Gene detail

Detailed information of OS493_001240-T1 in Lophelia pertusa

Genomic Location: scaffold_2:6768739...6783779
NR annotation: KAJ7387890.1, hypothetical protein OS493_001240 [Desmophyllum pertusum]
Species Lophelia pertusa · all data for this species · gene families

Gene Structure

More details in JBrowse

Sequence

CDS

Transcript

Protein

UniProt (Swiss-Prot top hit)

UniProt accession	Description
Q9CUU3	Synaptonemal complex protein 2 OS=Mus musculus OX=10090 GN=Sycp2 PE=1 SV=2
O70608	Synaptonemal complex protein 2 OS=Rattus norvegicus OX=10116 GN=Sycp2 PE=1 SV=1
Q9BX26	Synaptonemal complex protein 2 OS=Homo sapiens OX=9606 GN=SYCP2 PE=1 SV=2

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0002822 (this species only)

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF18584 all species →	SYCP2_SLD	Synaptonemal complex 2 Spt16M-like domain	Domain	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR040560 all species →	Domain	Synaptonemal complex protein 2, Spt16M-like domain	Interproscan
IPR024835 all species →	Family	Synaptonemal complex protein 2-like	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR15607 all species →	SYNAPTONEMAL COMPLEX PROTEIN-RELATED	Interproscan

Gene Ontology

No Gene Ontology signature was detected for OS493_001240-T1. This gene does have a gene model — the search simply returned no hit.

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_001240-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_001240-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

84TPM > 0

7Conditions

170.7Max TPM

5.0Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
polyp at pH7 9	18	8	0.67	2.32
polyp at pH7 6	18	9	0.80	2.10
coral polyp · control treatment	16	15	11.88	157.40
coral polyp · oil and dispersant treatment	16	15	14.18	170.72
coral polyp · oil treatment	16	15	2.34	6.79
coral polyp · dispersant treatment	16	16	3.84	17.35
Polyp	10	6	0.50	2.10

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

SRA run	Condition	Tissue	Developmental stage	Treatment	Study	TPM
SRR11359510	polyp at pH7 9	not recorded	not recorded	not recorded	-	2.32
SRR11359511	polyp at pH7 9	not recorded	not recorded	not recorded	-	2.23
SRR11359498	polyp at pH7 9	not recorded	not recorded	not recorded	-	1.83
SRR11359522	polyp at pH7 9	not recorded	not recorded	not recorded	-	1.51
SRR11359499	polyp at pH7 9	not recorded	not recorded	not recorded	-	1.32
SRR11359523	polyp at pH7 9	not recorded	not recorded	not recorded	-	1.24
SRR11359496	polyp at pH7 9	not recorded	not recorded	not recorded	-	1.12
SRR11359509	polyp at pH7 9	not recorded	not recorded	not recorded	-	0.55
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
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
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
SRR11359514	polyp at pH7 6	not recorded	not recorded	not recorded	-	2.10
SRR11359527	polyp at pH7 6	not recorded	not recorded	not recorded	-	2.01
SRR11359515	polyp at pH7 6	not recorded	not recorded	not recorded	-	1.94
SRR11359504	polyp at pH7 6	not recorded	not recorded	not recorded	-	1.61
SRR11359526	polyp at pH7 6	not recorded	not recorded	not recorded	-	1.56
SRR11359502	polyp at pH7 6	not recorded	not recorded	not recorded	-	1.56
SRR11359503	polyp at pH7 6	not recorded	not recorded	not recorded	-	1.42
SRR11359529	polyp at pH7 6	not recorded	not recorded	not recorded	-	1.41
SRR11359505	polyp at pH7 6	not recorded	not recorded	not recorded	-	0.85
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
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
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
SRR11359528	polyp at pH7 6	not recorded	not recorded	not recorded	-	0.00
SRR16705973	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	157.40
SRR16705942	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	10.81
SRR16705946	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	5.76
SRR16705991	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	5.27
SRR16705974	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	4.96
SRR16705972	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	0.86
SRR16705960	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	0.84
SRR16705971	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	0.68
SRR16705989	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	0.65
SRR16705965	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	0.65
SRR16705970	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	0.62
SRR16705992	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	0.56
SRR16705957	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	0.43
SRR16705975	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	0.37
SRR16705990	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	0.21
SRR16705943	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	0.00
SRR16705977	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	170.72
SRR16705978	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	15.08
SRR16705996	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	13.16
SRR16706004	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	8.25
SRR16705947	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	7.87
SRR16705995	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	2.64
SRR16705948	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	2.32
SRR16705997	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	2.10
SRR16705976	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	1.24
SRR16705982	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.90
SRR16705945	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.67
SRR16706005	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.59
SRR16705979	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.53
SRR16705993	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.47
SRR16705944	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.41
SRR16705994	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	6.79
SRR16705951	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	6.73
SRR16706000	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	6.18
SRR16705983	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	3.87
SRR16705998	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	2.77
SRR16705950	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	2.41
SRR16705999	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	2.26
SRR16705961	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	1.32
SRR16706001	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	1.19
SRR16705980	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	1.17
SRR16705949	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	0.74
SRR16705964	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	0.67
SRR16705984	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	0.62
SRR16705952	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	0.39
SRR16705981	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	0.25
SRR16705962	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	0.00
SRR16705987	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	17.35
SRR16705968	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	11.40
SRR16705955	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	10.60
SRR16705958	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	9.41
SRR16705988	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	2.29
SRR16706002	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1.57
SRR16705985	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1.45
SRR16706003	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1.40
SRR16705954	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1.22
SRR16705967	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1.16
SRR16705969	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1.02
SRR16705966	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.75
SRR16705956	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.70
SRR16705986	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.63
SRR16705953	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.30
SRR16705959	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.24
SRR23025711	Polyp	not recorded	not recorded	not recorded	-	2.10
SRR23025712	Polyp	not recorded	not recorded	not recorded	-	0.95
SRR23025709	Polyp	not recorded	not recorded	not recorded	-	0.79
SRR7746666	Polyp	not recorded	not recorded	not recorded	-	0.44
SRR23025713	Polyp	not recorded	not recorded	not recorded	-	0.41
SRR7746668	Polyp	not recorded	not recorded	not recorded	-	0.27
SRR23025708	Polyp	not recorded	not recorded	not recorded	-	0.00
SRR23025710	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.