Gene detail

Detailed information of OS493_012536-T1 in Lophelia pertusa

Genomic Location: scaffold_33:283293...287834
NR annotation: KAJ7379790.1, Regulator of chromosome condensation [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
P18754	Regulator of chromosome condensation OS=Homo sapiens OX=9606 GN=RCC1 PE=1 SV=1
P23800	Regulator of chromosome condensation OS=Mesocricetus auratus OX=10036 GN=RCC1 PE=1 SV=1
Q8VE37	Regulator of chromosome condensation OS=Mus musculus OX=10090 GN=Rcc1 PE=1 SV=1

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0007688 (this species only)

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF00415 all species →	RCC1	Regulator of chromosome condensation (RCC1) repeat	Repeat	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR000408 all species →	Repeat	Regulator of chromosome condensation, RCC1	Interproscan
IPR051553 all species →	Family	Ran GTPase-activating	Interproscan
IPR009091 all species →	Homologous_superfamily	Regulator of chromosome condensation 1/beta-lactamase-inhibitor protein II	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR45982 all species →	REGULATOR OF CHROMOSOME CONDENSATION	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0005085 all species →	Molecular Function	guanyl-nucleotide exchange factor activity	Interproscan
GO:0005737 all species →	Cellular Component	cytoplasm	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
K11493	RCC1; regulator of chromosome condensation	-	Chromosome and associated proteins	ko03036	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_012536-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

110TPM > 0

7Conditions

43.3Max TPM

17.1Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
polyp at pH7 9	18	18	11.04	18.49
polyp at pH7 6	18	18	14.39	26.77
coral polyp · control treatment	16	16	22.81	43.32
coral polyp · oil and dispersant treatment	16	16	23.31	41.90
coral polyp · oil treatment	16	16	18.00	40.21
coral polyp · dispersant treatment	16	16	15.72	34.13
Polyp	10	10	14.33	31.23

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

SRA run	Condition	Tissue	Developmental stage	Treatment	Study	TPM
SRR11359519	polyp at pH7 9	not recorded	not recorded	not recorded	-	18.49
SRR11359495	polyp at pH7 9	not recorded	not recorded	not recorded	-	17.38
SRR11359494	polyp at pH7 9	not recorded	not recorded	not recorded	-	16.23
SRR11359518	polyp at pH7 9	not recorded	not recorded	not recorded	-	14.91
SRR11359523	polyp at pH7 9	not recorded	not recorded	not recorded	-	13.82
SRR11359522	polyp at pH7 9	not recorded	not recorded	not recorded	-	13.75
SRR11359497	polyp at pH7 9	not recorded	not recorded	not recorded	-	11.07
SRR11359520	polyp at pH7 9	not recorded	not recorded	not recorded	-	10.98
SRR11359507	polyp at pH7 9	not recorded	not recorded	not recorded	-	10.98
SRR11359496	polyp at pH7 9	not recorded	not recorded	not recorded	-	10.53
SRR11359521	polyp at pH7 9	not recorded	not recorded	not recorded	-	9.41
SRR11359499	polyp at pH7 9	not recorded	not recorded	not recorded	-	9.02
SRR11359506	polyp at pH7 9	not recorded	not recorded	not recorded	-	8.15
SRR11359498	polyp at pH7 9	not recorded	not recorded	not recorded	-	7.76
SRR11359509	polyp at pH7 9	not recorded	not recorded	not recorded	-	7.24
SRR11359511	polyp at pH7 9	not recorded	not recorded	not recorded	-	6.83
SRR11359508	polyp at pH7 9	not recorded	not recorded	not recorded	-	6.70
SRR11359510	polyp at pH7 9	not recorded	not recorded	not recorded	-	5.54
SRR11359524	polyp at pH7 6	not recorded	not recorded	not recorded	-	26.77
SRR11359525	polyp at pH7 6	not recorded	not recorded	not recorded	-	23.85
SRR11359504	polyp at pH7 6	not recorded	not recorded	not recorded	-	18.90
SRR11359505	polyp at pH7 6	not recorded	not recorded	not recorded	-	18.60
SRR11359529	polyp at pH7 6	not recorded	not recorded	not recorded	-	16.51
SRR11359517	polyp at pH7 6	not recorded	not recorded	not recorded	-	15.71
SRR11359516	polyp at pH7 6	not recorded	not recorded	not recorded	-	15.42
SRR11359528	polyp at pH7 6	not recorded	not recorded	not recorded	-	15.28
SRR11359526	polyp at pH7 6	not recorded	not recorded	not recorded	-	14.26
SRR11359527	polyp at pH7 6	not recorded	not recorded	not recorded	-	13.26
SRR11359513	polyp at pH7 6	not recorded	not recorded	not recorded	-	12.82
SRR11359501	polyp at pH7 6	not recorded	not recorded	not recorded	-	11.28
SRR11359500	polyp at pH7 6	not recorded	not recorded	not recorded	-	11.27
SRR11359512	polyp at pH7 6	not recorded	not recorded	not recorded	-	10.84
SRR11359515	polyp at pH7 6	not recorded	not recorded	not recorded	-	9.40
SRR11359514	polyp at pH7 6	not recorded	not recorded	not recorded	-	9.37
SRR11359502	polyp at pH7 6	not recorded	not recorded	not recorded	-	7.84
SRR11359503	polyp at pH7 6	not recorded	not recorded	not recorded	-	7.71
SRR16705973	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	43.32
SRR16705965	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	32.85
SRR16705971	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	31.36
SRR16705957	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	30.10
SRR16705990	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	29.56
SRR16705960	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	23.94
SRR16705972	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	21.98
SRR16705974	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	21.72
SRR16705946	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	20.11
SRR16705942	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	19.57
SRR16705943	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	17.06
SRR16705975	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	15.83
SRR16705991	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	14.49
SRR16705989	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	14.48
SRR16705970	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	14.37
SRR16705992	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	14.20
SRR16705977	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	41.90
SRR16705993	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	41.88
SRR16705995	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	36.39
SRR16705945	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	29.49
SRR16706004	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	24.51
SRR16706005	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	24.13
SRR16705979	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	22.52
SRR16705982	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	21.70
SRR16705978	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	19.93
SRR16705944	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	19.66
SRR16705947	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	18.78
SRR16705996	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	16.36
SRR16705976	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	15.00
SRR16705948	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	14.69
SRR16705997	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	13.90
SRR16705994	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	12.21
SRR16705999	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	40.21
SRR16705949	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	27.51
SRR16705981	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	21.69
SRR16705962	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	21.50
SRR16705952	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	20.42
SRR16705983	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	20.09
SRR16706000	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	19.59
SRR16706001	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	17.30
SRR16705984	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	15.93
SRR16705951	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	14.64
SRR16705961	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	14.09
SRR16705980	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	13.75
SRR16705963	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	12.12
SRR16705998	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	11.32
SRR16705950	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	9.95
SRR16705964	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	7.93
SRR16705958	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	34.13
SRR16705986	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	25.10
SRR16705969	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	20.15
SRR16705967	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	19.51
SRR16705968	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	19.05
SRR16705959	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	19.03
SRR16705955	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	17.12
SRR16705988	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	15.86
SRR16706003	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	15.09
SRR16705954	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	14.86
SRR16705956	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	14.68
SRR16705987	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	12.04
SRR16706002	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	9.74
SRR16705966	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	9.36
SRR16705985	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	4.41
SRR16705953	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1.42
SRR7746667	Polyp	not recorded	not recorded	not recorded	-	31.23
SRR23025710	Polyp	not recorded	not recorded	not recorded	-	26.97
SRR7746669	Polyp	not recorded	not recorded	not recorded	-	19.35
SRR23025713	Polyp	not recorded	not recorded	not recorded	-	13.08
SRR23025712	Polyp	not recorded	not recorded	not recorded	-	12.00
SRR7746668	Polyp	not recorded	not recorded	not recorded	-	11.34
SRR23025708	Polyp	not recorded	not recorded	not recorded	-	11.26
SRR23025709	Polyp	not recorded	not recorded	not recorded	-	7.50
SRR23025711	Polyp	not recorded	not recorded	not recorded	-	6.87
SRR7746666	Polyp	not recorded	not recorded	not recorded	-	3.70

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.