Gene detail

Detailed information of OS493_020758-T1 in Lophelia pertusa

Genomic Location: scaffold_77:1327559...1343643
NR annotation: KAJ7358917.1, hypothetical protein OS493_020758 [Desmophyllum pertusum]
Species Lophelia pertusa · all data for this species · gene families

Gene Structure

More details in JBrowse

Sequence

CDS

OS493_020758-T1

ATGAAGGTGAGCTTCGAGCTTCGTAGACGGGCAGACAACAAGGGACCCGACGAAGAAAGGTTTAATCAGTTGGCAAATTCCGTAGAGAAGTTCACTCATTGTTTACTTGATCCACTGAGATCTGATCAAGAAAAACGTGAACAATTTGGAGAAAACATCCTGGATGATATCGTGGACGACGCCATTGATTTAGATCAAAAACAGTTTTTCACGCATCCAGTGGTACATGATGAGATGACTCGTAAATGGCATGGTCGTGCTGAATGTATGAAGAAAACATGGCGTGGTCGTGATTTTAAGAAGAGCGAAATTGGAAGCTGGCTGAAGCTATTACTGTTCCGCTTCTGGTGTATTTTCGATTTGGTGTTTTCTCCAATCCTGTTTTCTGTGTTTTCACTGGTGAAGAAAAGAAGCGAACAATGCGAAAGAAGCCAAGTAGCGAACAGGGACGATCGTCATGTAACAGTGGCAGAGATGTACCTAATATACTTGGAGACGCCATACTTCAAGTTTGTTCGCGACACGCTGAGCTATATAGTGCTTGTTGTTCTGCACTATGCTCTGTGCTTATCGCCATCAACGATAGCGCTCAGCGGATTAGAGTTGGCCATCCTCGTTTTCTTCATAGGCCGCTATCTGGTAGAGGGCAAACAAATCTGCGACATATTGCAACGCATAAAGCAACGGAGAGAGAAGGGGGATGTTGGAGCTCAATCAAAATGGATTCGTCTAAAGACGCTCTCAATATATCTCAGTGACTGCTGGAACAGGCTCGACTTCGTCAGTCTACTTGTCTATCTGATAATTTTCACACTGCGGTTAGTCATCGTGGTCATGTCTGGATCTGAGATGAACAACCGAGCTCTTGCCATTGCTGGTTACTTCTACAGCTTTAACACCTTGTGTCTCACACTAAGGGTATTTGGTTACGTAATGGAACACTCGAGACAAATTGGCCCCATCCAGATGGCTTTATTTAGCATTCTCGCAGATATTCGCGTCATATTCTGGCAGTTTGCAGCTGCCATTCTGGCTTTCTCCATCGCTATAACCAAAGTGTACATGGCTGAGAAATCTTTTATTGCCAATGGAAGTGATGGAAATGACATTTGGTGGACGATAATCACTCACCTGGTCTGGACTCTGTTGGGGGCATCAGAGGAGACCGAACCTGTGACGTCCGTGGACGTTCCTTCTGTGACTCTTGCCCGACTGCTCTACGCCACCTTTCATATCTTTGGAGTCATCCTTCTTTTCAATATGCTGATAGCTTTGCTATCCAACACGTATCAGCGAACACAGGACAACTCGTTAAAGGAGTGGTCAATCAAACGAGCGACTGTAATTCAGACATACGATGGCTATGGTCCAATACCAGTACCACTTAATATCATCTACAGTTTTCTCAAACTACTTGTGAGAGGAAAAGAAAAAGAAACGGCATGGGCCGACGTCGACGAGGGCGTAAGAATAGAGGGTCTCCTATTAACTTGTGAATGTATGTCATGCCAAGATGATGAGACTTGCCATGGTGCTAGACATGGCAAATCCTTTTCTTCCGAGGTTCCTCATTTTGAGGTCGCCATTTTAGAAACTGGAGAAAAAAGATGGCTGGCGGTGGGAGTGGTAACTGAAGAGTACAGTACTAAATGCATGCCGGGATGGAAGAATGGAGCTGTAGGTTACCATACTGATGATGGAATGATCATTCGCGACAATATTACAATGGAAACTAAAGGACCTGCTATGGCTCGTCGAGGTGATCGGATTCGTTGCACAGTCATGTTTGAGAATAAACGAGAGGAAGATGGGAAAGTTCCAGTTGTCTTTACTCTGAACGGCAAGAAGATAATCATGATCATGAAAGAAGGAGACGATCAAATCTTCATGGACGCTGATAAACCATTGTACCCCTGCATTAGCATGACTGACGGGTGTAGTGTGTTGGTTAAGATGTGCTCGAGGGAAGATCTTGACAGCAAGGCTACCGCACAAAGCATGGAGAAGAGAACGACAGAGATCAAACAACAAAACGAGTCATCAATTGCAAGGCGGCTTGCAAAACTTGAGAAAGGGGTTGAGGACGTGTTAGCGATATTGAAAGATATCCTCAAAAAAGACCCACCCAAGGTCTAG

Transcript

OS493_020758-T1

Protein

UniProt (Swiss-Prot top hit)

UniProt accession	Description
Q9R244	Short transient receptor potential channel 2 OS=Mus musculus OX=10090 GN=Trpc2 PE=2 SV=2
Q9UBN4	Short transient receptor potential channel 4 OS=Homo sapiens OX=9606 GN=TRPC4 PE=1 SV=1
P79100	Short transient receptor potential channel 4 OS=Bos taurus OX=9913 GN=TRPC4 PE=2 SV=2

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0000221 (this species only)

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF00622 all species →	SPRY	SPRY domain	Family	Interproscan
PF00520 all species →	Ion_trans	Ion transport protein	Family	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR002153 all species →	Family	Transient receptor potential channel, canonical	Interproscan
IPR003877 all species →	Domain	SPRY domain	Interproscan
IPR013320 all species →	Homologous_superfamily	Concanavalin A-like lectin/glucanase domain superfamily	Interproscan
IPR043136 all species →	Homologous_superfamily	B30.2/SPRY domain superfamily	Interproscan
IPR005821 all species →	Domain	Ion transport domain	Interproscan
IPR044736 all species →	Domain	Ran-binding protein Vid30/RanBPM/SPLA, SPRY domain	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR10117 all species →	TRANSIENT RECEPTOR POTENTIAL CHANNEL	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0005262 all species →	Molecular Function	calcium channel activity	Interproscan
GO:0005886 all species →	Cellular Component	plasma membrane	Interproscan
GO:0005887 all species →	Cellular Component	plasma membrane	Interproscan
GO:0015279 all species →	Molecular Function	store-operated calcium channel activity	Interproscan
GO:0016020 all species →	Cellular Component	membrane	Interproscan
GO:0034703 all species →	Cellular Component	cation channel complex	Interproscan
GO:0051480 all species →	Biological Process	regulation of cytosolic calcium ion concentration	Interproscan
GO:0070588 all species →	Biological Process	calcium ion transmembrane transport	Interproscan
GO:0070679 all species →	Molecular Function	inositol 1,4,5 trisphosphate binding	Interproscan
GO:0005515 all species →	Molecular Function	protein binding	Interproscan
GO:0005216 all species →	Molecular Function	monoatomic ion channel activity	Interproscan
GO:0006811 all species →	Biological Process	monoatomic ion transport	Interproscan
GO:0055085 all species →	Biological Process	transmembrane 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 OS493_020758-T1.

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

Expression pattern (RNA-seq)

Transcript abundance of OS493_020758-T1 across 110 RNA-seq samples of Lophelia pertusa. 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.

110Samples

38TPM > 0

7Conditions

1.3Max TPM

0.1Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
polyp at pH7 9	18	3	0.03	0.27
polyp at pH7 6	18	5	0.17	1.26
coral polyp · control treatment	16	9	0.10	0.47
coral polyp · oil and dispersant treatment	16	7	0.09	0.59
coral polyp · oil treatment	16	7	0.11	0.79
coral polyp · dispersant treatment	16	6	0.08	0.37
Polyp	10	1	0.02	0.15

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

SRA run	Condition	Tissue	Developmental stage	Treatment	Study	TPM
SRR11359523	polyp at pH7 9	not recorded	not recorded	not recorded	-	0.27
SRR11359522	polyp at pH7 9	not recorded	not recorded	not recorded	-	0.26
SRR11359496	polyp at pH7 9	not recorded	not recorded	not recorded	-	0.08
SRR11359494	polyp at pH7 9	not recorded	not recorded	not recorded	-	0.00
SRR11359495	polyp at pH7 9	not recorded	not recorded	not recorded	-	0.00
SRR11359497	polyp at pH7 9	not recorded	not recorded	not recorded	-	0.00
SRR11359498	polyp at pH7 9	not recorded	not recorded	not recorded	-	0.00
SRR11359499	polyp at pH7 9	not recorded	not recorded	not recorded	-	0.00
SRR11359506	polyp at pH7 9	not recorded	not recorded	not recorded	-	0.00
SRR11359507	polyp at pH7 9	not recorded	not recorded	not recorded	-	0.00
SRR11359508	polyp at pH7 9	not recorded	not recorded	not recorded	-	0.00
SRR11359509	polyp at pH7 9	not recorded	not recorded	not recorded	-	0.00
SRR11359510	polyp at pH7 9	not recorded	not recorded	not recorded	-	0.00
SRR11359511	polyp at pH7 9	not recorded	not recorded	not recorded	-	0.00
SRR11359518	polyp at pH7 9	not recorded	not recorded	not recorded	-	0.00
SRR11359519	polyp at pH7 9	not recorded	not recorded	not recorded	-	0.00
SRR11359520	polyp at pH7 9	not recorded	not recorded	not recorded	-	0.00
SRR11359521	polyp at pH7 9	not recorded	not recorded	not recorded	-	0.00
SRR11359517	polyp at pH7 6	not recorded	not recorded	not recorded	-	1.26
SRR11359516	polyp at pH7 6	not recorded	not recorded	not recorded	-	1.23
SRR11359504	polyp at pH7 6	not recorded	not recorded	not recorded	-	0.41
SRR11359514	polyp at pH7 6	not recorded	not recorded	not recorded	-	0.07
SRR11359515	polyp at pH7 6	not recorded	not recorded	not recorded	-	0.06
SRR11359500	polyp at pH7 6	not recorded	not recorded	not recorded	-	0.00
SRR11359501	polyp at pH7 6	not recorded	not recorded	not recorded	-	0.00
SRR11359502	polyp at pH7 6	not recorded	not recorded	not recorded	-	0.00
SRR11359503	polyp at pH7 6	not recorded	not recorded	not recorded	-	0.00
SRR11359505	polyp at pH7 6	not recorded	not recorded	not recorded	-	0.00
SRR11359512	polyp at pH7 6	not recorded	not recorded	not recorded	-	0.00
SRR11359513	polyp at pH7 6	not recorded	not recorded	not recorded	-	0.00
SRR11359524	polyp at pH7 6	not recorded	not recorded	not recorded	-	0.00
SRR11359525	polyp at pH7 6	not recorded	not recorded	not recorded	-	0.00
SRR11359526	polyp at pH7 6	not recorded	not recorded	not recorded	-	0.00
SRR11359527	polyp at pH7 6	not recorded	not recorded	not recorded	-	0.00
SRR11359528	polyp at pH7 6	not recorded	not recorded	not recorded	-	0.00
SRR11359529	polyp at pH7 6	not recorded	not recorded	not recorded	-	0.00
SRR16705972	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	0.47
SRR16705970	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	0.40
SRR16705957	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	0.18
SRR16705942	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	0.16
SRR16705989	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	0.15
SRR16705973	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	0.12
SRR16705990	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	0.08
SRR16705965	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	0.07
SRR16705943	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	0.05
SRR16705946	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	0.00
SRR16705960	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	0.00
SRR16705971	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	0.00
SRR16705974	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	0.00
SRR16705975	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	0.00
SRR16705991	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	0.00
SRR16705992	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	0.00
SRR16705944	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.59
SRR16705997	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.20
SRR16705976	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.18
SRR16705948	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.18
SRR16705995	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.16
SRR16705945	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.07
SRR16706005	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.05
SRR16705947	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.00
SRR16705977	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.00
SRR16705978	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.00
SRR16705979	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.00
SRR16705982	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.00
SRR16705993	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.00
SRR16705994	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.00
SRR16705996	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.00
SRR16706004	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.00
SRR16705950	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	0.79
SRR16705961	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	0.32
SRR16705949	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	0.27
SRR16705999	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	0.20
SRR16705952	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	0.14
SRR16706001	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	0.04
SRR16705981	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	0.04
SRR16705951	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	0.00
SRR16705962	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	0.00
SRR16705963	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	0.00
SRR16705964	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	0.00
SRR16705980	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	0.00
SRR16705983	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	0.00
SRR16705984	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	0.00
SRR16705998	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	0.00
SRR16706000	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	0.00
SRR16705988	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.37
SRR16705967	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.31
SRR16705959	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.29
SRR16705956	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.23
SRR16705969	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.10
SRR16705966	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.06
SRR16705953	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.00
SRR16705954	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.00
SRR16705955	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.00
SRR16705958	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.00
SRR16705968	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.00
SRR16705985	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.00
SRR16705986	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.00
SRR16705987	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.00
SRR16706002	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.00
SRR16706003	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.00
SRR23025708	Polyp	not recorded	not recorded	not recorded	-	0.15
SRR23025709	Polyp	not recorded	not recorded	not recorded	-	0.00
SRR23025710	Polyp	not recorded	not recorded	not recorded	-	0.00
SRR23025711	Polyp	not recorded	not recorded	not recorded	-	0.00
SRR23025712	Polyp	not recorded	not recorded	not recorded	-	0.00
SRR23025713	Polyp	not recorded	not recorded	not recorded	-	0.00
SRR7746666	Polyp	not recorded	not recorded	not recorded	-	0.00
SRR7746667	Polyp	not recorded	not recorded	not recorded	-	0.00
SRR7746668	Polyp	not recorded	not recorded	not recorded	-	0.00
SRR7746669	Polyp	not recorded	not recorded	not recorded	-	0.00

Source: CnidoSite RNA-seq expression matrices (LPERT_TPM, StringTie quantification over 110 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.