Gene detail

Detailed information of OS493_036683-T1 in Lophelia pertusa

Genomic Location: scaffold_379:88700...107067
NR annotation: KAJ7388610.1, Hemicentin-1 [Desmophyllum pertusum]
Species Lophelia pertusa · all data for this species · gene families

Gene Structure

More details in JBrowse

Sequence

CDS

OS493_036683-T1

ATGGTAATTGGAGCAAATGGAACCTATGGAGTGTCTGTACTAAGACAGTCAGTGGTATACAAACAAGGACGAGAGAATGCACTAATCCAGAGCCAGCATATGGTGGAAAACGCTTGTAATGAAACCAGAGCAGTAGTAAGGGAGTGTAGCAACATGTCTAGCTGCCATGACGTTCCTGTACGCTTAAATGGTGCAGATATAGAATATGGTGGAAGAGTGGAAGTATTTTACAAGGGAAAATGGGGAAAGATCTGCCGTAATGAATGGGATTTCAATGATGTAAAAGTTATTTGCCGTCAACTTGGCTTCAAAGGCGCGCTGGCTGAATTCATTGGGTCGGATGTCAAGGATGAGGGACATCCTTTCGTAATGTCTGGTGTAACCTGCACTGGAGATGAGTCTGAACTGGCATCCTGTGCACGCATTGATGGAAAGCTTAATATTGACTGTCAAAACGATGACGAAGGTGCTCAGTATTGTGCGAACCAAGTAAAGAATAAAGAAGTCTTGGAAAAGAAACAATTAGAATTTAACATCGACGCCAGCGAAACAGTTAGCTGCTCCATTCAAAACAAAACCAATTTCATTAAATGGTTTGTTAACAACAAAGAAGTCAATTCTACATCCGGGACGAGGATTAGGGTGACAGAAAATGGAAAATTGTTCATAGACAAAGTTCAGTTGTCTGATGGAGGAATTTATGAATGCAGGAGATTAGAATATGCAAAGTACTACACCATCTACATTAATGCGAGATTTTCGGAGAAGGCTCCTAAACAAAGTCTTATTGTTGACACATCTGGGATTATAAACTGTAGTGCTGAGGGAACGCCAAGCCCACTGATTAGTTGGAACAAACAAGATGGAGTACTGATGTACAAGCCAAAGGGCAGATTCAGACAATTTTCTAATGGGAGTTTGCATGTTGATCCAGTTCACCCCGGAGACAATGGAACATATATCTGTACAATGAAACAATATAAAGGAACTGACAGGGTCACAAGCACGCCTCAAACCATAAAAGTTTCTGTTATAATTCCTCCAAATGTTCAGTTGTTGGGACCAAACAAGCCCATACGAGAAGGAGACAGTGTCAACCTGACATGTAAAATTAACAAAGGTTTTCCTAAACCACAAATATCCTGGTCTAAAGATGGCACAGAGCGTAAAGAAAAGAGTACAACTTTGATCTTAACAGGGGTAAAAGATGAAGACGAGGGAATGTACACCTGTAAAGCAGAAAATGCCGGTGGTGCTTTCAGACACAGCTATAGCAAATATGTTACTGTTGATGTTCCACCTAAAGTGAATCCTGAACTCAGGAATCGTTCTGTTGAATTGAACTCCACGTTGACAATGACATGCTTTGTGAGAGGTGCTCCACTACCAAAAGTCAACTGGACTAAGAATGGAGTGGGTCTTGGTAACAACAATAACACATTCACTATTGAGCATGTGACATTCAAGCACGCAGGCTTGTATGGGTGTGCAGCTGTAAACCGGGTGGGAAAAACTCACACCACGTTTTGGATTAACATAACAGTCTCTCCTCAGGTTTATGTGTCTCCGAGAAACCAATCTGTTCCGGAAGGCTACCCAACCAACTTTACTTGCAAAGCCACCGGTATTCCAAAGCCGACATTGTCCTGGAATTTTAATGATGGGGACCTCCCATCGGGTGTCAGTCAAAGCGATACTAAGGAAGGATCATTCCTGGAGTTGTTAAACACAACTAAAAGTATGGAAGGGACATACAAGTGTACAGCGAAAAACAAAGCGAATGCGACAACTTCCTCTGCAATTCTTCGTGTTTTTGAAAACCCCACTGCTAAAATTAGTCCAAATCCATATCCAACACTTACGGTAGGAGATGAGCTCAGATTAACATGCAAAGTCAATGAAGCAACACTGGAGATCAAATGGAAGAAAAATAGTGACCCAATAAGCCACAGAGCACGCATTGATACACGAGTAGATGAAAAATGGAGCAATTTTTTTATTGAGGAAGTTGTGGGAGGGGATAGTGGTAAATATTCTTGCGAAGCACGTAACAAACCAGGCATTGTGGCCCACTCTACTGTGAAGATCGATGTCAAGGATTCTAATGCCAGGCCGGCTGTTGAGTGGTATTACATTGTTGGACCCATGTCTGCTTGCATTGTCATATTTTTGGTTGGTTGGTACATTCGTAAACGTCAAAGGGCAGCCATGCCCAAATTCCCTAGTAAAGAGCAAGACATTGAGATGGAGCTGCTCAATGTAGAAGTGGATGAATGGGAGATTGCATTTGACCGTATACTACTTCAAGAGGTCATTGGCAGAGGGGCATTTGGAGCAGTCTGGAGAGCACTGTTGAGTCAACCAGATGGAAAACCTGGAAATTGCACAGTTGCTGCGAAATGTTTTACACCCACTTCTGGAGAAGATGGAAGAAAATCTCTGACGAGAGAAATTGAGCTTGGAAAACTTCTTGGAGAAAATCCTCAGCCAAACATTTTCATCCGATACTGGTCATGGAATACTTGGCATGCGGTGACTTGCTGGTTATCTGAGAAAAGCCGAGGAATTCACGATAAGTATCATCTCGGACAGGGGAGTGTTCAAAAGCTGGAAACATATGACCTTGTGTTGTTTGCCAAACAAATCGCTGCTGGCATGGTGTACCTTGGATCAAGAGGGGTTAGTGAACATGTCCCAAAAATTACACTACGACAAAATTCCTTCAAAAACTCCAACTTTCCAAATTCAATCCGAATTCTTCATGTGGGTCACTGCGGATGTTTTACTTACACATTGTTTTAG

Transcript

OS493_036683-T1

Protein

UniProt (Swiss-Prot top hit)

UniProt accession	Description
Q96RW7	Hemicentin-1 OS=Homo sapiens OX=9606 GN=HMCN1 PE=1 SV=2
Q8NDA2	Hemicentin-2 OS=Homo sapiens OX=9606 GN=HMCN2 PE=1 SV=4
D3YXG0	Hemicentin-1 OS=Mus musculus OX=10090 GN=Hmcn1 PE=1 SV=1

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0000305 (this species only)

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF00530 all species →	SRCR	Scavenger receptor cysteine-rich domain	Domain	Interproscan
PF13927 all species →	Ig_3	Immunoglobulin domain	Domain	Interproscan
PF07714 all species →	PK_Tyr_Ser-Thr	Protein tyrosine and serine/threonine kinase	Domain	Interproscan
PF07679 all species →	I-set	Immunoglobulin I-set domain	Domain	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR000719 all species →	Domain	Protein kinase domain	Interproscan
IPR001190 all species →	Domain	SRCR domain	Interproscan
IPR036179 all species →	Homologous_superfamily	Immunoglobulin-like domain superfamily	Interproscan
IPR050831 all species →	Family	Carcinoembryonic antigen-related cell adhesion	Interproscan
IPR003599 all species →	Domain	Immunoglobulin subtype	Interproscan
IPR007110 all species →	Domain	Immunoglobulin-like domain	Interproscan
IPR013783 all species →	Homologous_superfamily	Immunoglobulin-like fold	Interproscan
IPR017448 all species →	Domain	SRCR-like domain	Interproscan
IPR036772 all species →	Homologous_superfamily	SRCR-like domain superfamily	Interproscan
IPR003598 all species →	Domain	Immunoglobulin subtype 2	Interproscan
IPR001245 all species →	Domain	Serine-threonine/tyrosine-protein kinase, catalytic domain	Interproscan
IPR013098 all species →	Domain	Immunoglobulin I-set	Interproscan
IPR017441 all species →	Binding_site	Protein kinase, ATP binding site	Interproscan
IPR011009 all species →	Homologous_superfamily	Protein kinase-like domain superfamily	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR44427 all species →	CARCINOEMBRYONIC ANTIGEN-RELATED CELL ADHESION MOLECULE 19	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0004672 all species →	Molecular Function	protein kinase activity	Interproscan
GO:0005524 all species →	Molecular Function	ATP binding	Interproscan
GO:0006468 all species →	Biological Process	protein phosphorylation	Interproscan
GO:0016020 all species →	Cellular Component	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 OS493_036683-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_036683-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

49TPM > 0

7Conditions

1.1Max TPM

0.2Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
polyp at pH7 9	18	3	0.08	0.81
polyp at pH7 6	18	0	0.00	0.00
coral polyp · control treatment	16	9	0.29	0.83
coral polyp · oil and dispersant treatment	16	12	0.35	1.10
coral polyp · oil treatment	16	12	0.36	1.07
coral polyp · dispersant treatment	16	9	0.18	0.70
Polyp	10	4	0.09	0.32

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

SRA run	Condition	Tissue	Developmental stage	Treatment	Study	TPM
SRR11359498	polyp at pH7 9	not recorded	not recorded	not recorded	-	0.81
SRR11359508	polyp at pH7 9	not recorded	not recorded	not recorded	-	0.34
SRR11359511	polyp at pH7 9	not recorded	not recorded	not recorded	-	0.29
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
SRR11359496	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
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
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
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
SRR11359522	polyp at pH7 9	not recorded	not recorded	not recorded	-	0.00
SRR11359523	polyp at pH7 9	not recorded	not recorded	not recorded	-	0.00
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
SRR11359504	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
SRR11359514	polyp at pH7 6	not recorded	not recorded	not recorded	-	0.00
SRR11359515	polyp at pH7 6	not recorded	not recorded	not recorded	-	0.00
SRR11359516	polyp at pH7 6	not recorded	not recorded	not recorded	-	0.00
SRR11359517	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
SRR16705991	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	0.83
SRR16705946	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	0.76
SRR16705974	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	0.65
SRR16705972	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	0.57
SRR16705942	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	0.52
SRR16705990	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	0.50
SRR16705971	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	0.38
SRR16705965	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	0.32
SRR16705943	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	0.17
SRR16705957	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
SRR16705970	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	0.00
SRR16705973	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
SRR16705989	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
SRR16705996	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	1.10
SRR16706004	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.84
SRR16705978	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.81
SRR16705995	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.67
SRR16705993	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.62
SRR16705947	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.40
SRR16705976	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.29
SRR16705945	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.29
SRR16705994	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.20
SRR16705944	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.19
SRR16706005	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.14
SRR16705948	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.13
SRR16705977	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
SRR16705997	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.00
SRR16705963	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	1.07
SRR16705951	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	1.01
SRR16706000	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	0.88
SRR16705983	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	0.83
SRR16705999	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	0.70
SRR16705980	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	0.32
SRR16705981	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	0.26
SRR16705950	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	0.23
SRR16705949	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	0.18
SRR16705961	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	0.16
SRR16705984	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	0.15
SRR16705962	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	0.04
SRR16705952	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
SRR16705998	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	0.00
SRR16706001	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	0.00
SRR16705958	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.70
SRR16705968	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.57
SRR16705986	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.42
SRR16705955	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.31
SRR16705987	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.26
SRR16705954	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.21
SRR16705967	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.18
SRR16705959	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.10
SRR16705988	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.09
SRR16705953	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.00
SRR16705956	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.00
SRR16705966	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.00
SRR16705969	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
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
SRR23025709	Polyp	not recorded	not recorded	not recorded	-	0.32
SRR23025708	Polyp	not recorded	not recorded	not recorded	-	0.30
SRR7746668	Polyp	not recorded	not recorded	not recorded	-	0.14
SRR23025711	Polyp	not recorded	not recorded	not recorded	-	0.12
SRR23025710	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
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.