGTCTCTTGTACACCGTCATCCTCAACTTCGTTTGTATCGCTACATGGCGAGCTGTCAAGTACGACACGGGGGACCTCGATTTTGACGGACCGCGGTTTACTATGGGAATCTTCGATATCTTCTATGCTCCTTCTGTCGGCCGGTTTAAAAGGCTTGCTATTGCTGTTGTCGCCCCCTGGTGGCCTATGGCATACGCTGCTCATAAGGTGGACGGATCACGTCGCTGGCTCGTCATGCTCACCATCGCTGTCCCATTCTACGGATGGCTTCTCCTGCTGGCGTTACATCCCCTTGAGGCCGGCTTAGCTTACATCGGATGGTCTATTCTGATGGGCTTTGTCGTCCTTGGCGCTGGCATTCGTGGGAAGATACGAGAGAGGTACTTCATCATCGGCAACATGGCGGAAGACTTCTTCGCGGTTCTTCTCCTGTACCCTTTCGCAGCTATACAAATGCAGGAACACATGATGTTCTCTAAGAACCCGCACGCTGACCCAGGTCAAAGCCATCCATCTACAGCCAATGGCGGGATCGATGCCAAAGTCAACGTGACCGTAGATATGAATGGGCTGAACGGAAGCAATAACGTGTTCTCAAGACCATCTAAGCTGACAAGAGACAATTtttcaatgacgtcatatctTTAAGGGTGCTTTGAATGTCTACCCGTGATGCAATTTTCTTATAGCTATAGTAGTCCCAATAGATGCAGGTCTGGTTATAGTGATTCTAACATTTTGATTATAGATATACCACAATGTTCCAATGCATTATAACTTATTGCACCCGCCTTTACTTGATGTCACGACCAAGATGTTAATGTTATTGCAAACTTTCTAACAATCATTGCTAATAAGCAAGATTCATAAAAAAGGCATTCAATTAAACTACGAATACACA

Protein

UniProt (Swiss-Prot top hit)

UniProt accession	Description
Q87NG3	Glycine betaine transporter 1 OS=Vibrio parahaemolyticus serotype O3:K6 (strain RIMD 2210633) OX=223926 GN=VP1905 PE=1 SV=1
P9WPR6	Uncharacterized transporter MT0942 OS=Mycobacterium tuberculosis (strain CDC 1551 / Oshkosh) OX=83331 GN=MT0942 PE=3 SV=1
P9WPR7	Uncharacterized transporter Rv0917 OS=Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) OX=83332 GN=Rv0917 PE=3 SV=1

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0000591 (this species only)

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF02028 all species →	BCCT	BCCT, betaine/carnitine/choline family transporter	Family	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR000060 all species →	Family	BCCT transporter family	Interproscan
IPR018093 all species →	Conserved_site	BCCT transporter, conserved site	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR30047 all species →	HIGH-AFFINITY CHOLINE TRANSPORT PROTEIN-RELATED	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0005886 all species →	Cellular Component	plasma membrane	Interproscan
GO:0006810 all species →	Biological Process	transport	Interproscan
GO:0016020 all species →	Cellular Component	membrane	Interproscan
GO:0016021 all species →	Cellular Component	membrane	Interproscan
GO:0022857 all species →	Molecular Function	transmembrane transporter activity	Interproscan
GO:0071705 all species →	Biological Process	nitrogen compound transport	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 XP_001640384.2.

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

Expression pattern (RNA-seq)

Transcript abundance of XP_001640384.2 across 48 RNA-seq samples of Nematostella vectensis. 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.

48Samples

43TPM > 0

16Conditions

35.9Max TPM

14.3Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
whole 6 week old aboral regenerate · regenerate 96hpa	3	3	25.20	29.35
whole 6 week old aboral regenerate · regenerate 144hpa	3	3	19.74	26.59
whole 6 week old aboral regenerate · regenerate 0hpa	3	3	13.88	14.79
whole 6 week old aboral regenerate · regenerate 2hpa	3	3	10.88	12.62
whole 6 week old aboral regenerate · regenerate uncut	3	3	21.36	24.56
whole 6 week old aboral regenerate · regenerate 4hpa	3	2	4.42	7.96
whole 6 week old aboral regenerate · regenerate 120hpa	3	3	22.79	26.81
whole 6 week old aboral regenerate · regenerate 36hpa	3	3	14.22	16.41
whole 6 week old aboral regenerate · regenerate 24hpa	3	2	7.00	11.70
whole 6 week old aboral regenerate · regenerate 20hpa	3	3	10.12	11.75
whole 6 week old aboral regenerate · regenerate 16hpa	3	3	10.25	10.51
whole 6 week old aboral regenerate · regenerate 72hpa	3	2	12.66	21.08
whole 6 week old aboral regenerate · regenerate 60hpa	3	3	16.65	17.28
whole 6 week old aboral regenerate · regenerate 48hpa	3	3	24.77	35.86
whole 6 week old aboral regenerate · regenerate 8hpa	3	3	11.20	12.70
whole 6 week old aboral regenerate · regenerate 12hpa	3	1	3.65	10.95

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

SRA run	Condition	Tissue	Developmental stage	Treatment	Study	TPM
SRR6320863	whole 6 week old aboral regenerate · regenerate 96hpa	whole 6 week old aboral regenerate	six weeks	regenerate 96hpa	SRP125570	29.35
SRR6320836	whole 6 week old aboral regenerate · regenerate 96hpa	whole 6 week old aboral regenerate	six weeks	regenerate 96hpa	SRP125570	26.04
SRR6320837	whole 6 week old aboral regenerate · regenerate 96hpa	whole 6 week old aboral regenerate	six weeks	regenerate 96hpa	SRP125570	20.22
SRR6320847	whole 6 week old aboral regenerate · regenerate 144hpa	whole 6 week old aboral regenerate	six weeks	regenerate 144hpa	SRP125570	26.59
SRR6320838	whole 6 week old aboral regenerate · regenerate 144hpa	whole 6 week old aboral regenerate	six weeks	regenerate 144hpa	SRP125570	17.18
SRR6320841	whole 6 week old aboral regenerate · regenerate 144hpa	whole 6 week old aboral regenerate	six weeks	regenerate 144hpa	SRP125570	15.45
SRR6320846	whole 6 week old aboral regenerate · regenerate 0hpa	whole 6 week old aboral regenerate	six weeks	regenerate 0hpa	SRP125570	14.79
SRR6320840	whole 6 week old aboral regenerate · regenerate 0hpa	whole 6 week old aboral regenerate	six weeks	regenerate 0hpa	SRP125570	14.25
SRR6320839	whole 6 week old aboral regenerate · regenerate 0hpa	whole 6 week old aboral regenerate	six weeks	regenerate 0hpa	SRP125570	12.61
SRR6320848	whole 6 week old aboral regenerate · regenerate 2hpa	whole 6 week old aboral regenerate	six weeks	regenerate 2hpa	SRP125570	12.62
SRR6320861	whole 6 week old aboral regenerate · regenerate 2hpa	whole 6 week old aboral regenerate	six weeks	regenerate 2hpa	SRP125570	10.05
SRR6320842	whole 6 week old aboral regenerate · regenerate 2hpa	whole 6 week old aboral regenerate	six weeks	regenerate 2hpa	SRP125570	9.96
SRR6320844	whole 6 week old aboral regenerate · regenerate uncut	whole 6 week old aboral regenerate	six weeks	regenerate uncut	SRP125570	24.56
SRR6320845	whole 6 week old aboral regenerate · regenerate uncut	whole 6 week old aboral regenerate	six weeks	regenerate uncut	SRP125570	20.92
SRR6320843	whole 6 week old aboral regenerate · regenerate uncut	whole 6 week old aboral regenerate	six weeks	regenerate uncut	SRP125570	18.59
SRR6320872	whole 6 week old aboral regenerate · regenerate 4hpa	whole 6 week old aboral regenerate	six weeks	regenerate 4hpa	SRP125570	7.96
SRR6320849	whole 6 week old aboral regenerate · regenerate 4hpa	whole 6 week old aboral regenerate	six weeks	regenerate 4hpa	SRP125570	5.31
SRR6320873	whole 6 week old aboral regenerate · regenerate 4hpa	whole 6 week old aboral regenerate	six weeks	regenerate 4hpa	SRP125570	0.00
SRR6320882	whole 6 week old aboral regenerate · regenerate 120hpa	whole 6 week old aboral regenerate	six weeks	regenerate 120hpa	SRP125570	26.81
SRR6320883	whole 6 week old aboral regenerate · regenerate 120hpa	whole 6 week old aboral regenerate	six weeks	regenerate 120hpa	SRP125570	23.21
SRR6320850	whole 6 week old aboral regenerate · regenerate 120hpa	whole 6 week old aboral regenerate	six weeks	regenerate 120hpa	SRP125570	18.36
SRR6320851	whole 6 week old aboral regenerate · regenerate 36hpa	whole 6 week old aboral regenerate	six weeks	regenerate 36hpa	SRP125570	16.41
SRR6320855	whole 6 week old aboral regenerate · regenerate 36hpa	whole 6 week old aboral regenerate	six weeks	regenerate 36hpa	SRP125570	13.59
SRR6320852	whole 6 week old aboral regenerate · regenerate 36hpa	whole 6 week old aboral regenerate	six weeks	regenerate 36hpa	SRP125570	12.66
SRR6320854	whole 6 week old aboral regenerate · regenerate 24hpa	whole 6 week old aboral regenerate	six weeks	regenerate 24hpa	SRP125570	11.70
SRR6320853	whole 6 week old aboral regenerate · regenerate 24hpa	whole 6 week old aboral regenerate	six weeks	regenerate 24hpa	SRP125570	9.32
SRR6320856	whole 6 week old aboral regenerate · regenerate 24hpa	whole 6 week old aboral regenerate	six weeks	regenerate 24hpa	SRP125570	0.00
SRR6320859	whole 6 week old aboral regenerate · regenerate 20hpa	whole 6 week old aboral regenerate	six weeks	regenerate 20hpa	SRP125570	11.75
SRR6320860	whole 6 week old aboral regenerate · regenerate 20hpa	whole 6 week old aboral regenerate	six weeks	regenerate 20hpa	SRP125570	10.03
SRR6320857	whole 6 week old aboral regenerate · regenerate 20hpa	whole 6 week old aboral regenerate	six weeks	regenerate 20hpa	SRP125570	8.60
SRR6320858	whole 6 week old aboral regenerate · regenerate 16hpa	whole 6 week old aboral regenerate	six weeks	regenerate 16hpa	SRP125570	10.51
SRR6320880	whole 6 week old aboral regenerate · regenerate 16hpa	whole 6 week old aboral regenerate	six weeks	regenerate 16hpa	SRP125570	10.30
SRR6320881	whole 6 week old aboral regenerate · regenerate 16hpa	whole 6 week old aboral regenerate	six weeks	regenerate 16hpa	SRP125570	9.93
SRR6320862	whole 6 week old aboral regenerate · regenerate 72hpa	whole 6 week old aboral regenerate	six weeks	regenerate 72hpa	SRP125570	21.08
SRR6320865	whole 6 week old aboral regenerate · regenerate 72hpa	whole 6 week old aboral regenerate	six weeks	regenerate 72hpa	SRP125570	16.91
SRR6320864	whole 6 week old aboral regenerate · regenerate 72hpa	whole 6 week old aboral regenerate	six weeks	regenerate 72hpa	SRP125570	0.00
SRR6320866	whole 6 week old aboral regenerate · regenerate 60hpa	whole 6 week old aboral regenerate	six weeks	regenerate 60hpa	SRP125570	17.28
SRR6320867	whole 6 week old aboral regenerate · regenerate 60hpa	whole 6 week old aboral regenerate	six weeks	regenerate 60hpa	SRP125570	17.27
SRR6320869	whole 6 week old aboral regenerate · regenerate 60hpa	whole 6 week old aboral regenerate	six weeks	regenerate 60hpa	SRP125570	15.40
SRR6320868	whole 6 week old aboral regenerate · regenerate 48hpa	whole 6 week old aboral regenerate	six weeks	regenerate 48hpa	SRP125570	35.86
SRR6320871	whole 6 week old aboral regenerate · regenerate 48hpa	whole 6 week old aboral regenerate	six weeks	regenerate 48hpa	SRP125570	19.57
SRR6320870	whole 6 week old aboral regenerate · regenerate 48hpa	whole 6 week old aboral regenerate	six weeks	regenerate 48hpa	SRP125570	18.88
SRR6320874	whole 6 week old aboral regenerate · regenerate 8hpa	whole 6 week old aboral regenerate	six weeks	regenerate 8hpa	SRP125570	12.70
SRR6320875	whole 6 week old aboral regenerate · regenerate 8hpa	whole 6 week old aboral regenerate	six weeks	regenerate 8hpa	SRP125570	11.88
SRR6320876	whole 6 week old aboral regenerate · regenerate 8hpa	whole 6 week old aboral regenerate	six weeks	regenerate 8hpa	SRP125570	9.02
SRR6320877	whole 6 week old aboral regenerate · regenerate 12hpa	whole 6 week old aboral regenerate	six weeks	regenerate 12hpa	SRP125570	10.95
SRR6320878	whole 6 week old aboral regenerate · regenerate 12hpa	whole 6 week old aboral regenerate	six weeks	regenerate 12hpa	SRP125570	0.00
SRR6320879	whole 6 week old aboral regenerate · regenerate 12hpa	whole 6 week old aboral regenerate	six weeks	regenerate 12hpa	SRP125570	0.00

Source: CnidoSite RNA-seq expression matrices (NVECT_TPM, StringTie quantification over 48 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.