Rh1AG098600

transposition, RNA-mediated

Design Primers CRISPR Design

Basic Information

Type: gene
Biological Identity
rosa_samantha
Chr1A
OG0000370
Physical Location & Seq
Forward (+)
17173088 .. 17173594
507 bp
Loading structure...
UTR
Exon/CDS
Intron
Rh1AG098600.1

Sequence Viewer

Length: 507 bp
ATGGAAGCTAATGTTTCATTTGTTAAAATACAGCAAGATACTAGAACAGTTGGAGCTACTTCATCCACTACTGGGCTTCCACATGATGAGGAGGTGGCTAAGTTATTTCAAGCCTTACTGCGAATGGCTTCCCTCGAGCTTGAGGGCACAAACGGGTTCAATAGGAGGCTGAAATTTTTGAAGATGTTCATTAGTCTGTCACCTCCGGAGTACGCAGGAAATCTTGATAATTCTTTGGAAGGGCTGGAGTGGTTACGAAGGGTAAAGCAATGTTTTGATGTTCTCGATGTACCTGGAGACCTTAGAGTTGAGTTTGCAGTCTACACTTTTACTGGAGCGGCTAGCTACTGGTGGGATTTTGTTAAAAGGACCTCTGATGTGGAATCGATGAATTGGGATGACTTTGAGCAGATATTTTTGAATAGGTACTTTCCTGAGACTATAAGGGAAGCTAAAGAAGAAGAATTTCTCAATTTGACACGGGGAAATGACAGTTTCTCAGTATGA
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
Retrotrans_gag zf-CCHC

Protein Analysis

168

Amino Acids

19.4

Weight (kDa)

4.68

Isoelectric Point (pI)

37.16

Instability Index
Protein Domains (Pfam)
Domain Name Pfam ID Position E-value Description
Retrotrans_gag PF03732 105 - 166 1.5e-10 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
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Orthologous Genes (Group: OG0000370)

Species Orthologous Gene IDs
fragaria_vesca FvH4_1g29481 FvH4_2g11454 FvH4_3g19661 FvH4_3g28463 FvH4_3g31691 FvH4_3g34551 FvH4_3g35241 FvH4_4g06575 FvH4_4g09082 FvH4_4g15804 FvH4_4g15805 FvH4_4g16178 FvH4_4g16282 FvH4_5g25163 FvH4_6g27413 FvH4_7g02962 FvH4_7g04361
malus_domestica MD01G1095000.v1.1 MD02G1270200.v1.1 MD02G1270300.v1.1 MD02G1270400.v1.1 MD06G1059100.v1.1 MD08G1226500.v1.1
prunus_persica Prupe.1G169500_v2.0.a1 Prupe.5G195800_v2.0.a1
pyrus_communis pycom01g00010 pycom01g00770 pycom02g23140 pycom03g11760 pycom04g06090 pycom05g06900 pycom05g08070 pycom05g14500 pycom06g03050 pycom07g06250 pycom07g07540 pycom07g10580 pycom08g04990 pycom1146g00060 pycom11g01080 pycom11g15270 pycom11g15460 pycom11g24900 pycom12419g00150 pycom12424g00120 pycom13g08740 pycom13g24950 pycom13g25960 pycom13g26030 pycom13g27820 pycom16g23270 pycom16g25020 pycom16g25960 pycom17g07780 pycom17g08210 pycom17g13100
rosa_chinensis RchiOBHm_Chr1g0329421 RchiOBHm_Chr4g0397711 RchiOBHm_Chr4g0403481 RchiOBHm_Chr5g0019091 RchiOBHm_Chr5g0049101
rosa_laevigata RLG00000029892
rosa_multiflora Rmu_sc0001866.1_g000007
rosa_roxburghii Rroxscaffold_2G00094160 Rroxscaffold_3G00229110 Rroxscaffold_4G00321100 Rroxscaffold_7G00196040 Rroxscaffold_7G00196280
rosa_rugosa Rorug05G0160500 Rorug06G0096500
rosa_samantha Rh1AG098600 Rh1AG098800 Rh1BG078200 Rh1BG078700 Rh1BG178500 Rh1CG094600 Rh1CG094900 Rh1DG101700 Rh1DG109600 Rh2AG175800 Rh2AG175900 Rh2AG511400 Rh2BG114700 Rh2CG042200 Rh2CG116600 Rh2CG317500 Rh2DG327700 Rh2DG337800 Rh4CG142700 Rh4DG113100 Rh5BG335800 Rh5CG360600 Rh5DG352000 Rh6BG071400 Rh6BG417100 Rh6CG463300 Rh6CG463400 Rh7BG186600 Rh7CG196500 Rh7CG196600 Rh7CG448900 Rh7DG228300
rosa_wichuraiana Rw4G006560 Rw4G017340 Rw5G030450

Restriction Enzyme Sites

1 / 10
Enzyme Recognition Site Cut Count Positions (bp)
AccBSI CCGCTC 1 cut(s) 338
AccI GTMKAC 1 cut(s) 321
AccIII TCCGGA 1 cut(s) 205
AciI CCGC 1 cut(s) 338
AcsI RAATTY 2 cut(s) 173, 464
AfaI GTAC 3 cut(s) 212, 291, 428
AfiI CCNNNNNNNGG 1 cut(s) 72
AgsI TTSAA 4 cut(s) 110, 160, 181, 421
AjnI CCWGG 1 cut(s) 292
AluBI AGCT 5 cut(s) 8, 56, 139, 345, 452
AluI AGCT 5 cut(s) 8, 56, 139, 345, 452
Alw26I GTCTC 2 cut(s) 291, 431
Ama87I CYCGRG 1 cut(s) 134
Aor13HI TCCGGA 1 cut(s) 205
ApoI RAATTY 2 cut(s) 173, 464
Asp700I GAANNNNTTC 3 cut(s) 127, 185, 465
AspS9I GGNCC 1 cut(s) 369
AsuHPI GGTGA 1 cut(s) 192
AsuNHI GCTAGC 1 cut(s) 341
AvaI CYCGRG 1 cut(s) 134
AvaII GGWCC 1 cut(s) 369
BaeGI GKGCMC 1 cut(s) 149
BciT130I CCWGG 1 cut(s) 294
BcoDI GTCTC 2 cut(s) 291, 431
BfaI CTAG 2 cut(s) 42, 342
BisI GCNGC 1 cut(s) 339
BlsI GCNGC 1 cut(s) 340
Bme1390I CCNGG 1 cut(s) 294
Bme18I GGWCC 1 cut(s) 369
BmeT110I CYCGRG 1 cut(s) 134
BmgT120I GGNCC 1 cut(s) 369
BmrFI CCNGG 1 cut(s) 294
BmrI ACTGGG 1 cut(s) 81
BmtI GCTAGC 1 cut(s) 345
BmuI ACTGGG 1 cut(s) 81
BpmI CTGGAG 3 cut(s) 266, 315, 354
BpuEI CTTGAG 1 cut(s) 161
Bsa29I ATCGAT 1 cut(s) 386
BsaI GGTCTC 1 cut(s) 291
BsaWI WCCGGW 1 cut(s) 205
Bsc4I CCNNNNNNNGG 1 cut(s) 72
Bse1I ACTGG 3 cut(s) 76, 337, 353
Bse3DI GCAATG 1 cut(s) 275
BseAI TCCGGA 1 cut(s) 205
BseBI CCWGG 1 cut(s) 294
BseCI ATCGAT 1 cut(s) 386
BseGI GGATG 2 cut(s) 62, 403
BseLI CCNNNNNNNGG 1 cut(s) 72
BseMI GCAATG 1 cut(s) 275
BseMII CTCAG 1 cut(s) 426
BseNI ACTGG 3 cut(s) 76, 337, 353
BseRI GAGGAG 1 cut(s) 104
BseSI GKGCMC 1 cut(s) 149
BshVI ATCGAT 1 cut(s) 386
BsiHKCI CYCGRG 1 cut(s) 134
BsiSI CCGG 1 cut(s) 206
BslI CCNNNNNNNGG 1 cut(s) 72
BsmAI GTCTC 2 cut(s) 291, 431
Bso31I GGTCTC 1 cut(s) 291
BsoBI CYCGRG 1 cut(s) 134
Bsp1286I GDGCHC 1 cut(s) 149
Bsp13I TCCGGA 1 cut(s) 205
BspACI CCGC 1 cut(s) 338
BspCNI CTCAG 1 cut(s) 427
BspDI ATCGAT 1 cut(s) 386
BspEI TCCGGA 1 cut(s) 205
BspOI GCTAGC 1 cut(s) 345
BspTNI GGTCTC 1 cut(s) 291
BsrBI CCGCTC 1 cut(s) 338
BsrDI GCAATG 1 cut(s) 275
BsrI ACTGG 3 cut(s) 76, 337, 353
Bst2UI CCWGG 1 cut(s) 294
Bst4CI ACNGT 2 cut(s) 49, 494
BstC8I GCNNGC 1 cut(s) 343
BstDEI CTNAG 4 cut(s) 99, 302, 435, 499
BstF5I GGATG 2 cut(s) 62, 403
BstMAI GTCTC 2 cut(s) 291, 431
BstNI CCWGG 1 cut(s) 294
BstSCI CCNGG 1 cut(s) 292
BstSLI GKGCMC 1 cut(s) 149
Bsu15I ATCGAT 1 cut(s) 386
BsuTUI ATCGAT 1 cut(s) 386
BtsCI GGATG 2 cut(s) 62, 403
Cac8I GCNNGC 1 cut(s) 343
Cfr13I GGNCC 1 cut(s) 369
ClaI ATCGAT 1 cut(s) 386
Csp6I GTAC 3 cut(s) 211, 290, 427
CviAII CATG 1 cut(s) 83
CviQI GTAC 3 cut(s) 211, 290, 427
DdeI CTNAG 4 cut(s) 99, 302, 435, 499
Eco31I GGTCTC 1 cut(s) 291
Eco47I GGWCC 1 cut(s) 369
Eco88I CYCGRG 1 cut(s) 134
EcoO109I RGGNCCY 1 cut(s) 369
EcoRII CCWGG 1 cut(s) 292
FaeI CATG 1 cut(s) 86
FaiI YATR 3 cut(s) 84, 443, 505
FatI CATG 1 cut(s) 82
FblI GTMKAC 1 cut(s) 321
Fnu4HI GCNGC 1 cut(s) 339
FokI GGATG 2 cut(s) 49, 410
Fsp4HI GCNGC 1 cut(s) 339
FspBI CTAG 2 cut(s) 42, 342
GluI GCNGC 1 cut(s) 339
GsuI CTGGAG 3 cut(s) 266, 315, 354
HapII CCGG 1 cut(s) 206
Hin1II CATG 1 cut(s) 86
HinfI GANTC 1 cut(s) 383
HpaII CCGG 1 cut(s) 206
HphI GGTGA 1 cut(s) 192
Hpy166II GTNNAC 1 cut(s) 322
Hpy188I TCNGA 1 cut(s) 376
Hpy188III TCNNGA 4 cut(s) 206, 224, 284, 434
Hpy8I GTNNAC 1 cut(s) 322
HpyAV CCTTC 2 cut(s) 233, 252
HpyCH4III ACNGT 2 cut(s) 49, 494
HpyCH4V TGCA 1 cut(s) 317
HpyF3I CTNAG 4 cut(s) 99, 302, 435, 499
Hsp92II CATG 1 cut(s) 86
Kpn2I TCCGGA 1 cut(s) 205
LmnI GCTCC 2 cut(s) 53, 335
LpnPI CCDG 9 cut(s) 57, 201, 219, 230, 279, 306, 318, 334, 447
MaeI CTAG 2 cut(s) 42, 342
MaeIII GTNAC 2 cut(s) 198, 252
MbiI CCGCTC 1 cut(s) 338
MboII GAAGA 3 cut(s) 193, 470, 473
MhlI GDGCHC 1 cut(s) 149
MluCI AATT 5 cut(s) 173, 229, 391, 464, 472
MmeI TCCRAC 1 cut(s) 31
MnlI CCTC 7 cut(s) 82, 85, 136, 143, 159, 213, 382
MroI TCCGGA 1 cut(s) 205
MroXI GAANNNNTTC 3 cut(s) 127, 185, 465
MseI TTAA 2 cut(s) 24, 363
MspI CCGG 1 cut(s) 206
MspR9I CCNGG 1 cut(s) 294
MvaI CCWGG 1 cut(s) 294
NheI GCTAGC 1 cut(s) 341
NlaIII CATG 1 cut(s) 86
NmuCI GTSAC 1 cut(s) 198
PaeR7I CTCGAG 1 cut(s) 134
PdmI GAANNNNTTC 3 cut(s) 127, 185, 465
PfeI GAWTC 1 cut(s) 383
PkrI GCNGC 1 cut(s) 340
PpuMI RGGWCCY 1 cut(s) 369
Psp5II RGGWCCY 1 cut(s) 369
Psp6I CCWGG 1 cut(s) 292
PspGI CCWGG 1 cut(s) 292
PspPI GGNCC 1 cut(s) 369
PspPPI RGGWCCY 1 cut(s) 369
PspXI VCTCGAGB 1 cut(s) 134
RsaI GTAC 3 cut(s) 212, 291, 428
RsaNI GTAC 3 cut(s) 211, 290, 427
SaqAI TTAA 2 cut(s) 24, 363
SatI GCNGC 1 cut(s) 339
Sau96I GGNCC 1 cut(s) 369
ScrFI CCNGG 1 cut(s) 294
SduI GDGCHC 1 cut(s) 149
Sfr274I CTCGAG 1 cut(s) 134
SinI GGWCC 1 cut(s) 369
SlaI CTCGAG 1 cut(s) 134
SmlI CTYRAG 2 cut(s) 134, 140
SmoI CTYRAG 2 cut(s) 134, 140
Sse9I AATT 5 cut(s) 173, 229, 391, 464, 472
SsiI CCGC 1 cut(s) 338
SspMI CTAG 2 cut(s) 42, 342
StyD4I CCNGG 1 cut(s) 292
TaaI ACNGT 2 cut(s) 49, 494
TaqI TCGA 3 cut(s) 135, 285, 386
TasI AATT 5 cut(s) 173, 229, 391, 464, 472
TauI GCSGC 1 cut(s) 341
TfiI GAWTC 1 cut(s) 383
Tru1I TTAA 2 cut(s) 24, 363
Tru9I TTAA 2 cut(s) 24, 363
TseFI GTSAC 1 cut(s) 198
Tsp45I GTSAC 1 cut(s) 198
TspDTI ATGAA 4 cut(s) 6, 51, 178, 404
VpaK11BI GGWCC 1 cut(s) 369
XapI RAATTY 2 cut(s) 173, 464
XhoI CTCGAG 1 cut(s) 134
XmiI GTMKAC 1 cut(s) 321
XmnI GAANNNNTTC 3 cut(s) 127, 185, 465
XspI CTAG 2 cut(s) 42, 342
Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.