Basic Information

Type: gene

Biological Identity

Species

rosa_samantha

Chromosome

Chr2C

Orthogroup ID

OG0004536

Physical Location & Seq

Genomic Coordinates Reverse (-)

1265639 .. 1265914

Gene Structure 276 bp

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UTR

Exon/CDS

Intron

Transcript / Protein ID

Rh2CG016000.1

Sequence Viewer

CDS Protein Promoter (2k)

Length: 276 bp

ATGACATGGTTGGGTGTTTGGCCGAGTGACCTATGTGCGCTTGACATACCCTGCGACGATATGAGTCCAAAAGAGATTAGAGACATGGATAATCTTTTGAAAGAAGATTTTGTGAAAGATAATCCGAGGTTGGTTGAGGAGCTGGAACATATGAAAGCGACGGAGAAAAAAGGGAATCTTGAAGCTTTGAAGGAGTTTGGGCCCACTTGTTTGTCCAAGTGCTATTTGCCATATAAGTTTAATTATCTTTTGACCGCCGTTCGCCGTGACAAGTAA

Functional Annotation

Gene Ontology

Molecular Function
Biological Process
Cellular Component

GO:0000003 GO:0000228 GO:0000280 GO:0000706 GO:0000729 GO:0003674 GO:0003676 GO:0003677 GO:0003824 GO:0003916 GO:0003918 GO:0004518 GO:0004519 GO:0004520 GO:0004536 GO:0005488 GO:0005515 GO:0005575 GO:0005622 GO:0005623 GO:0005634 GO:0005694 GO:0006139 GO:0006259 GO:0006281 GO:0006302 GO:0006310 GO:0006725 GO:0006807 GO:0006950 GO:0006974 GO:0006996 GO:0007049 GO:0007127 GO:0007131 GO:0008094 GO:0008134 GO:0008150 GO:0008152 GO:0009987 GO:0016043 GO:0016462 GO:0016787 GO:0016788 GO:0016817 GO:0016818 GO:0016853 GO:0016887 GO:0016889 GO:0016894 GO:0017111 GO:0022402 GO:0022414 GO:0030957 GO:0031974 GO:0031981 GO:0033554 GO:0034641 GO:0035825 GO:0042138 GO:0042623 GO:0042802 GO:0042803 GO:0043170 GO:0043226 GO:0043227 GO:0043228 GO:0043229 GO:0043231 GO:0043232 GO:0043233 GO:0044237 GO:0044238 GO:0044260 GO:0044422 GO:0044424 GO:0044428 GO:0044446 GO:0044464 GO:0046483 GO:0046983 GO:0048285 GO:0050896 GO:0051321 GO:0051716 GO:0061505 GO:0061982 GO:0070013 GO:0071704 GO:0071840 GO:0090304 GO:0090305 GO:0097159 GO:0140013 GO:0140097 GO:1901360 GO:1901363 GO:1903046

KEGG Pathways

Metabolic & Signaling

ko04113 map04113

Pfam Domains

Protein Families

TP6A_N

Protein Analysis

91

Amino Acids

10.63

Weight (kDa)

5.12

Isoelectric Point (pI)

34.7

Instability Index

Protein Domains (Pfam)

Domain Name	Pfam ID	Position	E-value	Description
TOP6A-Spo11_Toprim	PF21180	2 - 79	8.1e-14	Topoisomerase 6 subunit A/Spo11, Toprim domain

Hydrophobicity Profile (Kyte-Doolittle)

AI Structure Prediction Report

Calculating structure properties...

Genomic Context

Gene Family Tree

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Orthologous Genes (Group: OG0004536)

Species	Orthologous Gene IDs
fragaria_vesca	FvH4_3g43731 FvH4_3g43753
rosa_chinensis	RchiOBHm_Chr2g0086091 RchiOBHm_Chr2g0089291 RchiOBHm_Chr2g0089851 RchiOBHm_Chr5g0083311
rosa_laevigata	RLG00000015741 RLG00000016061 RLG00000017209
rosa_multiflora	Rmu_co8293021.1_g000001 Rmu_co8360049.1_g000001 Rmu_sc0000388.1_g000047 Rmu_sc0002384.1_g000009 Rmu_sc0003382.1_g000021 Rmu_sc0017765.1_g000002 Rmu_ssc0000355.1_g000016
rosa_roxburghii	Rroxscaffold_2G00140180 Rroxscaffold_2G00151540
rosa_rugosa	Rorug01G0465600 Rorug01G0488800 Rorug02G0003700
rosa_samantha	Rh2AG015000 Rh2AG045100 Rh2AG048900 Rh2BG047800 Rh2CG016000 Rh2CG016100 Rh2CG045000 Rh2CG049900 Rh5BG561000 Rh5CG583600
rosa_wichuraiana	Rw2G001320

Restriction Enzyme Sites

1 / 10

Enzyme	Recognition Site	Cut Count	Positions (bp)
AciI	CCGC	1 cut(s)	255
AcoI	YGGCCR	1 cut(s)	20
AgsI	TTSAA	3 cut(s)	100, 182, 190
AluBI	AGCT	2 cut(s)	142, 185
AluI	AGCT	2 cut(s)	142, 185
Alw26I	GTCTC	1 cut(s)	75
AoxI	GGCC	2 cut(s)	20, 200
ApaI	GGGCCC	1 cut(s)	204
AspLEI	GCGC	1 cut(s)	40
AspS9I	GGNCC	2 cut(s)	200, 201
BaeGI	GKGCMC	1 cut(s)	204
BanII	GRGCYC	1 cut(s)	204
BceAI	ACGGC	2 cut(s)	242, 249
BcoDI	GTCTC	1 cut(s)	75
BmgT120I	GGNCC	2 cut(s)	200, 201
BmiI	GGNNCC	1 cut(s)	202
BsaJI	CCNNGG	1 cut(s)	125
BseDI	CCNNGG	1 cut(s)	125
BseRI	GAGGAG	1 cut(s)	152
BseSI	GKGCMC	1 cut(s)	204
BshFI	GGCC	2 cut(s)	22, 202
BsmAI	GTCTC	1 cut(s)	75
BsnI	GGCC	2 cut(s)	22, 202
Bsp120I	GGGCCC	1 cut(s)	200
Bsp1286I	GDGCHC	1 cut(s)	204
BspACI	CCGC	1 cut(s)	255
BspANI	GGCC	2 cut(s)	22, 202
BspLI	GGNNCC	1 cut(s)	202
BssECI	CCNNGG	1 cut(s)	125
BstHHI	GCGC	1 cut(s)	40
BstMAI	GTCTC	1 cut(s)	75
BstSLI	GKGCMC	1 cut(s)	204
BsuRI	GGCC	2 cut(s)	22, 202
CfoI	GCGC	1 cut(s)	40
Cfr13I	GGNCC	2 cut(s)	200, 201
CviAII	CATG	2 cut(s)	6, 85
CviJI	RGCY	4 cut(s)	22, 142, 185, 202
CviKI_1	RGCY	4 cut(s)	22, 142, 185, 202
EaeI	YGGCCR	1 cut(s)	20
Eco24I	GRGCYC	1 cut(s)	204
EcoT38I	GRGCYC	1 cut(s)	204
FaeI	CATG	2 cut(s)	9, 88
FaiI	YATR	9 cut(s)	7, 34, 47, 62, 86, 150, 152, 232, 234
FalI	AAGNNNNNCTT	2 cut(s)	162, 194
FatI	CATG	2 cut(s)	5, 84
FauNDI	CATATG	1 cut(s)	150
FriOI	GRGCYC	1 cut(s)	204
GlaI	GCGC	1 cut(s)	39
HaeIII	GGCC	2 cut(s)	22, 202
HhaI	GCGC	1 cut(s)	40
Hin1II	CATG	2 cut(s)	9, 88
Hin6I	GCGC	1 cut(s)	38
HinP1I	GCGC	1 cut(s)	38
HindIII	AAGCTT	1 cut(s)	183
HinfI	GANTC	2 cut(s)	64, 175
Hpy188I	TCNGA	1 cut(s)	126
Hpy188III	TCNNGA	1 cut(s)	179
Hpy99I	CGWCG	2 cut(s)	59, 163
HpyAV	CCTTC	1 cut(s)	184
Hsp92II	CATG	2 cut(s)	9, 88
HspAI	GCGC	1 cut(s)	38
LmnI	GCTCC	1 cut(s)	139
LpnPI	CCDG	2 cut(s)	64, 128
MaeIII	GTNAC	2 cut(s)	26, 266
MboII	GAAGA	1 cut(s)	116
MhlI	GDGCHC	1 cut(s)	204
MluCI	AATT	1 cut(s)	241
MlyI	GAGTC	1 cut(s)	73
MnlI	CCTC	2 cut(s)	120, 130
MseI	TTAA	1 cut(s)	240
NdeI	CATATG	1 cut(s)	150
NlaIII	CATG	2 cut(s)	9, 88
NlaIV	GGNNCC	1 cut(s)	202
NmeAIII	GCCGAG	1 cut(s)	48
NmuCI	GTSAC	2 cut(s)	26, 266
PfeI	GAWTC	1 cut(s)	175
PleI	GAGTC	1 cut(s)	72
PpsI	GAGTC	1 cut(s)	72
PspN4I	GGNNCC	1 cut(s)	202
PspOMI	GGGCCC	1 cut(s)	200
PspPI	GGNCC	2 cut(s)	200, 201
SaqAI	TTAA	1 cut(s)	240
Sau96I	GGNCC	2 cut(s)	200, 201
SchI	GAGTC	1 cut(s)	73
SduI	GDGCHC	1 cut(s)	204
SetI	ASST	4 cut(s)	33, 131, 144, 187
Sse9I	AATT	1 cut(s)	241
SsiI	CCGC	1 cut(s)	255
TasI	AATT	1 cut(s)	241
TfiI	GAWTC	1 cut(s)	175
Tru1I	TTAA	1 cut(s)	240
Tru9I	TTAA	1 cut(s)	240
TseFI	GTSAC	2 cut(s)	26, 266
Tsp45I	GTSAC	2 cut(s)	26, 266
TspDTI	ATGAA	1 cut(s)	167
TspGWI	ACGGA	1 cut(s)	176

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