MD15G1306600.v1.1

transposition, RNA-mediated

Design Primers CRISPR Design

Basic Information

Type: gene
Biological Identity
malus_domestica
Chr15
OG0000437
Physical Location & Seq
Forward (+)
30436492 .. 30439326
2835 bp
Loading structure...
UTR
Exon/CDS
Intron
MD15G1306600.v1.1.491

Sequence Viewer

Length: 642 bp
ATGGCAGCGGACAATCGAACAATCAAGGAGCTTTCTGCTTCAGGATTGGACAATGCCGCTCCCCTATGCATCCAATACCCCATGGCTGCCCTAGGGAAGACGGACGAGTTCGAATTGAAATCAAGTTTGTTGCATCACATTCCTAAGTTCCACGGGATGTCCATGGAAGATCCTAATAAACACTTGAAGGAGTTTGAGGTTGTTTGCTCGAGCATGACCCCTGTGAACGTTGATGGAAGCATTCTGAAAATGAAGGTTTTTCCCTTTTCTCTCTTAGAAAAGGCTAAATATTGGTTGTATGAGCTAGCCCCCGGAACTATCACATCATGGGAGAGTATGAAACGGGCATTTTTGGAGAAGTTTTTCCCAACCTCTCGAGTCATTCTACTACGCAAAAGGATTAGTGGCATTCAGCAAAACCAAGGTGAATCATTTCCCACTTACTATGAGTGTTTTAAAACCCTTGTTGCTTCATGTCCACAACACCAGATGAAGGAGAAGCTTCTTCTTCAATATTTCTACGAAGGGCTTTTACCAATTGAAAGCCAAATGCTAGACGCCTCAGCGGGAGGAGCTTTGGTGGACAAAACACCTATGGCTGCCAAGACCTTAATTGCTAACCGAGCATTGAATGCTCAATAA
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
RVT_1 Retrotrans_gag rve

Protein Analysis

214

Amino Acids

23.94

Weight (kDa)

8.27

Isoelectric Point (pI)

41.12

Instability Index
Protein Domains (Pfam)
Domain Name Pfam ID Position E-value Description
Retrotrans_gag PF03732 85 - 178 1.3e-18 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: OG0000437)

Species Orthologous Gene IDs
arabidopsis_thaliana AT2G06105
fragaria_vesca FvH4_1g09709 FvH4_4g02101 FvH4_4g08975 FvH4_6g23372 FvH4_6g39851 FvH4_c1g00300
malus_domestica MD01G1176100.v1.1 MD09G1284900.v1.1 MD15G1306600.v1.1
prunus_persica Prupe.1G227700_v2.0.a1
pyrus_communis pycom01g00630 pycom01g01020 pycom01g01690 pycom01g01760 pycom01g04190 pycom01g04400 pycom02g18130 pycom03g10160 pycom05g06370 pycom05g08930 pycom06g05590 pycom10g06320 pycom11g14330 pycom11g15320 pycom11g16240 pycom12416g00050 pycom12420g00010 pycom12420g00120 pycom12426g00180 pycom12426g00710 pycom12531g00010 pycom1256g00020 pycom1256g00050 pycom1341g00030 pycom1353g00030 pycom13g23070 pycom13g23210 pycom13g26260 pycom13g26370 pycom13g26470 pycom13g26980 pycom14g08550 pycom14g08850 pycom1534g00040 pycom15g28760 pycom15g31230 pycom1604g00040 pycom16g21900 pycom16g26030 pycom1739g00020 pycom1739g00050 pycom17g12970 pycom17g17960 pycom17g18300 pycom17g18650 pycom2172g00020 pycom2438g00020 pycom436g00370 pycom436g00390 pycom576g00050 pycom76g00020
rosa_chinensis RchiOBHm_Chr1g0320811 RchiOBHm_Chr2g0135321 RchiOBHm_Chr3g0485721 RchiOBHm_Chr7g0236571
rosa_multiflora Rmu_sc0000185.1_g000007 Rmu_sc0002094.1_g000030 Rmu_sc0002764.1_g000007 Rmu_sc0002809.1_g000014 Rmu_sc0003005.1_g000007 Rmu_sc0003798.1_g000005 Rmu_sc0004646.1_g000027 Rmu_sc0004665.1_g000009 Rmu_sc0004818.1_g000001 Rmu_sc0004988.1_g000031 Rmu_sc0006373.1_g000007 Rmu_sc0007142.1_g000015 Rmu_sc0009930.1_g000001 Rmu_sc0011451.1_g000001 Rmu_sc0020424.1_g000001 Rmu_sc0036944.1_g000001 Rmu_ssc0000062.1_g000010
rosa_roxburghii Rroxscaffold_2G00123930 Rroxscaffold_3G00231480 Rroxscaffold_6G00413880
rosa_rugosa Rorug04G0084800
rosa_samantha Rh3BG150500 Rh6DG232400
rosa_wichuraiana Rw2G018400 Rw3G027860 Rw4G021220 Rw6G020670 Rw6G037970

Restriction Enzyme Sites

1 / 10
Enzyme Recognition Site Cut Count Positions (bp)
AccBSI CCGCTC 1 cut(s) 59
AciI CCGC 3 cut(s) 8, 57, 566
AclI AACGTT 1 cut(s) 228
AclWI GGATC 1 cut(s) 164
AcuI CTGAAG 1 cut(s) 24
AcyI GRCGYC 1 cut(s) 558
AfiI CCNNNNNNNGG 1 cut(s) 493
AgsI TTSAA 5 cut(s) 118, 187, 512, 542, 631
AluBI AGCT 4 cut(s) 31, 304, 502, 575
AluI AGCT 4 cut(s) 31, 304, 502, 575
AlwI GGATC 1 cut(s) 164
Ama87I CYCGRG 2 cut(s) 208, 375
ApeKI GCWGC 3 cut(s) 5, 86, 599
Asp700I GAANNNNTTC 2 cut(s) 362, 432
AspA2I CCTAGG 1 cut(s) 91
AsuC2I CCSGG 1 cut(s) 312
AsuHPI GGTGA 1 cut(s) 437
AsuII TTCGAA 1 cut(s) 111
AsuNHI GCTAGC 1 cut(s) 304
AvaI CYCGRG 2 cut(s) 208, 375
AvrII CCTAGG 1 cut(s) 91
BarI GAAGNNNNNNTAC 2 cut(s) 516, 548
BbsI GAAGAC 1 cut(s) 104
BbvCI CCTCAGC 1 cut(s) 562
BbvI GCAGC 3 cut(s) 17, 73, 586
BccI CCATC 1 cut(s) 227
BcnI CCSGG 1 cut(s) 312
BfaI CTAG 3 cut(s) 92, 305, 554
BisI GCNGC 4 cut(s) 6, 57, 87, 600
BlnI CCTAGG 1 cut(s) 91
BlsI GCNGC 4 cut(s) 7, 58, 88, 601
Bme1390I CCNGG 1 cut(s) 312
BmeT110I CYCGRG 2 cut(s) 208, 375
BmrFI CCNGG 1 cut(s) 312
BmsI GCATC 2 cut(s) 78, 142
BmtI GCTAGC 1 cut(s) 308
BpiI GAAGAC 1 cut(s) 104
Bpu10I CCTNAGC 1 cut(s) 562
Bpu14I TTCGAA 1 cut(s) 111
BpuMI CCSGG 1 cut(s) 312
BsaHI GRCGYC 1 cut(s) 558
BsaJI CCNNGG 6 cut(s) 81, 91, 151, 162, 310, 421
BsaXI ACNNNNNCTCC 2 cut(s) 564, 594
Bsc4I CCNNNNNNNGG 1 cut(s) 493
BseDI CCNNGG 6 cut(s) 81, 91, 151, 162, 310, 421
BseGI GGATG 2 cut(s) 69, 162
BseLI CCNNNNNNNGG 1 cut(s) 493
BseMII CTCAG 1 cut(s) 576
BseRI GAGGAG 1 cut(s) 585
BseXI GCAGC 3 cut(s) 17, 73, 586
BsiHKCI CYCGRG 2 cut(s) 208, 375
BsiSI CCGG 1 cut(s) 312
BslI CCNNNNNNNGG 1 cut(s) 493
BsmI GAATGC 3 cut(s) 240, 408, 637
BsoBI CYCGRG 2 cut(s) 208, 375
Bsp119I TTCGAA 1 cut(s) 111
Bsp143I GATC 1 cut(s) 169
Bsp19I CCATGG 2 cut(s) 81, 162
BspACI CCGC 3 cut(s) 8, 57, 566
BspCNI CTCAG 1 cut(s) 575
BspOI GCTAGC 1 cut(s) 308
BspPI GGATC 1 cut(s) 164
BspT104I TTCGAA 1 cut(s) 111
BsrBI CCGCTC 1 cut(s) 59
BssECI CCNNGG 6 cut(s) 81, 91, 151, 162, 310, 421
BssMI GATC 1 cut(s) 169
BssNI GRCGYC 1 cut(s) 558
BssT1I CCWWGG 4 cut(s) 81, 91, 162, 421
BstACI GRCGYC 1 cut(s) 558
BstAPI GCANNNNNTGC 1 cut(s) 632
BstBI TTCGAA 1 cut(s) 111
BstC8I GCNNGC 1 cut(s) 306
BstDEI CTNAG 3 cut(s) 144, 274, 562
BstDSI CCRYGG 3 cut(s) 81, 151, 162
BstF5I GGATG 2 cut(s) 69, 162
BstKTI GATC 1 cut(s) 172
BstMBI GATC 1 cut(s) 169
BstMWI GCNNNNNNNGC 3 cut(s) 572, 623, 632
BstSCI CCNGG 1 cut(s) 310
BstV1I GCAGC 3 cut(s) 17, 73, 586
BstV2I GAAGAC 1 cut(s) 104
BstX2I RGATCY 1 cut(s) 169
BstYI RGATCY 1 cut(s) 169
BtgI CCRYGG 3 cut(s) 81, 151, 162
BtsCI GGATG 2 cut(s) 69, 162
Cac8I GCNNGC 1 cut(s) 306
CseI GACGC 1 cut(s) 566
CviAII CATG 5 cut(s) 82, 163, 214, 327, 474
DdeI CTNAG 3 cut(s) 144, 274, 562
DpnI GATC 1 cut(s) 171
DpnII GATC 1 cut(s) 169
DraI TTTAAA 1 cut(s) 457
Eco130I CCWWGG 4 cut(s) 81, 91, 162, 421
Eco57I CTGAAG 1 cut(s) 24
Eco88I CYCGRG 2 cut(s) 208, 375
EcoT14I CCWWGG 4 cut(s) 81, 91, 162, 421
EcoT22I ATGCAT 1 cut(s) 71
ErhI CCWWGG 4 cut(s) 81, 91, 162, 421
FaeI CATG 5 cut(s) 85, 166, 217, 330, 477
FatI CATG 5 cut(s) 81, 162, 213, 326, 473
FauI CCCGC 1 cut(s) 559
Fnu4HI GCNGC 4 cut(s) 6, 57, 87, 600
FokI GGATG 2 cut(s) 56, 169
Fsp4HI GCNGC 4 cut(s) 6, 57, 87, 600
FspBI CTAG 3 cut(s) 92, 305, 554
GluI GCNGC 4 cut(s) 6, 57, 87, 600
HapII CCGG 1 cut(s) 312
HgaI GACGC 1 cut(s) 566
Hin1I GRCGYC 1 cut(s) 558
Hin1II CATG 5 cut(s) 85, 166, 217, 330, 477
HindIII AAGCTT 1 cut(s) 500
HinfI GANTC 2 cut(s) 378, 428
HpaII CCGG 1 cut(s) 312
HphI GGTGA 1 cut(s) 437
Hpy166II GTNNAC 3 cut(s) 226, 479, 583
Hpy188I TCNGA 1 cut(s) 246
Hpy188III TCNNGA 2 cut(s) 42, 375
Hpy8I GTNNAC 3 cut(s) 226, 479, 583
HpyAV CCTTC 4 cut(s) 181, 247, 487, 518
HpyCH4IV ACGT 1 cut(s) 228
HpyCH4V TGCA 2 cut(s) 69, 133
HpyF10VI GCNNNNNNNGC 3 cut(s) 572, 623, 632
HpyF3I CTNAG 3 cut(s) 144, 274, 562
HpySE526I ACGT 1 cut(s) 228
Hsp92I GRCGYC 1 cut(s) 558
Hsp92II CATG 5 cut(s) 85, 166, 217, 330, 477
Kzo9I GATC 1 cut(s) 169
LmnI GCTCC 3 cut(s) 28, 64, 572
LpnPI CCDG 4 cut(s) 27, 234, 325, 500
Lsp1109I GCAGC 3 cut(s) 17, 73, 586
LweI GCATC 2 cut(s) 78, 142
MaeI CTAG 3 cut(s) 92, 305, 554
MaeII ACGT 1 cut(s) 228
MalI GATC 1 cut(s) 171
MbiI CCGCTC 1 cut(s) 59
MboI GATC 1 cut(s) 169
MboII GAAGA 4 cut(s) 109, 179, 497, 500
MfeI CAATTG 1 cut(s) 537
MflI RGATCY 1 cut(s) 169
MluCI AATT 3 cut(s) 113, 537, 612
MlyI GAGTC 1 cut(s) 387
MnlI CCTC 4 cut(s) 190, 382, 563, 571
Mph1103I ATGCAT 1 cut(s) 71
MroXI GAANNNNTTC 2 cut(s) 362, 432
MseI TTAA 2 cut(s) 456, 611
MspA1I CMGCKG 2 cut(s) 8, 566
MspI CCGG 1 cut(s) 312
MspR9I CCNGG 1 cut(s) 312
MunI CAATTG 1 cut(s) 537
Mva1269I GAATGC 3 cut(s) 240, 408, 637
MwoI GCNNNNNNNGC 3 cut(s) 572, 623, 632
NciI CCSGG 1 cut(s) 312
NcoI CCATGG 2 cut(s) 81, 162
NdeII GATC 1 cut(s) 169
NheI GCTAGC 1 cut(s) 304
NlaIII CATG 5 cut(s) 85, 166, 217, 330, 477
NsiI ATGCAT 1 cut(s) 71
NspV TTCGAA 1 cut(s) 111
PaeR7I CTCGAG 2 cut(s) 208, 375
PctI GAATGC 3 cut(s) 240, 408, 637
PdmI GAANNNNTTC 2 cut(s) 362, 432
PfeI GAWTC 1 cut(s) 428
PkrI GCNGC 4 cut(s) 7, 58, 88, 601
PleI GAGTC 1 cut(s) 386
PpsI GAGTC 1 cut(s) 386
Psp1406I AACGTT 1 cut(s) 228
PspXI VCTCGAGB 1 cut(s) 208
PsuI RGATCY 1 cut(s) 169
SaqAI TTAA 2 cut(s) 456, 611
SatI GCNGC 4 cut(s) 6, 57, 87, 600
Sau3AI GATC 1 cut(s) 169
SchI GAGTC 1 cut(s) 387
ScrFI CCNGG 1 cut(s) 312
SfaNI GCATC 2 cut(s) 78, 142
Sfr274I CTCGAG 2 cut(s) 208, 375
SfuI TTCGAA 1 cut(s) 111
SlaI CTCGAG 2 cut(s) 208, 375
SmlI CTYRAG 2 cut(s) 208, 375
SmoI CTYRAG 2 cut(s) 208, 375
Sse9I AATT 3 cut(s) 113, 537, 612
SsiI CCGC 3 cut(s) 8, 57, 566
SspI AATATT 2 cut(s) 290, 515
SspMI CTAG 3 cut(s) 92, 305, 554
StyD4I CCNGG 1 cut(s) 310
StyI CCWWGG 4 cut(s) 81, 91, 162, 421
TaiI ACGT 1 cut(s) 231
TaqI TCGA 4 cut(s) 16, 111, 209, 376
TasI AATT 3 cut(s) 113, 537, 612
TauI GCSGC 1 cut(s) 59
TfiI GAWTC 1 cut(s) 428
Tru1I TTAA 2 cut(s) 456, 611
Tru9I TTAA 2 cut(s) 456, 611
TseI GCWGC 3 cut(s) 5, 86, 599
TspDTI ATGAA 4 cut(s) 266, 353, 462, 506
TspGWI ACGGA 1 cut(s) 116
XhoI CTCGAG 2 cut(s) 208, 375
XmaJI CCTAGG 1 cut(s) 91
XmnI GAANNNNTTC 2 cut(s) 362, 432
XspI CTAG 3 cut(s) 92, 305, 554
Zsp2I ATGCAT 1 cut(s) 71
Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.