Rh7CG448900

transposition, RNA-mediated

Design Primers CRISPR Design

Basic Information

Type: gene
Biological Identity
rosa_samantha
Chr7C
OG0000370
Physical Location & Seq
Reverse (-)
58975991 .. 58977278
1288 bp
Loading structure...
UTR
Exon/CDS
Intron
Rh7CG448900.1

Sequence Viewer

Length: 498 bp
ATGCATCATCCCCTTAGTTTTAAAGGAAGTCCTGATCCTTTGGAGGTTGAGGCTTGGATTGAGAAACTAGAGAAGATTTATGATGTTCTACCTGGTGAAGCTGATCAGTGGTGGAAGGTGTCTAGAGCACAAGTTGGTGGCCATCCACCAACTTGGGACAAGTTTCTAAAATTGTTTTGGGAGAAATTTTTTCCAGATTCTGTTCGAGATCGCATGGAGTTGGAATTTGCTGAGTTACAACAAGAAAGTATGTCTATCGCTAATTATGAGGCTCTTTTTACAAAACTTTATCATTTATCTCAGCCTCTTACTGAAGAAAGAAAGGCAAAGAAGTTTATGAGAAGTTTGAAGGAGTCTATTCGAGATCGCCTTTTAGTTTTGAAACTTGTGAGTTATTTTAACATGGTGGACCGAGCAATGATTATTAAAGATAACTTGAACCGTACCAACTTCAAGAAAAGATCAAGACTAGATGATTTTCATTCTGTTGGAAGTTAA
Functional Annotation
Gene Ontology
Molecular Function
Biological Process
Cellular Component
No ontology terms assigned.
KEGG Pathways
Metabolic & Signaling
ko00909 map00909
Pfam Domains
Protein Families
Retrotrans_gag Terpene_synth_C

Protein Analysis

165

Amino Acids

19.64

Weight (kDa)

8.73

Isoelectric Point (pI)

32.66

Instability Index
Protein Domains (Pfam)
Domain Name Pfam ID Position E-value Description
Ty3_capsid PF19259 29 - 129 1.7e-06 Ty3 transposon capsid-like protein
Retrotrans_gag PF03732 30 - 118 5.8e-14 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)
AclWI GGATC 1 cut(s) 29
AcoI YGGCCR 1 cut(s) 139
AcsI RAATTY 2 cut(s) 185, 224
AcuI CTGAAG 1 cut(s) 333
AfaI GTAC 1 cut(s) 445
AgsI TTSAA 4 cut(s) 349, 382, 439, 454
AjnI CCWGG 1 cut(s) 91
AluBI AGCT 1 cut(s) 101
AluI AGCT 1 cut(s) 101
Alw21I GWGCWC 1 cut(s) 130
AlwI GGATC 1 cut(s) 29
AlwNI CAGNNNCTG 1 cut(s) 200
AoxI GGCC 1 cut(s) 139
ApoI RAATTY 2 cut(s) 185, 224
AspS9I GGNCC 1 cut(s) 409
AsuHPI GGTGA 1 cut(s) 107
AvaII GGWCC 1 cut(s) 409
BalI TGGCCA 1 cut(s) 141
Bbv12I GWGCWC 1 cut(s) 130
BccI CCATC 1 cut(s) 150
BciT130I CCWGG 1 cut(s) 93
BclI TGATCA 1 cut(s) 103
BfaI CTAG 3 cut(s) 68, 123, 470
Bme1390I CCNGG 1 cut(s) 93
Bme18I GGWCC 1 cut(s) 409
BmgT120I GGNCC 1 cut(s) 409
BmrFI CCNGG 1 cut(s) 93
BmsI GCATC 1 cut(s) 13
Bse3DI GCAATG 1 cut(s) 423
BseBI CCWGG 1 cut(s) 93
BseGI GGATG 2 cut(s) 7, 142
BseMI GCAATG 1 cut(s) 423
BseMII CTCAG 2 cut(s) 222, 314
BshFI GGCC 1 cut(s) 141
BsiHKAI GWGCWC 1 cut(s) 130
BslFI GGGAC 1 cut(s) 170
BsmFI GGGAC 1 cut(s) 170
BsnI GGCC 1 cut(s) 141
Bsp1286I GDGCHC 1 cut(s) 130
Bsp143I GATC 5 cut(s) 34, 103, 208, 364, 461
BspANI GGCC 1 cut(s) 141
BspCNI CTCAG 2 cut(s) 223, 313
BspPI GGATC 1 cut(s) 29
BsrDI GCAATG 1 cut(s) 423
BssMI GATC 5 cut(s) 34, 103, 208, 364, 461
Bst2UI CCWGG 1 cut(s) 93
Bst4CI ACNGT 1 cut(s) 443
BstDEI CTNAG 3 cut(s) 14, 231, 300
BstF5I GGATG 2 cut(s) 7, 142
BstKTI GATC 5 cut(s) 37, 106, 211, 367, 464
BstMBI GATC 5 cut(s) 34, 103, 208, 364, 461
BstNI CCWGG 1 cut(s) 93
BstSCI CCNGG 1 cut(s) 91
BstXI CCANNNNNNTGG 1 cut(s) 153
BsuRI GGCC 1 cut(s) 141
BtsCI GGATG 2 cut(s) 7, 142
BtsIMutI CAGTG 1 cut(s) 113
CaiI CAGNNNCTG 1 cut(s) 200
Cfr13I GGNCC 1 cut(s) 409
CsiI ACCWGGT 1 cut(s) 91
Csp6I GTAC 1 cut(s) 444
CviAII CATG 2 cut(s) 214, 403
CviJI RGCY 5 cut(s) 53, 101, 141, 272, 304
CviKI_1 RGCY 5 cut(s) 53, 101, 141, 272, 304
CviQI GTAC 1 cut(s) 444
DdeI CTNAG 3 cut(s) 14, 231, 300
DpnI GATC 5 cut(s) 36, 105, 210, 366, 463
DpnII GATC 5 cut(s) 34, 103, 208, 364, 461
DraI TTTAAA 1 cut(s) 22
EaeI YGGCCR 1 cut(s) 139
Eco47I GGWCC 1 cut(s) 409
Eco57I CTGAAG 1 cut(s) 333
EcoRII CCWGG 1 cut(s) 91
EcoT22I ATGCAT 1 cut(s) 6
FaeI CATG 2 cut(s) 217, 406
FaiI YATR 6 cut(s) 81, 215, 251, 267, 338, 404
FaqI GGGAC 1 cut(s) 170
FatI CATG 2 cut(s) 213, 402
FbaI TGATCA 1 cut(s) 103
FokI GGATG 1 cut(s) 129
FspBI CTAG 3 cut(s) 68, 123, 470
HaeIII GGCC 1 cut(s) 141
Hin1II CATG 2 cut(s) 217, 406
HinfI GANTC 2 cut(s) 197, 353
HphI GGTGA 1 cut(s) 107
Hpy166II GTNNAC 1 cut(s) 409
Hpy188III TCNNGA 7 cut(s) 32, 123, 194, 206, 362, 454, 465
Hpy8I GTNNAC 1 cut(s) 409
HpyAV CCTTC 2 cut(s) 109, 343
HpyCH4III ACNGT 1 cut(s) 443
HpyCH4V TGCA 1 cut(s) 4
HpyF3I CTNAG 3 cut(s) 14, 231, 300
Hsp92II CATG 2 cut(s) 217, 406
Ksp22I TGATCA 1 cut(s) 103
Kzo9I GATC 5 cut(s) 34, 103, 208, 364, 461
LpnPI CCDG 4 cut(s) 45, 78, 105, 207
LweI GCATC 1 cut(s) 13
MabI ACCWGGT 1 cut(s) 91
MaeI CTAG 3 cut(s) 68, 123, 470
MaeIII GTNAC 1 cut(s) 234
MalI GATC 5 cut(s) 36, 105, 210, 366, 463
MboI GATC 5 cut(s) 34, 103, 208, 364, 461
MboII GAAGA 2 cut(s) 85, 326
MhlI GDGCHC 1 cut(s) 130
MlsI TGGCCA 1 cut(s) 141
MluCI AATT 4 cut(s) 170, 185, 224, 262
MluNI TGGCCA 1 cut(s) 141
MlyI GAGTC 1 cut(s) 362
MmeI TCCRAC 2 cut(s) 201, 469
MnlI CCTC 4 cut(s) 37, 43, 262, 315
Mox20I TGGCCA 1 cut(s) 141
Mph1103I ATGCAT 1 cut(s) 6
MscI TGGCCA 1 cut(s) 141
MseI TTAA 4 cut(s) 21, 399, 426, 496
Msp20I TGGCCA 1 cut(s) 141
MspR9I CCNGG 1 cut(s) 93
MvaI CCWGG 1 cut(s) 93
NdeII GATC 5 cut(s) 34, 103, 208, 364, 461
NlaIII CATG 2 cut(s) 217, 406
NsiI ATGCAT 1 cut(s) 6
PfeI GAWTC 1 cut(s) 197
PleI GAGTC 1 cut(s) 361
PpsI GAGTC 1 cut(s) 361
Psp6I CCWGG 1 cut(s) 91
PspGI CCWGG 1 cut(s) 91
PspPI GGNCC 1 cut(s) 409
PstNI CAGNNNCTG 1 cut(s) 200
RsaI GTAC 1 cut(s) 445
RsaNI GTAC 1 cut(s) 444
SaqAI TTAA 4 cut(s) 21, 399, 426, 496
Sau3AI GATC 5 cut(s) 34, 103, 208, 364, 461
Sau96I GGNCC 1 cut(s) 409
SchI GAGTC 1 cut(s) 362
ScrFI CCNGG 1 cut(s) 93
SduI GDGCHC 1 cut(s) 130
SetI ASST 4 cut(s) 48, 94, 103, 120
SexAI ACCWGGT 1 cut(s) 91
SfaNI GCATC 1 cut(s) 13
SinI GGWCC 1 cut(s) 409
Sse9I AATT 4 cut(s) 170, 185, 224, 262
SspMI CTAG 3 cut(s) 68, 123, 470
StyD4I CCNGG 1 cut(s) 91
TaaI ACNGT 1 cut(s) 443
TaqI TCGA 2 cut(s) 205, 361
TaqII GACCGA 1 cut(s) 426
TasI AATT 4 cut(s) 170, 185, 224, 262
TfiI GAWTC 1 cut(s) 197
Tru1I TTAA 4 cut(s) 21, 399, 426, 496
Tru9I TTAA 4 cut(s) 21, 399, 426, 496
TscAI CASTG 1 cut(s) 113
TspDTI ATGAA 1 cut(s) 470
TspRI CASTG 1 cut(s) 113
VpaK11BI GGWCC 1 cut(s) 409
XapI RAATTY 2 cut(s) 185, 224
XbaI TCTAGA 1 cut(s) 122
XspI CTAG 3 cut(s) 68, 123, 470
Zsp2I ATGCAT 1 cut(s) 6
Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.