Rroxscaffold_3G00239080

transposition, RNA-mediated

Design Primers CRISPR Design

Basic Information

Type: gene
Biological Identity
rosa_roxburghii
GWHEROQ00000003
OG0000094
Physical Location & Seq
Reverse (-)
28528181 .. 28529476
1296 bp
Loading structure...
UTR
Exon/CDS
Intron
Rroxscaffold_3G00239080.1

Sequence Viewer

Length: 399 bp
ATGAAGGGTGTGGTGAGATTTGGCAAGAAAGGGAAGTTATCACCAAGGTTTGTCGGACCTTTTGAAATTCTGGAAAGGGTAGGAGATTTGGCTTATAGGCTTGCCTTACCTCCTAGTATGTCCGGTGTGCATAATGTGTTCCATGTGTCTATGTTGAGGAAGTATGTCCAGGATGAGTCACATGTGATCGATTATGGCACGATTAAGGTGCATGCGGATACGACCTTTGTTGTTGAACCTGTTCGTATTTTGGATAGGTCAACAAAGCAACTTCGAAGGAAGGAAGTTGACTTGGTCAAGGTATTGTGGAGTCACCATGACGAGGGTGATGCTTCTTGGGAATTGGAGTCGGATATGAGAGCGAAGTACCCACAGTTGTTTGTTGATGAGCAAGCGTGA
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
No domains found.

Protein Analysis

132

Amino Acids

15.21

Weight (kDa)

8.02

Isoelectric Point (pI)

39.85

Instability Index
Protein Domains (Pfam)
Domain Name Pfam ID Position E-value Description
SH3_Tf2-1 PF24626 5 - 56 2.8e-25 Tf2-1-like, SH3 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)
AciI CCGC 1 cut(s) 215
AcsI RAATTY 1 cut(s) 66
AfaI GTAC 1 cut(s) 368
AfiI CCNNNNNNNGG 1 cut(s) 322
AflIII ACRYGT 1 cut(s) 181
AgsI TTSAA 2 cut(s) 65, 236
AjnI CCWGG 1 cut(s) 168
ApoI RAATTY 1 cut(s) 66
Asp700I GAANNNNTTC 1 cut(s) 240
AspS9I GGNCC 1 cut(s) 56
AsuHPI GGTGA 4 cut(s) 25, 33, 305, 338
AsuII TTCGAA 1 cut(s) 274
AvaII GGWCC 1 cut(s) 56
BcgI CGANNNNNNTGC 4 cut(s) 190, 224, 311, 345
BciT130I CCWGG 1 cut(s) 170
BciVI GTATCC 1 cut(s) 211
BfaI CTAG 1 cut(s) 114
BfuI GTATCC 1 cut(s) 211
Bme1390I CCNGG 1 cut(s) 170
Bme18I GGWCC 1 cut(s) 56
BmgT120I GGNCC 1 cut(s) 56
BmrFI CCNGG 1 cut(s) 170
BmsI GCATC 1 cut(s) 319
Bpu14I TTCGAA 1 cut(s) 274
Bsa29I ATCGAT 1 cut(s) 189
BsaJI CCNNGG 1 cut(s) 44
BsaWI WCCGGW 1 cut(s) 122
Bsc4I CCNNNNNNNGG 1 cut(s) 322
BseBI CCWGG 1 cut(s) 170
BseCI ATCGAT 1 cut(s) 189
BseDI CCNNGG 1 cut(s) 44
BseGI GGATG 1 cut(s) 178
BseLI CCNNNNNNNGG 1 cut(s) 322
BshVI ATCGAT 1 cut(s) 189
BsiSI CCGG 1 cut(s) 123
BslI CCNNNNNNNGG 1 cut(s) 322
Bsp119I TTCGAA 1 cut(s) 274
Bsp143I GATC 1 cut(s) 186
BspACI CCGC 1 cut(s) 215
BspDI ATCGAT 1 cut(s) 189
BspT104I TTCGAA 1 cut(s) 274
BssECI CCNNGG 1 cut(s) 44
BssMI GATC 1 cut(s) 186
BssT1I CCWWGG 1 cut(s) 44
Bst2UI CCWGG 1 cut(s) 170
Bst4CI ACNGT 1 cut(s) 375
BstBI TTCGAA 1 cut(s) 274
BstC8I GCNNGC 3 cut(s) 102, 213, 393
BstF5I GGATG 1 cut(s) 178
BstKTI GATC 1 cut(s) 189
BstMBI GATC 1 cut(s) 186
BstNI CCWGG 1 cut(s) 170
BstNSI RCATGY 2 cut(s) 185, 215
BstSCI CCNGG 1 cut(s) 168
Bsu15I ATCGAT 1 cut(s) 189
BsuI GTATCC 1 cut(s) 211
BsuTUI ATCGAT 1 cut(s) 189
BtsCI GGATG 1 cut(s) 178
Cac8I GCNNGC 3 cut(s) 102, 213, 393
Cfr13I GGNCC 1 cut(s) 56
ClaI ATCGAT 1 cut(s) 189
Csp6I GTAC 1 cut(s) 367
CviAII CATG 4 cut(s) 143, 182, 212, 317
CviJI RGCY 2 cut(s) 92, 100
CviKI_1 RGCY 2 cut(s) 92, 100
CviQI GTAC 1 cut(s) 367
DpnI GATC 1 cut(s) 188
DpnII GATC 1 cut(s) 186
Eco130I CCWWGG 1 cut(s) 44
Eco47I GGWCC 1 cut(s) 56
EcoRII CCWGG 1 cut(s) 168
EcoT14I CCWWGG 1 cut(s) 44
ErhI CCWWGG 1 cut(s) 44
FaeI CATG 4 cut(s) 146, 185, 215, 320
FatI CATG 4 cut(s) 142, 181, 211, 316
FokI GGATG 1 cut(s) 185
FspBI CTAG 1 cut(s) 114
HapII CCGG 1 cut(s) 123
Hin1II CATG 4 cut(s) 146, 185, 215, 320
HincII GTYRAC 2 cut(s) 261, 289
HindII GTYRAC 2 cut(s) 261, 289
HinfI GANTC 3 cut(s) 176, 310, 347
HpaII CCGG 1 cut(s) 123
HphI GGTGA 4 cut(s) 25, 33, 305, 338
Hpy166II GTNNAC 2 cut(s) 261, 289
Hpy188I TCNGA 2 cut(s) 56, 352
Hpy188III TCNNGA 1 cut(s) 71
Hpy8I GTNNAC 2 cut(s) 261, 289
HpyAV CCTTC 2 cut(s) 270, 274
HpyCH4III ACNGT 1 cut(s) 375
HpyCH4V TGCA 2 cut(s) 130, 211
Hsp92II CATG 4 cut(s) 146, 185, 215, 320
Kzo9I GATC 1 cut(s) 186
LpnPI CCDG 5 cut(s) 56, 136, 155, 182, 252
LweI GCATC 1 cut(s) 319
MaeI CTAG 1 cut(s) 114
MaeIII GTNAC 2 cut(s) 177, 311
MalI GATC 1 cut(s) 188
MboI GATC 1 cut(s) 186
MluCI AATT 2 cut(s) 66, 341
MlyI GAGTC 3 cut(s) 185, 319, 356
MmeI TCCRAC 2 cut(s) 34, 330
MnlI CCTC 3 cut(s) 120, 150, 316
MroXI GAANNNNTTC 1 cut(s) 240
MseI TTAA 1 cut(s) 204
MspI CCGG 1 cut(s) 123
MspR9I CCNGG 1 cut(s) 170
MvaI CCWGG 1 cut(s) 170
NdeII GATC 1 cut(s) 186
NlaIII CATG 4 cut(s) 146, 185, 215, 320
NmuCI GTSAC 2 cut(s) 177, 311
NspI RCATGY 2 cut(s) 185, 215
NspV TTCGAA 1 cut(s) 274
PaeI GCATGC 1 cut(s) 215
PciI ACATGT 1 cut(s) 181
PdmI GAANNNNTTC 1 cut(s) 240
PflFI GACNNNGTC 1 cut(s) 293
PfoI TCCNGGA 1 cut(s) 168
PleI GAGTC 3 cut(s) 184, 318, 355
PpsI GAGTC 3 cut(s) 184, 318, 355
PscI ACATGT 1 cut(s) 181
Psp6I CCWGG 1 cut(s) 168
PspGI CCWGG 1 cut(s) 168
PspPI GGNCC 1 cut(s) 56
PsyI GACNNNGTC 1 cut(s) 293
RsaI GTAC 1 cut(s) 368
RsaNI GTAC 1 cut(s) 367
SaqAI TTAA 1 cut(s) 204
Sau3AI GATC 1 cut(s) 186
Sau96I GGNCC 1 cut(s) 56
SchI GAGTC 3 cut(s) 185, 319, 356
ScrFI CCNGG 1 cut(s) 170
SetI ASST 8 cut(s) 50, 61, 112, 210, 227, 241, 260, 303
SfaNI GCATC 1 cut(s) 319
SfuI TTCGAA 1 cut(s) 274
SinI GGWCC 1 cut(s) 56
SphI GCATGC 1 cut(s) 215
Sse9I AATT 2 cut(s) 66, 341
SsiI CCGC 1 cut(s) 215
SspMI CTAG 1 cut(s) 114
StyD4I CCNGG 1 cut(s) 168
StyI CCWWGG 1 cut(s) 44
TaaI ACNGT 1 cut(s) 375
TaqI TCGA 2 cut(s) 189, 274
TasI AATT 2 cut(s) 66, 341
Tru1I TTAA 1 cut(s) 204
Tru9I TTAA 1 cut(s) 204
TseFI GTSAC 2 cut(s) 177, 311
Tsp45I GTSAC 2 cut(s) 177, 311
TspDTI ATGAA 1 cut(s) 17
Tth111I GACNNNGTC 1 cut(s) 293
VpaK11BI GGWCC 1 cut(s) 56
XapI RAATTY 1 cut(s) 66
XceI RCATGY 2 cut(s) 185, 215
XmnI GAANNNNTTC 1 cut(s) 240
XspI CTAG 1 cut(s) 114
Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.