RchiOBHm_Chr5g0053791

transposition, RNA-mediated

Design Primers CRISPR Design

Basic Information

Type: gene
Biological Identity
rosa_chinensis
5
OG0000094
Physical Location & Seq
Forward (+)
56142036 .. 56143796
1761 bp
Loading structure...
UTR
Exon/CDS
Intron
PRQ33104

Sequence Viewer

Length: 1041 bp
ATGGATTTTATTTACAAGTTACCTCGTACGCAGGATGGTAATGATGGTATTTGGGTGATTGTAGATCGACTCACCAAATCAGCTCATTTTCTGGCGGTTAAGGAAACCTTTAGTTTGGATAAACTGGCAAAGTTGTATGTGGACGAAATTGTAAAGCTTCATGGTGTCCCTGAGTCCATTGTTTCTGATCGTGATGCTCGATTCACATCAAAGTTTTGGAGGAAAGTTCACAAATTTATGGGAACAAAATTACAATTTAGCACTGCTTTCCATCCTCAAACTGATGGACAATCTGAGCGGACTATACAAACTTTGGAAGACATGTTGAGGGCTTGTTCTCTACAATTTAAAGGAAGTTGGGATAAGCACTTGGCTTTGATGGAGTTTGCATATAACAACAGTTACCATTCGAGTATTGGTATGGCTCCCTACGAAGCTTTGTATGGGAAACAGTGTAGGACCCCCTTGTGTTGGGATGAAGTGGGAGAAAGACAACTTATTGGTCCAGAGATCGTTGAAATCACAACAAATAAAGTCAAAGTGATCAGAGAGAAACTCAAGACGGCTCAAAGCAGACAGAAGAGCTACGCAGATAAACACAGGAAGCATCTTGAATTTCAAGTTGGTGATTGGGTATTTCTGAAGTTATCTCCTTGGAAGGGTGTGGTAAGGTTTGGTAAACGAGGAAAACTAAGTCCAAGGTATATTGGTCCCTATGAGATTGTGGAACGAATTGGTCTGGTTGCTTACCGCTTGGCTTTACCTCCACAACTATCTCAAGTACATGATGTATTCCACGTCTCCATGCTTCGCAAGTACATCACTGATCCTTCACATGTGTTACCAGCTCAACCCATTACACTTACAGAAGATCTAACATATGAAGAAGAACCAGTACAGATCCTTGATCGTCGTGAGCAAGTACTCCGAAGTAAGATTATACCTTTGGTTAAGGTATTATGGAGGAATCACCTGTTTGAAGAAGCTACTTGGGAACCAGAGGATCAAATGAGGCAACAGTATCCACATCTTTTTTCTTGA
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

346

Amino Acids

40.47

Weight (kDa)

9.09

Isoelectric Point (pI)

35.12

Instability Index
Protein Domains (Pfam)
Domain Name Pfam ID Position E-value Description
SH3_Tf2-1 PF24626 209 - 273 1.6e-28 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)
AccBSI CCGCTC 1 cut(s) 298
AciI CCGC 3 cut(s) 95, 298, 751
AclWI GGATC 3 cut(s) 821, 895, 1011
AcsI RAATTY 2 cut(s) 233, 614
AcuI CTGAAG 1 cut(s) 662
AfaI GTAC 5 cut(s) 28, 783, 818, 897, 924
AfiI CCNNNNNNNGG 2 cut(s) 471, 659
AflIII ACRYGT 2 cut(s) 321, 835
AgsI TTSAA 4 cut(s) 518, 614, 620, 980
AjiI CACGTC 1 cut(s) 799
AjuI GAANNNNNNNTTGG 2 cut(s) 606, 638
AluBI AGCT 6 cut(s) 83, 157, 437, 585, 848, 986
AluI AGCT 6 cut(s) 83, 157, 437, 585, 848, 986
Alw26I GTCTC 1 cut(s) 805
AlwI GGATC 3 cut(s) 821, 895, 1011
ApoI RAATTY 2 cut(s) 233, 614
AspS9I GGNCC 3 cut(s) 459, 503, 710
AsuHPI GGTGA 4 cut(s) 64, 67, 638, 962
AvaII GGWCC 3 cut(s) 459, 503, 710
BarI GAAGNNNNNNTAC 2 cut(s) 879, 911
BbsI GAAGAC 1 cut(s) 324
BccI CCATC 5 cut(s) 29, 38, 278, 279, 373
BceAI ACGGC 1 cut(s) 579
BciVI GTATCC 1 cut(s) 1032
BclI TGATCA 1 cut(s) 543
BcoDI GTCTC 1 cut(s) 805
BfuI GTATCC 1 cut(s) 1032
BglII AGATCT 1 cut(s) 871
BmcAI AGTACT 1 cut(s) 924
Bme18I GGWCC 3 cut(s) 459, 503, 710
BmgBI CACGTC 1 cut(s) 799
BmgT120I GGNCC 3 cut(s) 459, 503, 710
BmiI GGNNCC 4 cut(s) 426, 461, 712, 996
BmsI GCATC 2 cut(s) 184, 616
BpiI GAAGAC 1 cut(s) 324
BplI GAGNNNNNCTC 2 cut(s) 540, 572
BpuEI CTTGAG 2 cut(s) 542, 762
BsaBI GATNNNNATC 1 cut(s) 205
BsaJI CCNNGG 2 cut(s) 653, 698
Bsc4I CCNNNNNNNGG 2 cut(s) 471, 659
Bse1I ACTGG 2 cut(s) 129, 893
Bse8I GATNNNNATC 1 cut(s) 205
BseDI CCNNGG 2 cut(s) 653, 698
BseGI GGATG 3 cut(s) 40, 271, 481
BseJI GATNNNNATC 1 cut(s) 205
BseLI CCNNNNNNNGG 2 cut(s) 471, 659
BseMII CTCAG 2 cut(s) 162, 285
BseNI ACTGG 2 cut(s) 129, 893
BsiWI CGTACG 1 cut(s) 26
BslFI GGGAC 2 cut(s) 152, 696
BslI CCNNNNNNNGG 2 cut(s) 471, 659
BsmAI GTCTC 1 cut(s) 805
BsmBI CGTCTC 1 cut(s) 805
BsmFI GGGAC 2 cut(s) 152, 696
Bsp143I GATC 9 cut(s) 64, 187, 510, 543, 826, 871, 900, 907, 1003
BspACI CCGC 3 cut(s) 95, 298, 751
BspCNI CTCAG 2 cut(s) 163, 286
BspLI GGNNCC 4 cut(s) 426, 461, 712, 996
BspPI GGATC 3 cut(s) 821, 895, 1011
BspQI GCTCTTC 1 cut(s) 575
BsrBI CCGCTC 1 cut(s) 298
BsrI ACTGG 2 cut(s) 129, 893
BssECI CCNNGG 2 cut(s) 653, 698
BssMI GATC 9 cut(s) 64, 187, 510, 543, 826, 871, 900, 907, 1003
BssT1I CCWWGG 2 cut(s) 653, 698
Bst4CI ACNGT 3 cut(s) 401, 453, 1020
Bst6I CTCTTC 1 cut(s) 575
BstDEI CTNAG 3 cut(s) 171, 294, 692
BstF5I GGATG 3 cut(s) 40, 271, 481
BstKTI GATC 9 cut(s) 67, 190, 513, 546, 829, 874, 903, 910, 1006
BstMAI GTCTC 1 cut(s) 805
BstMBI GATC 9 cut(s) 64, 187, 510, 543, 826, 871, 900, 907, 1003
BstNSI RCATGY 2 cut(s) 325, 839
BstV2I GAAGAC 1 cut(s) 324
BstX2I RGATCY 2 cut(s) 871, 900
BstYI RGATCY 2 cut(s) 871, 900
BsuI GTATCC 1 cut(s) 1032
BtrI CACGTC 1 cut(s) 799
BtsCI GGATG 3 cut(s) 40, 271, 481
BtsI GCAGTG 1 cut(s) 261
BtsIMutI CAGTG 3 cut(s) 261, 458, 822
Cfr13I GGNCC 3 cut(s) 459, 503, 710
Csp6I GTAC 5 cut(s) 27, 782, 817, 896, 923
CviAII CATG 5 cut(s) 161, 322, 785, 805, 836
CviQI GTAC 5 cut(s) 27, 782, 817, 896, 923
DdeI CTNAG 3 cut(s) 171, 294, 692
DpnI GATC 9 cut(s) 66, 189, 512, 545, 828, 873, 902, 909, 1005
DpnII GATC 9 cut(s) 64, 187, 510, 543, 826, 871, 900, 907, 1003
DraI TTTAAA 1 cut(s) 349
Eam1104I CTCTTC 1 cut(s) 575
EarI CTCTTC 1 cut(s) 575
Eco130I CCWWGG 2 cut(s) 653, 698
Eco47I GGWCC 3 cut(s) 459, 503, 710
Eco57I CTGAAG 1 cut(s) 662
EcoO109I RGGNCCY 1 cut(s) 459
EcoT14I CCWWGG 2 cut(s) 653, 698
ErhI CCWWGG 2 cut(s) 653, 698
Esp3I CGTCTC 1 cut(s) 805
FaeI CATG 5 cut(s) 164, 325, 788, 808, 839
FalI AAGNNNNNCTT 2 cut(s) 92, 124
FaqI GGGAC 2 cut(s) 152, 696
FatI CATG 5 cut(s) 160, 321, 784, 804, 835
FauNDI CATATG 1 cut(s) 880
FbaI TGATCA 1 cut(s) 543
FokI GGATG 3 cut(s) 47, 258, 488
Hin1II CATG 5 cut(s) 164, 325, 788, 808, 839
HindIII AAGCTT 2 cut(s) 155, 435
HinfI GANTC 4 cut(s) 69, 173, 201, 967
HphI GGTGA 4 cut(s) 64, 67, 638, 962
Hpy166II GTNNAC 3 cut(s) 142, 229, 680
Hpy188I TCNGA 5 cut(s) 187, 295, 548, 642, 929
Hpy188III TCNNGA 6 cut(s) 191, 506, 559, 611, 914, 1038
Hpy8I GTNNAC 3 cut(s) 142, 229, 680
Hpy99I CGWCG 1 cut(s) 915
HpyAV CCTTC 2 cut(s) 652, 840
HpyCH4III ACNGT 3 cut(s) 401, 453, 1020
HpyCH4IV ACGT 1 cut(s) 798
HpyCH4V TGCA 1 cut(s) 389
HpyF3I CTNAG 3 cut(s) 171, 294, 692
HpySE526I ACGT 1 cut(s) 798
Hsp92II CATG 5 cut(s) 164, 325, 788, 808, 839
Ksp22I TGATCA 1 cut(s) 543
Kzo9I GATC 9 cut(s) 64, 187, 510, 543, 826, 871, 900, 907, 1003
LguI GCTCTTC 1 cut(s) 575
LmnI GCTCC 1 cut(s) 430
LweI GCATC 2 cut(s) 184, 616
MaeII ACGT 1 cut(s) 798
MaeIII GTNAC 3 cut(s) 18, 401, 840
MalI GATC 9 cut(s) 66, 189, 512, 545, 828, 873, 902, 909, 1005
MbiI CCGCTC 1 cut(s) 298
MboI GATC 9 cut(s) 64, 187, 510, 543, 826, 871, 900, 907, 1003
MboII GAAGA 6 cut(s) 329, 592, 881, 896, 899, 992
MflI RGATCY 2 cut(s) 871, 900
MluCI AATT 7 cut(s) 147, 233, 248, 254, 344, 614, 732
MlyI GAGTC 2 cut(s) 63, 182
MnlI CCTC 9 cut(s) 33, 213, 285, 321, 677, 774, 957, 994, 1005
MseI TTAA 3 cut(s) 99, 348, 951
NdeI CATATG 1 cut(s) 880
NdeII GATC 9 cut(s) 64, 187, 510, 543, 826, 871, 900, 907, 1003
NlaIII CATG 5 cut(s) 164, 325, 788, 808, 839
NlaIV GGNNCC 4 cut(s) 426, 461, 712, 996
NspI RCATGY 2 cut(s) 325, 839
PciI ACATGT 2 cut(s) 321, 835
PciSI GCTCTTC 1 cut(s) 575
PcsI WCGNNNNNNNCGW 1 cut(s) 196
PfeI GAWTC 2 cut(s) 201, 967
Pfl23II CGTACG 1 cut(s) 26
PleI GAGTC 2 cut(s) 63, 181
PpsI GAGTC 2 cut(s) 63, 181
PpuMI RGGWCCY 1 cut(s) 459
PscI ACATGT 2 cut(s) 321, 835
Psp5II RGGWCCY 1 cut(s) 459
PspLI CGTACG 1 cut(s) 26
PspN4I GGNNCC 4 cut(s) 426, 461, 712, 996
PspPI GGNCC 3 cut(s) 459, 503, 710
PspPPI RGGWCCY 1 cut(s) 459
PsuI RGATCY 2 cut(s) 871, 900
RsaI GTAC 5 cut(s) 28, 783, 818, 897, 924
RsaNI GTAC 5 cut(s) 27, 782, 817, 896, 923
SapI GCTCTTC 1 cut(s) 575
SaqAI TTAA 3 cut(s) 99, 348, 951
Sau3AI GATC 9 cut(s) 64, 187, 510, 543, 826, 871, 900, 907, 1003
Sau96I GGNCC 3 cut(s) 459, 503, 710
ScaI AGTACT 1 cut(s) 924
SchI GAGTC 2 cut(s) 63, 182
SfaNI GCATC 2 cut(s) 184, 616
SinI GGWCC 3 cut(s) 459, 503, 710
SmlI CTYRAG 2 cut(s) 557, 777
SmoI CTYRAG 2 cut(s) 557, 777
Sse9I AATT 7 cut(s) 147, 233, 248, 254, 344, 614, 732
SsiI CCGC 3 cut(s) 95, 298, 751
StyI CCWWGG 2 cut(s) 653, 698
TaaI ACNGT 3 cut(s) 401, 453, 1020
TaiI ACGT 1 cut(s) 801
TaqI TCGA 3 cut(s) 67, 199, 410
TasI AATT 7 cut(s) 147, 233, 248, 254, 344, 614, 732
TatI WGTACW 4 cut(s) 781, 816, 895, 922
TfiI GAWTC 2 cut(s) 201, 967
Tru1I TTAA 3 cut(s) 99, 348, 951
Tru9I TTAA 3 cut(s) 99, 348, 951
TscAI CASTG 3 cut(s) 268, 458, 829
TspDTI ATGAA 3 cut(s) 149, 492, 897
TspRI CASTG 3 cut(s) 268, 458, 829
VpaK11BI GGWCC 3 cut(s) 459, 503, 710
XapI RAATTY 2 cut(s) 233, 614
XceI RCATGY 2 cut(s) 325, 839
XcmI CCANNNNNNNNNTGG 1 cut(s) 413
ZrmI AGTACT 1 cut(s) 924
Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.