Basic Information

Type: gene

Biological Identity

Species

rosa_wichuraiana

Chromosome

Chr4

Orthogroup ID

OG0003287

Physical Location & Seq

Genomic Coordinates Reverse (-)

31804661 .. 31805287

Gene Structure 627 bp

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UTR

Exon/CDS

Intron

Transcript / Protein ID

Rw4G013620.1

Sequence Viewer

CDS Protein Promoter (2k)

Length: 627 bp

ATGTCATACGTGGAGTTGAATGAAGCAAGGAGAGAAGACGTGTGGTTTCTGGATTCAGGATGCTCCAACCACATGTGTGGAGACAAAACCTTGTTTAATGATCTCAACGAAGGGTTCAGGCAGATGGTGAAACTTGGAGATAACTCGAAAATGTCAGTGATGGGTAAAGGGAAGGTGAGGCTGATAGTGAGTGGTTTTGTGCATGTGATTACCGAGGTATTTTATGTTCCAGAGTTAAGGAACAACTTGTTGAGTATCGGTCAGCTACAGGAGAAAGGGTTGGCAATTCTAATCCAACATGGTCTGTGCCGGATTAACCATCCAATGAATGGCTTGATTATCCAAACCAAGATGTCAGCCAATAGAATGTTCTTTCTGTTGGCTAGGACTCAACCAAGAGAGATAGCTTGCTTTTATACAACCTCTCAAGATTCATCTCATTTGTGGCATTGTAGGTTCGGTCATCTGAGTTATAAAGGGCTACGAACTCTTCAGTTCAAGAAAATGGTGCATGGATTGCCGCAATTCTCTGCCTCCACAACATTATGTAAAGCATGCATGGTAGGGAAACAGCACCGAGACCCTATTCCAAAGAAGAGCAATTGGAGGGCAACACATAAGCTCTAA

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

208

Amino Acids

23.83

Weight (kDa)

9.68

Isoelectric Point (pI)

47.05

Instability Index

Protein Domains (Pfam)

Domain Name	Pfam ID	Position	E-value	Description
Pol_BBD	PF22936	15 - 93	3.6e-28	Pol polyprotein, beta-barrel domain
gag_pre-integrs	PF13976	134 - 191	4.7e-14	GAG-pre-integrase domain

Hydrophobicity Profile (Kyte-Doolittle)

AI Structure Prediction Report

Calculating structure properties...

Genomic Context

Gene Family Tree

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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: 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)
AanI	TTATAA	1 cut(s)	474
AccB7I	CCANNNNNTGG	1 cut(s)	329
AciI	CCGC	1 cut(s)	521
AcuI	CTGAAG	1 cut(s)	476
AfiI	CCNNNNNNNGG	1 cut(s)	329
AflIII	ACRYGT	2 cut(s)	39, 72
AgsI	TTSAA	2 cut(s)	19, 499
AjiI	CACGTC	1 cut(s)	40
AjuI	GAANNNNNNNTTGG	2 cut(s)	353, 385
AleI	CACNNNNGTG	1 cut(s)	75
AluBI	AGCT	3 cut(s)	265, 407, 622
AluI	AGCT	3 cut(s)	265, 407, 622
Alw26I	GTCTC	2 cut(s)	75, 573
AsuHPI	GGTGA	2 cut(s)	139, 187
BbsI	GAAGAC	1 cut(s)	42
BccI	CCATC	3 cut(s)	118, 154, 327
BcoDI	GTCTC	2 cut(s)	75, 573
BfaI	CTAG	1 cut(s)	384
BfmI	CTRYAG	1 cut(s)	266
BisI	GCNGC	1 cut(s)	521
BlsI	GCNGC	1 cut(s)	522
BmgBI	CACGTC	1 cut(s)	40
BmsI	GCATC	1 cut(s)	50
BpiI	GAAGAC	1 cut(s)	42
BpuEI	CTTGAG	1 cut(s)	411
BsaAI	YACGTR	1 cut(s)	10
BsaI	GGTCTC	1 cut(s)	573
BsaJI	CCNNGG	1 cut(s)	213
BsaXI	ACNNNNNCTCC	2 cut(s)	263, 293
Bsc4I	CCNNNNNNNGG	1 cut(s)	329
BseDI	CCNNGG	1 cut(s)	213
BseGI	GGATG	2 cut(s)	65, 319
BseLI	CCNNNNNNNGG	1 cut(s)	329
BseMII	CTCAG	1 cut(s)	458
BsiSI	CCGG	1 cut(s)	310
BslI	CCNNNNNNNGG	1 cut(s)	329
BsmAI	GTCTC	2 cut(s)	75, 573
Bso31I	GGTCTC	1 cut(s)	573
Bsp143I	GATC	1 cut(s)	100
BspACI	CCGC	1 cut(s)	521
BspCNI	CTCAG	1 cut(s)	459
BspQI	GCTCTTC	1 cut(s)	590
BspTNI	GGTCTC	1 cut(s)	573
BssECI	CCNNGG	1 cut(s)	213
BssMI	GATC	1 cut(s)	100
Bst6I	CTCTTC	2 cut(s)	495, 590
BstAPI	GCANNNNNTGC	1 cut(s)	517
BstBAI	YACGTR	1 cut(s)	10
BstC8I	GCNNGC	2 cut(s)	409, 556
BstDEI	CTNAG	1 cut(s)	467
BstF5I	GGATG	2 cut(s)	65, 319
BstKTI	GATC	1 cut(s)	103
BstMAI	GTCTC	2 cut(s)	75, 573
BstMBI	GATC	1 cut(s)	100
BstMWI	GCNNNNNNNGC	1 cut(s)	517
BstNSI	RCATGY	3 cut(s)	76, 206, 558
BstSFI	CTRYAG	1 cut(s)	266
BstV2I	GAAGAC	1 cut(s)	42
BstXI	CCANNNNNNTGG	1 cut(s)	77
BtrI	CACGTC	1 cut(s)	40
BtsCI	GGATG	2 cut(s)	65, 319
BtsIMutI	CAGTG	1 cut(s)	162
Cac8I	GCNNGC	2 cut(s)	409, 556
CviAII	CATG	6 cut(s)	73, 203, 299, 512, 555, 559
CviJI	RGCY	8 cut(s)	181, 265, 333, 359, 383, 407, 481, 622
CviKI_1	RGCY	8 cut(s)	181, 265, 333, 359, 383, 407, 481, 622
DdeI	CTNAG	1 cut(s)	467
DpnI	GATC	1 cut(s)	102
DpnII	GATC	1 cut(s)	100
Eam1104I	CTCTTC	2 cut(s)	495, 590
EarI	CTCTTC	2 cut(s)	495, 590
Eco31I	GGTCTC	1 cut(s)	573
Eco57I	CTGAAG	1 cut(s)	476
EcoT22I	ATGCAT	1 cut(s)	560
FaeI	CATG	6 cut(s)	76, 206, 302, 515, 558, 562
FatI	CATG	6 cut(s)	72, 202, 298, 511, 554, 558
Fnu4HI	GCNGC	1 cut(s)	521
FokI	GGATG	2 cut(s)	72, 306
Fsp4HI	GCNGC	1 cut(s)	521
FspBI	CTAG	1 cut(s)	384
GluI	GCNGC	1 cut(s)	521
HapII	CCGG	1 cut(s)	310
Hin1II	CATG	6 cut(s)	76, 206, 302, 515, 558, 562
HinfI	GANTC	3 cut(s)	53, 388, 431
HpaII	CCGG	1 cut(s)	310
HphI	GGTGA	2 cut(s)	139, 187
Hpy188I	TCNGA	1 cut(s)	468
Hpy188III	TCNNGA	5 cut(s)	50, 57, 230, 428, 499
HpyAV	CCTTC	2 cut(s)	104, 166
HpyCH4IV	ACGT	2 cut(s)	9, 39
HpyCH4V	TGCA	3 cut(s)	202, 511, 558
HpyF10VI	GCNNNNNNNGC	1 cut(s)	517
HpyF3I	CTNAG	1 cut(s)	467
HpySE526I	ACGT	2 cut(s)	9, 39
Hsp92II	CATG	6 cut(s)	76, 206, 302, 515, 558, 562
Kzo9I	GATC	1 cut(s)	100
LguI	GCTCTTC	1 cut(s)	590
LmnI	GCTCC	1 cut(s)	68
LpnPI	CCDG	6 cut(s)	35, 42, 103, 243, 254, 323
LweI	GCATC	1 cut(s)	50
MaeI	CTAG	1 cut(s)	384
MaeII	ACGT	2 cut(s)	9, 39
MalI	GATC	1 cut(s)	102
MboI	GATC	1 cut(s)	100
MboII	GAAGA	3 cut(s)	47, 482, 607
MfeI	CAATTG	1 cut(s)	601
MluCI	AATT	3 cut(s)	285, 524, 601
MlyI	GAGTC	1 cut(s)	382
MmeI	TCCRAC	2 cut(s)	90, 319
MnlI	CCTC	5 cut(s)	171, 208, 433, 544, 600
Mph1103I	ATGCAT	1 cut(s)	560
MseI	TTAA	3 cut(s)	96, 236, 315
MslI	CAYNNNNRTG	1 cut(s)	75
MspI	CCGG	1 cut(s)	310
MunI	CAATTG	1 cut(s)	601
MwoI	GCNNNNNNNGC	1 cut(s)	517
NdeII	GATC	1 cut(s)	100
NlaIII	CATG	6 cut(s)	76, 206, 302, 515, 558, 562
NsiI	ATGCAT	1 cut(s)	560
NspI	RCATGY	3 cut(s)	76, 206, 558
OliI	CACNNNNGTG	1 cut(s)	75
PaeI	GCATGC	1 cut(s)	558
PciI	ACATGT	1 cut(s)	72
PciSI	GCTCTTC	1 cut(s)	590
PfeI	GAWTC	2 cut(s)	53, 431
PflMI	CCANNNNNTGG	1 cut(s)	329
PkrI	GCNGC	1 cut(s)	522
PleI	GAGTC	1 cut(s)	382
PpsI	GAGTC	1 cut(s)	382
Ppu21I	YACGTR	1 cut(s)	10
PscI	ACATGT	1 cut(s)	72
PsiI	TTATAA	1 cut(s)	474
PsrI	GAACNNNNNNTAC	2 cut(s)	210, 242
RseI	CAYNNNNRTG	1 cut(s)	75
SapI	GCTCTTC	1 cut(s)	590
SaqAI	TTAA	3 cut(s)	96, 236, 315
SatI	GCNGC	1 cut(s)	521
Sau3AI	GATC	1 cut(s)	100
SchI	GAGTC	1 cut(s)	382
SfaNI	GCATC	1 cut(s)	50
SfcI	CTRYAG	1 cut(s)	266
SmiMI	CAYNNNNRTG	1 cut(s)	75
SmlI	CTYRAG	1 cut(s)	426
SmoI	CTYRAG	1 cut(s)	426
SphI	GCATGC	1 cut(s)	558
Sse9I	AATT	3 cut(s)	285, 524, 601
SsiI	CCGC	1 cut(s)	521
SspMI	CTAG	1 cut(s)	384
TaiI	ACGT	2 cut(s)	12, 42
TaqI	TCGA	1 cut(s)	146
TaqII	GACCGA	2 cut(s)	248, 449
TasI	AATT	3 cut(s)	285, 524, 601
TauI	GCSGC	1 cut(s)	523
TfiI	GAWTC	2 cut(s)	53, 431
Tru1I	TTAA	3 cut(s)	96, 236, 315
Tru9I	TTAA	3 cut(s)	96, 236, 315
TscAI	CASTG	1 cut(s)	162
TspDTI	ATGAA	3 cut(s)	36, 341, 423
TspRI	CASTG	1 cut(s)	162
Van91I	CCANNNNNTGG	1 cut(s)	329
XceI	RCATGY	3 cut(s)	76, 206, 558
XcmI	CCANNNNNNNNNTGG	1 cut(s)	326
XspI	CTAG	1 cut(s)	384
Zsp2I	ATGCAT	1 cut(s)	560

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