Rw2G048420

gag-polypeptide of LTR copia-type

Design Primers CRISPR Design

Basic Information

Type: gene
Biological Identity
rosa_wichuraiana
Chr2
OG0000154
Physical Location & Seq
Reverse (-)
75994348 .. 75995153
806 bp
Loading structure...
UTR
Exon/CDS
Intron
Rw2G048420.1

Sequence Viewer

Length: 774 bp
ATGGCGACAGAGAACAATTATGTTCAGCCTGCCATACCTAGATTCGATGGTCATTATGACCATTGGTCTATGCTCATGGAAAACTTCTTGCGATCAAAGGAGTATTGGGGCTTGGTAGAAAATGGGATTCCGGTAGTAGCAGATGGAATTGAACCCACTGAGGCACAGCGCAAGGCCATTGAAGATGCAAGATTGAAAGACCTAAAGGTGAAAAATTACCTTTTCCAAGCCATTGACAGAACAATTATGGAGACAATTCTCATCAAAGAGACAGCCAAAAACATTTGGGACTCAATGAGGCAGAAGTACCAAGGTTCTACAAAGGTGAAGAGAGCTCAGCTGCAGGCACTTCGAAGAGAGTTTGAGGTGCTCCAAATGAAAGATGGAGAGACGGTAGATGAATACTTTGCTCGGACATTAACCATTGTCAACAAGATGAAAGCTCATGGTGAAAGAATGGAGCAGCTTGTGATTGTGGAGAAAATTCTAAGGTCGATGCCTGTCAAATTTAATTACGTGGTGTGCTCCATAGAAGAATCCAACAATCTCACCACAATGTCTATTGATGAACTACAAAGCAGTCTGCTTGTTCATGAGCAAAGAATGCGTATCCATACCGGAGAGGAGCAAGCTCTGAAGGTGTCCTATGAAGACGGAAGGAGAGGAAGGGGCAGGCAACAGTTCAACAAGGCACTGGTGGAATGCTATAAATGCCACAAATTAGGACATTTCCAATACGAATGCCTGATTGGGAGAAAGGTGCACATTATGTAG
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

257

Amino Acids

30.15

Weight (kDa)

8.54

Isoelectric Point (pI)

56.07

Instability Index
Protein Domains (Pfam)
Domain Name Pfam ID Position E-value Description
Retrotran_gag_2 PF14223 26 - 203 1.7e-29 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)
AcsI RAATTY 2 cut(s) 483, 506
AcuI CTGAAG 1 cut(s) 656
AfaI GTAC 1 cut(s) 308
AgsI TTSAA 4 cut(s) 152, 182, 196, 685
AhdI GACNNNNNGTC 1 cut(s) 64
AjuI GAANNNNNNNTTGG 2 cut(s) 732, 764
AluBI AGCT 5 cut(s) 335, 340, 443, 466, 632
AluI AGCT 5 cut(s) 335, 340, 443, 466, 632
Alw21I GWGCWC 4 cut(s) 337, 372, 527, 765
Alw26I GTCTC 3 cut(s) 245, 263, 383
Alw44I GTGCAC 1 cut(s) 761
AoxI GGCC 1 cut(s) 174
ApaLI GTGCAC 1 cut(s) 761
ApeKI GCWGC 2 cut(s) 340, 463
ApoI RAATTY 2 cut(s) 483, 506
AspLEI GCGC 1 cut(s) 171
AsuHPI GGTGA 4 cut(s) 220, 337, 461, 541
AsuII TTCGAA 1 cut(s) 352
BaeGI GKGCMC 1 cut(s) 765
BanII GRGCYC 1 cut(s) 337
BbsI GAAGAC 1 cut(s) 657
Bbv12I GWGCWC 4 cut(s) 337, 372, 527, 765
BbvI GCAGC 2 cut(s) 327, 475
BccI CCATC 3 cut(s) 41, 137, 377
BcgI CGANNNNNNTGC 2 cut(s) 332, 366
BciVI GTATCC 1 cut(s) 620
BcoDI GTCTC 3 cut(s) 245, 263, 383
BfaI CTAG 1 cut(s) 39
BfmI CTRYAG 1 cut(s) 341
BfuI GTATCC 1 cut(s) 620
BisI GCNGC 2 cut(s) 341, 464
BlpI GCTNAGC 1 cut(s) 336
BlsI GCNGC 2 cut(s) 342, 465
BmeRI GACNNNNNGTC 1 cut(s) 64
BmsI GCATC 2 cut(s) 175, 486
BpiI GAAGAC 1 cut(s) 657
Bpu1102I GCTNAGC 1 cut(s) 336
Bpu14I TTCGAA 1 cut(s) 352
BsaAI YACGTR 1 cut(s) 517
BsaJI CCNNGG 1 cut(s) 310
BsaWI WCCGGW 2 cut(s) 130, 617
BsaXI ACNNNNNCTCC 2 cut(s) 378, 408
Bse1I ACTGG 1 cut(s) 699
BseDI CCNNGG 1 cut(s) 310
BseMII CTCAG 2 cut(s) 150, 350
BseNI ACTGG 1 cut(s) 699
BseRI GAGGAG 1 cut(s) 638
BseSI GKGCMC 1 cut(s) 765
BseXI GCAGC 2 cut(s) 327, 475
BshFI GGCC 1 cut(s) 176
BsiHKAI GWGCWC 4 cut(s) 337, 372, 527, 765
BsiSI CCGG 2 cut(s) 131, 618
BslFI GGGAC 1 cut(s) 302
BsmAI GTCTC 3 cut(s) 245, 263, 383
BsmBI CGTCTC 1 cut(s) 383
BsmFI GGGAC 1 cut(s) 302
BsmI GAATGC 3 cut(s) 609, 707, 746
BsnI GGCC 1 cut(s) 176
Bsp119I TTCGAA 1 cut(s) 352
Bsp1286I GDGCHC 4 cut(s) 337, 372, 527, 765
Bsp143I GATC 1 cut(s) 92
Bsp1720I GCTNAGC 1 cut(s) 336
BspANI GGCC 1 cut(s) 176
BspCNI CTCAG 2 cut(s) 151, 349
BspHI TCATGA 1 cut(s) 592
BspMAI CTGCAG 1 cut(s) 345
BspT104I TTCGAA 1 cut(s) 352
BsrI ACTGG 1 cut(s) 699
BssECI CCNNGG 1 cut(s) 310
BssMI GATC 1 cut(s) 92
BssT1I CCWWGG 1 cut(s) 310
Bst4CI ACNGT 2 cut(s) 394, 681
Bst6I CTCTTC 2 cut(s) 323, 349
BstAPI GCANNNNNTGC 1 cut(s) 604
BstBAI YACGTR 1 cut(s) 517
BstBI TTCGAA 1 cut(s) 352
BstC8I GCNNGC 4 cut(s) 30, 345, 630, 674
BstDEI CTNAG 3 cut(s) 159, 336, 488
BstHHI GCGC 1 cut(s) 171
BstKTI GATC 1 cut(s) 95
BstMAI GTCTC 3 cut(s) 245, 263, 383
BstMBI GATC 1 cut(s) 92
BstMWI GCNNNNNNNGC 2 cut(s) 604, 711
BstSFI CTRYAG 1 cut(s) 341
BstSLI GKGCMC 1 cut(s) 765
BstV1I GCAGC 2 cut(s) 327, 475
BstV2I GAAGAC 1 cut(s) 657
BsuI GTATCC 1 cut(s) 620
BsuRI GGCC 1 cut(s) 176
BtsIMutI CAGTG 2 cut(s) 156, 692
Cac8I GCNNGC 4 cut(s) 30, 345, 630, 674
CciI TCATGA 1 cut(s) 592
CfoI GCGC 1 cut(s) 171
Csp6I GTAC 1 cut(s) 307
CviAII CATG 3 cut(s) 76, 446, 593
CviQI GTAC 1 cut(s) 307
DdeI CTNAG 3 cut(s) 159, 336, 488
DpnI GATC 1 cut(s) 94
DpnII GATC 1 cut(s) 92
DriI GACNNNNNGTC 1 cut(s) 64
Eam1104I CTCTTC 2 cut(s) 323, 349
Eam1105I GACNNNNNGTC 1 cut(s) 64
EarI CTCTTC 2 cut(s) 323, 349
Ecl136II GAGCTC 1 cut(s) 335
Eco130I CCWWGG 1 cut(s) 310
Eco24I GRGCYC 1 cut(s) 337
Eco53kI GAGCTC 1 cut(s) 335
Eco57I CTGAAG 1 cut(s) 656
EcoICRI GAGCTC 1 cut(s) 335
EcoT14I CCWWGG 1 cut(s) 310
EcoT38I GRGCYC 1 cut(s) 337
ErhI CCWWGG 1 cut(s) 310
Esp3I CGTCTC 1 cut(s) 383
FaeI CATG 3 cut(s) 79, 449, 596
FaqI GGGAC 1 cut(s) 302
FatI CATG 3 cut(s) 75, 445, 592
Fnu4HI GCNGC 2 cut(s) 341, 464
FriOI GRGCYC 1 cut(s) 337
Fsp4HI GCNGC 2 cut(s) 341, 464
FspBI CTAG 1 cut(s) 39
GlaI GCGC 1 cut(s) 170
GluI GCNGC 2 cut(s) 341, 464
HaeIII GGCC 1 cut(s) 176
HapII CCGG 2 cut(s) 131, 618
HhaI GCGC 1 cut(s) 171
Hin1II CATG 3 cut(s) 79, 449, 596
Hin6I GCGC 1 cut(s) 169
HinP1I GCGC 1 cut(s) 169
HincII GTYRAC 1 cut(s) 430
HindII GTYRAC 1 cut(s) 430
HinfI GANTC 4 cut(s) 42, 127, 290, 536
HpaII CCGG 2 cut(s) 131, 618
HphI GGTGA 4 cut(s) 220, 337, 461, 541
Hpy166II GTNNAC 2 cut(s) 430, 763
Hpy188I TCNGA 2 cut(s) 414, 636
Hpy188III TCNNGA 1 cut(s) 593
Hpy8I GTNNAC 2 cut(s) 430, 763
HpyAV CCTTC 3 cut(s) 631, 651, 660
HpyCH4III ACNGT 2 cut(s) 394, 681
HpyCH4IV ACGT 1 cut(s) 516
HpyCH4V TGCA 3 cut(s) 188, 343, 763
HpyF10VI GCNNNNNNNGC 2 cut(s) 604, 711
HpyF3I CTNAG 3 cut(s) 159, 336, 488
HpySE526I ACGT 1 cut(s) 516
Hsp92II CATG 3 cut(s) 79, 449, 596
HspAI GCGC 1 cut(s) 169
Kzo9I GATC 1 cut(s) 92
LmnI GCTCC 4 cut(s) 375, 460, 530, 625
LpnPI CCDG 8 cut(s) 42, 144, 329, 513, 631, 658, 680, 758
Lsp1109I GCAGC 2 cut(s) 327, 475
LweI GCATC 2 cut(s) 175, 486
MaeI CTAG 1 cut(s) 39
MaeII ACGT 1 cut(s) 516
MalI GATC 1 cut(s) 94
MboI GATC 1 cut(s) 92
MboII GAAGA 5 cut(s) 194, 340, 366, 545, 662
MhlI GDGCHC 4 cut(s) 337, 372, 527, 765
MluCI AATT 9 cut(s) 16, 147, 214, 243, 255, 483, 506, 511, 719
MlyI GAGTC 1 cut(s) 284
MmeI TCCRAC 1 cut(s) 564
MnlI CCTC 5 cut(s) 154, 291, 358, 616, 656
MseI TTAA 2 cut(s) 419, 510
MslI CAYNNNNRTG 1 cut(s) 554
MspA1I CMGCKG 1 cut(s) 340
MspI CCGG 2 cut(s) 131, 618
Mva1269I GAATGC 3 cut(s) 609, 707, 746
MwoI GCNNNNNNNGC 2 cut(s) 604, 711
NdeII GATC 1 cut(s) 92
NlaIII CATG 3 cut(s) 79, 449, 596
NspV TTCGAA 1 cut(s) 352
PagI TCATGA 1 cut(s) 592
PctI GAATGC 3 cut(s) 609, 707, 746
PfeI GAWTC 3 cut(s) 42, 127, 536
PkrI GCNGC 2 cut(s) 342, 465
PleI GAGTC 1 cut(s) 284
PpsI GAGTC 1 cut(s) 284
Ppu21I YACGTR 1 cut(s) 517
Psp124BI GAGCTC 1 cut(s) 337
PstI CTGCAG 1 cut(s) 345
PvuII CAGCTG 1 cut(s) 340
RsaI GTAC 1 cut(s) 308
RsaNI GTAC 1 cut(s) 307
RseI CAYNNNNRTG 1 cut(s) 554
SacI GAGCTC 1 cut(s) 337
SaqAI TTAA 2 cut(s) 419, 510
SatI GCNGC 2 cut(s) 341, 464
Sau3AI GATC 1 cut(s) 92
SchI GAGTC 1 cut(s) 284
SduI GDGCHC 4 cut(s) 337, 372, 527, 765
SfaNI GCATC 2 cut(s) 175, 486
SfcI CTRYAG 1 cut(s) 341
SfuI TTCGAA 1 cut(s) 352
SmiMI CAYNNNNRTG 1 cut(s) 554
Sse9I AATT 9 cut(s) 16, 147, 214, 243, 255, 483, 506, 511, 719
SspMI CTAG 1 cut(s) 39
SstI GAGCTC 1 cut(s) 337
StyI CCWWGG 1 cut(s) 310
TaaI ACNGT 2 cut(s) 394, 681
TaiI ACGT 1 cut(s) 519
TaqI TCGA 3 cut(s) 45, 352, 494
TasI AATT 9 cut(s) 16, 147, 214, 243, 255, 483, 506, 511, 719
TfiI GAWTC 3 cut(s) 42, 127, 536
Tru1I TTAA 2 cut(s) 419, 510
Tru9I TTAA 2 cut(s) 419, 510
TscAI CASTG 2 cut(s) 163, 699
TseI GCWGC 2 cut(s) 340, 463
TspDTI ATGAA 6 cut(s) 392, 414, 452, 581, 582, 663
TspGWI ACGGA 1 cut(s) 669
TspRI CASTG 2 cut(s) 163, 699
VneI GTGCAC 1 cut(s) 761
XapI RAATTY 2 cut(s) 483, 506
XcmI CCANNNNNNNNNTGG 1 cut(s) 380
XspI CTAG 1 cut(s) 39
Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.