Rw4G019270

transposition, RNA-mediated

Design Primers CRISPR Design

Basic Information

Type: gene
Biological Identity
rosa_wichuraiana
Chr4
OG0000562
Physical Location & Seq
Forward (+)
42480702 .. 42481630
929 bp
Loading structure...
UTR
Exon/CDS
Intron
Rw4G019270.1

Sequence Viewer

Length: 822 bp
ATGGCTGGGAAATCGAGTTCTAAAGGTGAGGAGCCTCTTGTGTCCTCCGATGTTGAGTTTAATCCAAACCAACGTCTTAGTTCTGTTTTGTTAAATGAATTCAACTATCTTTCTTGGGCTAGAGCTGTTACACTTGCACTTGGAGGAAGGTTCAAGCTTGGCTATGTCAATGGAGTCATACAAAAGCCTAAAGATGACTCTCCTACATATGACTCTTGGCTGTGCAAGGATCAGTTGGTTATGTCTTGGCTACTCAACTCTATGGAGAAGATGTATGGAAATCAGAATAATACAGCTCGAGTTTTTCAACTCAAACTAGATATTGCTGATCTTCAACAAGAAGGTAAGCTTTTTGTTCAACATCTTGGTAGTCTTACAAGCATGTGGAATGAGCTAGATGTTTATAGACCTCATACCATCGAGGCTAGTGTTTTGTTAAAGAGAGCTGAAGAGGACAAGATTTTTCAACTCCTTGCAAGCTTAAACTCAAAGTATGAAGATTTAAGAAGTCATATTCTTATGAATGCTAAGTTGCCATCTTTCAACAATGTGATGAATATGGAGATCAAGACAAGTGTATCTGAAACTAGAGCTTATGTTTCTAATCACAGGCAAGTTGAAGCTAAGGTGTACAAAGGCAAGAAACCAGACTTGAAATGCAGCTACTATAAGAGTGTTGGACATGTTAAGGATAGATGTTGGGTTCTCCATCCTGAACAAAAGCCGAAGTTTCTAAAGGAAGGCAAAGGTCCTCAAAGGGTTGGAATCCACCAAAACAAAACCTTACAGCAGCTTCTTCTACTCCTTCTGAGGGTATGCTGA
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

273

Amino Acids

31.28

Weight (kDa)

9.32

Isoelectric Point (pI)

33.48

Instability Index
Protein Domains (Pfam)
Domain Name Pfam ID Position E-value Description
Retrotran_gag_3 PF14244 24 - 64 1.2e-13 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 1 cut(s) 237
AcsI RAATTY 1 cut(s) 98
AcuI CTGAAG 1 cut(s) 468
AfaI GTAC 1 cut(s) 632
AfiI CCNNNNNNNGG 1 cut(s) 811
AflIII ACRYGT 1 cut(s) 682
AgsI TTSAA 9 cut(s) 103, 154, 308, 335, 359, 467, 544, 620, 655
AloI GAACNNNNNNTCC 1 cut(s) 33
AlwI GGATC 1 cut(s) 237
Ama87I CYCGRG 1 cut(s) 297
ApeKI GCWGC 2 cut(s) 660, 790
ApoI RAATTY 1 cut(s) 98
AspS9I GGNCC 1 cut(s) 749
AsuHPI GGTGA 1 cut(s) 38
AvaI CYCGRG 1 cut(s) 297
AvaII GGWCC 1 cut(s) 749
BaeI ACNNNNGTAYC 2 cut(s) 561, 594
BbvI GCAGC 2 cut(s) 672, 802
BccI CCATC 3 cut(s) 425, 544, 717
BfaI CTAG 5 cut(s) 120, 317, 395, 426, 588
BisI GCNGC 2 cut(s) 661, 791
BlsI GCNGC 2 cut(s) 662, 792
Bme18I GGWCC 1 cut(s) 749
BmeT110I CYCGRG 1 cut(s) 297
BmgT120I GGNCC 1 cut(s) 749
BmiI GGNNCC 1 cut(s) 33
Bpu10I CCTNAGC 1 cut(s) 624
BsaXI ACNNNNNCTCC 2 cut(s) 257, 287
Bsc4I CCNNNNNNNGG 1 cut(s) 811
BseGI GGATG 1 cut(s) 709
BseLI CCNNNNNNNGG 1 cut(s) 811
BseMII CTCAG 1 cut(s) 800
BseRI GAGGAG 1 cut(s) 44
BseXI GCAGC 2 cut(s) 672, 802
BseYI CCCAGC 1 cut(s) 5
BsiHKCI CYCGRG 1 cut(s) 297
BslI CCNNNNNNNGG 1 cut(s) 811
BsmI GAATGC 1 cut(s) 529
BsoBI CYCGRG 1 cut(s) 297
Bsp1407I TGTACA 1 cut(s) 630
Bsp143I GATC 3 cut(s) 229, 328, 564
BspCNI CTCAG 1 cut(s) 801
BspLI GGNNCC 1 cut(s) 33
BspPI GGATC 1 cut(s) 237
BsrGI TGTACA 1 cut(s) 630
BssMI GATC 3 cut(s) 229, 328, 564
Bst6I CTCTTC 1 cut(s) 444
BstAUI TGTACA 1 cut(s) 630
BstC8I GCNNGC 1 cut(s) 478
BstDEI CTNAG 4 cut(s) 77, 528, 624, 809
BstF5I GGATG 1 cut(s) 709
BstKTI GATC 3 cut(s) 232, 331, 567
BstMBI GATC 3 cut(s) 229, 328, 564
BstNSI RCATGY 2 cut(s) 385, 686
BstV1I GCAGC 2 cut(s) 672, 802
BtsCI GGATG 1 cut(s) 709
Cac8I GCNNGC 1 cut(s) 478
Cfr13I GGNCC 1 cut(s) 749
Csp6I GTAC 1 cut(s) 631
CviAII CATG 2 cut(s) 382, 683
CviQI GTAC 1 cut(s) 631
DdeI CTNAG 4 cut(s) 77, 528, 624, 809
DpnI GATC 3 cut(s) 231, 330, 566
DpnII GATC 3 cut(s) 229, 328, 564
Eam1104I CTCTTC 1 cut(s) 444
EarI CTCTTC 1 cut(s) 444
Eco47I GGWCC 1 cut(s) 749
Eco57I CTGAAG 1 cut(s) 468
Eco88I CYCGRG 1 cut(s) 297
EcoO109I RGGNCCY 1 cut(s) 749
EcoRI GAATTC 1 cut(s) 98
FaeI CATG 2 cut(s) 385, 686
FalI AAGNNNNNCTT 2 cut(s) 333, 365
FatI CATG 2 cut(s) 381, 682
FauNDI CATATG 1 cut(s) 208
Fnu4HI GCNGC 2 cut(s) 661, 791
FokI GGATG 1 cut(s) 696
Fsp4HI GCNGC 2 cut(s) 661, 791
FspBI CTAG 5 cut(s) 120, 317, 395, 426, 588
GluI GCNGC 2 cut(s) 661, 791
GsaI CCCAGC 1 cut(s) 9
Hin1II CATG 2 cut(s) 385, 686
HindIII AAGCTT 3 cut(s) 155, 347, 478
HinfI GANTC 4 cut(s) 174, 197, 212, 765
HphI GGTGA 1 cut(s) 38
Hpy166II GTNNAC 1 cut(s) 631
Hpy188I TCNGA 4 cut(s) 49, 285, 583, 810
Hpy188III TCNNGA 2 cut(s) 568, 713
Hpy8I GTNNAC 1 cut(s) 631
HpyAV CCTTC 4 cut(s) 141, 335, 734, 815
HpyCH4IV ACGT 1 cut(s) 73
HpyCH4V TGCA 4 cut(s) 137, 225, 476, 660
HpyF3I CTNAG 4 cut(s) 77, 528, 624, 809
HpySE526I ACGT 1 cut(s) 73
Hsp92II CATG 2 cut(s) 385, 686
Kzo9I GATC 3 cut(s) 229, 328, 564
LmnI GCTCC 1 cut(s) 31
LpnPI CCDG 3 cut(s) 595, 660, 726
Lsp1109I GCAGC 2 cut(s) 672, 802
MaeI CTAG 5 cut(s) 120, 317, 395, 426, 588
MaeII ACGT 1 cut(s) 73
MaeIII GTNAC 1 cut(s) 127
MalI GATC 3 cut(s) 231, 330, 566
MboI GATC 3 cut(s) 229, 328, 564
MboII GAAGA 5 cut(s) 280, 323, 461, 509, 788
MluCI AATT 1 cut(s) 98
MlyI GAGTC 3 cut(s) 183, 191, 206
MmeI TCCRAC 2 cut(s) 658, 742
MnlI CCTC 9 cut(s) 22, 45, 55, 137, 415, 420, 445, 762, 804
MseI TTAA 6 cut(s) 60, 92, 437, 482, 503, 687
Mva1269I GAATGC 1 cut(s) 529
NdeI CATATG 1 cut(s) 208
NdeII GATC 3 cut(s) 229, 328, 564
NlaIII CATG 2 cut(s) 385, 686
NlaIV GGNNCC 1 cut(s) 33
NspI RCATGY 2 cut(s) 385, 686
PaeR7I CTCGAG 1 cut(s) 297
PciI ACATGT 1 cut(s) 682
PctI GAATGC 1 cut(s) 529
PfeI GAWTC 1 cut(s) 765
PkrI GCNGC 2 cut(s) 662, 792
PleI GAGTC 3 cut(s) 182, 191, 206
PpsI GAGTC 3 cut(s) 182, 191, 206
PpuMI RGGWCCY 1 cut(s) 749
PscI ACATGT 1 cut(s) 682
Psp5II RGGWCCY 1 cut(s) 749
PspFI CCCAGC 1 cut(s) 5
PspN4I GGNNCC 1 cut(s) 33
PspPI GGNCC 1 cut(s) 749
PspPPI RGGWCCY 1 cut(s) 749
PspXI VCTCGAGB 1 cut(s) 297
RsaI GTAC 1 cut(s) 632
RsaNI GTAC 1 cut(s) 631
SaqAI TTAA 6 cut(s) 60, 92, 437, 482, 503, 687
SatI GCNGC 2 cut(s) 661, 791
Sau3AI GATC 3 cut(s) 229, 328, 564
Sau96I GGNCC 1 cut(s) 749
SchI GAGTC 3 cut(s) 183, 191, 206
Sfr274I CTCGAG 1 cut(s) 297
SinI GGWCC 1 cut(s) 749
SlaI CTCGAG 1 cut(s) 297
SmlI CTYRAG 1 cut(s) 297
SmoI CTYRAG 1 cut(s) 297
Sse9I AATT 1 cut(s) 98
SspMI CTAG 5 cut(s) 120, 317, 395, 426, 588
TaiI ACGT 1 cut(s) 76
TaqI TCGA 3 cut(s) 14, 298, 420
TasI AATT 1 cut(s) 98
TatI WGTACW 1 cut(s) 630
TfiI GAWTC 1 cut(s) 765
Tru1I TTAA 6 cut(s) 60, 92, 437, 482, 503, 687
Tru9I TTAA 6 cut(s) 60, 92, 437, 482, 503, 687
TseI GCWGC 2 cut(s) 660, 790
TspDTI ATGAA 4 cut(s) 111, 510, 536, 569
VpaK11BI GGWCC 1 cut(s) 749
XapI RAATTY 1 cut(s) 98
XceI RCATGY 2 cut(s) 385, 686
XhoI CTCGAG 1 cut(s) 297
XspI CTAG 5 cut(s) 120, 317, 395, 426, 588
Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.