Rw3G028810

gag-polypeptide of LTR copia-type

Design Primers CRISPR Design

Basic Information

Type: gene
Biological Identity
rosa_wichuraiana
Chr3
OG0000154
Physical Location & Seq
Forward (+)
43518557 .. 43519402
846 bp
Loading structure...
UTR
Exon/CDS
Intron
Rw3G028810.1

Sequence Viewer

Length: 816 bp
ATGGCAACAGAGGGGAGCTTTGTTCAGCCTGCCATACCTAGGTTTGATGATCACTACGACCATTGGGCCATGCTCATGGAGAATTTTCTCCTGTTAAAGGAGTATTGGAGTTTAGTAGAAAGCGGGATCCTCACGGTTACTGACGGAGTAGAGCCAACTGATGGACAACGAAAGACCATTGAGGAACAGCGTCTGAAGGATTTAAAGGTAAAGAATTACCTTTTCCAGGCCATTGACAGAACCATTATGGAAACGATCCTCAATAAGGAGACAAAAAAGAATATTTGGGATTCGATGAAACAGAAGTATCAGGGAACAACGAGAGTGAAGCATGCTCAGTTGCAGGCACTTCAAAGGGAGTTCGAAGTTCTCCAGATGAGAGAAGGCGAGAAGGTAAATCAGTATTTTGCTCGAACCCTCTCAATTGCAAACAAGATGAAGATACATGGAGAAACGATGGGAGAAGTGGTGATTGTTGAGAAAATCTTGAGGTCAATGACCAAAAGATTTGATTATGTGGTATGCTCAGTAGAAGAATCCAACGATCTAGAGGTGTTGACGATTGATGAGTTACAAAGCAGCTTGTTAGTGCATGAGCAGAGAATGAATAGCCATGATGAAGAAGAACAAGCCCTCAAGATTACTTATGATGAGAGGTTTGGAGGCAGAGGAAGAGGCAGAGGCAGGCAGTCTTTGAACAAAGCTATAGTGGAGTGTTTTAAATGCCACAAACTAGGGCACTTTCAATATGAATGCCCTAATTGGAGAAAGGAATCAATTATGCTGAGATCGATGAAGAGGAAGAGATGCTCCTAA
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
Retrotran_gag_2

Protein Analysis

271

Amino Acids

31.92

Weight (kDa)

8.18

Isoelectric Point (pI)

49.94

Instability Index
Protein Domains (Pfam)
Domain Name Pfam ID Position E-value Description
Retrotran_gag_2 PF14223 29 - 205 3.5e-25 gag-polypeptide of LTR copia-type
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: OG0000154)

Species Orthologous Gene IDs
fragaria_vesca FvH4_1g02351 FvH4_1g18383 FvH4_1g18442 FvH4_1g19622 FvH4_2g08148 FvH4_2g16312 FvH4_3g06912 FvH4_3g10761 FvH4_3g12332 FvH4_3g12332 FvH4_3g14182 FvH4_3g21021 FvH4_3g35231 FvH4_3g45132 FvH4_4g08663 FvH4_4g30271 FvH4_4g30272 FvH4_4g30901 FvH4_4g30902 FvH4_5g12471 FvH4_5g22951 FvH4_6g07331 FvH4_6g07332 FvH4_6g41872 FvH4_6g43841 FvH4_6g43842 FvH4_6g48811 FvH4_7g03911 FvH4_7g13272 FvH4_7g21181 FvH4_7g29024 FvH4_7g33702
malus_domestica MD00G1037700.v1.1 MD01G1037300.v1.1 MD01G1096700.v1.1 MD01G1101100.v1.1 MD01G1129400.v1.1 MD02G1295200.v1.1 MD03G1131300.v1.1 MD04G1072100.v1.1 MD05G1104800.v1.1 MD07G1028600.v1.1 MD07G1274600.v1.1 MD08G1027200.v1.1 MD09G1044400.v1.1 MD09G1044700.v1.1 MD09G1129500.v1.1 MD09G1238700.v1.1 MD10G1011700.v1.1 MD10G1071400.v1.1 MD10G1108600.v1.1 MD10G1162100.v1.1 MD10G1162300.v1.1 MD11G1016700.v1.1 MD11G1074500.v1.1 MD15G1058600.v1.1 MD15G1383000.v1.1 MD16G1192200.v1.1 MD17G1077400.v1.1 MD17G1077500.v1.1
pyrus_communis pycom01g03520 pycom02g00350 pycom03g09910 pycom03g13960 pycom03g13970 pycom03g19180 pycom04g08410 pycom04g10140 pycom06g03750 pycom07g09240 pycom07g09260 pycom08g20130 pycom09g11020 pycom10g12690 pycom14g04140 pycom14g05710 pycom16g06380 pycom17g05500 pycom808g00140
rosa_chinensis RchiOBHm_Chr1g0316211 RchiOBHm_Chr1g0319901 RchiOBHm_Chr1g0321811 RchiOBHm_Chr1g0329831 RchiOBHm_Chr1g0330721 RchiOBHm_Chr1g0330731 RchiOBHm_Chr1g0368461 RchiOBHm_Chr1g0381111 RchiOBHm_Chr2g0154461 RchiOBHm_Chr2g0164521 RchiOBHm_Chr2g0175301 RchiOBHm_Chr3g0451301 RchiOBHm_Chr3g0453691 RchiOBHm_Chr3g0470191 RchiOBHm_Chr3g0486561 RchiOBHm_Chr4g0409141 RchiOBHm_Chr4g0409151 RchiOBHm_Chr4g0421231 RchiOBHm_Chr4g0440701 RchiOBHm_Chr5g0018211 RchiOBHm_Chr5g0023611 RchiOBHm_Chr5g0045971 RchiOBHm_Chr5g0056061 RchiOBHm_Chr5g0063381 RchiOBHm_Chr5g0064011 RchiOBHm_Chr5g0064021 RchiOBHm_Chr5g0064041 RchiOBHm_Chr6g0259681 RchiOBHm_Chr6g0259691 RchiOBHm_Chr6g0296531 RchiOBHm_Chr7g0186421 RchiOBHm_Chr7g0192321 RchiOBHm_Chr7g0198271 RchiOBHm_Chr7g0198951 RchiOBHm_Chr7g0237911
rosa_laevigata RLG00000026946
rosa_roxburghii Rroxscaffold_1G00014460 Rroxscaffold_1G00014610 Rroxscaffold_1G00028950 Rroxscaffold_1G00052630 Rroxscaffold_2G00104760 Rroxscaffold_2G00138900 Rroxscaffold_2G00145210 Rroxscaffold_3G00220110 Rroxscaffold_4G00297860 Rroxscaffold_4G00321570 Rroxscaffold_5G00332990 Rroxscaffold_5G00360870
rosa_samantha Rh1AG319600 Rh1CG299100 Rh4DG385900 Rh5BG032200
rosa_wichuraiana Rw0G002380 Rw0G003050 Rw0G003940 Rw1G002730 Rw1G003260 Rw1G005490 Rw1G016140 Rw1G016150 Rw1G017930 Rw1G017940 Rw1G022540 Rw1G022630 Rw1G031080 Rw1G039680 Rw2G003340 Rw2G003720 Rw2G006640 Rw2G020790 Rw2G025650 Rw2G028430 Rw2G029550 Rw2G034920 Rw2G040820 Rw2G048420 Rw2G048570 Rw3G010040 Rw3G022790 Rw3G023350 Rw3G025140 Rw3G028810 Rw4G000680 Rw4G003350 Rw4G004640 Rw4G026650 Rw4G034500 Rw5G008490 Rw5G020650 Rw5G023000 Rw5G033610 Rw5G037280 Rw5G046620 Rw5G050250 Rw6G001410 Rw6G005690 Rw6G005820 Rw6G010920 Rw6G022790 Rw6G023940 Rw6G026290 Rw6G028610 Rw6G031260 Rw6G036550 Rw6G036560 Rw7G015300 Rw7G017250 Rw7G018150 Rw7G031960 Rw7G036490

Restriction Enzyme Sites

1 / 10
Enzyme Recognition Site Cut Count Positions (bp)
AccB7I CCANNNNNTGG 1 cut(s) 161
AciI CCGC 1 cut(s) 123
AclWI GGATC 3 cut(s) 121, 134, 250
AcsI RAATTY 1 cut(s) 82
AcuI CTGAAG 1 cut(s) 215
AfiI CCNNNNNNNGG 5 cut(s) 39, 97, 161, 226, 265
AgsI TTSAA 3 cut(s) 353, 697, 746
AjnI CCWGG 1 cut(s) 225
AluBI AGCT 3 cut(s) 18, 582, 704
AluI AGCT 3 cut(s) 18, 582, 704
Alw26I GTCTC 1 cut(s) 263
AlwI GGATC 3 cut(s) 121, 134, 250
AlwNI CAGNNNCTG 1 cut(s) 193
AoxI GGCC 2 cut(s) 66, 228
ApeKI GCWGC 1 cut(s) 579
ApoI RAATTY 1 cut(s) 82
AspA2I CCTAGG 1 cut(s) 38
AspS9I GGNCC 1 cut(s) 66
AsuHPI GGTGA 1 cut(s) 481
AsuII TTCGAA 1 cut(s) 363
AvrII CCTAGG 1 cut(s) 38
BaeGI GKGCMC 1 cut(s) 741
BaeI ACNNNNGTAYC 2 cut(s) 290, 323
BamHI GGATCC 1 cut(s) 126
BbvI GCAGC 1 cut(s) 591
BccI CCATC 2 cut(s) 155, 451
BciT130I CCWGG 1 cut(s) 227
BclI TGATCA 1 cut(s) 49
BcoDI GTCTC 1 cut(s) 263
BfaI CTAG 3 cut(s) 39, 548, 734
BfmI CTRYAG 1 cut(s) 705
BisI GCNGC 1 cut(s) 580
BlnI CCTAGG 1 cut(s) 38
BlsI GCNGC 1 cut(s) 581
Bme1390I CCNGG 1 cut(s) 227
BmgT120I GGNCC 1 cut(s) 66
BmiI GGNNCC 1 cut(s) 128
BmrFI CCNGG 1 cut(s) 227
BmsI GCATC 1 cut(s) 797
BpmI CTGGAG 1 cut(s) 356
Bpu14I TTCGAA 1 cut(s) 363
BpuEI CTTGAG 2 cut(s) 508, 620
Bsa29I ATCGAT 1 cut(s) 791
BsaJI CCNNGG 1 cut(s) 38
BsaXI ACNNNNNCTCC 2 cut(s) 453, 483
Bsc4I CCNNNNNNNGG 5 cut(s) 39, 97, 161, 226, 265
BseBI CCWGG 1 cut(s) 227
BseCI ATCGAT 1 cut(s) 791
BseDI CCNNGG 1 cut(s) 38
BseLI CCNNNNNNNGG 5 cut(s) 39, 97, 161, 226, 265
BseMII CTCAG 3 cut(s) 350, 540, 776
BseSI GKGCMC 1 cut(s) 741
BseXI GCAGC 1 cut(s) 591
BshFI GGCC 2 cut(s) 68, 230
BshVI ATCGAT 1 cut(s) 791
BslI CCNNNNNNNGG 5 cut(s) 39, 97, 161, 226, 265
BsmAI GTCTC 1 cut(s) 263
BsmI GAATGC 1 cut(s) 758
BsnI GGCC 2 cut(s) 68, 230
Bsp119I TTCGAA 1 cut(s) 363
Bsp1286I GDGCHC 1 cut(s) 741
Bsp143I GATC 5 cut(s) 49, 126, 255, 544, 788
BspACI CCGC 1 cut(s) 123
BspANI GGCC 2 cut(s) 68, 230
BspCNI CTCAG 3 cut(s) 349, 539, 777
BspDI ATCGAT 1 cut(s) 791
BspLI GGNNCC 1 cut(s) 128
BspPI GGATC 3 cut(s) 121, 134, 250
BspT104I TTCGAA 1 cut(s) 363
BssECI CCNNGG 1 cut(s) 38
BssMI GATC 5 cut(s) 49, 126, 255, 544, 788
BssT1I CCWWGG 1 cut(s) 38
Bst2UI CCWGG 1 cut(s) 227
Bst4CI ACNGT 1 cut(s) 136
Bst6I CTCTTC 3 cut(s) 667, 791, 797
BstBI TTCGAA 1 cut(s) 363
BstC8I GCNNGC 4 cut(s) 30, 333, 345, 686
BstDEI CTNAG 3 cut(s) 336, 526, 785
BstENI CCTNNNNNAGG 3 cut(s) 95, 224, 263
BstKTI GATC 5 cut(s) 52, 129, 258, 547, 791
BstMAI GTCTC 1 cut(s) 263
BstMBI GATC 5 cut(s) 49, 126, 255, 544, 788
BstNI CCWGG 1 cut(s) 227
BstNSI RCATGY 1 cut(s) 335
BstSCI CCNGG 1 cut(s) 225
BstSFI CTRYAG 1 cut(s) 705
BstSLI GKGCMC 1 cut(s) 741
BstV1I GCAGC 1 cut(s) 591
BstX2I RGATCY 1 cut(s) 126
BstXI CCANNNNNNTGG 1 cut(s) 76
BstYI RGATCY 1 cut(s) 126
Bsu15I ATCGAT 1 cut(s) 791
BsuRI GGCC 2 cut(s) 68, 230
BsuTUI ATCGAT 1 cut(s) 791
Cac8I GCNNGC 4 cut(s) 30, 333, 345, 686
CaiI CAGNNNCTG 1 cut(s) 193
Cfr13I GGNCC 1 cut(s) 66
ClaI ATCGAT 1 cut(s) 791
CseI GACGC 1 cut(s) 179
CviAII CATG 6 cut(s) 70, 76, 332, 446, 593, 614
CviJI RGCY 9 cut(s) 18, 28, 68, 154, 230, 582, 612, 632, 704
CviKI_1 RGCY 9 cut(s) 18, 28, 68, 154, 230, 582, 612, 632, 704
DdeI CTNAG 3 cut(s) 336, 526, 785
DpnI GATC 5 cut(s) 51, 128, 257, 546, 790
DpnII GATC 5 cut(s) 49, 126, 255, 544, 788
DraI TTTAAA 2 cut(s) 204, 721
Eam1104I CTCTTC 3 cut(s) 667, 791, 797
EarI CTCTTC 3 cut(s) 667, 791, 797
Eco130I CCWWGG 1 cut(s) 38
Eco57I CTGAAG 1 cut(s) 215
EcoNI CCTNNNNNAGG 3 cut(s) 95, 224, 263
EcoRII CCWGG 1 cut(s) 225
EcoT14I CCWWGG 1 cut(s) 38
ErhI CCWWGG 1 cut(s) 38
FaeI CATG 6 cut(s) 73, 79, 335, 449, 596, 617
FatI CATG 6 cut(s) 69, 75, 331, 445, 592, 613
FauI CCCGC 1 cut(s) 116
FbaI TGATCA 1 cut(s) 49
Fnu4HI GCNGC 1 cut(s) 580
Fsp4HI GCNGC 1 cut(s) 580
FspBI CTAG 3 cut(s) 39, 548, 734
GluI GCNGC 1 cut(s) 580
GsuI CTGGAG 1 cut(s) 356
HaeIII GGCC 2 cut(s) 68, 230
HgaI GACGC 1 cut(s) 179
Hin1II CATG 6 cut(s) 73, 79, 335, 449, 596, 617
HincII GTYRAC 1 cut(s) 558
HindII GTYRAC 1 cut(s) 558
HinfI GANTC 3 cut(s) 290, 536, 773
HphI GGTGA 1 cut(s) 481
Hpy166II GTNNAC 1 cut(s) 558
Hpy188I TCNGA 1 cut(s) 195
Hpy188III TCNNGA 4 cut(s) 373, 487, 548, 637
Hpy8I GTNNAC 1 cut(s) 558
HpyAV CCTTC 3 cut(s) 190, 377, 385
HpyCH4III ACNGT 1 cut(s) 136
HpyCH4V TGCA 3 cut(s) 343, 428, 592
HpyF3I CTNAG 3 cut(s) 336, 526, 785
Hsp92II CATG 6 cut(s) 73, 79, 335, 449, 596, 617
Ksp22I TGATCA 1 cut(s) 49
Kzo9I GATC 5 cut(s) 49, 126, 255, 544, 788
LmnI GCTCC 2 cut(s) 15, 815
LpnPI CCDG 8 cut(s) 42, 104, 212, 239, 296, 329, 386, 670
Lsp1109I GCAGC 1 cut(s) 591
LweI GCATC 1 cut(s) 797
MaeI CTAG 3 cut(s) 39, 548, 734
MaeIII GTNAC 2 cut(s) 136, 570
MalI GATC 5 cut(s) 51, 128, 257, 546, 790
MboI GATC 5 cut(s) 49, 126, 255, 544, 788
MboII GAAGA 7 cut(s) 451, 545, 632, 635, 684, 808, 814
MfeI CAATTG 1 cut(s) 423
MflI RGATCY 1 cut(s) 126
MhlI GDGCHC 1 cut(s) 741
MluCI AATT 5 cut(s) 82, 214, 423, 760, 777
MmeI TCCRAC 1 cut(s) 564
MseI TTAA 3 cut(s) 95, 203, 720
MslI CAYNNNNRTG 1 cut(s) 74
MspR9I CCNGG 1 cut(s) 227
MunI CAATTG 1 cut(s) 423
Mva1269I GAATGC 1 cut(s) 758
MvaI CCWGG 1 cut(s) 227
NdeII GATC 5 cut(s) 49, 126, 255, 544, 788
NlaIII CATG 6 cut(s) 73, 79, 335, 449, 596, 617
NlaIV GGNNCC 1 cut(s) 128
NspI RCATGY 1 cut(s) 335
NspV TTCGAA 1 cut(s) 363
PaeI GCATGC 1 cut(s) 335
PctI GAATGC 1 cut(s) 758
PfeI GAWTC 3 cut(s) 290, 536, 773
PflMI CCANNNNNTGG 1 cut(s) 161
PkrI GCNGC 1 cut(s) 581
Psp6I CCWGG 1 cut(s) 225
PspGI CCWGG 1 cut(s) 225
PspN4I GGNNCC 1 cut(s) 128
PspPI GGNCC 1 cut(s) 66
PstNI CAGNNNCTG 1 cut(s) 193
PsuI RGATCY 1 cut(s) 126
RseI CAYNNNNRTG 1 cut(s) 74
SaqAI TTAA 3 cut(s) 95, 203, 720
SatI GCNGC 1 cut(s) 580
Sau3AI GATC 5 cut(s) 49, 126, 255, 544, 788
Sau96I GGNCC 1 cut(s) 66
ScrFI CCNGG 1 cut(s) 227
SduI GDGCHC 1 cut(s) 741
SfaNI GCATC 1 cut(s) 797
SfcI CTRYAG 1 cut(s) 705
SfuI TTCGAA 1 cut(s) 363
SmiMI CAYNNNNRTG 1 cut(s) 74
SmlI CTYRAG 2 cut(s) 487, 635
SmoI CTYRAG 2 cut(s) 487, 635
SphI GCATGC 1 cut(s) 335
Sse9I AATT 5 cut(s) 82, 214, 423, 760, 777
SsiI CCGC 1 cut(s) 123
SspI AATATT 1 cut(s) 283
SspMI CTAG 3 cut(s) 39, 548, 734
StyD4I CCNGG 1 cut(s) 225
StyI CCWWGG 1 cut(s) 38
TaaI ACNGT 1 cut(s) 136
TaqI TCGA 4 cut(s) 293, 363, 412, 791
TasI AATT 5 cut(s) 82, 214, 423, 760, 777
TfiI GAWTC 3 cut(s) 290, 536, 773
Tru1I TTAA 3 cut(s) 95, 203, 720
Tru9I TTAA 3 cut(s) 95, 203, 720
TseI GCWGC 1 cut(s) 579
TspDTI ATGAA 6 cut(s) 311, 452, 620, 633, 765, 809
TspGWI ACGGA 1 cut(s) 159
Van91I CCANNNNNTGG 1 cut(s) 161
XagI CCTNNNNNAGG 3 cut(s) 95, 224, 263
XapI RAATTY 1 cut(s) 82
XbaI TCTAGA 1 cut(s) 547
XceI RCATGY 1 cut(s) 335
XmaJI CCTAGG 1 cut(s) 38
XspI CTAG 3 cut(s) 39, 548, 734
Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.