Rw1G031370

transposition, RNA-mediated

Design Primers CRISPR Design

Basic Information

Type: gene
Biological Identity
rosa_wichuraiana
Chr1
OG0000562
Physical Location & Seq
Reverse (-)
59534618 .. 59535811
1194 bp
Loading structure...
UTR
Exon/CDS
Intron
Rw1G031370.1

Sequence Viewer

Length: 864 bp
ATGTTCTGGCTAATTAACTCCATGGAAACCAGAATAGCAGAAATTTTCAGTTTTTCTGAGTCATCTATGCATCTATGGAATAATGTCAAAGAGATGTATGGAAATCAGAATAATGCTGCTCGAGTTTTTCAACTGAAACTAGATATTGCTGATCTTCAACAGGAAGGTAAACCCTTTGTCCAGCATCTTGGTAGCCTTACTAGTATGTGGAATGAGCTAGATGTTTATAGACCTCACACTACCGAGGCTAGTGTGTTGTTAAAAAGAGCTGAGGAGGACAAGATTTTTCAGCTTCTTGCAAGCTTAAGCTCAGAATATGAAGATTTGAGAAGCCATATTCTTATGAATACTAAGTTACCATCTTTTAACAACGTGTGTGCTACCGTTCAAAGAGAAGAAGTTCGAAAAAATGTGATGAATATGGAGTCAAAGACTAGTGCATATGAAACTAGAGCATATGCCTCTAATCACAGGCAAGCTGAAGCTAAACTGTACAAGGGCAAGAAACCTGACTTGAAATGCAGCTACTATGAGGGAGTTGGACATGTTAGGGATAGATGTTGGATTCTCCATCCGGAACAGAAGTTAAAGTTTTTGAAGGAAGGCAAAGGCAAACCTGGCAGCAATTCCTTTAATCCTTCTGAGGTTAGGCTAAACTTCACCGCCAATCCCACTACTTTAATCAATGAATTTGCTGCTTATCTCAGCAAGAAGCAGATGCATAGTGGCAGTGAAGAAACAGACATTCCTGGGATTGAAGGCCATACTGCACTCCTTGGCAAACTTGCTGGCTTTCTTGCAGAGACTGATTGTGTTCCACATGAAGAAGCTTCAGGATCTCATCACCAAGAAGACGATTGGTGA
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 Retrotrans_gag rve

Protein Analysis

287

Amino Acids

32.76

Weight (kDa)

6.07

Isoelectric Point (pI)

37.51

Instability Index
Protein Domains (Pfam)
Domain Name Pfam ID Position E-value Description
Retrotran_gag_2 PF14223 4 - 138 7.4e-09 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)
AccIII TCCGGA 1 cut(s) 574
AciI CCGC 1 cut(s) 663
AclWI GGATC 1 cut(s) 844
AcsI RAATTY 2 cut(s) 42, 689
AcuI CTGAAG 2 cut(s) 501, 816
AfaI GTAC 1 cut(s) 494
AflII CTTAAG 1 cut(s) 304
AflIII ACRYGT 2 cut(s) 372, 544
AgsI TTSAA 6 cut(s) 131, 158, 389, 517, 598, 758
AhlI ACTAGT 2 cut(s) 200, 434
AjnI CCWGG 2 cut(s) 616, 748
AluBI AGCT 9 cut(s) 217, 269, 292, 303, 309, 479, 485, 525, 830
AluI AGCT 9 cut(s) 217, 269, 292, 303, 309, 479, 485, 525, 830
Alw26I GTCTC 1 cut(s) 797
AlwI GGATC 1 cut(s) 844
AlwNI CAGNNNCTG 1 cut(s) 806
Ama87I CYCGRG 1 cut(s) 120
Aor13HI TCCGGA 1 cut(s) 574
AoxI GGCC 1 cut(s) 760
ApeKI GCWGC 4 cut(s) 116, 522, 621, 695
ApoI RAATTY 2 cut(s) 42, 689
Asp700I GAANNNNTTC 1 cut(s) 399
AsuHPI GGTGA 2 cut(s) 652, 836
AsuII TTCGAA 1 cut(s) 403
AvaI CYCGRG 1 cut(s) 120
BbsI GAAGAC 1 cut(s) 858
BbvCI CCTCAGC 1 cut(s) 270
BbvI GCAGC 4 cut(s) 103, 534, 633, 682
BccI CCATC 2 cut(s) 367, 579
BciT130I CCWGG 2 cut(s) 618, 750
BcoDI GTCTC 1 cut(s) 797
BcuI ACTAGT 2 cut(s) 200, 434
BfaI CTAG 6 cut(s) 140, 201, 218, 249, 435, 450
BfrI CTTAAG 1 cut(s) 304
BisI GCNGC 4 cut(s) 117, 523, 622, 696
BlsI GCNGC 4 cut(s) 118, 524, 623, 697
Bme1390I CCNGG 2 cut(s) 618, 750
BmeT110I CYCGRG 1 cut(s) 120
BmrFI CCNGG 2 cut(s) 618, 750
BmsI GCATC 3 cut(s) 79, 193, 708
BpiI GAAGAC 1 cut(s) 858
Bpu10I CCTNAGC 1 cut(s) 270
Bpu14I TTCGAA 1 cut(s) 403
BsaJI CCNNGG 4 cut(s) 21, 243, 749, 775
BsaWI WCCGGW 1 cut(s) 574
BseAI TCCGGA 1 cut(s) 574
BseBI CCWGG 2 cut(s) 618, 750
BseDI CCNNGG 4 cut(s) 21, 243, 749, 775
BseGI GGATG 1 cut(s) 571
BseMII CTCAG 5 cut(s) 48, 261, 324, 633, 718
BseRI GAGGAG 1 cut(s) 287
BseXI GCAGC 4 cut(s) 103, 534, 633, 682
BsgI GTGCAG 1 cut(s) 753
BshFI GGCC 1 cut(s) 762
BsiHKCI CYCGRG 1 cut(s) 120
BsiSI CCGG 1 cut(s) 575
BsmAI GTCTC 1 cut(s) 797
BsnI GGCC 1 cut(s) 762
BsoBI CYCGRG 1 cut(s) 120
Bsp119I TTCGAA 1 cut(s) 403
Bsp13I TCCGGA 1 cut(s) 574
Bsp1407I TGTACA 1 cut(s) 492
Bsp143I GATC 2 cut(s) 151, 836
Bsp19I CCATGG 1 cut(s) 21
BspACI CCGC 1 cut(s) 663
BspANI GGCC 1 cut(s) 762
BspCNI CTCAG 5 cut(s) 49, 262, 323, 634, 717
BspEI TCCGGA 1 cut(s) 574
BspPI GGATC 1 cut(s) 844
BspT104I TTCGAA 1 cut(s) 403
BspTI CTTAAG 1 cut(s) 304
BsrGI TGTACA 1 cut(s) 492
BssECI CCNNGG 4 cut(s) 21, 243, 749, 775
BssMI GATC 2 cut(s) 151, 836
BssT1I CCWWGG 2 cut(s) 21, 775
Bst2UI CCWGG 2 cut(s) 618, 750
Bst4CI ACNGT 2 cut(s) 385, 492
BstAFI CTTAAG 1 cut(s) 304
BstAUI TGTACA 1 cut(s) 492
BstBI TTCGAA 1 cut(s) 403
BstC8I GCNNGC 3 cut(s) 301, 477, 790
BstDEI CTNAG 6 cut(s) 57, 270, 310, 351, 642, 704
BstDSI CCRYGG 1 cut(s) 21
BstF5I GGATG 1 cut(s) 571
BstKTI GATC 2 cut(s) 154, 839
BstMAI GTCTC 1 cut(s) 797
BstMBI GATC 2 cut(s) 151, 836
BstMWI GCNNNNNNNGC 1 cut(s) 618
BstNI CCWGG 2 cut(s) 618, 750
BstNSI RCATGY 1 cut(s) 548
BstSCI CCNGG 2 cut(s) 616, 748
BstV1I GCAGC 4 cut(s) 103, 534, 633, 682
BstV2I GAAGAC 1 cut(s) 858
BstX2I RGATCY 1 cut(s) 836
BstXI CCANNNNNNTGG 1 cut(s) 188
BstYI RGATCY 1 cut(s) 836
BsuRI GGCC 1 cut(s) 762
BtgI CCRYGG 1 cut(s) 21
BtsCI GGATG 1 cut(s) 571
BtsI GCAGTG 1 cut(s) 736
BtsIMutI CAGTG 1 cut(s) 736
Cac8I GCNNGC 3 cut(s) 301, 477, 790
CaiI CAGNNNCTG 1 cut(s) 806
Csp6I GTAC 1 cut(s) 493
CviAII CATG 3 cut(s) 22, 545, 821
CviQI GTAC 1 cut(s) 493
DdeI CTNAG 6 cut(s) 57, 270, 310, 351, 642, 704
DpnI GATC 2 cut(s) 153, 838
DpnII GATC 2 cut(s) 151, 836
Eco130I CCWWGG 2 cut(s) 21, 775
Eco57I CTGAAG 2 cut(s) 501, 816
Eco88I CYCGRG 1 cut(s) 120
EcoRII CCWGG 2 cut(s) 616, 748
EcoT14I CCWWGG 2 cut(s) 21, 775
EcoT22I ATGCAT 2 cut(s) 72, 723
ErhI CCWWGG 2 cut(s) 21, 775
FaeI CATG 3 cut(s) 25, 548, 824
FatI CATG 3 cut(s) 21, 544, 820
FauNDI CATATG 2 cut(s) 442, 457
Fnu4HI GCNGC 4 cut(s) 117, 523, 622, 696
FokI GGATG 1 cut(s) 558
Fsp4HI GCNGC 4 cut(s) 117, 523, 622, 696
FspBI CTAG 6 cut(s) 140, 201, 218, 249, 435, 450
GluI GCNGC 4 cut(s) 117, 523, 622, 696
HaeIII GGCC 1 cut(s) 762
HapII CCGG 1 cut(s) 575
Hin1II CATG 3 cut(s) 25, 548, 824
HindIII AAGCTT 2 cut(s) 301, 828
HinfI GANTC 3 cut(s) 59, 425, 565
HpaII CCGG 1 cut(s) 575
HphI GGTGA 2 cut(s) 652, 836
Hpy166II GTNNAC 1 cut(s) 170
Hpy188I TCNGA 4 cut(s) 58, 108, 313, 643
Hpy188III TCNNGA 2 cut(s) 575, 834
Hpy8I GTNNAC 1 cut(s) 170
HpyAV CCTTC 5 cut(s) 158, 592, 596, 648, 752
HpyCH4III ACNGT 2 cut(s) 385, 492
HpyCH4IV ACGT 1 cut(s) 372
HpyCH4V TGCA 7 cut(s) 70, 299, 440, 522, 721, 770, 800
HpyF10VI GCNNNNNNNGC 1 cut(s) 618
HpyF3I CTNAG 6 cut(s) 57, 270, 310, 351, 642, 704
HpySE526I ACGT 1 cut(s) 372
Hsp92II CATG 3 cut(s) 25, 548, 824
Kpn2I TCCGGA 1 cut(s) 574
Kzo9I GATC 2 cut(s) 151, 836
Lsp1109I GCAGC 4 cut(s) 103, 534, 633, 682
LweI GCATC 3 cut(s) 79, 193, 708
MaeI CTAG 6 cut(s) 140, 201, 218, 249, 435, 450
MaeII ACGT 1 cut(s) 372
MaeIII GTNAC 1 cut(s) 354
MalI GATC 2 cut(s) 153, 838
MboI GATC 2 cut(s) 151, 836
MboII GAAGA 6 cut(s) 146, 332, 407, 746, 836, 863
MflI RGATCY 1 cut(s) 836
MluCI AATT 4 cut(s) 12, 42, 625, 689
MlyI GAGTC 2 cut(s) 68, 434
MmeI TCCRAC 2 cut(s) 520, 542
MnlI CCTC 7 cut(s) 238, 243, 265, 268, 472, 526, 637
Mph1103I ATGCAT 2 cut(s) 72, 723
MroI TCCGGA 1 cut(s) 574
MroXI GAANNNNTTC 1 cut(s) 399
MseI TTAA 7 cut(s) 15, 260, 305, 366, 587, 633, 680
MspCI CTTAAG 1 cut(s) 304
MspI CCGG 1 cut(s) 575
MspR9I CCNGG 2 cut(s) 618, 750
MvaI CCWGG 2 cut(s) 618, 750
MwoI GCNNNNNNNGC 1 cut(s) 618
NcoI CCATGG 1 cut(s) 21
NdeI CATATG 2 cut(s) 442, 457
NdeII GATC 2 cut(s) 151, 836
NlaIII CATG 3 cut(s) 25, 548, 824
NsiI ATGCAT 2 cut(s) 72, 723
NspI RCATGY 1 cut(s) 548
NspV TTCGAA 1 cut(s) 403
PaeR7I CTCGAG 1 cut(s) 120
PciI ACATGT 1 cut(s) 544
PdmI GAANNNNTTC 1 cut(s) 399
PfeI GAWTC 1 cut(s) 565
PkrI GCNGC 4 cut(s) 118, 524, 623, 697
PleI GAGTC 2 cut(s) 67, 433
PpsI GAGTC 2 cut(s) 67, 433
PscI ACATGT 1 cut(s) 544
Psp6I CCWGG 2 cut(s) 616, 748
PspGI CCWGG 2 cut(s) 616, 748
PspXI VCTCGAGB 1 cut(s) 120
PstNI CAGNNNCTG 1 cut(s) 806
PsuI RGATCY 1 cut(s) 836
RsaI GTAC 1 cut(s) 494
RsaNI GTAC 1 cut(s) 493
SaqAI TTAA 7 cut(s) 15, 260, 305, 366, 587, 633, 680
SatI GCNGC 4 cut(s) 117, 523, 622, 696
Sau3AI GATC 2 cut(s) 151, 836
SchI GAGTC 2 cut(s) 68, 434
ScrFI CCNGG 2 cut(s) 618, 750
SfaNI GCATC 3 cut(s) 79, 193, 708
Sfr274I CTCGAG 1 cut(s) 120
SfuI TTCGAA 1 cut(s) 403
SlaI CTCGAG 1 cut(s) 120
SmlI CTYRAG 2 cut(s) 120, 304
SmoI CTYRAG 2 cut(s) 120, 304
SpeI ACTAGT 2 cut(s) 200, 434
Sse9I AATT 4 cut(s) 12, 42, 625, 689
SsiI CCGC 1 cut(s) 663
SspMI CTAG 6 cut(s) 140, 201, 218, 249, 435, 450
StyD4I CCNGG 2 cut(s) 616, 748
StyI CCWWGG 2 cut(s) 21, 775
TaaI ACNGT 2 cut(s) 385, 492
TaiI ACGT 1 cut(s) 375
TaqI TCGA 2 cut(s) 121, 403
TasI AATT 4 cut(s) 12, 42, 625, 689
TatI WGTACW 1 cut(s) 492
TfiI GAWTC 1 cut(s) 565
Tru1I TTAA 7 cut(s) 15, 260, 305, 366, 587, 633, 680
Tru9I TTAA 7 cut(s) 15, 260, 305, 366, 587, 633, 680
TscAI CASTG 1 cut(s) 736
TseI GCWGC 4 cut(s) 116, 522, 621, 695
TspDTI ATGAA 6 cut(s) 333, 359, 431, 459, 702, 837
TspRI CASTG 1 cut(s) 736
Vha464I CTTAAG 1 cut(s) 304
XapI RAATTY 2 cut(s) 42, 689
XceI RCATGY 1 cut(s) 548
XhoI CTCGAG 1 cut(s) 120
XmnI GAANNNNTTC 1 cut(s) 399
XspI CTAG 6 cut(s) 140, 201, 218, 249, 435, 450
Zsp2I ATGCAT 2 cut(s) 72, 723
Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.