Rw2G042180

transposition, RNA-mediated

Design Primers CRISPR Design

Basic Information

Type: gene
Biological Identity
rosa_wichuraiana
Chr2
OG0000562
Physical Location & Seq
Forward (+)
68416835 .. 68417764
930 bp
Loading structure...
UTR
Exon/CDS
Intron
Rw2G042180.1

Sequence Viewer

Length: 885 bp
ATGGCTGGGAAATCTGGTTCTAAAGATGATGATCCTCTTACAAATTCTTCCGATGTGGAGTCTAATCCAAACCAACGTCTTAGCTCCGTTTTGTTGAATGAATTCAACTATCTTTCTTGGGCTAGAGCTGTTACTCTTGCTCTTGGAGGAAGGTCCAAGCTTGGCTATGTCAATGGACTGTGCAAGGATCAACTCGTCATGTCTTGGCTAATCAACTCCATGGAGAGCAGAATAGCAGAAATTTTTAGTTTTTCTGAGTCATCTATGCATCTCTGGAATAATGTCAAGGAGATGTATGGAAATCAGAATAATGTTGCTCGAGTATTTCAACTCAAACGAGATATTGCCGATCTTCAACAAGAAGGTAAGCACTTTGTTCAGCATCTTGGTAGTCTTACAAGTATGTGGAATGAGCTAGATGTTTATAGACCTCATACTACTGAGGCTAGTGTTTTGTTAAAAAGAGCTAAGGAGGATAAGATCTTTCAGCTTCTTGCAAGTTTAAGCTCAAAATATGAAGATTTGAGAAGTCATATTCTTATGAATACTGAGCTACCATCTTTCAACAATGTGTGTGCCACCATTCAAAGAGAAGAAATTCGAAAAAGGGTGATGAATATGGAGACCAAGACAAGTGCATCTGAAACCAGAGCTTATGCTTCTAATCACAGGCAAGCTGAAGCTAAAGTGTACAAAGGCAAGAGGCCTGACTTGAAATGCAGCTACTGTGAGGGGGTTGGACATGTCAGGGAAAAATGTTGGGTTCTCTATCCTGAGCAGAAGCCAAAGTTTCTAAAGGAAGGCAAAAGCTCTCAAAAGAGCTGGAATCCACCAAAAGCAAACCTGGCAACAACTTCTTCTTCTTCTTCTTCTGAGGATATATAG
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

294

Amino Acids

33.37

Weight (kDa)

8.94

Isoelectric Point (pI)

44.01

Instability Index
Protein Domains (Pfam)
Domain Name Pfam ID Position E-value Description
Retrotran_gag_3 PF14244 22 - 62 1.5e-12 gag-polypeptide of LTR copia-type
Retrotran_gag_2 PF14223 62 - 204 2e-10 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)
AclWI GGATC 2 cut(s) 26, 195
AcsI RAATTY 4 cut(s) 43, 101, 240, 597
AcuI CTGAAG 1 cut(s) 699
AfaI GTAC 1 cut(s) 692
AflIII ACRYGT 1 cut(s) 742
AgsI TTSAA 7 cut(s) 97, 106, 329, 356, 565, 587, 715
AjnI CCWGG 1 cut(s) 843
AloI GAACNNNNNNTCC 1 cut(s) 33
Alw26I GTCTC 1 cut(s) 617
AlwI GGATC 2 cut(s) 26, 195
AlwNI CAGNNNCTG 1 cut(s) 726
Ama87I CYCGRG 1 cut(s) 318
AoxI GGCC 1 cut(s) 704
ApeKI GCWGC 1 cut(s) 720
ApoI RAATTY 4 cut(s) 43, 101, 240, 597
Asp700I GAANNNNTTC 2 cut(s) 101, 597
AspS9I GGNCC 1 cut(s) 153
AsuHPI GGTGA 1 cut(s) 622
AsuII TTCGAA 1 cut(s) 601
AvaI CYCGRG 1 cut(s) 318
AvaII GGWCC 1 cut(s) 153
BbvI GCAGC 1 cut(s) 732
BccI CCATC 1 cut(s) 565
BciT130I CCWGG 1 cut(s) 845
BcoDI GTCTC 1 cut(s) 617
BfaI CTAG 3 cut(s) 123, 416, 447
BglII AGATCT 1 cut(s) 480
BisI GCNGC 1 cut(s) 721
BlsI GCNGC 1 cut(s) 722
Bme1390I CCNGG 1 cut(s) 845
Bme18I GGWCC 1 cut(s) 153
BmeT110I CYCGRG 1 cut(s) 318
BmgT120I GGNCC 1 cut(s) 153
BmrFI CCNGG 1 cut(s) 845
BmsI GCATC 3 cut(s) 277, 391, 647
Bpu10I CCTNAGC 2 cut(s) 468, 774
Bpu14I TTCGAA 1 cut(s) 601
BsaBI GATNNNNATC 1 cut(s) 30
BsaI GGTCTC 1 cut(s) 617
BsaJI CCNNGG 1 cut(s) 219
Bse8I GATNNNNATC 1 cut(s) 30
BseBI CCWGG 1 cut(s) 845
BseDI CCNNGG 1 cut(s) 219
BseJI GATNNNNATC 1 cut(s) 30
BseMII CTCAG 5 cut(s) 246, 432, 540, 765, 864
BseXI GCAGC 1 cut(s) 732
BseYI CCCAGC 1 cut(s) 5
BshFI GGCC 1 cut(s) 706
BsiHKCI CYCGRG 1 cut(s) 318
BsmAI GTCTC 1 cut(s) 617
BsnI GGCC 1 cut(s) 706
Bso31I GGTCTC 1 cut(s) 617
BsoBI CYCGRG 1 cut(s) 318
Bsp119I TTCGAA 1 cut(s) 601
Bsp1407I TGTACA 1 cut(s) 690
Bsp143I GATC 4 cut(s) 31, 187, 349, 480
Bsp19I CCATGG 1 cut(s) 219
BspANI GGCC 1 cut(s) 706
BspCNI CTCAG 5 cut(s) 247, 433, 541, 766, 865
BspPI GGATC 2 cut(s) 26, 195
BspT104I TTCGAA 1 cut(s) 601
BspTNI GGTCTC 1 cut(s) 617
BsrGI TGTACA 1 cut(s) 690
BssECI CCNNGG 1 cut(s) 219
BssMI GATC 4 cut(s) 31, 187, 349, 480
BssT1I CCWWGG 1 cut(s) 219
Bst2UI CCWGG 1 cut(s) 845
Bst4CI ACNGT 2 cut(s) 180, 728
BstAUI TGTACA 1 cut(s) 690
BstBI TTCGAA 1 cut(s) 601
BstC8I GCNNGC 1 cut(s) 675
BstDEI CTNAG 7 cut(s) 80, 255, 441, 468, 549, 774, 873
BstDSI CCRYGG 1 cut(s) 219
BstKTI GATC 4 cut(s) 34, 190, 352, 483
BstMAI GTCTC 1 cut(s) 617
BstMBI GATC 4 cut(s) 31, 187, 349, 480
BstMWI GCNNNNNNNGC 1 cut(s) 845
BstNI CCWGG 1 cut(s) 845
BstNSI RCATGY 1 cut(s) 746
BstSCI CCNGG 1 cut(s) 843
BstV1I GCAGC 1 cut(s) 732
BstX2I RGATCY 1 cut(s) 480
BstYI RGATCY 1 cut(s) 480
BsuRI GGCC 1 cut(s) 706
BtgI CCRYGG 1 cut(s) 219
Cac8I GCNNGC 1 cut(s) 675
CaiI CAGNNNCTG 1 cut(s) 726
Cfr13I GGNCC 1 cut(s) 153
Csp6I GTAC 1 cut(s) 691
CviAII CATG 3 cut(s) 199, 220, 743
CviQI GTAC 1 cut(s) 691
DdeI CTNAG 7 cut(s) 80, 255, 441, 468, 549, 774, 873
DpnI GATC 4 cut(s) 33, 189, 351, 482
DpnII GATC 4 cut(s) 31, 187, 349, 480
Eco130I CCWWGG 1 cut(s) 219
Eco147I AGGCCT 1 cut(s) 706
Eco31I GGTCTC 1 cut(s) 617
Eco47I GGWCC 1 cut(s) 153
Eco57I CTGAAG 1 cut(s) 699
Eco88I CYCGRG 1 cut(s) 318
EcoRI GAATTC 1 cut(s) 101
EcoRII CCWGG 1 cut(s) 843
EcoT14I CCWWGG 1 cut(s) 219
EcoT22I ATGCAT 1 cut(s) 270
ErhI CCWWGG 1 cut(s) 219
FaeI CATG 3 cut(s) 202, 223, 746
FatI CATG 3 cut(s) 198, 219, 742
Fnu4HI GCNGC 1 cut(s) 721
Fsp4HI GCNGC 1 cut(s) 721
FspBI CTAG 3 cut(s) 123, 416, 447
GluI GCNGC 1 cut(s) 721
GsaI CCCAGC 1 cut(s) 9
HaeIII GGCC 1 cut(s) 706
Hin1II CATG 3 cut(s) 202, 223, 746
HindIII AAGCTT 1 cut(s) 158
HinfI GANTC 3 cut(s) 59, 257, 826
HphI GGTGA 1 cut(s) 622
Hpy166II GTNNAC 1 cut(s) 691
Hpy188I TCNGA 5 cut(s) 52, 256, 306, 643, 874
Hpy188III TCNNGA 2 cut(s) 274, 773
Hpy8I GTNNAC 1 cut(s) 691
HpyAV CCTTC 3 cut(s) 144, 356, 794
HpyCH4III ACNGT 2 cut(s) 180, 728
HpyCH4IV ACGT 1 cut(s) 76
HpyCH4V TGCA 5 cut(s) 183, 268, 497, 638, 720
HpyF10VI GCNNNNNNNGC 1 cut(s) 845
HpyF3I CTNAG 7 cut(s) 80, 255, 441, 468, 549, 774, 873
HpySE526I ACGT 1 cut(s) 76
Hsp92II CATG 3 cut(s) 202, 223, 746
Kzo9I GATC 4 cut(s) 31, 187, 349, 480
LmnI GCTCC 1 cut(s) 89
LpnPI CCDG 9 cut(s) 259, 655, 661, 720, 733, 786, 808, 830, 857
Lsp1109I GCAGC 1 cut(s) 732
LweI GCATC 3 cut(s) 277, 391, 647
MaeI CTAG 3 cut(s) 123, 416, 447
MaeII ACGT 1 cut(s) 76
MaeIII GTNAC 1 cut(s) 130
MalI GATC 4 cut(s) 33, 189, 351, 482
MboI GATC 4 cut(s) 31, 187, 349, 480
MboII GAAGA 9 cut(s) 39, 344, 530, 605, 849, 852, 855, 858, 861
MflI RGATCY 1 cut(s) 480
MluCI AATT 4 cut(s) 43, 101, 240, 597
MlyI GAGTC 2 cut(s) 68, 266
MmeI TCCRAC 1 cut(s) 718
MnlI CCTC 8 cut(s) 45, 140, 436, 441, 466, 696, 724, 868
Mph1103I ATGCAT 1 cut(s) 270
MroXI GAANNNNTTC 2 cut(s) 101, 597
MseI TTAA 2 cut(s) 458, 503
MspR9I CCNGG 1 cut(s) 845
MvaI CCWGG 1 cut(s) 845
MwoI GCNNNNNNNGC 1 cut(s) 845
NcoI CCATGG 1 cut(s) 219
NdeII GATC 4 cut(s) 31, 187, 349, 480
NlaIII CATG 3 cut(s) 202, 223, 746
NsiI ATGCAT 1 cut(s) 270
NspI RCATGY 1 cut(s) 746
NspV TTCGAA 1 cut(s) 601
PaeR7I CTCGAG 1 cut(s) 318
PceI AGGCCT 1 cut(s) 706
PciI ACATGT 1 cut(s) 742
PdmI GAANNNNTTC 2 cut(s) 101, 597
PfeI GAWTC 1 cut(s) 826
PkrI GCNGC 1 cut(s) 722
PleI GAGTC 2 cut(s) 67, 265
PpsI GAGTC 2 cut(s) 67, 265
PscI ACATGT 1 cut(s) 742
Psp6I CCWGG 1 cut(s) 843
PspFI CCCAGC 1 cut(s) 5
PspGI CCWGG 1 cut(s) 843
PspPI GGNCC 1 cut(s) 153
PspXI VCTCGAGB 1 cut(s) 318
PstNI CAGNNNCTG 1 cut(s) 726
PsuI RGATCY 1 cut(s) 480
RsaI GTAC 1 cut(s) 692
RsaNI GTAC 1 cut(s) 691
SaqAI TTAA 2 cut(s) 458, 503
SatI GCNGC 1 cut(s) 721
Sau3AI GATC 4 cut(s) 31, 187, 349, 480
Sau96I GGNCC 1 cut(s) 153
SchI GAGTC 2 cut(s) 68, 266
ScrFI CCNGG 1 cut(s) 845
SfaNI GCATC 3 cut(s) 277, 391, 647
Sfr274I CTCGAG 1 cut(s) 318
SfuI TTCGAA 1 cut(s) 601
SinI GGWCC 1 cut(s) 153
SlaI CTCGAG 1 cut(s) 318
SmlI CTYRAG 1 cut(s) 318
SmoI CTYRAG 1 cut(s) 318
Sse9I AATT 4 cut(s) 43, 101, 240, 597
SseBI AGGCCT 1 cut(s) 706
SspMI CTAG 3 cut(s) 123, 416, 447
StuI AGGCCT 1 cut(s) 706
StyD4I CCNGG 1 cut(s) 843
StyI CCWWGG 1 cut(s) 219
TaaI ACNGT 2 cut(s) 180, 728
TaiI ACGT 1 cut(s) 79
TaqI TCGA 2 cut(s) 319, 601
TasI AATT 4 cut(s) 43, 101, 240, 597
TatI WGTACW 1 cut(s) 690
TfiI GAWTC 1 cut(s) 826
Tru1I TTAA 2 cut(s) 458, 503
Tru9I TTAA 2 cut(s) 458, 503
TseI GCWGC 1 cut(s) 720
TspDTI ATGAA 4 cut(s) 114, 531, 557, 629
TspGWI ACGGA 1 cut(s) 76
VpaK11BI GGWCC 1 cut(s) 153
XapI RAATTY 4 cut(s) 43, 101, 240, 597
XceI RCATGY 1 cut(s) 746
XhoI CTCGAG 1 cut(s) 318
XmnI GAANNNNTTC 2 cut(s) 101, 597
XspI CTAG 3 cut(s) 123, 416, 447
Zsp2I ATGCAT 1 cut(s) 270
Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.