Rroxscaffold_5G00340720

ribonuclease H protein

Design Primers CRISPR Design

Basic Information

Type: gene
Biological Identity
rosa_roxburghii
GWHEROQ00000005
OG0000204
Physical Location & Seq
Forward (+)
9203581 .. 9204474
894 bp
Loading structure...
UTR
Exon/CDS
Intron
Rroxscaffold_5G00340720.1

Sequence Viewer

Length: 357 bp
ATGGAAGTGATAGCCAAAGATGGAGATAGCTATAGGGGAAATGGATGGAGTCTGAAACTGTCGTTCCCGCCTCTTAGTTATCTTCAGATGAACTCTACACTAACTGGTGGATTTGCCTTCAGAAATGGTGAAGGTCTTCACATTTTAGCAGCCTACAAGAATCTTCATCAGGTGGATATCCTTTTAGCAGAAGGTCTTCCTCTTAGAGCAAGTCTACATGCAGCTTTGCTTTATGGTTACTCTTCTTTAGACATTGAGGGTGATTCAAAAGTTCTAATCGATGCAATAGCTGGCAAGATCCGGACTCATTGGCGTACGAAGTCAATTATTCGAGACATTAAACTTATAGCAAGTTAG
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
DUF4283 RVT_1 RVT_3 zf-RVT

Protein Analysis

118

Amino Acids

12.97

Weight (kDa)

8.96

Isoelectric Point (pI)

22.54

Instability Index
Protein Domains (Pfam)
Domain Name Pfam ID Position E-value Description
RVT_3 PF13456 36 - 116 7.4e-07 Reverse transcriptase-like
Hydrophobicity Profile (Kyte-Doolittle)
AI Structure Prediction Report
Calculating structure properties...

Genomic Context

Gene Family Tree

Species Filter
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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: OG0000204)

Species Orthologous Gene IDs
arabidopsis_thaliana AT1G04625 AT1G27220 AT1G27250 AT1G27870 AT1G47497 AT1G47497 AT1G50160 AT1G52990 AT1G52990 AT1G77815 AT2G02650 AT2G04420 AT2G11205 AT2G13980 AT2G33160 AT2G46460 AT3G09510 AT3G23320 AT3G25270 AT3G32130 AT4G03292 AT4G09775 AT5G26617 AT5G44470 AT5G52115 AT5G65005
fragaria_vesca FvH4_1g25222 FvH4_1g28481 FvH4_3g03751 FvH4_3g24081 FvH4_3g35341 FvH4_5g31961 FvH4_6g20891 FvH4_6g23253 FvH4_6g31361 FvH4_6g53051
malus_domestica MD14G1209300.v1.1
prunus_persica Prupe.1G168800_v2.0.a1 Prupe.1G509200_v2.0.a1 Prupe.2G042000_v2.0.a1 Prupe.2G133200_v2.0.a1 Prupe.2G140300_v2.0.a1 Prupe.3G103800_v2.0.a1 Prupe.4G217300_v2.0.a1 Prupe.4G245300_v2.0.a1 Prupe.5G002600_v2.0.a1 Prupe.5G134600_v2.0.a1 Prupe.6G185900_v2.0.a1 Prupe.6G308300_v2.0.a1 Prupe.7G010700_v2.0.a1 Prupe.8G078100_v2.0.a1 Prupe.8G128400_v2.0.a1
pyrus_communis pycom01g14230 pycom03g12410 pycom08g15160 pycom08g21670 pycom10g25730 pycom10g25740 pycom11g15380 pycom14g10440 pycom14g11510 pycom15g31840 pycom16g02370
rosa_chinensis RchiOBHm_Chr4g0440421 RchiOBHm_Chr5g0005841 RchiOBHm_Chr6g0289481 RchiOBHm_Chr7g0218671
rosa_laevigata RLG00000011653 RLG00000031330 RLG00000031331 RLG00000032722
rosa_multiflora Rmu_co8243061.1_g000001 Rmu_sc0000470.1_g000036 Rmu_sc0000581.1_g000008 Rmu_sc0000666.1_g000017 Rmu_sc0000905.1_g000019 Rmu_sc0000976.1_g000013 Rmu_sc0001066.1_g000001 Rmu_sc0001103.1_g000007 Rmu_sc0001180.1_g000001 Rmu_sc0001643.1_g000034 Rmu_sc0001759.1_g000007 Rmu_sc0001850.1_g000051 Rmu_sc0001910.1_g000008 Rmu_sc0001981.1_g000015 Rmu_sc0001981.1_g000029 Rmu_sc0002209.1_g000015 Rmu_sc0002406.1_g000010 Rmu_sc0003743.1_g000002 Rmu_sc0006416.1_g000026 Rmu_sc0006513.1_g000006 Rmu_sc0006577.1_g000010 Rmu_sc0014652.1_g000001 Rmu_sc0016202.1_g000003
rosa_roxburghii Rroxscaffold_1G00001530 Rroxscaffold_1G00047250 Rroxscaffold_5G00340720 Rroxscaffold_7G00171110 Rroxscaffold_7G00177650
rosa_rugosa Rorug01G0044800 Rorug01G0204500 Rorug01G0224700 Rorug01G0267800 Rorug02G0038400 Rorug02G0107100 Rorug02G0180700 Rorug02G0363800 Rorug02G0374300 Rorug02G0491400 Rorug02G0491400 Rorug03G0104200 Rorug03G0109800 Rorug03G0334200 Rorug04G0007100 Rorug04G0061400.1 Rorug04G0080000 Rorug05G0152200 Rorug05G0188800 Rorug05G0234800 Rorug05G0239900 Rorug05G0284800 Rorug06G0044700 Rorug06G0205700 Rorug06G0266900 Rorug06G0440700 Rorug07G0037400 Rorug07G0192100 Rorug07G0196900 Rorug07G0237500 Rorug07G0336400.1 RorugPtG0002500.1
rosa_samantha Rh1BG014800 Rh1CG017500 Rh2CG332500 Rh3BG371800 Rh5AG046000 Rh5AG046100 Rh5BG044700 Rh5BG044800 Rh5BG248000 Rh5CG053600 Rh5CG053700 Rh5DG044500 Rh5DG044600 Rh6AG052800 Rh6AG315400 Rh6DG021400 Rh7AG409500
rosa_wichuraiana Rw3G007750 Rw3G018750 Rw4G008820 Rw5G004630

Restriction Enzyme Sites

1 / 10
Enzyme Recognition Site Cut Count Positions (bp)
AccI GTMKAC 1 cut(s) 214
AccIII TCCGGA 1 cut(s) 300
AciI CCGC 1 cut(s) 68
AclWI GGATC 1 cut(s) 292
AcuI CTGAAG 2 cut(s) 68, 103
AfaI GTAC 1 cut(s) 316
AgsI TTSAA 1 cut(s) 267
AluBI AGCT 3 cut(s) 30, 224, 290
AluI AGCT 3 cut(s) 30, 224, 290
Alw26I GTCTC 1 cut(s) 327
AlwI GGATC 1 cut(s) 292
Aor13HI TCCGGA 1 cut(s) 300
ApeKI GCWGC 2 cut(s) 149, 221
Asp700I GAANNNNTTC 2 cut(s) 135, 195
AsuHPI GGTGA 2 cut(s) 140, 272
BbsI GAAGAC 2 cut(s) 128, 188
BbvI GCAGC 2 cut(s) 161, 233
BccI CCATC 2 cut(s) 14, 39
BcoDI GTCTC 1 cut(s) 327
BfmI CTRYAG 1 cut(s) 31
BisI GCNGC 2 cut(s) 150, 222
BlsI GCNGC 2 cut(s) 151, 223
BmsI GCATC 1 cut(s) 271
BpiI GAAGAC 2 cut(s) 128, 188
Bsa29I ATCGAT 1 cut(s) 279
BsaWI WCCGGW 1 cut(s) 300
Bse1I ACTGG 1 cut(s) 109
BseAI TCCGGA 1 cut(s) 300
BseCI ATCGAT 1 cut(s) 279
BseGI GGATG 1 cut(s) 50
BseNI ACTGG 1 cut(s) 109
BseXI GCAGC 2 cut(s) 161, 233
BshVI ATCGAT 1 cut(s) 279
BsiSI CCGG 1 cut(s) 301
BsiWI CGTACG 1 cut(s) 314
BsmAI GTCTC 1 cut(s) 327
Bsp13I TCCGGA 1 cut(s) 300
Bsp143I GATC 1 cut(s) 297
BspACI CCGC 1 cut(s) 68
BspDI ATCGAT 1 cut(s) 279
BspEI TCCGGA 1 cut(s) 300
BspPI GGATC 1 cut(s) 292
BsrI ACTGG 1 cut(s) 109
BssMI GATC 1 cut(s) 297
Bst4CI ACNGT 1 cut(s) 60
Bst6I CTCTTC 1 cut(s) 247
BstC8I GCNNGC 1 cut(s) 292
BstDEI CTNAG 2 cut(s) 74, 203
BstF5I GGATG 1 cut(s) 50
BstKTI GATC 1 cut(s) 300
BstMAI GTCTC 1 cut(s) 327
BstMBI GATC 1 cut(s) 297
BstNSI RCATGY 1 cut(s) 221
BstSFI CTRYAG 1 cut(s) 31
BstV1I GCAGC 2 cut(s) 161, 233
BstV2I GAAGAC 2 cut(s) 128, 188
BstX2I RGATCY 1 cut(s) 297
BstYI RGATCY 1 cut(s) 297
Bsu15I ATCGAT 1 cut(s) 279
BsuTUI ATCGAT 1 cut(s) 279
BtsCI GGATG 1 cut(s) 50
Cac8I GCNNGC 1 cut(s) 292
ClaI ATCGAT 1 cut(s) 279
Csp6I GTAC 1 cut(s) 315
CviAII CATG 1 cut(s) 218
CviJI RGCY 5 cut(s) 14, 30, 152, 224, 290
CviKI_1 RGCY 5 cut(s) 14, 30, 152, 224, 290
CviQI GTAC 1 cut(s) 315
DdeI CTNAG 2 cut(s) 74, 203
DpnI GATC 1 cut(s) 299
DpnII GATC 1 cut(s) 297
Eam1104I CTCTTC 1 cut(s) 247
EarI CTCTTC 1 cut(s) 247
Eco32I GATATC 1 cut(s) 178
Eco57I CTGAAG 2 cut(s) 68, 103
EcoRV GATATC 1 cut(s) 178
FaeI CATG 1 cut(s) 221
FaiI YATR 4 cut(s) 33, 219, 234, 347
FatI CATG 1 cut(s) 217
FauI CCCGC 1 cut(s) 75
FblI GTMKAC 1 cut(s) 214
Fnu4HI GCNGC 2 cut(s) 150, 222
FokI GGATG 1 cut(s) 57
Fsp4HI GCNGC 2 cut(s) 150, 222
GluI GCNGC 2 cut(s) 150, 222
HapII CCGG 1 cut(s) 301
Hin1II CATG 1 cut(s) 221
HinfI GANTC 4 cut(s) 49, 160, 263, 304
HpaII CCGG 1 cut(s) 301
HphI GGTGA 2 cut(s) 140, 272
Hpy166II GTNNAC 1 cut(s) 215
Hpy188I TCNGA 3 cut(s) 54, 87, 122
Hpy188III TCNNGA 2 cut(s) 301, 332
Hpy8I GTNNAC 1 cut(s) 215
HpyAV CCTTC 3 cut(s) 125, 127, 185
HpyCH4III ACNGT 1 cut(s) 60
HpyCH4V TGCA 2 cut(s) 221, 284
HpyF3I CTNAG 2 cut(s) 74, 203
Hsp92II CATG 1 cut(s) 221
Kpn2I TCCGGA 1 cut(s) 300
Kzo9I GATC 1 cut(s) 297
LpnPI CCDG 4 cut(s) 90, 155, 276, 314
Lsp1109I GCAGC 2 cut(s) 161, 233
LweI GCATC 1 cut(s) 271
MaeIII GTNAC 1 cut(s) 236
MalI GATC 1 cut(s) 299
MboI GATC 1 cut(s) 297
MboII GAAGA 5 cut(s) 74, 128, 155, 188, 234
MflI RGATCY 1 cut(s) 297
MluCI AATT 1 cut(s) 324
MlyI GAGTC 2 cut(s) 58, 298
MnlI CCTC 3 cut(s) 81, 210, 250
MroI TCCGGA 1 cut(s) 300
MroXI GAANNNNTTC 2 cut(s) 135, 195
MseI TTAA 1 cut(s) 339
MspI CCGG 1 cut(s) 301
NdeII GATC 1 cut(s) 297
NlaIII CATG 1 cut(s) 221
NspI RCATGY 1 cut(s) 221
PdmI GAANNNNTTC 2 cut(s) 135, 195
PfeI GAWTC 2 cut(s) 160, 263
Pfl23II CGTACG 1 cut(s) 314
PkrI GCNGC 2 cut(s) 151, 223
PleI GAGTC 2 cut(s) 57, 298
PpsI GAGTC 2 cut(s) 57, 298
PspLI CGTACG 1 cut(s) 314
PsuI RGATCY 1 cut(s) 297
RsaI GTAC 1 cut(s) 316
RsaNI GTAC 1 cut(s) 315
SaqAI TTAA 1 cut(s) 339
SatI GCNGC 2 cut(s) 150, 222
Sau3AI GATC 1 cut(s) 297
SchI GAGTC 2 cut(s) 58, 298
SetI ASST 6 cut(s) 32, 136, 174, 196, 226, 292
SfaNI GCATC 1 cut(s) 271
SfcI CTRYAG 1 cut(s) 31
Sse9I AATT 1 cut(s) 324
SsiI CCGC 1 cut(s) 68
TaaI ACNGT 1 cut(s) 60
TaqI TCGA 2 cut(s) 279, 331
TasI AATT 1 cut(s) 324
TfiI GAWTC 2 cut(s) 160, 263
Tru1I TTAA 1 cut(s) 339
Tru9I TTAA 1 cut(s) 339
TseI GCWGC 2 cut(s) 149, 221
TspDTI ATGAA 2 cut(s) 104, 155
XceI RCATGY 1 cut(s) 221
XmiI GTMKAC 1 cut(s) 214
XmnI GAANNNNTTC 2 cut(s) 135, 195
Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.