Rh1DG109600

Retrotransposon gag protein

Design Primers CRISPR Design

Basic Information

Type: gene
Biological Identity
rosa_samantha
Chr1D
OG0000370
Physical Location & Seq
Reverse (-)
20122195 .. 20132082
9888 bp
Loading structure...
UTR
Exon/CDS
Intron
Rh1DG109600.1

Sequence Viewer

Length: 729 bp
ATGGAAGAACAACATGAAGATAGCAACTCTGTAGTTATAGCTGCCATTCAAGATATGGCAAATGCCACTAGGGGAGGAAATAATAACCACCCAGAAGATACTGGAAGTCGAGTTATGAGGATTCAAGGAGAATTTCGGAAATCTCGACCACCAGTATTTAAAGGCATAATGGATCCAATGATGGCCGAGGAATCGCTACGTCAGATTACAAGGAGTATGAATAACCGAAGAGTTCCTGAAGATTTGAAAGTCATTATCGCTTGTACTTATCTGGAAGGACAAGCATATCATTGGTGGGAATCGATCTTAAGCATGCCAAACACTGAACTCACCACCTGGTCTGCATTTGAGAACATTTTCTTGGAAAAATATTTTCCTGACACTGTGAGAGGAATGAAAGTTCGAGAATTTATAAATCTTCTTCAGCGTGACCTATCTATGGCTGAATACCAGGCTATGTTTGAAGAACTAATGAGATTTGCACCAACCATGATTTCAACTGAACTTACCAAAGCAAAACGATTCCAGGATGGTCTTAGGCCTACTATTAAGGAAAAGGTGTCAATTCTCAAGCTAGAAAGGTATGCAGATGTGGTGGATCGAGCACTCATAGCTGAACAGAATCTCAATGAGACTAAGAGAATTTGGGAGAGTCGACAACCAAATGGAGGACAAAGAAACAACAAGCGCCAAAATTTTGGTGAACAGAAGGCGTGGGGTTTTGTTTGA
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
RVP_2 Retrotrans_gag

Protein Analysis

242

Amino Acids

28.23

Weight (kDa)

6.87

Isoelectric Point (pI)

49.91

Instability Index
Protein Domains (Pfam)
Domain Name Pfam ID Position E-value Description
Ty3_capsid PF19259 49 - 200 3e-09 Ty3 transposon capsid-like protein
Retrotrans_gag PF03732 86 - 181 5.5e-15 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)
AanI TTATAA 1 cut(s) 413
AccI GTMKAC 1 cut(s) 655
AclWI GGATC 3 cut(s) 167, 180, 606
AcoI YGGCCR 1 cut(s) 183
AcsI RAATTY 4 cut(s) 131, 407, 642, 694
AcuI CTGAAG 2 cut(s) 258, 407
AfaI GTAC 1 cut(s) 265
AfiI CCNNNNNNNGG 2 cut(s) 439, 668
AflII CTTAAG 1 cut(s) 307
AgsI TTSAA 5 cut(s) 50, 125, 247, 464, 498
AjnI CCWGG 3 cut(s) 335, 450, 525
AjuI GAANNNNNNNTTGG 4 cut(s) 344, 376, 478, 510
AloI GAACNNNNNNTCC 2 cut(s) 384, 416
AluBI AGCT 3 cut(s) 41, 574, 614
AluI AGCT 3 cut(s) 41, 574, 614
Alw21I GWGCWC 1 cut(s) 607
Alw26I GTCTC 1 cut(s) 626
AlwI GGATC 3 cut(s) 167, 180, 606
AoxI GGCC 2 cut(s) 183, 539
ApeKI GCWGC 1 cut(s) 41
ApoI RAATTY 4 cut(s) 131, 407, 642, 694
Asp700I GAANNNNTTC 1 cut(s) 356
AspLEI GCGC 1 cut(s) 690
AsuHPI GGTGA 2 cut(s) 322, 713
BamHI GGATCC 1 cut(s) 172
Bbv12I GWGCWC 1 cut(s) 607
BbvI GCAGC 1 cut(s) 28
BccI CCATC 2 cut(s) 175, 524
BciT130I CCWGG 3 cut(s) 337, 452, 527
BcoDI GTCTC 1 cut(s) 626
BfaI CTAG 2 cut(s) 69, 575
BfmI CTRYAG 1 cut(s) 30
BfoI RGCGCY 1 cut(s) 691
BfrI CTTAAG 1 cut(s) 307
BisI GCNGC 1 cut(s) 42
BlsI GCNGC 1 cut(s) 43
Bme1390I CCNGG 3 cut(s) 337, 452, 527
BmiI GGNNCC 1 cut(s) 174
BmrFI CCNGG 3 cut(s) 337, 452, 527
BpuEI CTTGAG 1 cut(s) 554
Bsa29I ATCGAT 1 cut(s) 302
BsaJI CCNNGG 1 cut(s) 186
Bsc4I CCNNNNNNNGG 2 cut(s) 439, 668
Bse1I ACTGG 2 cut(s) 106, 152
BseBI CCWGG 3 cut(s) 337, 452, 527
BseCI ATCGAT 1 cut(s) 302
BseDI CCNNGG 1 cut(s) 186
BseGI GGATG 1 cut(s) 535
BseLI CCNNNNNNNGG 2 cut(s) 439, 668
BseNI ACTGG 2 cut(s) 106, 152
BseXI GCAGC 1 cut(s) 28
BshFI GGCC 2 cut(s) 185, 541
BshVI ATCGAT 1 cut(s) 302
BsiHKAI GWGCWC 1 cut(s) 607
BslI CCNNNNNNNGG 2 cut(s) 439, 668
BsmAI GTCTC 1 cut(s) 626
BsnI GGCC 2 cut(s) 185, 541
Bsp1286I GDGCHC 1 cut(s) 607
Bsp143I GATC 3 cut(s) 172, 303, 598
BspANI GGCC 2 cut(s) 185, 541
BspDI ATCGAT 1 cut(s) 302
BspLI GGNNCC 1 cut(s) 174
BspPI GGATC 3 cut(s) 167, 180, 606
BspTI CTTAAG 1 cut(s) 307
BsrI ACTGG 2 cut(s) 106, 152
BssECI CCNNGG 1 cut(s) 186
BssMI GATC 3 cut(s) 172, 303, 598
Bst2UI CCWGG 3 cut(s) 337, 452, 527
Bst4CI ACNGT 1 cut(s) 385
Bst6I CTCTTC 1 cut(s) 223
BstAFI CTTAAG 1 cut(s) 307
BstC8I GCNNGC 1 cut(s) 314
BstDEI CTNAG 2 cut(s) 536, 636
BstF5I GGATG 1 cut(s) 535
BstH2I RGCGCY 1 cut(s) 691
BstHHI GCGC 1 cut(s) 690
BstKTI GATC 3 cut(s) 175, 306, 601
BstMAI GTCTC 1 cut(s) 626
BstMBI GATC 3 cut(s) 172, 303, 598
BstMWI GCNNNNNNNGC 1 cut(s) 611
BstNI CCWGG 3 cut(s) 337, 452, 527
BstNSI RCATGY 1 cut(s) 316
BstSCI CCNGG 3 cut(s) 335, 450, 525
BstSFI CTRYAG 1 cut(s) 30
BstV1I GCAGC 1 cut(s) 28
BstX2I RGATCY 1 cut(s) 172
BstXI CCANNNNNNTGG 1 cut(s) 698
BstYI RGATCY 1 cut(s) 172
Bsu15I ATCGAT 1 cut(s) 302
BsuRI GGCC 2 cut(s) 185, 541
BsuTUI ATCGAT 1 cut(s) 302
BtsCI GGATG 1 cut(s) 535
BtsIMutI CAGTG 2 cut(s) 321, 381
Cac8I GCNNGC 1 cut(s) 314
CfoI GCGC 1 cut(s) 690
ClaI ATCGAT 1 cut(s) 302
CsiI ACCWGGT 1 cut(s) 335
Csp6I GTAC 1 cut(s) 264
CviAII CATG 3 cut(s) 14, 313, 490
CviJI RGCY 7 cut(s) 41, 185, 443, 455, 541, 574, 614
CviKI_1 RGCY 7 cut(s) 41, 185, 443, 455, 541, 574, 614
CviQI GTAC 1 cut(s) 264
DdeI CTNAG 2 cut(s) 536, 636
DpnI GATC 3 cut(s) 174, 305, 600
DpnII GATC 3 cut(s) 172, 303, 598
DraI TTTAAA 1 cut(s) 160
EaeI YGGCCR 1 cut(s) 183
Eam1104I CTCTTC 1 cut(s) 223
EarI CTCTTC 1 cut(s) 223
Eco147I AGGCCT 1 cut(s) 541
Eco57I CTGAAG 2 cut(s) 258, 407
EcoRII CCWGG 3 cut(s) 335, 450, 525
FaeI CATG 3 cut(s) 17, 316, 493
FatI CATG 3 cut(s) 13, 312, 489
FblI GTMKAC 1 cut(s) 655
Fnu4HI GCNGC 1 cut(s) 42
FokI GGATG 1 cut(s) 542
Fsp4HI GCNGC 1 cut(s) 42
FspBI CTAG 2 cut(s) 69, 575
GlaI GCGC 1 cut(s) 689
GluI GCNGC 1 cut(s) 42
HaeII RGCGCY 1 cut(s) 691
HaeIII GGCC 2 cut(s) 185, 541
HhaI GCGC 1 cut(s) 690
Hin1II CATG 3 cut(s) 17, 316, 493
Hin6I GCGC 1 cut(s) 688
HinP1I GCGC 1 cut(s) 688
HincII GTYRAC 1 cut(s) 656
HindII GTYRAC 1 cut(s) 656
HinfI GANTC 6 cut(s) 121, 191, 299, 522, 622, 652
HphI GGTGA 2 cut(s) 322, 713
Hpy166II GTNNAC 2 cut(s) 656, 704
Hpy188I TCNGA 2 cut(s) 138, 204
Hpy188III TCNNGA 6 cut(s) 50, 144, 236, 272, 377, 404
Hpy8I GTNNAC 2 cut(s) 656, 704
HpyAV CCTTC 2 cut(s) 269, 703
HpyCH4III ACNGT 1 cut(s) 385
HpyCH4IV ACGT 1 cut(s) 199
HpyCH4V TGCA 3 cut(s) 344, 482, 587
HpyF10VI GCNNNNNNNGC 1 cut(s) 611
HpyF3I CTNAG 2 cut(s) 536, 636
HpySE526I ACGT 1 cut(s) 199
Hsp92II CATG 3 cut(s) 17, 316, 493
HspAI GCGC 1 cut(s) 688
Kzo9I GATC 3 cut(s) 172, 303, 598
Lsp1109I GCAGC 1 cut(s) 28
MabI ACCWGGT 1 cut(s) 335
MaeI CTAG 2 cut(s) 69, 575
MaeII ACGT 1 cut(s) 199
MaeIII GTNAC 1 cut(s) 428
MalI GATC 3 cut(s) 174, 305, 600
MboI GATC 3 cut(s) 172, 303, 598
MboII GAAGA 8 cut(s) 17, 29, 107, 240, 251, 410, 413, 476
MflI RGATCY 1 cut(s) 172
MhlI GDGCHC 1 cut(s) 607
MluCI AATT 5 cut(s) 131, 407, 564, 642, 694
MlyI GAGTC 1 cut(s) 661
MnlI CCTC 5 cut(s) 68, 111, 181, 383, 662
MroXI GAANNNNTTC 1 cut(s) 356
MseI TTAA 3 cut(s) 159, 308, 549
MspCI CTTAAG 1 cut(s) 307
MspR9I CCNGG 3 cut(s) 337, 452, 527
MvaI CCWGG 3 cut(s) 337, 452, 527
MwoI GCNNNNNNNGC 1 cut(s) 611
NdeII GATC 3 cut(s) 172, 303, 598
NlaIII CATG 3 cut(s) 17, 316, 493
NlaIV GGNNCC 1 cut(s) 174
NmeAIII GCCGAG 1 cut(s) 211
NmuCI GTSAC 1 cut(s) 428
NspI RCATGY 1 cut(s) 316
PaeI GCATGC 1 cut(s) 316
PceI AGGCCT 1 cut(s) 541
PcsI WCGNNNNNNNCGW 1 cut(s) 142
PdmI GAANNNNTTC 1 cut(s) 356
PfeI GAWTC 5 cut(s) 121, 191, 299, 522, 622
PfoI TCCNGGA 1 cut(s) 525
PkrI GCNGC 1 cut(s) 43
PleI GAGTC 1 cut(s) 660
PpsI GAGTC 1 cut(s) 660
PsiI TTATAA 1 cut(s) 413
Psp6I CCWGG 3 cut(s) 335, 450, 525
PspGI CCWGG 3 cut(s) 335, 450, 525
PspN4I GGNNCC 1 cut(s) 174
PsuI RGATCY 1 cut(s) 172
RsaI GTAC 1 cut(s) 265
RsaNI GTAC 1 cut(s) 264
SalI GTCGAC 1 cut(s) 654
SaqAI TTAA 3 cut(s) 159, 308, 549
SatI GCNGC 1 cut(s) 42
Sau3AI GATC 3 cut(s) 172, 303, 598
SchI GAGTC 1 cut(s) 661
ScrFI CCNGG 3 cut(s) 337, 452, 527
SduI GDGCHC 1 cut(s) 607
SetI ASST 8 cut(s) 43, 202, 338, 435, 561, 576, 584, 616
SexAI ACCWGGT 1 cut(s) 335
SfcI CTRYAG 1 cut(s) 30
SmlI CTYRAG 2 cut(s) 307, 569
SmoI CTYRAG 2 cut(s) 307, 569
SphI GCATGC 1 cut(s) 316
Sse9I AATT 5 cut(s) 131, 407, 564, 642, 694
SseBI AGGCCT 1 cut(s) 541
SspI AATATT 1 cut(s) 371
SspMI CTAG 2 cut(s) 69, 575
StuI AGGCCT 1 cut(s) 541
StyD4I CCNGG 3 cut(s) 335, 450, 525
TaaI ACNGT 1 cut(s) 385
TaiI ACGT 1 cut(s) 202
TaqI TCGA 6 cut(s) 109, 145, 302, 403, 601, 655
TasI AATT 5 cut(s) 131, 407, 564, 642, 694
TatI WGTACW 1 cut(s) 263
TfiI GAWTC 5 cut(s) 121, 191, 299, 522, 622
Tru1I TTAA 3 cut(s) 159, 308, 549
Tru9I TTAA 3 cut(s) 159, 308, 549
TscAI CASTG 2 cut(s) 328, 388
TseFI GTSAC 1 cut(s) 428
TseI GCWGC 1 cut(s) 41
Tsp45I GTSAC 1 cut(s) 428
TspDTI ATGAA 3 cut(s) 30, 233, 410
TspRI CASTG 2 cut(s) 328, 388
Vha464I CTTAAG 1 cut(s) 307
XapI RAATTY 4 cut(s) 131, 407, 642, 694
XceI RCATGY 1 cut(s) 316
XcmI CCANNNNNNNNNTGG 1 cut(s) 52
XmiI GTMKAC 1 cut(s) 655
XmnI GAANNNNTTC 1 cut(s) 356
XspI CTAG 2 cut(s) 69, 575
Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.