RchiOBHm_Chr1g0329421

transposition, RNA-mediated

Design Primers CRISPR Design

Basic Information

Type: gene
Biological Identity
rosa_chinensis
1
OG0000370
Physical Location & Seq
Forward (+)
19020533 .. 19023361
2829 bp
Loading structure...
UTR
Exon/CDS
Intron
PRQ55874

Sequence Viewer

Length: 813 bp
ATGGTCAAGGGCAAGAAAGATACTAGAACAGGTGGAGCTACTTCATCCACTACTGGGCTTCCACATGATGAGGAGGTGGCTAAGTTGTTTCAAGCCTTACTGCGAATGGCTTCCCTTGAGCTTGAGGGCACAAACGGGTTTAATAGGAGGCTGAAATTTTTGAAGATGTTCATTAGTCTGTCACCTCCGGAGTATGCAGGAAATCTTGATTATTCTTTGGAAGGGCTGGAGTGGTTACGAAGGGTAAAGCAATGTTTTGATGTTCTTGATGTACCTGGAGACCTAAGAGTTGGGTTTGCAGTCTATACTCTTACTGGAGCGGCTAGCTACTGGTGGGATTTTGTTAAAAGGACCTGTGATGTGGAATCGATGAATTGGGATGACTTTGAGCAGATATTTTTGAATAGGTACTTTCCTGAGACTATAAGGCTAGCTAAAGTAGAAGAATTCCTCAATTTGACACAGGGGGAAATGACAGTTTCTCAGTATGATTCTAAGTTCATTGAATTATCATGGCATGCACCTAATCTTCTGACTTCGGATAAAGATAGGGCAGGGAAGTTTTTACGCGGGTTGAGGCCTTCCATCGGTATGTCTATACCTAGTTTTATGTATAATACTTATCATGAGGCGGTGGCAGCAGCACTGAAAGTAGAACAAATTGAAATTATCGAGTATCAGTGTGTGCAAGAGTCATTTGAGGGAGCTTCTGGTAGAGGGGGAAAAAGGCAAAGATATACTTGCCACAACTGTGGTGAGCCTGGTCATATTCGGCCTCATTGCCCATATAATCCGTCATCTTCCTCACTGTAG
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
Retrotrans_gag zf-CCHC

Protein Analysis

270

Amino Acids

30.68

Weight (kDa)

6.11

Isoelectric Point (pI)

47.39

Instability Index
Protein Domains (Pfam)
Domain Name Pfam ID Position E-value Description
Ty3_capsid PF19259 96 - 222 2.7e-09 Ty3 transposon capsid-like protein
Retrotrans_gag PF03732 99 - 194 1.2e-17 Retrotransposon gag protein
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: OG0000370)

Species Orthologous Gene IDs
fragaria_vesca FvH4_1g29481 FvH4_2g11454 FvH4_3g19661 FvH4_3g28463 FvH4_3g31691 FvH4_3g34551 FvH4_3g35241 FvH4_4g06575 FvH4_4g09082 FvH4_4g15804 FvH4_4g15805 FvH4_4g16178 FvH4_4g16282 FvH4_5g25163 FvH4_6g27413 FvH4_7g02962 FvH4_7g04361
malus_domestica MD01G1095000.v1.1 MD02G1270200.v1.1 MD02G1270300.v1.1 MD02G1270400.v1.1 MD06G1059100.v1.1 MD08G1226500.v1.1
prunus_persica Prupe.1G169500_v2.0.a1 Prupe.5G195800_v2.0.a1
pyrus_communis pycom01g00010 pycom01g00770 pycom02g23140 pycom03g11760 pycom04g06090 pycom05g06900 pycom05g08070 pycom05g14500 pycom06g03050 pycom07g06250 pycom07g07540 pycom07g10580 pycom08g04990 pycom1146g00060 pycom11g01080 pycom11g15270 pycom11g15460 pycom11g24900 pycom12419g00150 pycom12424g00120 pycom13g08740 pycom13g24950 pycom13g25960 pycom13g26030 pycom13g27820 pycom16g23270 pycom16g25020 pycom16g25960 pycom17g07780 pycom17g08210 pycom17g13100
rosa_chinensis RchiOBHm_Chr1g0329421 RchiOBHm_Chr4g0397711 RchiOBHm_Chr4g0403481 RchiOBHm_Chr5g0019091 RchiOBHm_Chr5g0049101
rosa_laevigata RLG00000029892
rosa_multiflora Rmu_sc0001866.1_g000007
rosa_roxburghii Rroxscaffold_2G00094160 Rroxscaffold_3G00229110 Rroxscaffold_4G00321100 Rroxscaffold_7G00196040 Rroxscaffold_7G00196280
rosa_rugosa Rorug05G0160500 Rorug06G0096500
rosa_samantha Rh1AG098600 Rh1AG098800 Rh1BG078200 Rh1BG078700 Rh1BG178500 Rh1CG094600 Rh1CG094900 Rh1DG101700 Rh1DG109600 Rh2AG175800 Rh2AG175900 Rh2AG511400 Rh2BG114700 Rh2CG042200 Rh2CG116600 Rh2CG317500 Rh2DG327700 Rh2DG337800 Rh4CG142700 Rh4DG113100 Rh5BG335800 Rh5CG360600 Rh5DG352000 Rh6BG071400 Rh6BG417100 Rh6CG463300 Rh6CG463400 Rh7BG186600 Rh7CG196500 Rh7CG196600 Rh7CG448900 Rh7DG228300
rosa_wichuraiana Rw4G006560 Rw4G017340 Rw5G030450

Restriction Enzyme Sites

1 / 10
Enzyme Recognition Site Cut Count Positions (bp)
AccBSI CCGCTC 1 cut(s) 320
AccII CGCG 1 cut(s) 570
AccIII TCCGGA 1 cut(s) 187
AciI CCGC 3 cut(s) 320, 570, 632
AcsI RAATTY 2 cut(s) 155, 446
AfaI GTAC 2 cut(s) 273, 410
AfiI CCNNNNNNNGG 2 cut(s) 54, 587
AgsI TTSAA 5 cut(s) 92, 163, 403, 506, 665
AjnI CCWGG 2 cut(s) 274, 760
AleI CACNNNNGTG 1 cut(s) 750
AluBI AGCT 5 cut(s) 38, 121, 327, 434, 707
AluI AGCT 5 cut(s) 38, 121, 327, 434, 707
Alw26I GTCTC 2 cut(s) 273, 413
Aor13HI TCCGGA 1 cut(s) 187
AoxI GGCC 2 cut(s) 578, 773
ApeKI GCWGC 2 cut(s) 638, 641
ApoI RAATTY 2 cut(s) 155, 446
Asp700I GAANNNNTTC 2 cut(s) 109, 167
AspS9I GGNCC 1 cut(s) 351
AsuHPI GGTGA 2 cut(s) 174, 767
AsuNHI GCTAGC 2 cut(s) 323, 430
AvaII GGWCC 1 cut(s) 351
BaeGI GKGCMC 1 cut(s) 131
BbvI GCAGC 2 cut(s) 650, 653
BccI CCATC 1 cut(s) 593
BciT130I CCWGG 2 cut(s) 276, 762
BcoDI GTCTC 2 cut(s) 273, 413
BfaI CTAG 4 cut(s) 24, 324, 431, 603
BfmI CTRYAG 1 cut(s) 809
BisI GCNGC 3 cut(s) 321, 639, 642
BlsI GCNGC 3 cut(s) 322, 640, 643
Bme1390I CCNGG 2 cut(s) 276, 762
Bme18I GGWCC 1 cut(s) 351
BmgT120I GGNCC 1 cut(s) 351
BmrFI CCNGG 2 cut(s) 276, 762
BmrI ACTGGG 1 cut(s) 63
BmtI GCTAGC 2 cut(s) 327, 434
BmuI ACTGGG 1 cut(s) 63
BpmI CTGGAG 3 cut(s) 248, 297, 336
BpuEI CTTGAG 2 cut(s) 137, 143
Bsa29I ATCGAT 1 cut(s) 368
BsaI GGTCTC 1 cut(s) 273
BsaWI WCCGGW 1 cut(s) 187
Bsc4I CCNNNNNNNGG 2 cut(s) 54, 587
Bse1I ACTGG 3 cut(s) 58, 319, 335
Bse3DI GCAATG 2 cut(s) 257, 778
BseAI TCCGGA 1 cut(s) 187
BseBI CCWGG 2 cut(s) 276, 762
BseCI ATCGAT 1 cut(s) 368
BseGI GGATG 2 cut(s) 44, 385
BseLI CCNNNNNNNGG 2 cut(s) 54, 587
BseMI GCAATG 2 cut(s) 257, 778
BseMII CTCAG 2 cut(s) 408, 497
BseNI ACTGG 3 cut(s) 58, 319, 335
BseRI GAGGAG 1 cut(s) 86
BseSI GKGCMC 1 cut(s) 131
BseXI GCAGC 2 cut(s) 650, 653
Bsh1236I CGCG 1 cut(s) 570
BshFI GGCC 2 cut(s) 580, 775
BshVI ATCGAT 1 cut(s) 368
BsiSI CCGG 1 cut(s) 188
BslI CCNNNNNNNGG 2 cut(s) 54, 587
BsmAI GTCTC 2 cut(s) 273, 413
BsnI GGCC 2 cut(s) 580, 775
Bso31I GGTCTC 1 cut(s) 273
Bsp1286I GDGCHC 1 cut(s) 131
Bsp13I TCCGGA 1 cut(s) 187
BspACI CCGC 3 cut(s) 320, 570, 632
BspANI GGCC 2 cut(s) 580, 775
BspCNI CTCAG 2 cut(s) 409, 496
BspDI ATCGAT 1 cut(s) 368
BspEI TCCGGA 1 cut(s) 187
BspFNI CGCG 1 cut(s) 570
BspHI TCATGA 1 cut(s) 625
BspOI GCTAGC 2 cut(s) 327, 434
BspTNI GGTCTC 1 cut(s) 273
BsrBI CCGCTC 1 cut(s) 320
BsrDI GCAATG 2 cut(s) 257, 778
BsrI ACTGG 3 cut(s) 58, 319, 335
Bst2UI CCWGG 2 cut(s) 276, 762
Bst4CI ACNGT 3 cut(s) 478, 752, 810
BstC8I GCNNGC 3 cut(s) 325, 432, 519
BstDEI CTNAG 5 cut(s) 81, 284, 417, 483, 495
BstF5I GGATG 2 cut(s) 44, 385
BstFNI CGCG 1 cut(s) 570
BstMAI GTCTC 2 cut(s) 273, 413
BstMWI GCNNNNNNNGC 1 cut(s) 638
BstNI CCWGG 2 cut(s) 276, 762
BstNSI RCATGY 1 cut(s) 521
BstSCI CCNGG 2 cut(s) 274, 760
BstSFI CTRYAG 1 cut(s) 809
BstSLI GKGCMC 1 cut(s) 131
BstUI CGCG 1 cut(s) 570
BstV1I GCAGC 2 cut(s) 650, 653
BstXI CCANNNNNNTGG 1 cut(s) 752
Bsu15I ATCGAT 1 cut(s) 368
BsuRI GGCC 2 cut(s) 580, 775
BsuTUI ATCGAT 1 cut(s) 368
BtsCI GGATG 2 cut(s) 44, 385
BtsIMutI CAGTG 3 cut(s) 644, 686, 806
Cac8I GCNNGC 3 cut(s) 325, 432, 519
CciI TCATGA 1 cut(s) 625
Cfr13I GGNCC 1 cut(s) 351
ClaI ATCGAT 1 cut(s) 368
Csp6I GTAC 2 cut(s) 272, 409
CviAII CATG 4 cut(s) 65, 513, 518, 626
CviQI GTAC 2 cut(s) 272, 409
DdeI CTNAG 5 cut(s) 81, 284, 417, 483, 495
Eco147I AGGCCT 1 cut(s) 580
Eco31I GGTCTC 1 cut(s) 273
Eco47I GGWCC 1 cut(s) 351
EcoO109I RGGNCCY 1 cut(s) 351
EcoRI GAATTC 1 cut(s) 446
EcoRII CCWGG 2 cut(s) 274, 760
FaeI CATG 4 cut(s) 68, 516, 521, 629
FalI AAGNNNNNCTT 2 cut(s) 724, 756
FatI CATG 4 cut(s) 64, 512, 517, 625
FauI CCCGC 1 cut(s) 563
Fnu4HI GCNGC 3 cut(s) 321, 639, 642
FokI GGATG 2 cut(s) 31, 392
Fsp4HI GCNGC 3 cut(s) 321, 639, 642
FspBI CTAG 4 cut(s) 24, 324, 431, 603
GluI GCNGC 3 cut(s) 321, 639, 642
GsuI CTGGAG 3 cut(s) 248, 297, 336
HaeIII GGCC 2 cut(s) 580, 775
HapII CCGG 1 cut(s) 188
Hin1II CATG 4 cut(s) 68, 516, 521, 629
HinfI GANTC 3 cut(s) 365, 491, 692
HpaII CCGG 1 cut(s) 188
HphI GGTGA 2 cut(s) 174, 767
Hpy188I TCNGA 2 cut(s) 534, 541
Hpy188III TCNNGA 5 cut(s) 188, 206, 266, 416, 626
HpyAV CCTTC 3 cut(s) 215, 234, 591
HpyCH4III ACNGT 3 cut(s) 478, 752, 810
HpyCH4V TGCA 4 cut(s) 197, 299, 521, 688
HpyF10VI GCNNNNNNNGC 1 cut(s) 638
HpyF3I CTNAG 5 cut(s) 81, 284, 417, 483, 495
Hsp92II CATG 4 cut(s) 68, 516, 521, 629
Kpn2I TCCGGA 1 cut(s) 187
LmnI GCTCC 3 cut(s) 35, 317, 704
Lsp1109I GCAGC 2 cut(s) 650, 653
MaeI CTAG 4 cut(s) 24, 324, 431, 603
MaeIII GTNAC 2 cut(s) 180, 234
MbiI CCGCTC 1 cut(s) 320
MboII GAAGA 4 cut(s) 175, 455, 521, 792
MhlI GDGCHC 1 cut(s) 131
MluCI AATT 7 cut(s) 155, 373, 446, 454, 506, 660, 666
MlyI GAGTC 1 cut(s) 701
MroI TCCGGA 1 cut(s) 187
MroXI GAANNNNTTC 2 cut(s) 109, 167
MseI TTAA 2 cut(s) 141, 345
MslI CAYNNNNRTG 2 cut(s) 590, 750
MspI CCGG 1 cut(s) 188
MspR9I CCNGG 2 cut(s) 276, 762
MvaI CCWGG 2 cut(s) 276, 762
MvnI CGCG 1 cut(s) 570
MwoI GCNNNNNNNGC 1 cut(s) 638
NheI GCTAGC 2 cut(s) 323, 430
NlaIII CATG 4 cut(s) 68, 516, 521, 629
NmuCI GTSAC 1 cut(s) 180
NspI RCATGY 1 cut(s) 521
OliI CACNNNNGTG 1 cut(s) 750
PaeI GCATGC 1 cut(s) 521
PagI TCATGA 1 cut(s) 625
PceI AGGCCT 1 cut(s) 580
PdmI GAANNNNTTC 2 cut(s) 109, 167
PfeI GAWTC 2 cut(s) 365, 491
PkrI GCNGC 3 cut(s) 322, 640, 643
PleI GAGTC 1 cut(s) 700
PpsI GAGTC 1 cut(s) 700
PpuMI RGGWCCY 1 cut(s) 351
Psp5II RGGWCCY 1 cut(s) 351
Psp6I CCWGG 2 cut(s) 274, 760
PspGI CCWGG 2 cut(s) 274, 760
PspPI GGNCC 1 cut(s) 351
PspPPI RGGWCCY 1 cut(s) 351
RsaI GTAC 2 cut(s) 273, 410
RsaNI GTAC 2 cut(s) 272, 409
RseI CAYNNNNRTG 2 cut(s) 590, 750
SaqAI TTAA 2 cut(s) 141, 345
SatI GCNGC 3 cut(s) 321, 639, 642
Sau96I GGNCC 1 cut(s) 351
SchI GAGTC 1 cut(s) 701
ScrFI CCNGG 2 cut(s) 276, 762
SduI GDGCHC 1 cut(s) 131
SfcI CTRYAG 1 cut(s) 809
SinI GGWCC 1 cut(s) 351
SmiMI CAYNNNNRTG 2 cut(s) 590, 750
SmlI CTYRAG 2 cut(s) 116, 122
SmoI CTYRAG 2 cut(s) 116, 122
SphI GCATGC 1 cut(s) 521
Sse9I AATT 7 cut(s) 155, 373, 446, 454, 506, 660, 666
SseBI AGGCCT 1 cut(s) 580
SsiI CCGC 3 cut(s) 320, 570, 632
SspMI CTAG 4 cut(s) 24, 324, 431, 603
StuI AGGCCT 1 cut(s) 580
StyD4I CCNGG 2 cut(s) 274, 760
TaaI ACNGT 3 cut(s) 478, 752, 810
TaqI TCGA 2 cut(s) 368, 672
TasI AATT 7 cut(s) 155, 373, 446, 454, 506, 660, 666
TauI GCSGC 1 cut(s) 323
TfiI GAWTC 2 cut(s) 365, 491
Tru1I TTAA 2 cut(s) 141, 345
Tru9I TTAA 2 cut(s) 141, 345
TscAI CASTG 3 cut(s) 651, 686, 813
TseFI GTSAC 1 cut(s) 180
TseI GCWGC 2 cut(s) 638, 641
Tsp45I GTSAC 1 cut(s) 180
TspDTI ATGAA 4 cut(s) 33, 160, 386, 490
TspGWI ACGGA 1 cut(s) 783
TspRI CASTG 3 cut(s) 651, 686, 813
VpaK11BI GGWCC 1 cut(s) 351
XapI RAATTY 2 cut(s) 155, 446
XceI RCATGY 1 cut(s) 521
XmnI GAANNNNTTC 2 cut(s) 109, 167
XspI CTAG 4 cut(s) 24, 324, 431, 603
Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.