Rh5AG495300

transposition, RNA-mediated

Design Primers CRISPR Design

Basic Information

Type: gene
Biological Identity
rosa_samantha
Chr5A
OG0000276
Physical Location & Seq
Reverse (-)
84233537 .. 84237070
3534 bp
Loading structure...
UTR
Exon/CDS
Intron
Rh5AG495300.1

Sequence Viewer

Length: 666 bp
ATGATGCAAAAGATACTTGTGAAGTTGCACATTCATTGCGACAAATGCAGAACCAAGGCTTTAAAGATTGCAGCAACTGCACCAGGTGTGAACAAAGTGTCGATTGAAGGTGATCATATGGAGGTGATTGGGAATGGAGTTGACTCGGTATGCTTGACTAGGGCTTTAAGGAAGAAGCTTGGCTTCGCCAATCTAATCAAAGTCGAACAAGTGGGAGAATCCACAGCCACTACTGAGGAAGAAAACCCGACTCCGATTCAATATTGTACTACTACATCAAGCTATAGTCATTTTCAACATCCTCCGATAGTTTGTCCAATAACCATGATACAGAAAAAGATAGTAATGAAGGTGCAAATGAGCTCTGAGAAATGCAGAACCAAGGCCTTGAAGATTGCCGCAGTGGCCAAAGGCGAGAGCAAAGTGTCGATAGAACCGGAGAAAGATCAGGTGGAAGTGATCGGAAGCGGGATTGACTCCATGACCTTGACCATGACGATGAGGAAGAAGGTTGGGCATGCAGACATACTGAGTATTGAAGAAGTGAAAGCCGATGGGTCAATTCCAATTACTTGCACATCAAGCTATAGTTATGCTCACTATCCGCGATATCCCACGCACTATCATGTGGTTCGTGAGGAACCAACGACTTGCTCCATTATGTAA
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
HMA

Protein Analysis

221

Amino Acids

24.39

Weight (kDa)

8.7

Isoelectric Point (pI)

39.77

Instability Index
Protein Domains (Pfam)
No Pfam domains detected for this 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
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Orthologous Genes (Group: OG0000276)

Species Orthologous Gene IDs
arabidopsis_thaliana AT4G05030 AT4G05030
fragaria_vesca FvH4_3g24080 FvH4_3g24080 FvH4_3g24100 FvH4_3g24100 FvH4_3g42050 FvH4_3g42060 FvH4_3g42070 FvH4_3g42071 FvH4_3g42080 FvH4_3g42090 FvH4_3g42100 FvH4_3g42110
malus_domestica MD03G1038100.v1.1 MD03G1038400.v1.1 MD03G1038600.v1.1 MD03G1038900.v1.1 MD03G1039000.v1.1 MD03G1039100.v1.1 MD03G1188500.v1.1 MD10G1233100.v1.1 MD10G1233300.v1.1 MD10G1341200.v1.1 MD11G1039200.v1.1 MD11G1039300.v1.1 MD11G1204400.v1.1 MD11G1204600.v1.1
prunus_persica Prupe.2G123900_v2.0.a1 Prupe.4G001900_v2.0.a1 Prupe.4G234700_v2.0.a1 Prupe.4G234800_v2.0.a1 Prupe.6G025900_v2.0.a1 Prupe.6G030200_v2.0.a1 Prupe.6G030300_v2.0.a1 Prupe.6G030400_v2.0.a1 Prupe.6G030600_v2.0.a1 Prupe.6G030900_v2.0.a1 Prupe.6G031000_v2.0.a1 Prupe.6G031100_v2.0.a1 Prupe.6G031100_v2.0.a1
pyrus_communis pycom03g02940 pycom03g02950 pycom03g02980 pycom03g02990 pycom03g03010 pycom11g03310 pycom11g03320
rosa_chinensis RchiOBHm_Chr3g0484311 RchiOBHm_Chr5g0000231 RchiOBHm_Chr5g0042661 RchiOBHm_Chr5g0042671 RchiOBHm_Chr5g0075281 RchiOBHm_Chr5g0075291 RchiOBHm_Chr5g0075321 RchiOBHm_Chr5g0075331
rosa_laevigata RLG00000034149 RLG00000036545 RLG00000036546 RLG00000036547 RLG00000036548 RLG00000036549 RLG00000036550
rosa_multiflora Rmu_sc0000295.1_g000011 Rmu_sc0000770.1_g000041 Rmu_sc0000770.1_g000049 Rmu_sc0002564.1_g000002 Rmu_sc0002564.1_g000003 Rmu_sc0002564.1_g000016
rosa_roxburghii Rroxscaffold_1G00006200 Rroxscaffold_1G00006210 Rroxscaffold_1G00006220 Rroxscaffold_1G00006250 Rroxscaffold_1G00006270 Rroxscaffold_1G00037900 Rroxscaffold_1G00037980 Rroxscaffold_6G00397790
rosa_rugosa Rorug03G0210600 Rorug05G0203800 Rorug05G0203900 Rorug05G0438100 Rorug05G0438200 Rorug05G0438700 Rorug05G0438900 Rorug05G0438900
rosa_samantha Rh3AG259700 Rh3AG259800 Rh3BG296300 Rh3DG289900 Rh5AG001600 Rh5AG288900 Rh5AG289000 Rh5AG289200 Rh5AG494800 Rh5AG495000 Rh5AG495200 Rh5AG495300 Rh5BG293000 Rh5BG293100 Rh5BG293300 Rh5BG516400 Rh5BG516500 Rh5BG516900 Rh5BG517000 Rh5CG001900 Rh5CG325700 Rh5CG325900 Rh5CG326000 Rh5CG540200 Rh5CG540300 Rh5CG540500 Rh5CG540600 Rh5DG001900 Rh5DG302900 Rh5DG303000 Rh5DG303200 Rh5DG529100 Rh5DG529300 Rh5DG529400 Rh5DG532500
rosa_wichuraiana Rw3G023420 Rw3G023430 Rw5G000210 Rw5G026800 Rw5G045910 Rw5G045920 Rw5G045930 Rw5G045940 Rw5G045950

Restriction Enzyme Sites

1 / 10
Enzyme Recognition Site Cut Count Positions (bp)
AccII CGCG 1 cut(s) 607
AciI CCGC 3 cut(s) 399, 468, 605
AcoI YGGCCR 1 cut(s) 405
AdeI CACNNNGTG 1 cut(s) 86
AfaI GTAC 1 cut(s) 268
AgsI TTSAA 5 cut(s) 107, 260, 296, 391, 539
AjnI CCWGG 1 cut(s) 82
AluBI AGCT 4 cut(s) 178, 282, 363, 585
AluI AGCT 4 cut(s) 178, 282, 363, 585
Alw21I GWGCWC 1 cut(s) 365
AlwNI CAGNNNCTG 1 cut(s) 77
AoxI GGCC 2 cut(s) 384, 405
ApeKI GCWGC 1 cut(s) 71
AsuHPI GGTGA 2 cut(s) 122, 136
BalI TGGCCA 1 cut(s) 407
BanII GRGCYC 1 cut(s) 365
Bbv12I GWGCWC 1 cut(s) 365
BbvI GCAGC 1 cut(s) 83
BccI CCATC 1 cut(s) 548
BciT130I CCWGG 1 cut(s) 84
BclI TGATCA 1 cut(s) 112
BfaI CTAG 1 cut(s) 159
BfmI CTRYAG 2 cut(s) 283, 586
BglI GCCNNNNNGGC 1 cut(s) 404
BisI GCNGC 2 cut(s) 72, 399
BlsI GCNGC 2 cut(s) 73, 400
Bme1390I CCNGG 1 cut(s) 84
BmiI GGNNCC 1 cut(s) 642
BmrFI CCNGG 1 cut(s) 84
BsaJI CCNNGG 2 cut(s) 54, 381
BsaWI WCCGGW 1 cut(s) 436
Bse3DI GCAATG 1 cut(s) 34
BseBI CCWGG 1 cut(s) 84
BseDI CCNNGG 2 cut(s) 54, 381
BseGI GGATG 1 cut(s) 298
BseMI GCAATG 1 cut(s) 34
BseMII CTCAG 3 cut(s) 225, 357, 521
BseXI GCAGC 1 cut(s) 83
BsgI GTGCAG 1 cut(s) 63
Bsh1236I CGCG 1 cut(s) 607
BshFI GGCC 2 cut(s) 386, 407
BsiHKAI GWGCWC 1 cut(s) 365
BsiSI CCGG 1 cut(s) 437
BsnI GGCC 2 cut(s) 386, 407
Bsp1286I GDGCHC 1 cut(s) 365
Bsp143I GATC 3 cut(s) 112, 445, 459
BspACI CCGC 3 cut(s) 399, 468, 605
BspANI GGCC 2 cut(s) 386, 407
BspCNI CTCAG 3 cut(s) 226, 358, 522
BspFNI CGCG 1 cut(s) 607
BspLI GGNNCC 1 cut(s) 642
BsrDI GCAATG 1 cut(s) 34
BssECI CCNNGG 2 cut(s) 54, 381
BssMI GATC 3 cut(s) 112, 445, 459
BssT1I CCWWGG 2 cut(s) 54, 381
Bst2UI CCWGG 1 cut(s) 84
BstAPI GCANNNNNTGC 1 cut(s) 77
BstC8I GCNNGC 1 cut(s) 519
BstDEI CTNAG 3 cut(s) 234, 366, 530
BstF5I GGATG 1 cut(s) 298
BstFNI CGCG 1 cut(s) 607
BstKTI GATC 3 cut(s) 115, 448, 462
BstMBI GATC 3 cut(s) 112, 445, 459
BstMWI GCNNNNNNNGC 4 cut(s) 45, 77, 404, 582
BstNI CCWGG 1 cut(s) 84
BstNSI RCATGY 1 cut(s) 521
BstSCI CCNGG 1 cut(s) 82
BstSFI CTRYAG 2 cut(s) 283, 586
BstUI CGCG 1 cut(s) 607
BstV1I GCAGC 1 cut(s) 83
BsuRI GGCC 2 cut(s) 386, 407
BtsCI GGATG 1 cut(s) 298
BtsI GCAGTG 1 cut(s) 408
BtsIMutI CAGTG 1 cut(s) 408
Cac8I GCNNGC 1 cut(s) 519
CaiI CAGNNNCTG 1 cut(s) 77
CsiI ACCWGGT 1 cut(s) 82
Csp6I GTAC 1 cut(s) 267
CviAII CATG 5 cut(s) 325, 481, 493, 518, 626
CviQI GTAC 1 cut(s) 267
DdeI CTNAG 3 cut(s) 234, 366, 530
DpnI GATC 3 cut(s) 114, 447, 461
DpnII GATC 3 cut(s) 112, 445, 459
DraI TTTAAA 1 cut(s) 63
DraIII CACNNNGTG 1 cut(s) 86
EaeI YGGCCR 1 cut(s) 405
Ecl136II GAGCTC 1 cut(s) 363
Eco130I CCWWGG 2 cut(s) 54, 381
Eco147I AGGCCT 1 cut(s) 386
Eco24I GRGCYC 1 cut(s) 365
Eco32I GATATC 1 cut(s) 611
Eco53kI GAGCTC 1 cut(s) 363
EcoICRI GAGCTC 1 cut(s) 363
EcoRII CCWGG 1 cut(s) 82
EcoRV GATATC 1 cut(s) 611
EcoT14I CCWWGG 2 cut(s) 54, 381
EcoT38I GRGCYC 1 cut(s) 365
ErhI CCWWGG 2 cut(s) 54, 381
FaeI CATG 5 cut(s) 328, 484, 496, 521, 629
FalI AAGNNNNNCTT 2 cut(s) 167, 199
FatI CATG 5 cut(s) 324, 480, 492, 517, 625
FauI CCCGC 1 cut(s) 461
FauNDI CATATG 1 cut(s) 117
FbaI TGATCA 1 cut(s) 112
Fnu4HI GCNGC 2 cut(s) 72, 399
FokI GGATG 1 cut(s) 285
FriOI GRGCYC 1 cut(s) 365
Fsp4HI GCNGC 2 cut(s) 72, 399
FspBI CTAG 1 cut(s) 159
GluI GCNGC 2 cut(s) 72, 399
HaeIII GGCC 2 cut(s) 386, 407
HapII CCGG 1 cut(s) 437
Hin1II CATG 5 cut(s) 328, 484, 496, 521, 629
HincII GTYRAC 1 cut(s) 142
HindII GTYRAC 1 cut(s) 142
HindIII AAGCTT 1 cut(s) 176
HinfI GANTC 5 cut(s) 143, 218, 250, 256, 476
HpaII CCGG 1 cut(s) 437
HphI GGTGA 2 cut(s) 122, 136
Hpy166II GTNNAC 2 cut(s) 91, 142
Hpy188I TCNGA 4 cut(s) 255, 306, 367, 464
Hpy188III TCNNGA 1 cut(s) 635
Hpy8I GTNNAC 2 cut(s) 91, 142
HpyAV CCTTC 3 cut(s) 101, 343, 502
HpyCH4V TGCA 9 cut(s) 7, 28, 48, 71, 80, 355, 375, 521, 576
HpyF10VI GCNNNNNNNGC 4 cut(s) 45, 77, 404, 582
HpyF3I CTNAG 3 cut(s) 234, 366, 530
Hsp92II CATG 5 cut(s) 328, 484, 496, 521, 629
Ksp22I TGATCA 1 cut(s) 112
Kzo9I GATC 3 cut(s) 112, 445, 459
LmnI GCTCC 1 cut(s) 659
LpnPI CCDG 4 cut(s) 69, 96, 434, 450
Lsp1109I GCAGC 1 cut(s) 83
MabI ACCWGGT 1 cut(s) 82
MaeI CTAG 1 cut(s) 159
MalI GATC 3 cut(s) 114, 447, 461
MboI GATC 3 cut(s) 112, 445, 459
MboII GAAGA 5 cut(s) 184, 251, 403, 517, 551
MhlI GDGCHC 1 cut(s) 365
MlsI TGGCCA 1 cut(s) 407
MluCI AATT 2 cut(s) 561, 567
MluNI TGGCCA 1 cut(s) 407
MlyI GAGTC 3 cut(s) 137, 244, 470
MnlI CCTC 5 cut(s) 115, 229, 312, 495, 631
Mox20I TGGCCA 1 cut(s) 407
MscI TGGCCA 1 cut(s) 407
MseI TTAA 2 cut(s) 62, 167
MslI CAYNNNNRTG 2 cut(s) 497, 624
Msp20I TGGCCA 1 cut(s) 407
MspI CCGG 1 cut(s) 437
MspR9I CCNGG 1 cut(s) 84
MvaI CCWGG 1 cut(s) 84
MvnI CGCG 1 cut(s) 607
MwoI GCNNNNNNNGC 4 cut(s) 45, 77, 404, 582
NdeI CATATG 1 cut(s) 117
NdeII GATC 3 cut(s) 112, 445, 459
NlaIII CATG 5 cut(s) 328, 484, 496, 521, 629
NlaIV GGNNCC 1 cut(s) 642
NspI RCATGY 1 cut(s) 521
PaeI GCATGC 1 cut(s) 521
PceI AGGCCT 1 cut(s) 386
PfeI GAWTC 2 cut(s) 218, 256
PkrI GCNGC 2 cut(s) 73, 400
PleI GAGTC 3 cut(s) 137, 244, 470
PpsI GAGTC 3 cut(s) 137, 244, 470
Psp124BI GAGCTC 1 cut(s) 365
Psp6I CCWGG 1 cut(s) 82
PspGI CCWGG 1 cut(s) 82
PspN4I GGNNCC 1 cut(s) 642
PstNI CAGNNNCTG 1 cut(s) 77
RsaI GTAC 1 cut(s) 268
RsaNI GTAC 1 cut(s) 267
RseI CAYNNNNRTG 2 cut(s) 497, 624
SacI GAGCTC 1 cut(s) 365
SaqAI TTAA 2 cut(s) 62, 167
SatI GCNGC 2 cut(s) 72, 399
Sau3AI GATC 3 cut(s) 112, 445, 459
SchI GAGTC 3 cut(s) 137, 244, 470
ScrFI CCNGG 1 cut(s) 84
SduI GDGCHC 1 cut(s) 365
SexAI ACCWGGT 1 cut(s) 82
SfcI CTRYAG 2 cut(s) 283, 586
SmiMI CAYNNNNRTG 2 cut(s) 497, 624
SphI GCATGC 1 cut(s) 521
Sse9I AATT 2 cut(s) 561, 567
SseBI AGGCCT 1 cut(s) 386
SsiI CCGC 3 cut(s) 399, 468, 605
SspI AATATT 1 cut(s) 263
SspMI CTAG 1 cut(s) 159
SstI GAGCTC 1 cut(s) 365
StuI AGGCCT 1 cut(s) 386
StyD4I CCNGG 1 cut(s) 82
StyI CCWWGG 2 cut(s) 54, 381
TaqI TCGA 3 cut(s) 101, 204, 428
TasI AATT 2 cut(s) 561, 567
TatI WGTACW 1 cut(s) 266
TauI GCSGC 1 cut(s) 401
TfiI GAWTC 2 cut(s) 218, 256
Tru1I TTAA 2 cut(s) 62, 167
Tru9I TTAA 2 cut(s) 62, 167
TscAI CASTG 1 cut(s) 408
TseI GCWGC 1 cut(s) 71
TspDTI ATGAA 2 cut(s) 23, 362
TspRI CASTG 1 cut(s) 408
XceI RCATGY 1 cut(s) 521
XspI CTAG 1 cut(s) 159
Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.