Rroxscaffold_10G00433150

transposition, RNA-mediated

Design Primers CRISPR Design

Basic Information

Type: gene
Biological Identity
rosa_roxburghii
GWHEROQ00000010
OG0000094
Physical Location & Seq
Forward (+)
673590 .. 704148
30559 bp
Loading structure...
UTR
Exon/CDS
Intron
Rroxscaffold_10G00433150.1

Sequence Viewer

Length: 501 bp
ATGTTTGATAACAGGATCTATGTGCCTGATCATGATGATCTTAAAAGGGAAATCTTGGAGGAAGCTCACAGTTCTGCTTATGCTATGCATCCTGGTGGAACAAAAATGTACCATACTCTTAAGAAGTATTATTGGTGGCCTAGGATGAAGAGGAAAATCGCAGATTATGTGAGAAGATGTCTAATATGTCAGCAAGTGAAAGCGGAAAGACAAAAACCCTCGGGTTTGTTGCAGCCATTACCAATACCAGAATGGAAATGGGAGCACCTTACTATGGATTTCGTGTCGGGGTTACCACGAACTCGTAGTGATCATGATAGCATTTGGGTAATTGTGGATCGACTTACAAAATCCGCACATTTCTTACCCGTCAACAAGGCTTACAAAATGGATAGATATGCAGAGTTATTCATGAATGAGATAGTGAGACTCCATGGTACACCCGTCTCAATCACCTCGATCGAGATCCTCGTTTTACTTCGAAATTTTGGCGCGAGTTGA
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 rve zf-CCHC

Protein Analysis

166

Amino Acids

19.64

Weight (kDa)

9.34

Isoelectric Point (pI)

49.73

Instability Index
Protein Domains (Pfam)
Domain Name Pfam ID Position E-value Description
Integrase_H2C2 PF17921 12 - 68 7.5e-22 Integrase zinc binding domain
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: OG0000094)

Species Orthologous Gene IDs
arabidopsis_thaliana AT1G42190
fragaria_vesca FvH4_1g22371 FvH4_1g23261 FvH4_1g27933 FvH4_1g27934 FvH4_1g29231 FvH4_2g02781 FvH4_2g08031 FvH4_2g08581 FvH4_3g06961 FvH4_3g06962 FvH4_3g13531 FvH4_3g14391 FvH4_3g14392 FvH4_3g18622 FvH4_3g18964 FvH4_3g26314 FvH4_3g28781 FvH4_3g30771 FvH4_3g30772 FvH4_3g31752 FvH4_3g32803 FvH4_3g35751 FvH4_3g35752 FvH4_4g02151 FvH4_4g02642 FvH4_4g05523 FvH4_4g05524 FvH4_4g06574 FvH4_4g06722 FvH4_4g08644 FvH4_4g08645 FvH4_4g08646 FvH4_4g08851 FvH4_4g08971 FvH4_4g09081 FvH4_4g09243 FvH4_4g09244 FvH4_4g09283 FvH4_4g10021 FvH4_4g10032 FvH4_4g10033 FvH4_4g10182 FvH4_4g10361 FvH4_4g12502 FvH4_4g12503 FvH4_4g13341 FvH4_4g13942 FvH4_4g13943 FvH4_4g13944 FvH4_4g14432 FvH4_4g14822 FvH4_4g14823 FvH4_4g15291 FvH4_4g15292 FvH4_4g15293 FvH4_4g15471 FvH4_4g15583 FvH4_4g15584 FvH4_4g15585 FvH4_4g15586 FvH4_4g15587 FvH4_4g15591 FvH4_4g15592 FvH4_4g15593 FvH4_4g16179 FvH4_4g18131 FvH4_4g21031 FvH4_4g22021 FvH4_4g22021 FvH4_4g22042 FvH4_5g03402 FvH4_5g07411 FvH4_5g13881 FvH4_5g15792 FvH4_5g24682 FvH4_5g24911 FvH4_5g25322 FvH4_5g25641 FvH4_5g36692 FvH4_5g38072 FvH4_5g38171 FvH4_6g05202 FvH4_6g08531 FvH4_6g16342 FvH4_6g21771 FvH4_6g23303 FvH4_6g23961 FvH4_6g25381 FvH4_6g27021 FvH4_6g27022 FvH4_6g30091 FvH4_6g30092 FvH4_7g02051 FvH4_7g06031 FvH4_7g07031 FvH4_7g07581 FvH4_7g08381 FvH4_7g11551 FvH4_7g19711 FvH4_7g25621 FvH4_7g29722
malus_domestica MD06G1134500.v1.1 MD09G1067600.v1.1 MD13G1145500.v1.1 MD15G1166500.v1.1 MD16G1270000.v1.1
prunus_persica Prupe.7G030900_v2.0.a1
pyrus_communis pycom01g00710 pycom01g03760 pycom03g10770 pycom04g02180 pycom05g08050 pycom06g04140 pycom06g11110 pycom07g07550 pycom07g21570 pycom08g17240 pycom09g13900 pycom09g19570 pycom10g22300 pycom11g03210 pycom11g13750 pycom11g24890 pycom12561g00270 pycom12668g00020 pycom12g11280 pycom12g20720 pycom12g20730 pycom13g21410 pycom13g21660 pycom14g06010 pycom14g06370 pycom14g12800 pycom16g21440 pycom16g22530 pycom17g02030 pycom420g00170 pycom50g00020 pycom5153684g00110 pycom520g00860 pycom581g00060
rosa_chinensis RchiOBHm_Chr0c08g0498091 RchiOBHm_Chr0c08g0498101 RchiOBHm_Chr1g0326991 RchiOBHm_Chr2g0084311 RchiOBHm_Chr2g0090701 RchiOBHm_Chr2g0098591 RchiOBHm_Chr2g0109491 RchiOBHm_Chr2g0109501 RchiOBHm_Chr2g0130801 RchiOBHm_Chr2g0145931 RchiOBHm_Chr2g0168091 RchiOBHm_Chr3g0457081 RchiOBHm_Chr3g0457091 RchiOBHm_Chr3g0467781 RchiOBHm_Chr3g0467791 RchiOBHm_Chr3g0493771 RchiOBHm_Chr3g0494051 RchiOBHm_Chr3g0496881 RchiOBHm_Chr4g0401391 RchiOBHm_Chr4g0414861 RchiOBHm_Chr4g0424081 RchiOBHm_Chr5g0009611 RchiOBHm_Chr5g0049881 RchiOBHm_Chr5g0050351 RchiOBHm_Chr5g0053791 RchiOBHm_Chr5g0078031 RchiOBHm_Chr6g0256481 RchiOBHm_Chr6g0271231 RchiOBHm_Chr6g0286381 RchiOBHm_Chr7g0197101 RchiOBHm_Chr7g0221891 RchiOBHm_Chr7g0237801 RchiOBHm_Chr7g0237821
rosa_multiflora Rmu_sc0000509.1_g000034 Rmu_sc0004751.1_g000014 Rmu_sc0008546.1_g000002 Rmu_sc0009320.1_g000003 Rmu_sc0010661.1_g000006 Rmu_sc0029652.1_g000002
rosa_roxburghii Rroxscaffold_10G00433150 Rroxscaffold_15G00447630 Rroxscaffold_26G00447790 Rroxscaffold_29G00441810 Rroxscaffold_32G00442860 Rroxscaffold_33G00439800 Rroxscaffold_34G00443230 Rroxscaffold_3G00220560 Rroxscaffold_3G00227370 Rroxscaffold_3G00239080 Rroxscaffold_3G00239090 Rroxscaffold_3G00273190 Rroxscaffold_4G00323530 Rroxscaffold_4G00326840 Rroxscaffold_57G00443110 Rroxscaffold_5G00338590 Rroxscaffold_5G00347530 Rroxscaffold_68G00446990 Rroxscaffold_76G00448570 Rroxscaffold_90G00448860
rosa_rugosa Rorug06G0233600
rosa_samantha Rh3CG302700 Rh6DG286700
rosa_wichuraiana Rw0G002280 Rw0G004080 Rw0G011830 Rw1G003690 Rw1G008800 Rw1G009130 Rw1G009140 Rw1G009150 Rw1G009160 Rw1G009410 Rw1G009580 Rw1G012770 Rw1G015850 Rw1G026860 Rw2G003780 Rw2G006480 Rw2G016520 Rw2G016960 Rw2G018170 Rw2G025180 Rw2G025510 Rw2G025610 Rw2G025750 Rw2G025920 Rw2G029950 Rw2G046360 Rw2G046370 Rw2G046380 Rw3G009070 Rw3G025820 Rw3G027340 Rw3G027900 Rw3G028150 Rw3G029060 Rw4G002440 Rw4G005960 Rw4G007520 Rw4G011970 Rw4G011980 Rw4G012190 Rw4G012530 Rw4G018490 Rw4G026380 Rw5G003970 Rw5G030920 Rw5G031780 Rw5G031900 Rw5G033030 Rw5G033040 Rw5G036330 Rw5G039730 Rw5G048110 Rw6G006670 Rw6G007910 Rw6G009720 Rw6G010990 Rw6G012930 Rw6G012940 Rw6G013420 Rw6G014690 Rw6G015290 Rw6G015790 Rw6G015920 Rw6G036510 Rw7G016650 Rw7G023140 Rw7G028650 Rw7G036450 Rw7G036460 Rw7G036910

Restriction Enzyme Sites

1 / 10
Enzyme Recognition Site Cut Count Positions (bp)
AccII CGCG 1 cut(s) 494
AciI CCGC 2 cut(s) 203, 354
AclWI GGATC 3 cut(s) 23, 345, 460
AcsI RAATTY 1 cut(s) 484
AfaI GTAC 2 cut(s) 110, 439
AfiI CCNNNNNNNGG 1 cut(s) 274
AflII CTTAAG 1 cut(s) 119
AjnI CCWGG 1 cut(s) 91
AluBI AGCT 1 cut(s) 65
AluI AGCT 1 cut(s) 65
Alw21I GWGCWC 1 cut(s) 267
Alw26I GTCTC 2 cut(s) 421, 451
AlwI GGATC 3 cut(s) 23, 345, 460
Ama87I CYCGRG 1 cut(s) 220
AoxI GGCC 1 cut(s) 137
ApeKI GCWGC 1 cut(s) 232
ApoI RAATTY 1 cut(s) 484
AspA2I CCTAGG 1 cut(s) 140
AspLEI GCGC 1 cut(s) 494
AsuHPI GGTGA 1 cut(s) 445
AsuII TTCGAA 1 cut(s) 481
AvaI CYCGRG 1 cut(s) 220
AvrII CCTAGG 1 cut(s) 140
BaeI ACNNNNGTAYC 2 cut(s) 429, 462
Bbv12I GWGCWC 1 cut(s) 267
BbvI GCAGC 1 cut(s) 244
BciT130I CCWGG 1 cut(s) 93
BclI TGATCA 2 cut(s) 28, 310
BcoDI GTCTC 2 cut(s) 421, 451
BfaI CTAG 1 cut(s) 141
BfrI CTTAAG 1 cut(s) 119
BisI GCNGC 1 cut(s) 233
BlnI CCTAGG 1 cut(s) 140
BlsI GCNGC 1 cut(s) 234
Bme1390I CCNGG 1 cut(s) 93
BmeT110I CYCGRG 1 cut(s) 220
BmrFI CCNGG 1 cut(s) 93
BmsI GCATC 1 cut(s) 97
Bpu14I TTCGAA 1 cut(s) 481
BsaBI GATNNNNATC 1 cut(s) 464
BsaJI CCNNGG 3 cut(s) 140, 219, 433
Bsc4I CCNNNNNNNGG 1 cut(s) 274
Bse8I GATNNNNATC 1 cut(s) 464
BseBI CCWGG 1 cut(s) 93
BseDI CCNNGG 3 cut(s) 140, 219, 433
BseGI GGATG 2 cut(s) 88, 150
BseJI GATNNNNATC 1 cut(s) 464
BseLI CCNNNNNNNGG 1 cut(s) 274
BseXI GCAGC 1 cut(s) 244
Bsh1236I CGCG 1 cut(s) 494
Bsh1285I CGRYCG 1 cut(s) 462
BshFI GGCC 1 cut(s) 139
BsiEI CGRYCG 1 cut(s) 462
BsiHKAI GWGCWC 1 cut(s) 267
BsiHKCI CYCGRG 1 cut(s) 220
BslI CCNNNNNNNGG 1 cut(s) 274
BsmAI GTCTC 2 cut(s) 421, 451
BsmBI CGTCTC 1 cut(s) 451
BsnI GGCC 1 cut(s) 139
BsoBI CYCGRG 1 cut(s) 220
Bsp119I TTCGAA 1 cut(s) 481
Bsp1286I GDGCHC 1 cut(s) 267
Bsp143I GATC 7 cut(s) 15, 28, 37, 310, 337, 459, 465
Bsp19I CCATGG 1 cut(s) 433
BspACI CCGC 2 cut(s) 203, 354
BspANI GGCC 1 cut(s) 139
BspFNI CGCG 1 cut(s) 494
BspHI TCATGA 3 cut(s) 31, 313, 411
BspPI GGATC 3 cut(s) 23, 345, 460
BspT104I TTCGAA 1 cut(s) 481
BspTI CTTAAG 1 cut(s) 119
BssECI CCNNGG 3 cut(s) 140, 219, 433
BssMI GATC 7 cut(s) 15, 28, 37, 310, 337, 459, 465
BssT1I CCWWGG 2 cut(s) 140, 433
Bst2UI CCWGG 1 cut(s) 93
Bst4CI ACNGT 1 cut(s) 71
Bst6I CTCTTC 1 cut(s) 143
BstAFI CTTAAG 1 cut(s) 119
BstBI TTCGAA 1 cut(s) 481
BstDSI CCRYGG 1 cut(s) 433
BstEII GGTNACC 1 cut(s) 291
BstF5I GGATG 2 cut(s) 88, 150
BstFNI CGCG 1 cut(s) 494
BstHHI GCGC 1 cut(s) 494
BstKTI GATC 7 cut(s) 18, 31, 40, 313, 340, 462, 468
BstMAI GTCTC 2 cut(s) 421, 451
BstMBI GATC 7 cut(s) 15, 28, 37, 310, 337, 459, 465
BstMCI CGRYCG 1 cut(s) 462
BstNI CCWGG 1 cut(s) 93
BstPI GGTNACC 1 cut(s) 291
BstSCI CCNGG 1 cut(s) 91
BstUI CGCG 1 cut(s) 494
BstV1I GCAGC 1 cut(s) 244
BstX2I RGATCY 2 cut(s) 15, 465
BstYI RGATCY 2 cut(s) 15, 465
BsuRI GGCC 1 cut(s) 139
BtgI CCRYGG 1 cut(s) 433
BtsCI GGATG 2 cut(s) 88, 150
CciI TCATGA 3 cut(s) 31, 313, 411
CfoI GCGC 1 cut(s) 494
Csp6I GTAC 2 cut(s) 109, 438
CviAII CATG 4 cut(s) 32, 314, 412, 434
CviJI RGCY 4 cut(s) 65, 139, 235, 380
CviKI_1 RGCY 4 cut(s) 65, 139, 235, 380
CviQI GTAC 2 cut(s) 109, 438
DpnI GATC 7 cut(s) 17, 30, 39, 312, 339, 461, 467
DpnII GATC 7 cut(s) 15, 28, 37, 310, 337, 459, 465
Eam1104I CTCTTC 1 cut(s) 143
EarI CTCTTC 1 cut(s) 143
Eco130I CCWWGG 2 cut(s) 140, 433
Eco88I CYCGRG 1 cut(s) 220
Eco91I GGTNACC 1 cut(s) 291
EcoO65I GGTNACC 1 cut(s) 291
EcoRII CCWGG 1 cut(s) 91
EcoT14I CCWWGG 2 cut(s) 140, 433
EcoT22I ATGCAT 1 cut(s) 90
ErhI CCWWGG 2 cut(s) 140, 433
Esp3I CGTCTC 1 cut(s) 451
FaeI CATG 4 cut(s) 35, 317, 415, 437
FatI CATG 4 cut(s) 31, 313, 411, 433
FbaI TGATCA 2 cut(s) 28, 310
Fnu4HI GCNGC 1 cut(s) 233
FokI GGATG 2 cut(s) 75, 157
Fsp4HI GCNGC 1 cut(s) 233
FspBI CTAG 1 cut(s) 141
GlaI GCGC 1 cut(s) 493
GluI GCNGC 1 cut(s) 233
HaeIII GGCC 1 cut(s) 139
HhaI GCGC 1 cut(s) 494
Hin1II CATG 4 cut(s) 35, 317, 415, 437
Hin6I GCGC 1 cut(s) 492
HinP1I GCGC 1 cut(s) 492
HincII GTYRAC 1 cut(s) 373
HindII GTYRAC 1 cut(s) 373
HinfI GANTC 1 cut(s) 429
HphI GGTGA 1 cut(s) 445
Hpy166II GTNNAC 2 cut(s) 373, 440
Hpy188III TCNNGA 4 cut(s) 32, 314, 412, 463
Hpy8I GTNNAC 2 cut(s) 373, 440
HpyCH4III ACNGT 1 cut(s) 71
HpyCH4V TGCA 3 cut(s) 88, 232, 401
Hsp92II CATG 4 cut(s) 35, 317, 415, 437
HspAI GCGC 1 cut(s) 492
Ksp22I TGATCA 2 cut(s) 28, 310
Kzo9I GATC 7 cut(s) 15, 28, 37, 310, 337, 459, 465
LmnI GCTCC 1 cut(s) 262
LpnPI CCDG 4 cut(s) 39, 78, 105, 261
Lsp1109I GCAGC 1 cut(s) 244
LweI GCATC 1 cut(s) 97
MaeI CTAG 1 cut(s) 141
MaeIII GTNAC 1 cut(s) 291
MalI GATC 7 cut(s) 17, 30, 39, 312, 339, 461, 467
MboI GATC 7 cut(s) 15, 28, 37, 310, 337, 459, 465
MboII GAAGA 2 cut(s) 160, 186
MflI RGATCY 2 cut(s) 15, 465
MhlI GDGCHC 1 cut(s) 267
MluCI AATT 2 cut(s) 330, 484
MlyI GAGTC 1 cut(s) 423
MnlI CCTC 5 cut(s) 52, 144, 229, 466, 479
Mph1103I ATGCAT 1 cut(s) 90
MseI TTAA 2 cut(s) 42, 120
MslI CAYNNNNRTG 1 cut(s) 93
MspCI CTTAAG 1 cut(s) 119
MspR9I CCNGG 1 cut(s) 93
MvaI CCWGG 1 cut(s) 93
MvnI CGCG 1 cut(s) 494
NcoI CCATGG 1 cut(s) 433
NdeII GATC 7 cut(s) 15, 28, 37, 310, 337, 459, 465
NlaIII CATG 4 cut(s) 35, 317, 415, 437
NsiI ATGCAT 1 cut(s) 90
NspV TTCGAA 1 cut(s) 481
PagI TCATGA 3 cut(s) 31, 313, 411
PcsI WCGNNNNNNNCGW 1 cut(s) 468
PkrI GCNGC 1 cut(s) 234
Ple19I CGATCG 1 cut(s) 462
PleI GAGTC 1 cut(s) 423
PpsI GAGTC 1 cut(s) 423
Psp6I CCWGG 1 cut(s) 91
PspEI GGTNACC 1 cut(s) 291
PspGI CCWGG 1 cut(s) 91
PsuI RGATCY 2 cut(s) 15, 465
PvuI CGATCG 1 cut(s) 462
RsaI GTAC 2 cut(s) 110, 439
RsaNI GTAC 2 cut(s) 109, 438
RseI CAYNNNNRTG 1 cut(s) 93
SaqAI TTAA 2 cut(s) 42, 120
SatI GCNGC 1 cut(s) 233
Sau3AI GATC 7 cut(s) 15, 28, 37, 310, 337, 459, 465
SchI GAGTC 1 cut(s) 423
ScrFI CCNGG 1 cut(s) 93
SduI GDGCHC 1 cut(s) 267
SetI ASST 3 cut(s) 67, 270, 458
SfaNI GCATC 1 cut(s) 97
SfuI TTCGAA 1 cut(s) 481
SmiMI CAYNNNNRTG 1 cut(s) 93
SmlI CTYRAG 1 cut(s) 119
SmoI CTYRAG 1 cut(s) 119
Sse9I AATT 2 cut(s) 330, 484
SsiI CCGC 2 cut(s) 203, 354
SspMI CTAG 1 cut(s) 141
StyD4I CCNGG 1 cut(s) 91
StyI CCWWGG 2 cut(s) 140, 433
TaaI ACNGT 1 cut(s) 71
TaqI TCGA 4 cut(s) 340, 458, 462, 481
TasI AATT 2 cut(s) 330, 484
Tru1I TTAA 2 cut(s) 42, 120
Tru9I TTAA 2 cut(s) 42, 120
TseI GCWGC 1 cut(s) 232
TspDTI ATGAA 3 cut(s) 161, 400, 428
Vha464I CTTAAG 1 cut(s) 119
XapI RAATTY 1 cut(s) 484
XcmI CCANNNNNNNNNTGG 2 cut(s) 249, 255
XmaJI CCTAGG 1 cut(s) 140
XspI CTAG 1 cut(s) 141
Zsp2I ATGCAT 1 cut(s) 90
Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.