Gene detail

Detailed information of OS493_011686-T1 in Lophelia pertusa

Genomic Location: scaffold_30:160733...168441
NR annotation: KAJ7336485.1, DNA mismatch repair protein [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
P40692	DNA mismatch repair protein Mlh1 OS=Homo sapiens OX=9606 GN=MLH1 PE=1 SV=1
Q9JK91	DNA mismatch repair protein Mlh1 OS=Mus musculus OX=10090 GN=Mlh1 PE=1 SV=2
P97679	DNA mismatch repair protein Mlh1 OS=Rattus norvegicus OX=10116 GN=Mlh1 PE=2 SV=1

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0005246 (this species only)

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF01119 all species →	DNA_mis_repair	DNA mismatch repair protein, C-terminal domain	Family	Interproscan
PF16413 all species →	Mlh1_C	DNA mismatch repair protein Mlh1 C-terminus	Domain	Interproscan
PF13589 all species →	HATPase_c_3	Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase	Domain	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR013507 all species →	Domain	DNA mismatch repair protein, S5 domain 2-like	Interproscan
IPR036890 all species →	Homologous_superfamily	Histidine kinase/HSP90-like ATPase superfamily	Interproscan
IPR002099 all species →	Family	DNA mismatch repair protein MutL/Mlh/PMS	Interproscan
IPR014721 all species →	Homologous_superfamily	Small ribosomal subunit protein uS5 domain 2-type fold, subgroup	Interproscan
IPR038973 all species →	Family	DNA mismatch repair protein MutL/Mlh/Pms-like	Interproscan
IPR014762 all species →	Conserved_site	DNA mismatch repair, conserved site	Interproscan
IPR020568 all species →	Homologous_superfamily	Ribosomal protein uS5 domain 2-type superfamily	Interproscan
IPR032189 all species →	Domain	DNA mismatch repair protein Mlh1, C-terminal	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR10073 all species →	DNA MISMATCH REPAIR PROTEIN MLH, PMS, MUTL	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0005524 all species →	Molecular Function	ATP binding	Interproscan
GO:0006298 all species →	Biological Process	mismatch repair	Interproscan
GO:0030983 all species →	Molecular Function	mismatched DNA binding	Interproscan
GO:0016887 all species →	Molecular Function	ATP hydrolysis activity	Interproscan
GO:0032300 all species →	Cellular Component	mismatch repair complex	Interproscan
GO:0032389 all species →	Cellular Component	MutLalpha complex	Interproscan
GO:0140664 all species →	Molecular Function	ATP-dependent DNA damage sensor activity	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
K08734	MLH1; DNA mismatch repair protein MLH1	-	DNA repair and recombination proteins	ko03400	deepkoala

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

Expression pattern (RNA-seq)

Transcript abundance of OS493_011686-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

98TPM > 0

7Conditions

44.5Max TPM

1.2Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
polyp at pH7 9	18	16	0.98	1.91
polyp at pH7 6	18	14	0.71	1.61
coral polyp · control treatment	16	15	3.41	44.47
coral polyp · oil and dispersant treatment	16	16	1.65	19.25
coral polyp · oil treatment	16	15	0.74	1.58
coral polyp · dispersant treatment	16	15	0.53	1.21
Polyp	10	7	0.52	1.18

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

SRA run	Condition	Tissue	Developmental stage	Treatment	Study	TPM
SRR11359522	polyp at pH7 9	not recorded	not recorded	not recorded	-	1.91
SRR11359519	polyp at pH7 9	not recorded	not recorded	not recorded	-	1.83
SRR11359521	polyp at pH7 9	not recorded	not recorded	not recorded	-	1.74
SRR11359523	polyp at pH7 9	not recorded	not recorded	not recorded	-	1.69
SRR11359520	polyp at pH7 9	not recorded	not recorded	not recorded	-	1.63
SRR11359518	polyp at pH7 9	not recorded	not recorded	not recorded	-	1.52
SRR11359497	polyp at pH7 9	not recorded	not recorded	not recorded	-	1.15
SRR11359510	polyp at pH7 9	not recorded	not recorded	not recorded	-	1.01
SRR11359494	polyp at pH7 9	not recorded	not recorded	not recorded	-	0.98
SRR11359496	polyp at pH7 9	not recorded	not recorded	not recorded	-	0.91
SRR11359508	polyp at pH7 9	not recorded	not recorded	not recorded	-	0.90
SRR11359511	polyp at pH7 9	not recorded	not recorded	not recorded	-	0.69
SRR11359506	polyp at pH7 9	not recorded	not recorded	not recorded	-	0.52
SRR11359498	polyp at pH7 9	not recorded	not recorded	not recorded	-	0.50
SRR11359509	polyp at pH7 9	not recorded	not recorded	not recorded	-	0.47
SRR11359499	polyp at pH7 9	not recorded	not recorded	not recorded	-	0.18
SRR11359495	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
SRR11359528	polyp at pH7 6	not recorded	not recorded	not recorded	-	1.61
SRR11359515	polyp at pH7 6	not recorded	not recorded	not recorded	-	1.38
SRR11359514	polyp at pH7 6	not recorded	not recorded	not recorded	-	1.22
SRR11359527	polyp at pH7 6	not recorded	not recorded	not recorded	-	1.21
SRR11359529	polyp at pH7 6	not recorded	not recorded	not recorded	-	1.19
SRR11359526	polyp at pH7 6	not recorded	not recorded	not recorded	-	1.08
SRR11359524	polyp at pH7 6	not recorded	not recorded	not recorded	-	0.96
SRR11359513	polyp at pH7 6	not recorded	not recorded	not recorded	-	0.94
SRR11359505	polyp at pH7 6	not recorded	not recorded	not recorded	-	0.75
SRR11359504	polyp at pH7 6	not recorded	not recorded	not recorded	-	0.66
SRR11359517	polyp at pH7 6	not recorded	not recorded	not recorded	-	0.51
SRR11359502	polyp at pH7 6	not recorded	not recorded	not recorded	-	0.46
SRR11359503	polyp at pH7 6	not recorded	not recorded	not recorded	-	0.44
SRR11359516	polyp at pH7 6	not recorded	not recorded	not recorded	-	0.38
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
SRR11359525	polyp at pH7 6	not recorded	not recorded	not recorded	-	0.00
SRR16705973	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	44.47
SRR16705974	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	1.58
SRR16705960	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	1.22
SRR16705972	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	1.00
SRR16705975	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	0.99
SRR16705971	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	0.95
SRR16705965	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	0.92
SRR16705942	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	0.91
SRR16705946	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	0.84
SRR16705991	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	0.45
SRR16705970	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	0.43
SRR16705990	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	0.33
SRR16705943	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	0.31
SRR16705957	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	0.07
SRR16705992	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	0.03
SRR16705989	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	19.25
SRR16705948	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	1.02
SRR16705976	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.83
SRR16705997	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.80
SRR16705979	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.75
SRR16705993	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.71
SRR16705995	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.69
SRR16705996	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.44
SRR16706004	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.40
SRR16705978	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.39
SRR16705945	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.35
SRR16705982	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.24
SRR16705947	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.18
SRR16705994	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.17
SRR16706005	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.13
SRR16705944	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.08
SRR16705950	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	1.58
SRR16706000	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	1.44
SRR16705999	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	1.18
SRR16705964	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	1.04
SRR16705952	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	1.02
SRR16706001	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	1.02
SRR16705984	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	0.98
SRR16705998	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	0.72
SRR16705983	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	0.62
SRR16705951	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	0.62
SRR16705981	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	0.51
SRR16705961	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	0.40
SRR16705949	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	0.34
SRR16705962	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	0.23
SRR16705980	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	0.07
SRR16705963	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	0.00
SRR16705959	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1.21
SRR16705958	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1.17
SRR16706003	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1.16
SRR16705955	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.86
SRR16705954	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.78
SRR16705967	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.70
SRR16705986	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.52
SRR16705988	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.50
SRR16705956	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.46
SRR16705987	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.43
SRR16705968	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.24
SRR16706002	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.16
SRR16705985	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.13
SRR16705966	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.11
SRR16705969	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
SRR23025710	Polyp	not recorded	not recorded	not recorded	-	1.18
SRR23025713	Polyp	not recorded	not recorded	not recorded	-	1.00
SRR23025711	Polyp	not recorded	not recorded	not recorded	-	0.73
SRR23025709	Polyp	not recorded	not recorded	not recorded	-	0.72
SRR23025708	Polyp	not recorded	not recorded	not recorded	-	0.62
SRR23025712	Polyp	not recorded	not recorded	not recorded	-	0.48
SRR7746666	Polyp	not recorded	not recorded	not recorded	-	0.47
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.