RchiOBHm_Chr1g0365941

transposition, RNA-mediated

Design Primers CRISPR Design

Basic Information

Type: gene
Biological Identity
rosa_chinensis
1
OG0000562
Physical Location & Seq
Forward (+)
56693816 .. 56695060
1245 bp
Loading structure...
UTR
Exon/CDS
Intron
PRQ59053

Sequence Viewer

Length: 987 bp
ATGGCTAGGAAATCTGGTTCAAAAAATGAGGATTCTCTTCTAACCTCAATTTCTTCCGATGTTGAGTTTAATCCGAACCAACGTCTAAGCTCTGTTTTGTTGAATGAATTCAACTATCTTTCTTGGGCTAGAGCTGTTACACTTGCTCTTGGAGGAAGGCTTGCTCTTGGAGGAAGGTCCAAGCTTGGTTATATCAATGGAGTTATACATATGCCAGAAGCTAAGTCCCCTACATGTGATTCTTGGCTTTGCAAGGATCAACTTGTTATGTCTTGGTTACTCAATTCCATGGAGAGTAGAATAAGGGAGATTTTTAGTTTTTCTGAGTCTTCTATGCATCTCTGGAAATATGTTAAAGAGATGTATGGAAATCAGAATAATGCTGCTCGAGTGTTTCAACTCAAGCGAGATATTGCTGATCTACAACAAGAGGGTAAATCCTTTGTTCAACACCTTGGTAGCCTTACAAGCATGTGGAATGAGCTAGATGTTTACAGACCTCATACCACAGAGGCGAGTGTTTTGTTAAAGAGAGCAGAGGAGGACAAGATTTTTCAACTCCTTGCAAGTTTAAGCTCAGATTATGAAGATTTGAGAAGCCACATTCTCATGAATTCTGAGCTTCCATCTTTCAACACCGTATGTGCTACGATTCAAAGGGAAGAAGTTCGAAAAAAGGTGATGAATATGGAGAACAAGTCTAGACTGTCTGAAACTAGAGCCTATGTTTCAAATCATAGGCAAGTTGAAGAGAGAACATACAAAGGCAAGAGAACTGATTTGAAGTGCACTTACTGTGAAGGTGTTGGGTATGTCAAGGACAGATGTTGGATTCTCCATCCTGAGCAGAAGCCAAAGTTTTCAAAAGAAGGCAAAATTCTTCAAAAAGGCTGGAGTACTCCATCACACAGAGCAAAACTTGCTGATGCTTCTTCTACTGGGAGTATGATGAATTTCACCTCCAATCCCGCTGCGCTTATTAATTAA
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
Retrotran_gag_2 Retrotran_gag_3 rve

Protein Analysis

328

Amino Acids

37.43

Weight (kDa)

9.09

Isoelectric Point (pI)

44.57

Instability Index
Protein Domains (Pfam)
Domain Name Pfam ID Position E-value Description
Retrotran_gag_3 PF14244 27 - 72 9.8e-10 gag-polypeptide of LTR copia-type
Retrotran_gag_2 PF14223 60 - 227 2.8e-14 gag-polypeptide of LTR copia-type
Hydrophobicity Profile (Kyte-Doolittle)
AI Structure Prediction Report
Calculating structure properties...

Genomic Context

Gene Family Tree

Species Filter
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Publication-ready
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Orthologous Genes (Group: OG0000562)

Species Orthologous Gene IDs
fragaria_vesca FvH4_2g17331 FvH4_3g36541
malus_domestica MD07G1078600.v1.1 MD10G1237700.v1.1 MD10G1333400.v1.1 MD11G1102200.v1.1 MD13G1138400.v1.1 MD14G1033400.v1.1 MD15G1053300.v1.1
prunus_persica Prupe.1G465400_v2.0.a1 Prupe.3G136000_v2.0.a1 Prupe.7G119900_v2.0.a1
pyrus_communis pycom01g04630 pycom03g13050 pycom04g21190 pycom05g04910 pycom05g05510 pycom08g15850 pycom09g15040 pycom1094g00010 pycom11g02000 pycom12g06150 pycom13g24110 pycom13g24910 pycom14g00050 pycom15g21970 pycom15g35170 pycom15g35180 pycom16g14620 pycom16g14630 pycom808g00110
rosa_chinensis RchiOBHm_Chr1g0322851 RchiOBHm_Chr1g0365941 RchiOBHm_Chr3g0453341 RchiOBHm_Chr4g0388371 RchiOBHm_Chr4g0394021 RchiOBHm_Chr5g0013181 RchiOBHm_Chr6g0261721 RchiOBHm_Chr6g0261731 RchiOBHm_Chr7g0188861 RchiOBHm_Chr7g0192331 RchiOBHm_Chr7g0231721
rosa_multiflora Rmu_sc0002521.1_g000006 Rmu_sc0003255.1_g000026 Rmu_sc0004191.1_g000036 Rmu_sc0004414.1_g000014 Rmu_sc0005670.1_g000006 Rmu_sc0006081.1_g000001 Rmu_sc0007215.1_g000004 Rmu_sc0010088.1_g000010 Rmu_sc0020285.1_g000003 Rmu_sc0026896.1_g000002 Rmu_ssc0000019.1_g000029
rosa_roxburghii Rroxscaffold_3G00224890 Rroxscaffold_6G00400640 Rroxscaffold_7G00176590 Rroxscaffold_7G00189230
rosa_samantha Rh4BG046700
rosa_wichuraiana Rw1G012690 Rw1G031370 Rw2G042180 Rw2G043670 Rw2G046240 Rw2G049890 Rw2G050760 Rw2G051280 Rw2G053590 Rw3G007590 Rw3G026850 Rw4G001540 Rw4G009760 Rw4G019270 Rw5G000720 Rw5G005620 Rw5G041560 Rw6G007370 Rw6G009830 Rw6G015360 Rw6G031160 Rw7G004930 Rw7G011010 Rw7G024230 Rw7G028240

Restriction Enzyme Sites

1 / 10
Enzyme Recognition Site Cut Count Positions (bp)
AciI CCGC 1 cut(s) 969
AclWI GGATC 1 cut(s) 264
AcsI RAATTY 4 cut(s) 107, 613, 876, 952
AfaI GTAC 1 cut(s) 898
AflIII ACRYGT 1 cut(s) 233
AloI GAACNNNNNNTCC 1 cut(s) 33
AluBI AGCT 7 cut(s) 90, 134, 184, 221, 484, 576, 622
AluI AGCT 7 cut(s) 90, 134, 184, 221, 484, 576, 622
Alw21I GWGCWC 1 cut(s) 791
Alw44I GTGCAC 1 cut(s) 787
AlwI GGATC 1 cut(s) 264
Ama87I CYCGRG 1 cut(s) 387
ApaLI GTGCAC 1 cut(s) 787
ApeKI GCWGC 2 cut(s) 383, 971
ApoI RAATTY 4 cut(s) 107, 613, 876, 952
AseI ATTAAT 1 cut(s) 981
Asp700I GAANNNNTTC 2 cut(s) 107, 666
AspLEI GCGC 1 cut(s) 976
AspS9I GGNCC 1 cut(s) 177
AsuHPI GGTGA 2 cut(s) 691, 949
AsuII TTCGAA 1 cut(s) 670
AvaI CYCGRG 1 cut(s) 387
AvaII GGWCC 1 cut(s) 177
BaeGI GKGCMC 1 cut(s) 791
BarI GAAGNNNNNNTAC 2 cut(s) 776, 808
BbsI GAAGAC 1 cut(s) 321
Bbv12I GWGCWC 1 cut(s) 791
BbvI GCAGC 2 cut(s) 370, 958
BccI CCATC 3 cut(s) 634, 846, 910
BfaI CTAG 5 cut(s) 6, 129, 485, 702, 717
BisI GCNGC 2 cut(s) 384, 972
BlsI GCNGC 2 cut(s) 385, 973
BmcAI AGTACT 1 cut(s) 898
Bme18I GGWCC 1 cut(s) 177
BmeT110I CYCGRG 1 cut(s) 387
BmgT120I GGNCC 1 cut(s) 177
BmrI ACTGGG 1 cut(s) 948
BmsI GCATC 2 cut(s) 346, 916
BmuI ACTGGG 1 cut(s) 948
BpiI GAAGAC 1 cut(s) 321
BpmI CTGGAG 1 cut(s) 913
Bpu10I CCTNAGC 1 cut(s) 843
Bpu14I TTCGAA 1 cut(s) 670
BpuEI CTTGAG 1 cut(s) 386
BsaJI CCNNGG 2 cut(s) 288, 454
BsaXI ACNNNNNCTCC 2 cut(s) 683, 713
Bse1I ACTGG 1 cut(s) 943
BseDI CCNNGG 2 cut(s) 288, 454
BseGI GGATG 1 cut(s) 838
BseMII CTCAG 4 cut(s) 315, 591, 609, 834
BseNI ACTGG 1 cut(s) 943
BseRI GAGGAG 1 cut(s) 554
BseSI GKGCMC 1 cut(s) 791
BseXI GCAGC 2 cut(s) 370, 958
BsiHKAI GWGCWC 1 cut(s) 791
BsiHKCI CYCGRG 1 cut(s) 387
BslFI GGGAC 1 cut(s) 211
BsmFI GGGAC 1 cut(s) 211
BsoBI CYCGRG 1 cut(s) 387
Bsp119I TTCGAA 1 cut(s) 670
Bsp1286I GDGCHC 1 cut(s) 791
Bsp143I GATC 2 cut(s) 256, 418
Bsp19I CCATGG 1 cut(s) 288
BspACI CCGC 1 cut(s) 969
BspCNI CTCAG 4 cut(s) 316, 590, 610, 835
BspHI TCATGA 1 cut(s) 609
BspPI GGATC 1 cut(s) 264
BspT104I TTCGAA 1 cut(s) 670
BsrI ACTGG 1 cut(s) 943
BssECI CCNNGG 2 cut(s) 288, 454
BssMI GATC 2 cut(s) 256, 418
BssT1I CCWWGG 2 cut(s) 288, 454
Bst4CI ACNGT 3 cut(s) 640, 708, 797
Bst6I CTCTTC 2 cut(s) 42, 744
BstAPI GCANNNNNTGC 1 cut(s) 920
BstBI TTCGAA 1 cut(s) 670
BstC8I GCNNGC 1 cut(s) 162
BstDEI CTNAG 6 cut(s) 86, 222, 324, 577, 618, 843
BstDSI CCRYGG 1 cut(s) 288
BstF5I GGATG 1 cut(s) 838
BstHHI GCGC 1 cut(s) 976
BstKTI GATC 2 cut(s) 259, 421
BstMBI GATC 2 cut(s) 256, 418
BstMWI GCNNNNNNNGC 2 cut(s) 468, 920
BstNSI RCATGY 2 cut(s) 237, 475
BstSLI GKGCMC 1 cut(s) 791
BstV1I GCAGC 2 cut(s) 370, 958
BstV2I GAAGAC 1 cut(s) 321
BtgI CCRYGG 1 cut(s) 288
BtsCI GGATG 1 cut(s) 838
Cac8I GCNNGC 1 cut(s) 162
CciI TCATGA 1 cut(s) 609
CfoI GCGC 1 cut(s) 976
Cfr13I GGNCC 1 cut(s) 177
Csp6I GTAC 1 cut(s) 897
CviAII CATG 4 cut(s) 234, 289, 472, 610
CviQI GTAC 1 cut(s) 897
DdeI CTNAG 6 cut(s) 86, 222, 324, 577, 618, 843
DpnI GATC 2 cut(s) 258, 420
DpnII GATC 2 cut(s) 256, 418
Eam1104I CTCTTC 2 cut(s) 42, 744
EarI CTCTTC 2 cut(s) 42, 744
Eco130I CCWWGG 2 cut(s) 288, 454
Eco47I GGWCC 1 cut(s) 177
Eco88I CYCGRG 1 cut(s) 387
EcoRI GAATTC 2 cut(s) 107, 613
EcoT14I CCWWGG 2 cut(s) 288, 454
EcoT22I ATGCAT 1 cut(s) 339
ErhI CCWWGG 2 cut(s) 288, 454
FaeI CATG 4 cut(s) 237, 292, 475, 613
FaqI GGGAC 1 cut(s) 211
FatI CATG 4 cut(s) 233, 288, 471, 609
FauI CCCGC 1 cut(s) 976
FauNDI CATATG 1 cut(s) 210
Fnu4HI GCNGC 2 cut(s) 384, 972
FokI GGATG 1 cut(s) 825
Fsp4HI GCNGC 2 cut(s) 384, 972
FspBI CTAG 5 cut(s) 6, 129, 485, 702, 717
GlaI GCGC 1 cut(s) 975
GluI GCNGC 2 cut(s) 384, 972
GsuI CTGGAG 1 cut(s) 913
HhaI GCGC 1 cut(s) 976
Hin1II CATG 4 cut(s) 237, 292, 475, 613
Hin6I GCGC 1 cut(s) 974
HinP1I GCGC 1 cut(s) 974
HindIII AAGCTT 1 cut(s) 182
HinfI GANTC 5 cut(s) 32, 239, 326, 652, 832
HphI GGTGA 2 cut(s) 691, 949
Hpy166II GTNNAC 2 cut(s) 493, 789
Hpy188I TCNGA 7 cut(s) 58, 75, 325, 375, 580, 619, 712
Hpy188III TCNNGA 4 cut(s) 343, 610, 702, 842
Hpy8I GTNNAC 2 cut(s) 493, 789
HpyAV CCTTC 4 cut(s) 150, 168, 794, 863
HpyCH4III ACNGT 3 cut(s) 640, 708, 797
HpyCH4IV ACGT 1 cut(s) 82
HpyCH4V TGCA 4 cut(s) 252, 337, 566, 789
HpyF10VI GCNNNNNNNGC 2 cut(s) 468, 920
HpyF3I CTNAG 6 cut(s) 86, 222, 324, 577, 618, 843
HpySE526I ACGT 1 cut(s) 82
Hsp92II CATG 4 cut(s) 237, 292, 475, 613
HspAI GCGC 1 cut(s) 974
Kzo9I GATC 2 cut(s) 256, 418
LpnPI CCDG 5 cut(s) 228, 328, 855, 877, 924
Lsp1109I GCAGC 2 cut(s) 370, 958
LweI GCATC 2 cut(s) 346, 916
MaeI CTAG 5 cut(s) 6, 129, 485, 702, 717
MaeII ACGT 1 cut(s) 82
MaeIII GTNAC 2 cut(s) 136, 276
MalI GATC 2 cut(s) 258, 420
MboI GATC 2 cut(s) 256, 418
MboII GAAGA 8 cut(s) 29, 45, 321, 599, 674, 761, 872, 924
MhlI GDGCHC 1 cut(s) 791
MluCI AATT 7 cut(s) 48, 107, 283, 613, 876, 952, 982
MlyI GAGTC 1 cut(s) 335
MmeI TCCRAC 1 cut(s) 809
Mph1103I ATGCAT 1 cut(s) 339
MroXI GAANNNNTTC 2 cut(s) 107, 666
MseI TTAA 6 cut(s) 69, 354, 527, 572, 981, 985
MslI CAYNNNNRTG 1 cut(s) 608
MspA1I CMGCKG 1 cut(s) 971
MwoI GCNNNNNNNGC 2 cut(s) 468, 920
NcoI CCATGG 1 cut(s) 288
NdeI CATATG 1 cut(s) 210
NdeII GATC 2 cut(s) 256, 418
NlaIII CATG 4 cut(s) 237, 292, 475, 613
NsiI ATGCAT 1 cut(s) 339
NspI RCATGY 2 cut(s) 237, 475
NspV TTCGAA 1 cut(s) 670
PacI TTAATTAA 1 cut(s) 985
PaeR7I CTCGAG 1 cut(s) 387
PagI TCATGA 1 cut(s) 609
PciI ACATGT 1 cut(s) 233
PdmI GAANNNNTTC 2 cut(s) 107, 666
PfeI GAWTC 4 cut(s) 32, 239, 652, 832
PkrI GCNGC 2 cut(s) 385, 973
PleI GAGTC 1 cut(s) 334
PpsI GAGTC 1 cut(s) 334
PscI ACATGT 1 cut(s) 233
PshBI ATTAAT 1 cut(s) 981
PspPI GGNCC 1 cut(s) 177
PspXI VCTCGAGB 1 cut(s) 387
RsaI GTAC 1 cut(s) 898
RsaNI GTAC 1 cut(s) 897
RseI CAYNNNNRTG 1 cut(s) 608
SaqAI TTAA 6 cut(s) 69, 354, 527, 572, 981, 985
SatI GCNGC 2 cut(s) 384, 972
Sau3AI GATC 2 cut(s) 256, 418
Sau96I GGNCC 1 cut(s) 177
ScaI AGTACT 1 cut(s) 898
SchI GAGTC 1 cut(s) 335
SduI GDGCHC 1 cut(s) 791
SfaNI GCATC 2 cut(s) 346, 916
Sfr274I CTCGAG 1 cut(s) 387
SfuI TTCGAA 1 cut(s) 670
SinI GGWCC 1 cut(s) 177
SlaI CTCGAG 1 cut(s) 387
SmiMI CAYNNNNRTG 1 cut(s) 608
SmlI CTYRAG 2 cut(s) 387, 401
SmoI CTYRAG 2 cut(s) 387, 401
Sse9I AATT 7 cut(s) 48, 107, 283, 613, 876, 952, 982
SsiI CCGC 1 cut(s) 969
SspMI CTAG 5 cut(s) 6, 129, 485, 702, 717
StyI CCWWGG 2 cut(s) 288, 454
TaaI ACNGT 3 cut(s) 640, 708, 797
TaiI ACGT 1 cut(s) 85
TaqI TCGA 2 cut(s) 388, 670
TasI AATT 7 cut(s) 48, 107, 283, 613, 876, 952, 982
TatI WGTACW 1 cut(s) 896
TfiI GAWTC 4 cut(s) 32, 239, 652, 832
Tru1I TTAA 6 cut(s) 69, 354, 527, 572, 981, 985
Tru9I TTAA 6 cut(s) 69, 354, 527, 572, 981, 985
TseI GCWGC 2 cut(s) 383, 971
TspDTI ATGAA 5 cut(s) 120, 600, 626, 698, 965
VneI GTGCAC 1 cut(s) 787
VpaK11BI GGWCC 1 cut(s) 177
VspI ATTAAT 1 cut(s) 981
XapI RAATTY 4 cut(s) 107, 613, 876, 952
XbaI TCTAGA 1 cut(s) 701
XceI RCATGY 2 cut(s) 237, 475
XhoI CTCGAG 1 cut(s) 387
XmnI GAANNNNTTC 2 cut(s) 107, 666
XspI CTAG 5 cut(s) 6, 129, 485, 702, 717
ZrmI AGTACT 1 cut(s) 898
Zsp2I ATGCAT 1 cut(s) 339
Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.