Basic Information

Type: gene

Biological Identity

Species

rosa_samantha

Chromosome

Chr2C

Orthogroup ID

OG0006381

Physical Location & Seq

Genomic Coordinates Forward (+)

7492732 .. 7493139

Gene Structure 408 bp

Loading structure...

UTR

Exon/CDS

Intron

Transcript / Protein ID

Rh2CG091200.1

Sequence Viewer

CDS Protein Promoter (2k)

Length: 327 bp

ATGTGCTGGTACGAGTCTCGGTACCCGGCGAGTGCGCCGTGGTCGATTTTCCGGCACGAGTTTCTGAGGTTTTTCCGGCCGGAGACGCTCATCGCCGCCGTGTGTAATTTGGAGCAGAAGAGGTCGGTGAAGGAGTATGAGGTGGAGTTTCTGAGGCTGGCTGCCGGAGGTGGGGATCCGTCGCCGGAGTGGAGCGATGAGGAGTTGACGAGGCATTTTGTTGGTGGATTGAAGGAGGAGATACGGCGGAAGGTGGAGTCGTTTCGGCCCAAAACCCTAGCTGACGCCATGGATTTTGCTCGCAATGTGGAGGCTGAAAGTGCATAA

Functional Annotation

Gene Ontology

Molecular Function
Biological Process
Cellular Component

No ontology terms assigned.

KEGG Pathways

Metabolic & Signaling

No pathways identified.

Pfam Domains

Protein Families

RVP_2 RVT_1 Retrotrans_gag gag-asp_proteas rve

Protein Analysis

108

Amino Acids

12.59

Weight (kDa)

5.46

Isoelectric Point (pI)

61.46

Instability Index

Protein Domains (Pfam)

Domain Name	Pfam ID	Position	E-value	Description
Retrotrans_gag	PF03732	13 - 79	3.6e-06	Retrotransposon gag protein
Ty3_capsid	PF19259	17 - 102	2.6e-07	Ty3 transposon capsid-like protein

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

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Orthologous Genes (Group: OG0006381)

Species	Orthologous Gene IDs
fragaria_vesca	FvH4_1g06201 FvH4_1g08061 FvH4_1g08061 FvH4_5g27691 FvH4_6g16962 FvH4_7g30611
rosa_chinensis	RchiOBHm_Chr2g0094121 RchiOBHm_Chr6g0296601
rosa_laevigata	RLG00000008247 RLG00000016457
rosa_roxburghii	Rroxscaffold_2G00076380 Rroxscaffold_2G00132740 Rroxscaffold_2G00147460 Rroxscaffold_3G00257090 Rroxscaffold_7G00171340
rosa_rugosa	Rorug03G0253300 Rorug03G0304200
rosa_samantha	Rh1DG093900 Rh2AG088700 Rh2AG365300 Rh2BG088800 Rh2BG325600 Rh2CG091200 Rh2DG087800 Rh4AG227300 Rh4CG009100
rosa_wichuraiana	Rw4G001570

Restriction Enzyme Sites

1 / 10

Enzyme	Recognition Site	Cut Count	Positions (bp)
Acc65I	GGTACC	1 cut(s)	21
AccB1I	GGYRCC	1 cut(s)	21
AciI	CCGC	2 cut(s)	96, 247
AclWI	GGATC	2 cut(s)	170, 183
AcoI	YGGCCR	1 cut(s)	77
AcyI	GRCGYC	1 cut(s)	285
AfaI	GTAC	2 cut(s)	11, 23
AfiI	CCNNNNNNNGG	1 cut(s)	171
AgsI	TTSAA	1 cut(s)	232
AluBI	AGCT	1 cut(s)	281
AluI	AGCT	1 cut(s)	281
Alw26I	GTCTC	2 cut(s)	21, 77
AlwI	GGATC	2 cut(s)	170, 183
AoxI	GGCC	2 cut(s)	77, 266
ApeKI	GCWGC	1 cut(s)	161
Asp718I	GGTACC	1 cut(s)	21
AspLEI	GCGC	1 cut(s)	37
AspS9I	GGNCC	1 cut(s)	267
AsuC2I	CCSGG	1 cut(s)	26
AsuHPI	GGTGA	1 cut(s)	139
BamHI	GGATCC	1 cut(s)	175
BanI	GGYRCC	1 cut(s)	21
BauI	CACGAG	1 cut(s)	56
BbvI	GCAGC	1 cut(s)	148
BceAI	ACGGC	3 cut(s)	22, 83, 260
BcnI	CCSGG	1 cut(s)	26
BcoDI	GTCTC	2 cut(s)	21, 77
BfaI	CTAG	1 cut(s)	278
BisI	GCNGC	2 cut(s)	96, 162
BlsI	GCNGC	2 cut(s)	97, 163
Bme1390I	CCNGG	1 cut(s)	26
BmgT120I	GGNCC	1 cut(s)	267
BmiI	GGNNCC	2 cut(s)	23, 177
BmrFI	CCNGG	1 cut(s)	26
BpuMI	CCSGG	1 cut(s)	26
BsaHI	GRCGYC	1 cut(s)	285
BsaJI	CCNNGG	2 cut(s)	38, 288
Bsc4I	CCNNNNNNNGG	1 cut(s)	171
Bse3DI	GCAATG	1 cut(s)	310
BseDI	CCNNGG	2 cut(s)	38, 288
BseLI	CCNNNNNNNGG	1 cut(s)	171
BseMI	GCAATG	1 cut(s)	310
BseMII	CTCAG	2 cut(s)	56, 143
BseRI	GAGGAG	2 cut(s)	215, 251
BseX3I	CGGCCG	1 cut(s)	77
BseXI	GCAGC	1 cut(s)	148
Bsh1285I	CGRYCG	1 cut(s)	80
BshFI	GGCC	2 cut(s)	79, 268
BshNI	GGYRCC	1 cut(s)	21
BsiEI	CGRYCG	1 cut(s)	80
BsiSI	CCGG	6 cut(s)	26, 52, 76, 80, 165, 185
BslI	CCNNNNNNNGG	1 cut(s)	171
BsmAI	GTCTC	2 cut(s)	21, 77
BsmBI	CGTCTC	1 cut(s)	77
BsnI	GGCC	2 cut(s)	79, 268
Bsp143I	GATC	1 cut(s)	175
Bsp19I	CCATGG	1 cut(s)	288
BspACI	CCGC	2 cut(s)	96, 247
BspANI	GGCC	2 cut(s)	79, 268
BspCNI	CTCAG	2 cut(s)	57, 144
BspLI	GGNNCC	2 cut(s)	23, 177
BspPI	GGATC	2 cut(s)	170, 183
BspT107I	GGYRCC	1 cut(s)	21
BsrDI	GCAATG	1 cut(s)	310
BssECI	CCNNGG	2 cut(s)	38, 288
BssMI	GATC	1 cut(s)	175
BssNI	GRCGYC	1 cut(s)	285
BssSI	CACGAG	1 cut(s)	56
BssT1I	CCWWGG	1 cut(s)	288
Bst2BI	CACGAG	1 cut(s)	56
Bst6I	CTCTTC	1 cut(s)	113
BstACI	GRCGYC	1 cut(s)	285
BstC8I	GCNNGC	2 cut(s)	159, 301
BstDEI	CTNAG	2 cut(s)	65, 152
BstDSI	CCRYGG	2 cut(s)	38, 288
BstHHI	GCGC	1 cut(s)	37
BstKTI	GATC	1 cut(s)	178
BstMAI	GTCTC	2 cut(s)	21, 77
BstMBI	GATC	1 cut(s)	175
BstMCI	CGRYCG	1 cut(s)	80
BstMWI	GCNNNNNNNGC	2 cut(s)	85, 320
BstSCI	CCNGG	1 cut(s)	24
BstV1I	GCAGC	1 cut(s)	148
BstX2I	RGATCY	1 cut(s)	175
BstYI	RGATCY	1 cut(s)	175
BstZI	CGGCCG	1 cut(s)	77
BsuRI	GGCC	2 cut(s)	79, 268
BtgI	CCRYGG	2 cut(s)	38, 288
BtgZI	GCGATG	2 cut(s)	76, 210
Cac8I	GCNNGC	2 cut(s)	159, 301
CfoI	GCGC	1 cut(s)	37
Cfr13I	GGNCC	1 cut(s)	267
CseI	GACGC	2 cut(s)	94, 293
Csp6I	GTAC	2 cut(s)	10, 22
CviAII	CATG	1 cut(s)	289
CviJI	RGCY	6 cut(s)	79, 157, 161, 268, 281, 314
CviKI_1	RGCY	6 cut(s)	79, 157, 161, 268, 281, 314
CviQI	GTAC	2 cut(s)	10, 22
DdeI	CTNAG	2 cut(s)	65, 152
DpnI	GATC	1 cut(s)	177
DpnII	GATC	1 cut(s)	175
EaeI	YGGCCR	1 cut(s)	77
EagI	CGGCCG	1 cut(s)	77
Eam1104I	CTCTTC	1 cut(s)	113
EarI	CTCTTC	1 cut(s)	113
EciI	GGCGGA	1 cut(s)	262
EclXI	CGGCCG	1 cut(s)	77
Eco130I	CCWWGG	1 cut(s)	288
Eco52I	CGGCCG	1 cut(s)	77
EcoT14I	CCWWGG	1 cut(s)	288
ErhI	CCWWGG	1 cut(s)	288
Esp3I	CGTCTC	1 cut(s)	77
FaeI	CATG	1 cut(s)	292
FaiI	YATR	3 cut(s)	138, 290, 325
FatI	CATG	1 cut(s)	288
Fnu4HI	GCNGC	2 cut(s)	96, 162
Fsp4HI	GCNGC	2 cut(s)	96, 162
FspBI	CTAG	1 cut(s)	278
GlaI	GCGC	1 cut(s)	36
GluI	GCNGC	2 cut(s)	96, 162
HaeIII	GGCC	2 cut(s)	79, 268
HapII	CCGG	6 cut(s)	26, 52, 76, 80, 165, 185
HgaI	GACGC	2 cut(s)	94, 293
HhaI	GCGC	1 cut(s)	37
Hin1I	GRCGYC	1 cut(s)	285
Hin1II	CATG	1 cut(s)	292
Hin6I	GCGC	1 cut(s)	35
HinP1I	GCGC	1 cut(s)	35
HincII	GTYRAC	1 cut(s)	207
HindII	GTYRAC	1 cut(s)	207
HinfI	GANTC	2 cut(s)	14, 257
HpaII	CCGG	6 cut(s)	26, 52, 76, 80, 165, 185
HphI	GGTGA	1 cut(s)	139
Hpy166II	GTNNAC	1 cut(s)	207
Hpy188I	TCNGA	2 cut(s)	66, 153
Hpy8I	GTNNAC	1 cut(s)	207
Hpy99I	CGWCG	1 cut(s)	184
HpyAV	CCTTC	3 cut(s)	124, 226, 244
HpyCH4V	TGCA	1 cut(s)	323
HpyF10VI	GCNNNNNNNGC	2 cut(s)	85, 320
HpyF3I	CTNAG	2 cut(s)	65, 152
Hsp92I	GRCGYC	1 cut(s)	285
Hsp92II	CATG	1 cut(s)	292
HspAI	GCGC	1 cut(s)	35
KpnI	GGTACC	1 cut(s)	25
Kzo9I	GATC	1 cut(s)	175
LmnI	GCTCC	2 cut(s)	112, 192
LpnPI	CCDG	7 cut(s)	39, 65, 89, 93, 143, 178, 198
Lsp1109I	GCAGC	1 cut(s)	148
MaeI	CTAG	1 cut(s)	278
MalI	GATC	1 cut(s)	177
MboI	GATC	1 cut(s)	175
MboII	GAAGA	1 cut(s)	130
MflI	RGATCY	1 cut(s)	175
MluCI	AATT	1 cut(s)	106
MlyI	GAGTC	2 cut(s)	23, 266
MnlI	CCTC	9 cut(s)	60, 114, 133, 147, 161, 193, 204, 229, 304
MspI	CCGG	6 cut(s)	26, 52, 76, 80, 165, 185
MspR9I	CCNGG	1 cut(s)	26
MwoI	GCNNNNNNNGC	2 cut(s)	85, 320
NciI	CCSGG	1 cut(s)	26
NcoI	CCATGG	1 cut(s)	288
NdeII	GATC	1 cut(s)	175
NlaIII	CATG	1 cut(s)	292
NlaIV	GGNNCC	2 cut(s)	23, 177
PkrI	GCNGC	2 cut(s)	97, 163
PleI	GAGTC	2 cut(s)	22, 265
PpsI	GAGTC	2 cut(s)	22, 265
PspN4I	GGNNCC	2 cut(s)	23, 177
PspPI	GGNCC	1 cut(s)	267
PsuI	RGATCY	1 cut(s)	175
RsaI	GTAC	2 cut(s)	11, 23
RsaNI	GTAC	2 cut(s)	10, 22
SatI	GCNGC	2 cut(s)	96, 162
Sau3AI	GATC	1 cut(s)	175
Sau96I	GGNCC	1 cut(s)	267
SchI	GAGTC	2 cut(s)	23, 266
ScrFI	CCNGG	1 cut(s)	26
SetI	ASST	6 cut(s)	71, 125, 144, 172, 255, 283
Sse9I	AATT	1 cut(s)	106
SsiI	CCGC	2 cut(s)	96, 247
SspMI	CTAG	1 cut(s)	278
StyD4I	CCNGG	1 cut(s)	24
StyI	CCWWGG	1 cut(s)	288
TaqI	TCGA	1 cut(s)	44
TasI	AATT	1 cut(s)	106
TauI	GCSGC	1 cut(s)	98
TseI	GCWGC	1 cut(s)	161
TspGWI	ACGGA	1 cut(s)	168
XspI	CTAG	1 cut(s)	278

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