Rh1CG094600

transposition, RNA-mediated

Design Primers CRISPR Design

Basic Information

Type: gene
Biological Identity
rosa_samantha
Chr1C
OG0000370
Physical Location & Seq
Forward (+)
20232046 .. 20235648
3603 bp
Loading structure...
UTR
Exon/CDS
Intron
Rh1CG094600.1

Sequence Viewer

Length: 519 bp
ATGTTGGTGTCATCTTTGCTTTCGCTACTTCATTTGTACTCAAATAAAGATACTAGAACAGGTGGAGCTACTTCATCCACTACTGGGCTTCCACATGATGAGGAGGTGGCTAAGTTGTTTCAAGCCTTACTGCGAATGGCTTCCCTTGAGCTTGAGGGCACAAACGGGTTTAATAGGAGGCTGAAATTTTTGAAGATGTTCATTAGTCTGTCACCTCCGGAGTATGCAGGAAATCTTGATTATTCTTTGGAAGGGCTGGAGTGGTTACGAAGGGTAAAGCAATGTTTTGATGTTCTTGATGTACCTGGAGACCTAAGAGTTGGGTTTGCAGTCTATACTCTTACTGGAGCGGCTAGCTACTGGTGGGATTTTGTTAAAAGGACCTGTGATGTGGAATCGATGAATTGGGATGACTTTGAGCAGATATTTTTGAATAGGTACTTTCCTGAGACTATAAGGCTAGCTAAAGTAGAAGAATTCCTCAATTTGACACGGGGAAATGACAGTTTCTCAGTATGA
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

172

Amino Acids

19.7

Weight (kDa)

5.08

Isoelectric Point (pI)

35.68

Instability Index
Protein Domains (Pfam)
Domain Name Pfam ID Position E-value Description
Retrotrans_gag PF03732 109 - 170 5.1e-09 Retrotransposon gag protein
Hydrophobicity Profile (Kyte-Doolittle)
AI Structure Prediction Report
Calculating structure properties...

Genomic Context

Gene Family Tree

Species Filter
Loading...
Style Settings
Image
Tree File
Tip: Beautify your tree with professional tools

Download the Full Tree (.nwk) file, then upload it to any of the following tools to customize colors, fonts, annotations, clades, and branch support.

Publication-ready
iTOL Interactive Tree Of Life · Most popular EvolView Flexible annotations MEGA Desktop phylogenetics suite FigTree Desktop tree editor

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) 350
AccIII TCCGGA 1 cut(s) 217
AciI CCGC 1 cut(s) 350
AcsI RAATTY 2 cut(s) 185, 476
AfaI GTAC 3 cut(s) 38, 303, 440
AfiI CCNNNNNNNGG 1 cut(s) 84
AgsI TTSAA 3 cut(s) 122, 193, 433
AjnI CCWGG 1 cut(s) 304
AluBI AGCT 4 cut(s) 68, 151, 357, 464
AluI AGCT 4 cut(s) 68, 151, 357, 464
Alw26I GTCTC 2 cut(s) 303, 443
Aor13HI TCCGGA 1 cut(s) 217
ApoI RAATTY 2 cut(s) 185, 476
Asp700I GAANNNNTTC 2 cut(s) 139, 197
AspS9I GGNCC 1 cut(s) 381
AsuHPI GGTGA 1 cut(s) 204
AsuNHI GCTAGC 2 cut(s) 353, 460
AvaII GGWCC 1 cut(s) 381
BaeGI GKGCMC 1 cut(s) 161
BciT130I CCWGG 1 cut(s) 306
BcoDI GTCTC 2 cut(s) 303, 443
BfaI CTAG 3 cut(s) 54, 354, 461
BisI GCNGC 1 cut(s) 351
BlsI GCNGC 1 cut(s) 352
Bme1390I CCNGG 1 cut(s) 306
Bme18I GGWCC 1 cut(s) 381
BmgT120I GGNCC 1 cut(s) 381
BmrFI CCNGG 1 cut(s) 306
BmrI ACTGGG 1 cut(s) 93
BmtI GCTAGC 2 cut(s) 357, 464
BmuI ACTGGG 1 cut(s) 93
BpmI CTGGAG 3 cut(s) 278, 327, 366
BpuEI CTTGAG 2 cut(s) 167, 173
Bsa29I ATCGAT 1 cut(s) 398
BsaI GGTCTC 1 cut(s) 303
BsaWI WCCGGW 1 cut(s) 217
Bsc4I CCNNNNNNNGG 1 cut(s) 84
Bse1I ACTGG 3 cut(s) 88, 349, 365
Bse3DI GCAATG 1 cut(s) 287
BseAI TCCGGA 1 cut(s) 217
BseBI CCWGG 1 cut(s) 306
BseCI ATCGAT 1 cut(s) 398
BseGI GGATG 2 cut(s) 74, 415
BseLI CCNNNNNNNGG 1 cut(s) 84
BseMI GCAATG 1 cut(s) 287
BseMII CTCAG 1 cut(s) 438
BseNI ACTGG 3 cut(s) 88, 349, 365
BseRI GAGGAG 1 cut(s) 116
BseSI GKGCMC 1 cut(s) 161
BshVI ATCGAT 1 cut(s) 398
BsiSI CCGG 1 cut(s) 218
BslI CCNNNNNNNGG 1 cut(s) 84
BsmAI GTCTC 2 cut(s) 303, 443
Bso31I GGTCTC 1 cut(s) 303
Bsp1286I GDGCHC 1 cut(s) 161
Bsp13I TCCGGA 1 cut(s) 217
BspACI CCGC 1 cut(s) 350
BspCNI CTCAG 1 cut(s) 439
BspDI ATCGAT 1 cut(s) 398
BspEI TCCGGA 1 cut(s) 217
BspOI GCTAGC 2 cut(s) 357, 464
BspTNI GGTCTC 1 cut(s) 303
BsrBI CCGCTC 1 cut(s) 350
BsrDI GCAATG 1 cut(s) 287
BsrI ACTGG 3 cut(s) 88, 349, 365
Bst2UI CCWGG 1 cut(s) 306
Bst4CI ACNGT 1 cut(s) 506
BstC8I GCNNGC 2 cut(s) 355, 462
BstDEI CTNAG 4 cut(s) 111, 314, 447, 511
BstF5I GGATG 2 cut(s) 74, 415
BstMAI GTCTC 2 cut(s) 303, 443
BstNI CCWGG 1 cut(s) 306
BstSCI CCNGG 1 cut(s) 304
BstSLI GKGCMC 1 cut(s) 161
Bsu15I ATCGAT 1 cut(s) 398
BsuTUI ATCGAT 1 cut(s) 398
BtsCI GGATG 2 cut(s) 74, 415
Cac8I GCNNGC 2 cut(s) 355, 462
Cfr13I GGNCC 1 cut(s) 381
ClaI ATCGAT 1 cut(s) 398
Csp6I GTAC 3 cut(s) 37, 302, 439
CviAII CATG 1 cut(s) 95
CviQI GTAC 3 cut(s) 37, 302, 439
DdeI CTNAG 4 cut(s) 111, 314, 447, 511
Eco31I GGTCTC 1 cut(s) 303
Eco47I GGWCC 1 cut(s) 381
EcoO109I RGGNCCY 1 cut(s) 381
EcoRI GAATTC 1 cut(s) 476
EcoRII CCWGG 1 cut(s) 304
FaeI CATG 1 cut(s) 98
FaiI YATR 5 cut(s) 96, 225, 336, 455, 517
FatI CATG 1 cut(s) 94
Fnu4HI GCNGC 1 cut(s) 351
FokI GGATG 2 cut(s) 61, 422
Fsp4HI GCNGC 1 cut(s) 351
FspBI CTAG 3 cut(s) 54, 354, 461
GluI GCNGC 1 cut(s) 351
GsuI CTGGAG 3 cut(s) 278, 327, 366
HapII CCGG 1 cut(s) 218
Hin1II CATG 1 cut(s) 98
HinfI GANTC 1 cut(s) 395
HpaII CCGG 1 cut(s) 218
HphI GGTGA 1 cut(s) 204
Hpy188III TCNNGA 4 cut(s) 218, 236, 296, 446
HpyAV CCTTC 2 cut(s) 245, 264
HpyCH4III ACNGT 1 cut(s) 506
HpyCH4V TGCA 2 cut(s) 227, 329
HpyF3I CTNAG 4 cut(s) 111, 314, 447, 511
Hsp92II CATG 1 cut(s) 98
Kpn2I TCCGGA 1 cut(s) 217
LmnI GCTCC 2 cut(s) 65, 347
MaeI CTAG 3 cut(s) 54, 354, 461
MaeIII GTNAC 2 cut(s) 210, 264
MbiI CCGCTC 1 cut(s) 350
MboII GAAGA 2 cut(s) 205, 485
MhlI GDGCHC 1 cut(s) 161
MluCI AATT 4 cut(s) 185, 403, 476, 484
MnlI CCTC 6 cut(s) 94, 97, 148, 171, 225, 491
MroI TCCGGA 1 cut(s) 217
MroXI GAANNNNTTC 2 cut(s) 139, 197
MseI TTAA 2 cut(s) 171, 375
MspI CCGG 1 cut(s) 218
MspR9I CCNGG 1 cut(s) 306
MvaI CCWGG 1 cut(s) 306
NheI GCTAGC 2 cut(s) 353, 460
NlaIII CATG 1 cut(s) 98
NmuCI GTSAC 1 cut(s) 210
PdmI GAANNNNTTC 2 cut(s) 139, 197
PfeI GAWTC 1 cut(s) 395
PkrI GCNGC 1 cut(s) 352
PpuMI RGGWCCY 1 cut(s) 381
Psp5II RGGWCCY 1 cut(s) 381
Psp6I CCWGG 1 cut(s) 304
PspGI CCWGG 1 cut(s) 304
PspPI GGNCC 1 cut(s) 381
PspPPI RGGWCCY 1 cut(s) 381
RsaI GTAC 3 cut(s) 38, 303, 440
RsaNI GTAC 3 cut(s) 37, 302, 439
SaqAI TTAA 2 cut(s) 171, 375
SatI GCNGC 1 cut(s) 351
Sau96I GGNCC 1 cut(s) 381
ScrFI CCNGG 1 cut(s) 306
SduI GDGCHC 1 cut(s) 161
SinI GGWCC 1 cut(s) 381
SmlI CTYRAG 2 cut(s) 146, 152
SmoI CTYRAG 2 cut(s) 146, 152
Sse9I AATT 4 cut(s) 185, 403, 476, 484
SsiI CCGC 1 cut(s) 350
SspMI CTAG 3 cut(s) 54, 354, 461
StyD4I CCNGG 1 cut(s) 304
TaaI ACNGT 1 cut(s) 506
TaqI TCGA 1 cut(s) 398
TasI AATT 4 cut(s) 185, 403, 476, 484
TatI WGTACW 1 cut(s) 36
TauI GCSGC 1 cut(s) 353
TfiI GAWTC 1 cut(s) 395
Tru1I TTAA 2 cut(s) 171, 375
Tru9I TTAA 2 cut(s) 171, 375
TseFI GTSAC 1 cut(s) 210
Tsp45I GTSAC 1 cut(s) 210
TspDTI ATGAA 4 cut(s) 20, 63, 190, 416
VpaK11BI GGWCC 1 cut(s) 381
XapI RAATTY 2 cut(s) 185, 476
XmnI GAANNNNTTC 2 cut(s) 139, 197
XspI CTAG 3 cut(s) 54, 354, 461
Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.