Basic Information

Type: gene

Biological Identity

Species

rosa_samantha

Chromosome

Chr4C

Orthogroup ID

OG0006852

Physical Location & Seq

Genomic Coordinates Reverse (-)

49815155 .. 49815340

Gene Structure 186 bp

Loading structure...

UTR

Exon/CDS

Intron

Transcript / Protein ID

Rh4CG248500.1

Sequence Viewer

CDS Protein Promoter (2k)

Length: 186 bp

ATGGATGGTTTGTTGAACAAGGAAGAGTTGAAGGAGAAAACAGAAGAAGATAAGCTTGCTGTTTACTGGAATGCAAACAAGGAAGTTGCTATTTTTCTAAATCATCGGAGAGAAGTGTCAGATTTTGAAGAGAAACAAGCTTGGGAGCTTAGCATACAAATCTTTGAACTAGAGGCGCAAAAATAA

Functional Annotation

Gene Ontology

Molecular Function
Biological Process
Cellular Component

GO:0000228 GO:0003674 GO:0003824 GO:0003916 GO:0003917 GO:0005575 GO:0005622 GO:0005623 GO:0005634 GO:0005657 GO:0005694 GO:0005730 GO:0006139 GO:0006259 GO:0006260 GO:0006265 GO:0006325 GO:0006338 GO:0006725 GO:0006807 GO:0006996 GO:0007059 GO:0008150 GO:0008152 GO:0009058 GO:0009059 GO:0009987 GO:0016020 GO:0016043 GO:0016853 GO:0031298 GO:0031974 GO:0031981 GO:0032991 GO:0034641 GO:0034645 GO:0043170 GO:0043226 GO:0043227 GO:0043228 GO:0043229 GO:0043231 GO:0043232 GO:0043233 GO:0043596 GO:0044237 GO:0044238 GO:0044249 GO:0044260 GO:0044422 GO:0044424 GO:0044427 GO:0044428 GO:0044446 GO:0044454 GO:0044464 GO:0046483 GO:0051276 GO:0070013 GO:0071103 GO:0071704 GO:0071840 GO:0090304 GO:0140097 GO:1901360 GO:1901576

KEGG Pathways

Metabolic & Signaling

No pathways identified.

Pfam Domains

Protein Families

Topo_C_assoc Topoisom_I Topoisom_I_N

Protein Analysis

61

Amino Acids

7.33

Weight (kDa)

4.68

Isoelectric Point (pI)

46.89

Instability Index

Protein Domains (Pfam)

Domain Name	Pfam ID	Position	E-value	Description
Topoisom_I	PF01028	3 - 60	1e-07	Eukaryotic DNA topoisomerase I, catalytic core

Hydrophobicity Profile (Kyte-Doolittle)

AI Structure Prediction Report

Calculating structure properties...

Genomic Context

Gene Family Tree

Species Filter

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Align Labels (Cladogram)

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Publication-ready

iTOL Interactive Tree Of Life · Most popular EvolView Flexible annotations MEGA Desktop phylogenetics suite FigTree Desktop tree editor

Orthologous Genes (Group: OG0006852)

Species	Orthologous Gene IDs
arabidopsis_thaliana	AT4G26701
rosa_chinensis	RchiOBHm_Chr1g0370531 RchiOBHm_Chr4g0420291 RchiOBHm_Chr4g0421651 RchiOBHm_Chr4g0421661
rosa_laevigata	RLG00000007661 RLG00000027031
rosa_multiflora	Rmu_sc0022275.1_g000007 Rmu_sc0026595.1_g000002
rosa_roxburghii	Rroxscaffold_5G00362880 Rroxscaffold_5G00362920
rosa_rugosa	Rorug01G0357400 Rorug04G0161800 Rorug04G0174200
rosa_samantha	Rh1AG366300 Rh1BG328900 Rh1BG329600 Rh1BG329800 Rh1CG342300 Rh1CG342400 Rh1CG343500 Rh1CG343700 Rh4BG236700 Rh4BG236800 Rh4CG248500 Rh4CG248600

Restriction Enzyme Sites

1 / 10

Enzyme	Recognition Site	Cut Count	Positions (bp)
AgsI	TTSAA	4 cut(s)	16, 31, 128, 167
AluBI	AGCT	3 cut(s)	55, 140, 148
AluI	AGCT	3 cut(s)	55, 140, 148
AspLEI	GCGC	1 cut(s)	178
BfaI	CTAG	1 cut(s)	170
BlpI	GCTNAGC	1 cut(s)	149
Bpu1102I	GCTNAGC	1 cut(s)	149
Bse1I	ACTGG	1 cut(s)	71
BseGI	GGATG	1 cut(s)	10
BseNI	ACTGG	1 cut(s)	71
BsmI	GAATGC	1 cut(s)	76
Bsp1720I	GCTNAGC	1 cut(s)	149
BsrI	ACTGG	1 cut(s)	71
Bst6I	CTCTTC	2 cut(s)	18, 123
BstC8I	GCNNGC	1 cut(s)	57
BstDEI	CTNAG	1 cut(s)	149
BstF5I	GGATG	1 cut(s)	10
BstHHI	GCGC	1 cut(s)	178
BtsCI	GGATG	1 cut(s)	10
Cac8I	GCNNGC	1 cut(s)	57
CfoI	GCGC	1 cut(s)	178
CviJI	RGCY	3 cut(s)	55, 140, 148
CviKI_1	RGCY	3 cut(s)	55, 140, 148
DdeI	CTNAG	1 cut(s)	149
Eam1104I	CTCTTC	2 cut(s)	18, 123
EarI	CTCTTC	2 cut(s)	18, 123
FaiI	YATR	1 cut(s)	155
FalI	AAGNNNNNCTT	2 cut(s)	39, 71
FokI	GGATG	1 cut(s)	17
FspBI	CTAG	1 cut(s)	170
FspEI	CC	8 cut(s)	5, 17, 52, 65, 91, 127, 128, 158
GlaI	GCGC	1 cut(s)	177
HhaI	GCGC	1 cut(s)	178
Hin6I	GCGC	1 cut(s)	176
HinP1I	GCGC	1 cut(s)	176
HindIII	AAGCTT	2 cut(s)	53, 138
Hpy166II	GTNNAC	1 cut(s)	64
Hpy188I	TCNGA	2 cut(s)	108, 121
Hpy8I	GTNNAC	1 cut(s)	64
HpyAV	CCTTC	1 cut(s)	25
HpyCH4V	TGCA	1 cut(s)	74
HpyF3I	CTNAG	1 cut(s)	149
HspAI	GCGC	1 cut(s)	176
LmnI	GCTCC	1 cut(s)	145
LpnPI	CCDG	1 cut(s)	52
MaeI	CTAG	1 cut(s)	170
MboII	GAAGA	4 cut(s)	35, 56, 59, 140
MnlI	CCTC	1 cut(s)	166
Mva1269I	GAATGC	1 cut(s)	76
PctI	GAATGC	1 cut(s)	76
SetI	ASST	3 cut(s)	57, 142, 150
SgeI	CNNG	7 cut(s)	31, 68, 79, 91, 149, 153, 182
SspMI	CTAG	1 cut(s)	170
XspI	CTAG	1 cut(s)	170

Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.