Gene detail

Detailed information of XP_032230264.2 in Nematostella vectensis

Genomic Location: NC_064041.1:15084161...15091496
NR annotation: XP_032230264.2, geranylgeranyl transferase type-2 subunit beta-like isoform X1 [Nematostella vectensis]
Species Nematostella vectensis · all data for this species · gene families

Gene Structure

More details in JBrowse

Sequence

CDS

Transcript

rna-XM_032374373.2

GTCTGCATGGTTTAGGCCAGCGGTAACGCTAATTTGTAAATATGGCCGTGTACTTAGAAAGAAACAAATTTCTGCTGTGAATTAATAGCCATTAGAAGTATTGATCTACCATAAAGAGCGTGAAATGGGTACCCAAATCAAGGATGTCAAGATTTCCCAAGATGCACCCAAGACTCTGTTCCTTGATAAGCATGCAGAGTTTATTGCAAGCTATGGGAAAAAGAAAGACACAGACTATGATTACTGTATGACAGAGTATCTACGCATGAGTGGGGTCTACTGGGGGTTAACTGCGATGGCTTTGATGGACAAGTTAGATATGATGAATAGAGAGGAAGCTATTGATTTCGTCAAGTCTTGTCAGCATGACGATGGAGGGTTTGGCGCGAGTGTGTCACATGACCCGCACTTACTGTATACTTTGAGTGCTGTTCAGATTCTTTTCCTGTATGATGCAATAGATGCGGTTGATGTACCAAGTATTGTACAATATGTCAAAAAGCTTCAGCAAGAAGATGGGTCATTTGCGGGTGACAAGTGGGGTGAAATAGACACAAGGTTTTCATTTTGTGCGATAGCTTGCTTACAGCTACTGGACCGTCTGGATGCTATCAACGTTGATAAGGCAGTGGAATATGTAGTGGATTGTATGAATTTTGATGGAGGGTTTGGCTGCAGACCTGGTTCAGAATCACACGCAGGGCAGATCTACTGCTGTCTAGGGGCCCTGTCAATCACTCACTCCCTCCATCACGTTAATGTCGACATGCTGGGCTGGTGGCTTTGCGAGAGGCAGCTTCCATCAGGCGGCTTGAATGgGAGGCCTGAAAAACTACCTGATGTTTGTTATTCTTGGTGGGTTCTGGCTTCACTGAAAATTCTAGGAAAAGTTCACTGGATCAACAAGGAGAAATTAAAGATGTATATATTGGCATGTCAAGACGAGGAAACTGGAGGGTTTGCAGATCGACCAGGAGACATgGTCGACCCATTTCATACCCTGTTCGGACTGACTGGTCTTTCTCTGCTCGGCTCTTCTGAAGTCAAGGCTGTTAATCCTGTGTACTGCCTTCCACAGAGTGcaatattaaaattaaaaagtcAACCAGATATcttagactaaaaagaggtgGAAGGGTATTTAGGGAAATACGAACCTCTTACAAAGTATGTCATTTATATAGCGACGCGCGCTATTGTTTAAATAAAGTTAGCCAGTTAGCATGCGTGAGAACCAGAGCTTTCAGTGACGCGAGCATTTTATCTAGAAGGGCTCGCCTAGTCAGCCTTGGTCCTGTAAAATGAGATGAAATCAAACACATTACTTGACTGGCTTTTGTTTTTGCACTTCGGAAATTTAGTTGCCCACTtgatcgtttttttttttattcttttcttgGATCCGACGGTGTTCTCCTTTGTCAAGTACCCTTCTACGAACTTGCCTGAAAGATTGAAGTCATTTAGACGCATTTTTGTCGTAGCCTTTGAAAGTGAAAGAGTCAATTACTTGCACGATTTCTTTGGAAATGGTTTTTGTTGGACACTATGATACAACTACACATGTACATAAGCTAATCTGTACTGTATCATTTTGTCATTGTCGATTAATATTTGGCCAGAATTTGTCTTTTTGTGGATAACTACAAAATTGCGGACCAAGATACACACTGGCAAATTTTGCAACTTTTTAACTAATTAAGAACTCCATGTGCAAAGTGCCTACATTTTTACCGACAGACGACCAACAGATCAGTGTGACGTTTTGTAAGGAAAGTGTTGGCATTTGTTGCGAATATTACGAATATTTGGCCGAGATATTGAGAACAAACTACTAGTTCGCGGTGCTGTGAAAAGGCAGTATTTAGGGAGCGGCCATTAATTACTGGAGATGGTCCggcaattttgcaaaaccctgGGCTAAAAAATgttgccccccaccccccaccccccaaatcCAAGCCCAAAAATCGTGACCCTTCCTTGACCGGACGCCCAAAAATTTGCaaccccccaccaccaccacctttATATATTCAATAATTATATCTCTTTTAAACCACAGAGACTTGATATACATACTGAGTTTTACTGAATTTAACCTTCACTAAAATATAGATCAGCTAGCATGGCAATTTTGTCCTACTAAATTTAAAAGTATGAATCTTCACTTTCGCTAGTTTAAGAGTGGCACAGACAAGATTGGTACCTGAACAATATGGAACTAGATATACAAAAGTAGGAAACATTGTTAACTGAATAGAATTTTCAATTTAACAATGACTCTCTTGTTGAGTATTATATTAGAACCAGACTTTAATTCGACGCccaaaaaatgtgacccccctTTTAATGACAGCCAAAAAGAaattcgcccccccccccaaaaaaaaatccgcGCCCAAAAAACGAACCCACCCAGTAATAAATGACCGCTCCCTTAGAGATTTTACCCATCTCCTTTGGGCATGCTGGAATGCCAGGAATGAGGGTTGGGAGAGTTAAAAAATCAATCAATTGTTAGGTGAAATCAATTTTAATTAGTCATCTTTTAGCGTATAGATATTCAattaagaaaaagaaattgcCGGACTAGGGTACTAGCCGGACCAACGAA

Protein

UniProt (Swiss-Prot top hit)

UniProt accession	Description
P53611	Geranylgeranyl transferase type-2 subunit beta OS=Homo sapiens OX=9606 GN=RABGGTB PE=1 SV=2
Q08603	Geranylgeranyl transferase type-2 subunit beta OS=Rattus norvegicus OX=10116 GN=Rabggtb PE=1 SV=1
P53612	Geranylgeranyl transferase type-2 subunit beta OS=Mus musculus OX=10090 GN=Rabggtb PE=1 SV=2

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0006218 (this species only) · gene tree & orthology

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF00432 all species →	Prenyltrans	Prenyltransferase and squalene oxidase repeat	Repeat	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR008930 all species →	Homologous_superfamily	Terpenoid cyclases/protein prenyltransferase alpha-alpha toroid	Interproscan
IPR001330 all species →	Repeat	PFTB repeat	Interproscan
IPR026873 all species →	Family	Geranylgeranyl transferase type-2 subunit beta	Interproscan
IPR045089 all species →	Family	Prenyltransferase subunit beta	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR11774 all species →	GERANYLGERANYL TRANSFERASE TYPE BETA SUBUNIT	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0003824 all species →	Molecular Function	catalytic activity	Interproscan
GO:0004663 all species →	Molecular Function	Rab geranylgeranyltransferase activity	Interproscan
GO:0018344 all species →	Biological Process	protein geranylgeranylation	Interproscan
GO:0005968 all species →	Cellular Component	Rab-protein geranylgeranyltransferase complex	Interproscan
GO:0008318 all species →	Molecular Function	protein prenyltransferase activity	Interproscan
GO:0018342 all species →	Biological Process	protein prenylation	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
K05956	RABGGTB; geranylgeranyl transferase type-2 subunit beta	EC:2.5.1.60	Membrane trafficking	ko04131	deepkoala

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

Expression pattern (RNA-seq)

Transcript abundance of XP_032230264.2 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

37TPM > 0

16Conditions

12.2Max TPM

4.5Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
whole 6 week old aboral regenerate · regenerate 96hpa	3	2	4.53	7.29
whole 6 week old aboral regenerate · regenerate 144hpa	3	3	5.46	6.99
whole 6 week old aboral regenerate · regenerate 0hpa	3	3	4.23	5.15
whole 6 week old aboral regenerate · regenerate 2hpa	3	3	4.42	5.23
whole 6 week old aboral regenerate · regenerate uncut	3	3	4.55	5.68
whole 6 week old aboral regenerate · regenerate 4hpa	3	1	1.30	3.89
whole 6 week old aboral regenerate · regenerate 120hpa	3	2	4.57	7.43
whole 6 week old aboral regenerate · regenerate 36hpa	3	3	6.70	8.16
whole 6 week old aboral regenerate · regenerate 24hpa	3	2	3.67	5.61
whole 6 week old aboral regenerate · regenerate 20hpa	3	2	3.59	5.51
whole 6 week old aboral regenerate · regenerate 16hpa	3	3	4.83	5.28
whole 6 week old aboral regenerate · regenerate 72hpa	3	2	4.83	7.65
whole 6 week old aboral regenerate · regenerate 60hpa	3	3	8.37	12.22
whole 6 week old aboral regenerate · regenerate 48hpa	3	2	5.27	8.54
whole 6 week old aboral regenerate · regenerate 8hpa	3	2	3.57	6.04
whole 6 week old aboral regenerate · regenerate 12hpa	3	1	1.82	5.45

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	7.29
SRR6320836	whole 6 week old aboral regenerate · regenerate 96hpa	whole 6 week old aboral regenerate	six weeks	regenerate 96hpa	SRP125570	6.31
SRR6320837	whole 6 week old aboral regenerate · regenerate 96hpa	whole 6 week old aboral regenerate	six weeks	regenerate 96hpa	SRP125570	0.00
SRR6320847	whole 6 week old aboral regenerate · regenerate 144hpa	whole 6 week old aboral regenerate	six weeks	regenerate 144hpa	SRP125570	6.99
SRR6320838	whole 6 week old aboral regenerate · regenerate 144hpa	whole 6 week old aboral regenerate	six weeks	regenerate 144hpa	SRP125570	5.16
SRR6320841	whole 6 week old aboral regenerate · regenerate 144hpa	whole 6 week old aboral regenerate	six weeks	regenerate 144hpa	SRP125570	4.22
SRR6320839	whole 6 week old aboral regenerate · regenerate 0hpa	whole 6 week old aboral regenerate	six weeks	regenerate 0hpa	SRP125570	5.15
SRR6320846	whole 6 week old aboral regenerate · regenerate 0hpa	whole 6 week old aboral regenerate	six weeks	regenerate 0hpa	SRP125570	4.32
SRR6320840	whole 6 week old aboral regenerate · regenerate 0hpa	whole 6 week old aboral regenerate	six weeks	regenerate 0hpa	SRP125570	3.21
SRR6320861	whole 6 week old aboral regenerate · regenerate 2hpa	whole 6 week old aboral regenerate	six weeks	regenerate 2hpa	SRP125570	5.23
SRR6320842	whole 6 week old aboral regenerate · regenerate 2hpa	whole 6 week old aboral regenerate	six weeks	regenerate 2hpa	SRP125570	4.79
SRR6320848	whole 6 week old aboral regenerate · regenerate 2hpa	whole 6 week old aboral regenerate	six weeks	regenerate 2hpa	SRP125570	3.25
SRR6320843	whole 6 week old aboral regenerate · regenerate uncut	whole 6 week old aboral regenerate	six weeks	regenerate uncut	SRP125570	5.68
SRR6320844	whole 6 week old aboral regenerate · regenerate uncut	whole 6 week old aboral regenerate	six weeks	regenerate uncut	SRP125570	4.57
SRR6320845	whole 6 week old aboral regenerate · regenerate uncut	whole 6 week old aboral regenerate	six weeks	regenerate uncut	SRP125570	3.41
SRR6320872	whole 6 week old aboral regenerate · regenerate 4hpa	whole 6 week old aboral regenerate	six weeks	regenerate 4hpa	SRP125570	3.89
SRR6320849	whole 6 week old aboral regenerate · regenerate 4hpa	whole 6 week old aboral regenerate	six weeks	regenerate 4hpa	SRP125570	0.00
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	7.43
SRR6320883	whole 6 week old aboral regenerate · regenerate 120hpa	whole 6 week old aboral regenerate	six weeks	regenerate 120hpa	SRP125570	6.29
SRR6320850	whole 6 week old aboral regenerate · regenerate 120hpa	whole 6 week old aboral regenerate	six weeks	regenerate 120hpa	SRP125570	0.00
SRR6320855	whole 6 week old aboral regenerate · regenerate 36hpa	whole 6 week old aboral regenerate	six weeks	regenerate 36hpa	SRP125570	8.16
SRR6320852	whole 6 week old aboral regenerate · regenerate 36hpa	whole 6 week old aboral regenerate	six weeks	regenerate 36hpa	SRP125570	6.36
SRR6320851	whole 6 week old aboral regenerate · regenerate 36hpa	whole 6 week old aboral regenerate	six weeks	regenerate 36hpa	SRP125570	5.59
SRR6320854	whole 6 week old aboral regenerate · regenerate 24hpa	whole 6 week old aboral regenerate	six weeks	regenerate 24hpa	SRP125570	5.61
SRR6320853	whole 6 week old aboral regenerate · regenerate 24hpa	whole 6 week old aboral regenerate	six weeks	regenerate 24hpa	SRP125570	5.40
SRR6320856	whole 6 week old aboral regenerate · regenerate 24hpa	whole 6 week old aboral regenerate	six weeks	regenerate 24hpa	SRP125570	0.00
SRR6320860	whole 6 week old aboral regenerate · regenerate 20hpa	whole 6 week old aboral regenerate	six weeks	regenerate 20hpa	SRP125570	5.51
SRR6320857	whole 6 week old aboral regenerate · regenerate 20hpa	whole 6 week old aboral regenerate	six weeks	regenerate 20hpa	SRP125570	5.27
SRR6320859	whole 6 week old aboral regenerate · regenerate 20hpa	whole 6 week old aboral regenerate	six weeks	regenerate 20hpa	SRP125570	0.00
SRR6320881	whole 6 week old aboral regenerate · regenerate 16hpa	whole 6 week old aboral regenerate	six weeks	regenerate 16hpa	SRP125570	5.28
SRR6320880	whole 6 week old aboral regenerate · regenerate 16hpa	whole 6 week old aboral regenerate	six weeks	regenerate 16hpa	SRP125570	4.96
SRR6320858	whole 6 week old aboral regenerate · regenerate 16hpa	whole 6 week old aboral regenerate	six weeks	regenerate 16hpa	SRP125570	4.26
SRR6320862	whole 6 week old aboral regenerate · regenerate 72hpa	whole 6 week old aboral regenerate	six weeks	regenerate 72hpa	SRP125570	7.65
SRR6320865	whole 6 week old aboral regenerate · regenerate 72hpa	whole 6 week old aboral regenerate	six weeks	regenerate 72hpa	SRP125570	6.82
SRR6320864	whole 6 week old aboral regenerate · regenerate 72hpa	whole 6 week old aboral regenerate	six weeks	regenerate 72hpa	SRP125570	0.00
SRR6320869	whole 6 week old aboral regenerate · regenerate 60hpa	whole 6 week old aboral regenerate	six weeks	regenerate 60hpa	SRP125570	12.22
SRR6320866	whole 6 week old aboral regenerate · regenerate 60hpa	whole 6 week old aboral regenerate	six weeks	regenerate 60hpa	SRP125570	7.19
SRR6320867	whole 6 week old aboral regenerate · regenerate 60hpa	whole 6 week old aboral regenerate	six weeks	regenerate 60hpa	SRP125570	5.71
SRR6320871	whole 6 week old aboral regenerate · regenerate 48hpa	whole 6 week old aboral regenerate	six weeks	regenerate 48hpa	SRP125570	8.54
SRR6320870	whole 6 week old aboral regenerate · regenerate 48hpa	whole 6 week old aboral regenerate	six weeks	regenerate 48hpa	SRP125570	7.27
SRR6320868	whole 6 week old aboral regenerate · regenerate 48hpa	whole 6 week old aboral regenerate	six weeks	regenerate 48hpa	SRP125570	0.00
SRR6320874	whole 6 week old aboral regenerate · regenerate 8hpa	whole 6 week old aboral regenerate	six weeks	regenerate 8hpa	SRP125570	6.04
SRR6320875	whole 6 week old aboral regenerate · regenerate 8hpa	whole 6 week old aboral regenerate	six weeks	regenerate 8hpa	SRP125570	4.68
SRR6320876	whole 6 week old aboral regenerate · regenerate 8hpa	whole 6 week old aboral regenerate	six weeks	regenerate 8hpa	SRP125570	0.00
SRR6320877	whole 6 week old aboral regenerate · regenerate 12hpa	whole 6 week old aboral regenerate	six weeks	regenerate 12hpa	SRP125570	5.45
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.