Basic Information

Type: gene

Biological Identity

Species

rosa_wichuraiana

Chromosome

Chr4

Orthogroup ID

OG0006381

Physical Location & Seq

Genomic Coordinates Forward (+)

2895809 .. 2897185

Gene Structure 1377 bp

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UTR

Exon/CDS

Intron

Transcript / Protein ID

Rw4G001570.1

Sequence Viewer

CDS Protein Promoter (2k)

Length: 1134 bp

ATGCCCCTGACGCGAAAACAAAAAGATCAGTTAGGCATATCTGATCTGGAGAGTTATTCCATGGCTCCTAATCAGTCCTCTAAACCCATCGATGAAAGCCAATTGGAATCAAGGATTAAAGCAAAGCTTGTTGCCCAGTTTGATCAAAAGTTTGAGCAGCTTATGGTGGAGATAGCTTCAATTAACCTTGATGGAGATGCGATCCAGTGGTACGATTGGCTTGAGTCAAGCCATGGAGTCCCAACATGGAACGAGTTTGTCGAAGGCCTGCTTGTACGATTCGGACCTTCGAAATATGAGAATGTAGATGGAGAGCTTGCAAAGCTTCATCAAACAACGACCGTAGTGGAGTTTCAGAGTCGCTTTGAACGGTTATCCAATAGGGCTCGTGATTGGACTGAACGTCAGTTGGTGGGAACTTTCGTTGAAGGGCTTCGTCCAGACATTCGACGCGAGGTTAAGGCATATAGACCCCGAACTATGTCAGCTGCAATTTCTTTTGCTCGAATGCAGGAAGAGAGACTCAATGCAGAAAATCGTCGCCAACACAAGAGTTCCCATAAGTCTACGATTGAACAGGGTGTTGTTGGAGCTCGAAACTCTCCAAGAAGGCTTACAGAACAAGAGCTAAAGGAGCGGACATCAAAAGGATTGTGCTGGTATTGTGATGAAAAATTGAAGCGAGGCCATCAATGCAAACATAAGCGTATCTTGATGATTGAACCAGCAAGGGCCAATGAGGAAGAGGAAGAGTCAGAAAGAGAAATTGAGGCTCAGGGGACAGGTGATTGTAATTCGGATGACGATGATCAATTTCCCATTATTGTTCATGCCTTGGCCGGGTATGCAAATCCACAGACCATGCGAGTTGAAGGAAATGTGAAGAAACAATCAGTAACTGTTCTCATTGATTCGGGTAGCACTGATAATTTCCTTAACATAAAGGTGGCCAAGCGACTAGCCTGTTCAACCATTGAATGCAAGGCGTTCAAAGTTAAGGTTGCTGATGGAAGACCAGTGACTTGCTCTGGGAGATGCCCCAATGTGGAAATTTCGGTTCAAGGTCAGAAAATCACAGCTCCTTTCTTCTTGTTGCCATTAGATGGGTATGACTTGGTCCTTGGTGCACGATGA

Functional Annotation

Gene Ontology

Molecular Function
Biological Process
Cellular Component

GO:0000943 GO:0003674 GO:0003676 GO:0003723 GO:0003824 GO:0003887 GO:0003964 GO:0004518 GO:0004540 GO:0005488 GO:0005575 GO:0005622 GO:0005623 GO:0005634 GO:0006139 GO:0006259 GO:0006278 GO:0006508 GO:0006725 GO:0006807 GO:0008150 GO:0008152 GO:0008233 GO:0009058 GO:0009059 GO:0009987 GO:0016070 GO:0016740 GO:0016772 GO:0016779 GO:0016787 GO:0016788 GO:0018130 GO:0019438 GO:0019538 GO:0032196 GO:0032197 GO:0034061 GO:0034641 GO:0034645 GO:0034654 GO:0043170 GO:0043226 GO:0043227 GO:0043229 GO:0043231 GO:0044237 GO:0044238 GO:0044249 GO:0044260 GO:0044271 GO:0044422 GO:0044424 GO:0044428 GO:0044446 GO:0044464 GO:0046483 GO:0071704 GO:0071897 GO:0090304 GO:0090305 GO:0090501 GO:0097159 GO:0140096 GO:0140097 GO:0140098 GO:1901360 GO:1901362 GO:1901363 GO:1901564 GO:1901576

KEGG Pathways

Metabolic & Signaling

No pathways identified.

Pfam Domains

Protein Families

Chromo RVP_2 RVT_1 Retrotrans_gag rve

Protein Analysis

377

Amino Acids

42.83

Weight (kDa)

6.69

Isoelectric Point (pI)

54.46

Instability Index

Protein Domains (Pfam)

Domain Name	Pfam ID	Position	E-value	Description
Retrotrans_gag	PF03732	58 - 147	6.8e-16	Retrotransposon gag protein
Ty3_capsid	PF19259	59 - 171	5.4e-10	Ty3 transposon capsid-like protein
RVP_2	PF08284	293 - 375	3.1e-06	Retroviral aspartyl protease

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)

Image

Tree File

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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)
AccB7I	CCANNNNNTGG	1 cut(s)	1103
AccBSI	CCGCTC	1 cut(s)	637
AccI	GTMKAC	1 cut(s)	566
AccII	CGCG	2 cut(s)	13, 453
AciI	CCGC	1 cut(s)	637
AclWI	GGATC	1 cut(s)	196
AcoI	YGGCCR	2 cut(s)	837, 948
AcsI	RAATTY	1 cut(s)	1050
AfaI	GTAC	2 cut(s)	212, 276
AfiI	CCNNNNNNNGG	3 cut(s)	840, 1045, 1103
AhdI	GACNNNNNGTC	1 cut(s)	402
AluBI	AGCT	9 cut(s)	127, 160, 176, 316, 325, 488, 593, 628, 1079
AluI	AGCT	9 cut(s)	127, 160, 176, 316, 325, 488, 593, 628, 1079
Alw21I	GWGCWC	2 cut(s)	595, 1129
Alw26I	GTCTC	1 cut(s)	514
Alw44I	GTGCAC	1 cut(s)	1125
AlwI	GGATC	1 cut(s)	196
AlwNI	CAGNNNCTG	1 cut(s)	899
AoxI	GGCC	5 cut(s)	265, 685, 732, 837, 948
ApaLI	GTGCAC	1 cut(s)	1125
ApeKI	GCWGC	2 cut(s)	157, 488
ApoI	RAATTY	1 cut(s)	1050
Asp700I	GAANNNNTTC	1 cut(s)	432
AspS9I	GGNCC	3 cut(s)	284, 732, 1117
AsuC2I	CCSGG	1 cut(s)	841
AsuHPI	GGTGA	1 cut(s)	797
AsuII	TTCGAA	1 cut(s)	290
AvaII	GGWCC	2 cut(s)	284, 1117
BaeGI	GKGCMC	1 cut(s)	1129
BalI	TGGCCA	1 cut(s)	950
BanII	GRGCYC	2 cut(s)	388, 595
BauI	CACGAG	1 cut(s)	387
BbsI	GAAGAC	1 cut(s)	1018
Bbv12I	GWGCWC	2 cut(s)	595, 1129
BbvI	GCAGC	2 cut(s)	169, 475
BccI	CCATC	6 cut(s)	95, 185, 302, 696, 1001, 1097
BclI	TGATCA	2 cut(s)	142, 808
BcnI	CCSGG	1 cut(s)	841
BcoDI	GTCTC	1 cut(s)	514
BfaI	CTAG	1 cut(s)	959
BisI	GCNGC	2 cut(s)	158, 489
BlsI	GCNGC	2 cut(s)	159, 490
Bme1390I	CCNGG	1 cut(s)	841
Bme18I	GGWCC	2 cut(s)	284, 1117
BmeRI	GACNNNNNGTC	1 cut(s)	402
BmgT120I	GGNCC	3 cut(s)	284, 732, 1117
BmiI	GGNNCC	1 cut(s)	66
BmrFI	CCNGG	1 cut(s)	841
BmrI	ACTGGG	1 cut(s)	130
BmsI	GCATC	2 cut(s)	187, 1025
BmuI	ACTGGG	1 cut(s)	130
BpiI	GAAGAC	1 cut(s)	1018
BpmI	CTGGAG	1 cut(s)	68
Bpu10I	CCTNAGC	1 cut(s)	774
Bpu14I	TTCGAA	1 cut(s)	290
BpuEI	CTTGAG	1 cut(s)	242
BpuMI	CCSGG	1 cut(s)	841
Bsa29I	ATCGAT	1 cut(s)	90
BsaJI	CCNNGG	4 cut(s)	60, 232, 834, 1120
Bsc4I	CCNNNNNNNGG	3 cut(s)	840, 1045, 1103
Bse1I	ACTGG	3 cut(s)	136, 205, 1016
BseCI	ATCGAT	1 cut(s)	90
BseDI	CCNNGG	4 cut(s)	60, 232, 834, 1120
BseGI	GGATG	1 cut(s)	805
BseLI	CCNNNNNNNGG	3 cut(s)	840, 1045, 1103
BseMII	CTCAG	1 cut(s)	788
BseNI	ACTGG	3 cut(s)	136, 205, 1016
BseSI	GKGCMC	1 cut(s)	1129
BseXI	GCAGC	2 cut(s)	169, 475
Bsh1236I	CGCG	2 cut(s)	13, 453
Bsh1285I	CGRYCG	1 cut(s)	342
BshFI	GGCC	5 cut(s)	267, 687, 734, 839, 950
BshVI	ATCGAT	1 cut(s)	90
BsiEI	CGRYCG	1 cut(s)	342
BsiHKAI	GWGCWC	2 cut(s)	595, 1129
BsiSI	CCGG	1 cut(s)	840
BslFI	GGGAC	2 cut(s)	224, 793
BslI	CCNNNNNNNGG	3 cut(s)	840, 1045, 1103
BsmAI	GTCTC	1 cut(s)	514
BsmFI	GGGAC	2 cut(s)	224, 793
BsmI	GAATGC	2 cut(s)	513, 983
BsnI	GGCC	5 cut(s)	267, 687, 734, 839, 950
Bsp119I	TTCGAA	1 cut(s)	290
Bsp1286I	GDGCHC	3 cut(s)	388, 595, 1129
Bsp143I	GATC	5 cut(s)	25, 43, 142, 201, 808
Bsp19I	CCATGG	2 cut(s)	60, 232
BspACI	CCGC	1 cut(s)	637
BspANI	GGCC	5 cut(s)	267, 687, 734, 839, 950
BspCNI	CTCAG	1 cut(s)	787
BspDI	ATCGAT	1 cut(s)	90
BspFNI	CGCG	2 cut(s)	13, 453
BspLI	GGNNCC	1 cut(s)	66
BspPI	GGATC	1 cut(s)	196
BspT104I	TTCGAA	1 cut(s)	290
BsrBI	CCGCTC	1 cut(s)	637
BsrI	ACTGG	3 cut(s)	136, 205, 1016
BssECI	CCNNGG	4 cut(s)	60, 232, 834, 1120
BssMI	GATC	5 cut(s)	25, 43, 142, 201, 808
BssSI	CACGAG	1 cut(s)	387
BssT1I	CCWWGG	4 cut(s)	60, 232, 834, 1120
Bst2BI	CACGAG	1 cut(s)	387
Bst4CI	ACNGT	3 cut(s)	343, 372, 901
Bst6I	CTCTTC	3 cut(s)	510, 738, 744
BstBI	TTCGAA	1 cut(s)	290
BstC8I	GCNNGC	2 cut(s)	269, 318
BstDEI	CTNAG	1 cut(s)	774
BstDSI	CCRYGG	2 cut(s)	60, 232
BstF5I	GGATG	1 cut(s)	805
BstFNI	CGCG	2 cut(s)	13, 453
BstKTI	GATC	5 cut(s)	28, 46, 145, 204, 811
BstMAI	GTCTC	1 cut(s)	514
BstMBI	GATC	5 cut(s)	25, 43, 142, 201, 808
BstMCI	CGRYCG	1 cut(s)	342
BstMWI	GCNNNNNNNGC	5 cut(s)	10, 322, 634, 693, 845
BstSCI	CCNGG	1 cut(s)	839
BstSLI	GKGCMC	1 cut(s)	1129
BstUI	CGCG	2 cut(s)	13, 453
BstV1I	GCAGC	2 cut(s)	169, 475
BstV2I	GAAGAC	1 cut(s)	1018
Bsu15I	ATCGAT	1 cut(s)	90
BsuRI	GGCC	5 cut(s)	267, 687, 734, 839, 950
BsuTUI	ATCGAT	1 cut(s)	90
BtgI	CCRYGG	2 cut(s)	60, 232
BtsCI	GGATG	1 cut(s)	805
BtsIMutI	CAGTG	3 cut(s)	212, 921, 1023
Cac8I	GCNNGC	2 cut(s)	269, 318
CaiI	CAGNNNCTG	1 cut(s)	899
Cfr13I	GGNCC	3 cut(s)	284, 732, 1117
ClaI	ATCGAT	1 cut(s)	90
CseI	GACGC	2 cut(s)	19, 459
Csp6I	GTAC	2 cut(s)	211, 275
CviAII	CATG	5 cut(s)	61, 233, 246, 830, 862
CviQI	GTAC	2 cut(s)	211, 275
DdeI	CTNAG	1 cut(s)	774
DpnI	GATC	5 cut(s)	27, 45, 144, 203, 810
DpnII	GATC	5 cut(s)	25, 43, 142, 201, 808
DriI	GACNNNNNGTC	1 cut(s)	402
EaeI	YGGCCR	2 cut(s)	837, 948
Eam1104I	CTCTTC	3 cut(s)	510, 738, 744
Eam1105I	GACNNNNNGTC	1 cut(s)	402
EarI	CTCTTC	3 cut(s)	510, 738, 744
Ecl136II	GAGCTC	1 cut(s)	593
Eco130I	CCWWGG	4 cut(s)	60, 232, 834, 1120
Eco147I	AGGCCT	1 cut(s)	267
Eco24I	GRGCYC	2 cut(s)	388, 595
Eco47I	GGWCC	2 cut(s)	284, 1117
Eco53kI	GAGCTC	1 cut(s)	593
EcoICRI	GAGCTC	1 cut(s)	593
EcoT14I	CCWWGG	4 cut(s)	60, 232, 834, 1120
EcoT38I	GRGCYC	2 cut(s)	388, 595
ErhI	CCWWGG	4 cut(s)	60, 232, 834, 1120
FaeI	CATG	5 cut(s)	64, 236, 249, 833, 865
FalI	AAGNNNNNCTT	6 cut(s)	111, 143, 255, 287, 695, 727
FaqI	GGGAC	2 cut(s)	224, 793
FatI	CATG	5 cut(s)	60, 232, 245, 829, 861
FbaI	TGATCA	2 cut(s)	142, 808
FblI	GTMKAC	1 cut(s)	566
Fnu4HI	GCNGC	2 cut(s)	158, 489
FokI	GGATG	1 cut(s)	812
FriOI	GRGCYC	2 cut(s)	388, 595
Fsp4HI	GCNGC	2 cut(s)	158, 489
FspBI	CTAG	1 cut(s)	959
GluI	GCNGC	2 cut(s)	158, 489
GsuI	CTGGAG	1 cut(s)	68
HaeIII	GGCC	5 cut(s)	267, 687, 734, 839, 950
HapII	CCGG	1 cut(s)	840
HgaI	GACGC	2 cut(s)	19, 459
Hin1II	CATG	5 cut(s)	64, 236, 249, 833, 865
HindIII	AAGCTT	2 cut(s)	125, 323
HinfI	GANTC	8 cut(s)	107, 224, 237, 279, 358, 522, 752, 911
HpaII	CCGG	1 cut(s)	840
HphI	GGTGA	1 cut(s)	797
Hpy166II	GTNNAC	2 cut(s)	567, 1127
Hpy188I	TCNGA	6 cut(s)	43, 284, 357, 757, 799, 1068
Hpy188III	TCNNGA	4 cut(s)	47, 389, 440, 712
Hpy8I	GTNNAC	2 cut(s)	567, 1127
Hpy99I	CGWCG	2 cut(s)	453, 543
HpyAV	CCTTC	5 cut(s)	257, 297, 422, 603, 866
HpyCH4III	ACNGT	3 cut(s)	343, 372, 901
HpyCH4IV	ACGT	1 cut(s)	403
HpyCH4V	TGCA	8 cut(s)	320, 491, 511, 530, 696, 848, 981, 1127
HpyF10VI	GCNNNNNNNGC	5 cut(s)	10, 322, 634, 693, 845
HpyF3I	CTNAG	1 cut(s)	774
HpySE526I	ACGT	1 cut(s)	403
Hsp92II	CATG	5 cut(s)	64, 236, 249, 833, 865
Ksp22I	TGATCA	2 cut(s)	142, 808
Kzo9I	GATC	5 cut(s)	25, 43, 142, 201, 808
LmnI	GCTCC	4 cut(s)	70, 590, 634, 1084
Lsp1109I	GCAGC	2 cut(s)	169, 475
LweI	GCATC	2 cut(s)	187, 1025
MaeI	CTAG	1 cut(s)	959
MaeII	ACGT	1 cut(s)	403
MaeIII	GTNAC	2 cut(s)	895, 1018
MalI	GATC	5 cut(s)	27, 45, 144, 203, 810
MbiI	CCGCTC	1 cut(s)	637
MboI	GATC	5 cut(s)	25, 43, 142, 201, 808
MboII	GAAGA	6 cut(s)	527, 755, 761, 895, 1023, 1078
MfeI	CAATTG	1 cut(s)	101
MhlI	GDGCHC	3 cut(s)	388, 595, 1129
MlsI	TGGCCA	1 cut(s)	950
MluCI	AATT	9 cut(s)	101, 180, 492, 674, 765, 793, 812, 928, 1050
MluNI	TGGCCA	1 cut(s)	950
MlyI	GAGTC	5 cut(s)	233, 246, 367, 516, 761
MmeI	TCCRAC	1 cut(s)	568
MnlI	CCTC	6 cut(s)	88, 448, 677, 733, 739, 763
Mox20I	TGGCCA	1 cut(s)	950
MroXI	GAANNNNTTC	1 cut(s)	432
MscI	TGGCCA	1 cut(s)	950
MseI	TTAA	5 cut(s)	117, 183, 459, 936, 996
MslI	CAYNNNNRTG	1 cut(s)	944
Msp20I	TGGCCA	1 cut(s)	950
MspA1I	CMGCKG	1 cut(s)	488
MspI	CCGG	1 cut(s)	840
MspR9I	CCNGG	1 cut(s)	841
MunI	CAATTG	1 cut(s)	101
Mva1269I	GAATGC	2 cut(s)	513, 983
MvnI	CGCG	2 cut(s)	13, 453
MwoI	GCNNNNNNNGC	5 cut(s)	10, 322, 634, 693, 845
NciI	CCSGG	1 cut(s)	841
NcoI	CCATGG	2 cut(s)	60, 232
NdeII	GATC	5 cut(s)	25, 43, 142, 201, 808
NlaIII	CATG	5 cut(s)	64, 236, 249, 833, 865
NlaIV	GGNNCC	1 cut(s)	66
NmuCI	GTSAC	1 cut(s)	1018
NspV	TTCGAA	1 cut(s)	290
PceI	AGGCCT	1 cut(s)	267
PcsI	WCGNNNNNNNCGW	1 cut(s)	258
PctI	GAATGC	2 cut(s)	513, 983
PdmI	GAANNNNTTC	1 cut(s)	432
PfeI	GAWTC	3 cut(s)	107, 279, 911
PflFI	GACNNNGTC	1 cut(s)	1115
PflMI	CCANNNNNTGG	1 cut(s)	1103
PkrI	GCNGC	2 cut(s)	159, 490
PleI	GAGTC	5 cut(s)	232, 245, 366, 516, 760
PpsI	GAGTC	5 cut(s)	232, 245, 366, 516, 760
Psp124BI	GAGCTC	1 cut(s)	595
PspN4I	GGNNCC	1 cut(s)	66
PspPI	GGNCC	3 cut(s)	284, 732, 1117
PstNI	CAGNNNCTG	1 cut(s)	899
PsyI	GACNNNGTC	1 cut(s)	1115
PvuII	CAGCTG	1 cut(s)	488
RsaI	GTAC	2 cut(s)	212, 276
RsaNI	GTAC	2 cut(s)	211, 275
RseI	CAYNNNNRTG	1 cut(s)	944
SacI	GAGCTC	1 cut(s)	595
SaqAI	TTAA	5 cut(s)	117, 183, 459, 936, 996
SatI	GCNGC	2 cut(s)	158, 489
Sau3AI	GATC	5 cut(s)	25, 43, 142, 201, 808
Sau96I	GGNCC	3 cut(s)	284, 732, 1117
SchI	GAGTC	5 cut(s)	233, 246, 367, 516, 761
ScrFI	CCNGG	1 cut(s)	841
SduI	GDGCHC	3 cut(s)	388, 595, 1129
SfaNI	GCATC	2 cut(s)	187, 1025
SfuI	TTCGAA	1 cut(s)	290
SinI	GGWCC	2 cut(s)	284, 1117
SmiMI	CAYNNNNRTG	1 cut(s)	944
SmlI	CTYRAG	1 cut(s)	221
SmoI	CTYRAG	1 cut(s)	221
Sse9I	AATT	9 cut(s)	101, 180, 492, 674, 765, 793, 812, 928, 1050
SseBI	AGGCCT	1 cut(s)	267
SsiI	CCGC	1 cut(s)	637
SspMI	CTAG	1 cut(s)	959
SstI	GAGCTC	1 cut(s)	595
StuI	AGGCCT	1 cut(s)	267
StyD4I	CCNGG	1 cut(s)	839
StyI	CCWWGG	4 cut(s)	60, 232, 834, 1120
TaaI	ACNGT	3 cut(s)	343, 372, 901
TaiI	ACGT	1 cut(s)	406
TaqI	TCGA	6 cut(s)	90, 261, 290, 448, 505, 595
TasI	AATT	9 cut(s)	101, 180, 492, 674, 765, 793, 812, 928, 1050
TfiI	GAWTC	3 cut(s)	107, 279, 911
Tru1I	TTAA	5 cut(s)	117, 183, 459, 936, 996
Tru9I	TTAA	5 cut(s)	117, 183, 459, 936, 996
TscAI	CASTG	3 cut(s)	212, 928, 1023
TseFI	GTSAC	1 cut(s)	1018
TseI	GCWGC	2 cut(s)	157, 488
Tsp45I	GTSAC	1 cut(s)	1018
TspDTI	ATGAA	4 cut(s)	108, 317, 684, 818
TspRI	CASTG	3 cut(s)	212, 928, 1023
Tth111I	GACNNNGTC	1 cut(s)	1115
Van91I	CCANNNNNTGG	1 cut(s)	1103
VneI	GTGCAC	1 cut(s)	1125
VpaK11BI	GGWCC	2 cut(s)	284, 1117
XapI	RAATTY	1 cut(s)	1050
XmiI	GTMKAC	1 cut(s)	566
XmnI	GAANNNNTTC	1 cut(s)	432
XspI	CTAG	1 cut(s)	959

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