Basic Information

Type: gene

Biological Identity

Species

rosa_roxburghii

Chromosome

GWHEROQ00000001

Orthogroup ID

OG0003287

Physical Location & Seq

Genomic Coordinates Forward (+)

56201139 .. 56202848

Gene Structure 1710 bp

Loading structure...

UTR

Exon/CDS

Intron

Transcript / Protein ID

Rroxscaffold_1G00038680.1

Sequence Viewer

CDS Protein Promoter (2k)

Length: 468 bp

ATGATTGTGATGGGGAGAGGGAATATTAGACTCAATGTTGGTGGAGTGACTCAAGTGGTTAGTGAGGTGTTCTATATCCTGGAGCTAAAGAACAACCTATTGAGCATAGGATTGTTACAGGAGAAGGGCTTAGCCATACTTATTCAACATGGTTTTTCCAAGTTGTTTTATCCCTCGAAAGGCTTAATTATGCAAACTGCAATGTCAGCTAATAAGATGTTTGTGTTGTTGGCCTCTATGACTTCAAAAGAATCAGCATGCTTCCAAGCAATTGGTGAGAACGATACTCATCCGTGGCACTTCCGCTTTGGTCACCTAAGTTTTAAAGGATTAAGGACCTTGCATTACAAGAAAATGGTCAAGGAACTACCTTCACTTAAAGCCCCTGCTAAGGTGTGTGTAGATTGCTTAGTTGACAAACAACATAGGGACTCCATCCCTAAGAAGAGCCTCTGGAGAGCCACATAA

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

RVT_2 Retrotran_gag_2 Retrotran_gag_3 Retrotrans_gag gag_pre-integrs rve zf-CCHC

Protein Analysis

155

Amino Acids

17.43

Weight (kDa)

9.84

Isoelectric Point (pI)

39.95

Instability Index

Protein Domains (Pfam)

Domain Name	Pfam ID	Position	E-value	Description
Pol_BBD	PF22936	3 - 43	2.7e-07	Pol polyprotein, beta-barrel domain
gag_pre-integrs	PF13976	74 - 141	7.7e-12	GAG-pre-integrase domain

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: OG0003287)

Species	Orthologous Gene IDs
arabidopsis_thaliana	AT1G11591
fragaria_vesca	FvH4_2g20411 FvH4_2g29931 FvH4_3g14181 FvH4_4g00781 FvH4_4g12541 FvH4_5g22143 FvH4_7g24581
pyrus_communis	pycom04g03170 pycom05g18080 pycom12g05030 pycom13g18540
rosa_chinensis	RchiOBHm_Chr1g0313681 RchiOBHm_Chr1g0344501 RchiOBHm_Chr2g0157511
rosa_laevigata	RLG00000008144 RLG00000008360
rosa_multiflora	Rmu_sc0003765.1_g000035 Rmu_sc0004343.1_g000026 Rmu_sc0006087.1_g000011
rosa_roxburghii	Rroxscaffold_1G00038680 Rroxscaffold_3G00247490 Rroxscaffold_4G00315330 Rroxscaffold_5G00355970 Rroxscaffold_7G00214090
rosa_rugosa	Rorug04G0109300 Rorug04G0109400
rosa_samantha	Rh1AG403200 Rh4AG167500 Rh4BG164600 Rh4CG179400 Rh4DG162300
rosa_wichuraiana	Rw4G013620 Rw4G013850 Rw4G013950 Rw6G038170

Restriction Enzyme Sites

1 / 10

Enzyme	Recognition Site	Cut Count	Positions (bp)
AciI	CCGC	1 cut(s)	304
AfiI	CCNNNNNNNGG	2 cut(s)	179, 391
AgsI	TTSAA	2 cut(s)	146, 246
AjnI	CCWGG	1 cut(s)	78
AluBI	AGCT	2 cut(s)	85, 209
AluI	AGCT	2 cut(s)	85, 209
AoxI	GGCC	1 cut(s)	231
AspS9I	GGNCC	1 cut(s)	336
AsuHPI	GGTGA	2 cut(s)	287, 305
AvaII	GGWCC	1 cut(s)	336
BccI	CCATC	2 cut(s)	4, 443
BciT130I	CCWGG	1 cut(s)	80
BlpI	GCTNAGC	1 cut(s)	130
Bme1390I	CCNGG	1 cut(s)	80
Bme18I	GGWCC	1 cut(s)	336
BmgT120I	GGNCC	1 cut(s)	336
BmrFI	CCNGG	1 cut(s)	80
BpmI	CTGGAG	1 cut(s)	101
Bpu10I	CCTNAGC	1 cut(s)	390
Bpu1102I	GCTNAGC	1 cut(s)	130
BpuEI	CTTGAG	1 cut(s)	36
BsaBI	GATNNNNATC	1 cut(s)	288
BsaJI	CCNNGG	1 cut(s)	293
Bsc4I	CCNNNNNNNGG	2 cut(s)	179, 391
Bse3DI	GCAATG	1 cut(s)	207
Bse8I	GATNNNNATC	1 cut(s)	288
BseBI	CCWGG	1 cut(s)	80
BseDI	CCNNGG	1 cut(s)	293
BseGI	GGATG	2 cut(s)	289, 435
BseJI	GATNNNNATC	1 cut(s)	288
BseLI	CCNNNNNNNGG	2 cut(s)	179, 391
BseMI	GCAATG	1 cut(s)	207
BshFI	GGCC	1 cut(s)	233
BslFI	GGGAC	1 cut(s)	443
BslI	CCNNNNNNNGG	2 cut(s)	179, 391
BsmFI	GGGAC	1 cut(s)	443
BsnI	GGCC	1 cut(s)	233
Bsp1720I	GCTNAGC	1 cut(s)	130
BspACI	CCGC	1 cut(s)	304
BspANI	GGCC	1 cut(s)	233
BspQI	GCTCTTC	1 cut(s)	440
BsrDI	GCAATG	1 cut(s)	207
BssECI	CCNNGG	1 cut(s)	293
Bst2UI	CCWGG	1 cut(s)	80
Bst6I	CTCTTC	1 cut(s)	440
BstC8I	GCNNGC	1 cut(s)	259
BstDEI	CTNAG	5 cut(s)	130, 317, 390, 409, 441
BstDSI	CCRYGG	1 cut(s)	293
BstEII	GGTNACC	1 cut(s)	311
BstF5I	GGATG	2 cut(s)	289, 435
BstMWI	GCNNNNNNNGC	1 cut(s)	206
BstNI	CCWGG	1 cut(s)	80
BstNSI	RCATGY	1 cut(s)	261
BstPI	GGTNACC	1 cut(s)	311
BstSCI	CCNGG	1 cut(s)	78
BstXI	CCANNNNNNTGG	1 cut(s)	272
BsuRI	GGCC	1 cut(s)	233
BtgI	CCRYGG	1 cut(s)	293
BtsCI	GGATG	2 cut(s)	289, 435
Cac8I	GCNNGC	1 cut(s)	259
Cfr13I	GGNCC	1 cut(s)	336
CspCI	CAANNNNNGTGG	2 cut(s)	22, 57
CviAII	CATG	2 cut(s)	149, 258
CviJI	RGCY	9 cut(s)	85, 129, 134, 183, 209, 233, 383, 450, 461
CviKI_1	RGCY	9 cut(s)	85, 129, 134, 183, 209, 233, 383, 450, 461
DdeI	CTNAG	5 cut(s)	130, 317, 390, 409, 441
DraI	TTTAAA	1 cut(s)	325
Eam1104I	CTCTTC	1 cut(s)	440
EarI	CTCTTC	1 cut(s)	440
Eco47I	GGWCC	1 cut(s)	336
Eco91I	GGTNACC	1 cut(s)	311
EcoO109I	RGGNCCY	1 cut(s)	336
EcoO65I	GGTNACC	1 cut(s)	311
EcoRII	CCWGG	1 cut(s)	78
FaeI	CATG	2 cut(s)	152, 261
FaiI	YATR	9 cut(s)	75, 107, 137, 150, 191, 239, 259, 426, 466
FaqI	GGGAC	1 cut(s)	443
FatI	CATG	2 cut(s)	148, 257
FokI	GGATG	2 cut(s)	276, 422
GsuI	CTGGAG	1 cut(s)	101
HaeIII	GGCC	1 cut(s)	233
Hin1II	CATG	2 cut(s)	152, 261
HincII	GTYRAC	1 cut(s)	415
HindII	GTYRAC	1 cut(s)	415
HinfI	GANTC	4 cut(s)	30, 49, 251, 431
HphI	GGTGA	2 cut(s)	287, 305
Hpy166II	GTNNAC	1 cut(s)	415
Hpy188III	TCNNGA	1 cut(s)	454
Hpy8I	GTNNAC	1 cut(s)	415
HpyAV	CCTTC	2 cut(s)	118, 381
HpyCH4V	TGCA	3 cut(s)	193, 200, 343
HpyF10VI	GCNNNNNNNGC	1 cut(s)	206
HpyF3I	CTNAG	5 cut(s)	130, 317, 390, 409, 441
Hsp92II	CATG	2 cut(s)	152, 261
LguI	GCTCTTC	1 cut(s)	440
LmnI	GCTCC	1 cut(s)	82
LpnPI	CCDG	5 cut(s)	65, 92, 104, 399, 439
MaeIII	GTNAC	3 cut(s)	46, 114, 311
MboII	GAAGA	1 cut(s)	457
MfeI	CAATTG	1 cut(s)	270
MluCI	AATT	2 cut(s)	186, 270
MlyI	GAGTC	3 cut(s)	24, 43, 425
MnlI	CCTC	5 cut(s)	11, 58, 184, 244, 461
MseI	TTAA	4 cut(s)	185, 324, 332, 378
MspR9I	CCNGG	1 cut(s)	80
MunI	CAATTG	1 cut(s)	270
MvaI	CCWGG	1 cut(s)	80
MwoI	GCNNNNNNNGC	1 cut(s)	206
NlaIII	CATG	2 cut(s)	152, 261
NmuCI	GTSAC	2 cut(s)	46, 311
NspI	RCATGY	1 cut(s)	261
PaeI	GCATGC	1 cut(s)	261
PciSI	GCTCTTC	1 cut(s)	440
PfeI	GAWTC	1 cut(s)	251
PfoI	TCCNGGA	1 cut(s)	78
PleI	GAGTC	3 cut(s)	24, 43, 425
PpsI	GAGTC	3 cut(s)	24, 43, 425
PpuMI	RGGWCCY	1 cut(s)	336
Psp5II	RGGWCCY	1 cut(s)	336
Psp6I	CCWGG	1 cut(s)	78
PspEI	GGTNACC	1 cut(s)	311
PspGI	CCWGG	1 cut(s)	78
PspPI	GGNCC	1 cut(s)	336
PspPPI	RGGWCCY	1 cut(s)	336
SapI	GCTCTTC	1 cut(s)	440
SaqAI	TTAA	4 cut(s)	185, 324, 332, 378
Sau96I	GGNCC	1 cut(s)	336
SchI	GAGTC	3 cut(s)	24, 43, 425
ScrFI	CCNGG	1 cut(s)	80
SetI	ASST	8 cut(s)	69, 87, 99, 211, 318, 341, 373, 396
SinI	GGWCC	1 cut(s)	336
SmlI	CTYRAG	1 cut(s)	51
SmoI	CTYRAG	1 cut(s)	51
SphI	GCATGC	1 cut(s)	261
Sse9I	AATT	2 cut(s)	186, 270
SsiI	CCGC	1 cut(s)	304
SspI	AATATT	1 cut(s)	25
StyD4I	CCNGG	1 cut(s)	78
TaqI	TCGA	1 cut(s)	176
TasI	AATT	2 cut(s)	186, 270
TfiI	GAWTC	1 cut(s)	251
Tru1I	TTAA	4 cut(s)	185, 324, 332, 378
Tru9I	TTAA	4 cut(s)	185, 324, 332, 378
TseFI	GTSAC	2 cut(s)	46, 311
Tsp45I	GTSAC	2 cut(s)	46, 311
TspGWI	ACGGA	1 cut(s)	282
VpaK11BI	GGWCC	1 cut(s)	336
XceI	RCATGY	1 cut(s)	261

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