Rw1G016140

gag-polypeptide of LTR copia-type

Design Primers CRISPR Design

Basic Information

Type: gene
Biological Identity
rosa_wichuraiana
Chr1
OG0000154
Physical Location & Seq
Forward (+)
35831612 .. 35832541
930 bp
Loading structure...
UTR
Exon/CDS
Intron
Rw1G016140.1

Sequence Viewer

Length: 879 bp
ATGGCAGCAGAGTCAAGTAACTTTGCGCAACCTTGCATCCCAAAGTTTGATGGGGATTATGAGCATTGGAACATGCTAATGGAGAATCTTTTACGTTCAAAGGAGTTTTGGAGTGTTATTGAGACGGGGTATGCAGAACCTGCTACTGGAGAAGTTTTAACTAGTGCACAGAGAAAAACCTTGGAGGAGACAAAGCTAAAGGATCTGAAGGCTAAGAATTATCTTTTCCAATCCATTGACAAGTCCATTATGAAGACAATTGCTCAGAAGGTGATGGCAAAGCAGTTGTGGGATTCCATGAAGGTCAAGTACCAAGGAAACGCTATGGTGCAGCGTGCTCAACTTCAAATCCTTCGCAGGAATTTTGAAGTGTTGGAGATGAAACTTGGAGAATCTGTCACAGATTACTTTGCAAGGGTGATGCTGGTGGCAAACGATATGAGGAATCTTGGAGAGAACATGCTTGATGTGAAGATCGTTGAGAAGATCTTGCGCACACTTACTGAGAAGTTCAACTACATAGTTTGTTCGATCGAGGAGTCAAAAGACCTCAATCGTCTTTCAAATGAAGGAAATGACCAAGCACTGAGGGTCTATGAGGAAAGAGTTGGAGGAAGAGGCCGAGGAAGAAGCAATTACAGAGGAAGAGGTCGTGGAAGAGGACAAGTGTTTAATAGGGCCACGGTGGAATGCTTCAAGTGCCACAAACTTGGACATTTCCAATATGAATGTCCAAGTTTGAACAAGGAAGCCAATTACGCAGAGCTGAATGAAGAGGATGAGATGCTACTGATGTCGTATGTTGAATTACATGATGTGAAACGGAATGATGCGTGGTTTCTTGACTCAGGGTGCTCCAATCATATGTATGGATATTGA
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

292

Amino Acids

33.9

Weight (kDa)

6.97

Isoelectric Point (pI)

39.45

Instability Index
Protein Domains (Pfam)
Domain Name Pfam ID Position E-value Description
Retrotran_gag_2 PF14223 27 - 185 8.7e-28 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)
Acc16I TGCGCA 2 cut(s) 27, 494
Acc36I ACCTGC 1 cut(s) 148
AclWI GGATC 1 cut(s) 210
AcsI RAATTY 1 cut(s) 361
AcuI CTGAAG 1 cut(s) 227
AfaI GTAC 1 cut(s) 311
AfiI CCNNNNNNNGG 1 cut(s) 146
AgsI TTSAA 8 cut(s) 99, 347, 368, 514, 564, 697, 742, 806
AhlI ACTAGT 1 cut(s) 161
AluBI AGCT 2 cut(s) 196, 766
AluI AGCT 2 cut(s) 196, 766
Alw21I GWGCWC 3 cut(s) 169, 340, 857
Alw26I GTCTC 2 cut(s) 116, 182
Alw44I GTGCAC 1 cut(s) 165
AlwI GGATC 1 cut(s) 210
AlwNI CAGNNNCTG 1 cut(s) 140
AoxI GGCC 2 cut(s) 619, 678
ApaLI GTGCAC 1 cut(s) 165
ApeKI GCWGC 2 cut(s) 5, 331
ApoI RAATTY 1 cut(s) 361
AspLEI GCGC 2 cut(s) 28, 495
AspS9I GGNCC 1 cut(s) 678
AsuHPI GGTGA 2 cut(s) 283, 430
BaeGI GKGCMC 1 cut(s) 169
BarI GAAGNNNNNNTAC 4 cut(s) 293, 325, 500, 532
BbsI GAAGAC 1 cut(s) 260
Bbv12I GWGCWC 3 cut(s) 169, 340, 857
BbvI GCAGC 2 cut(s) 17, 343
BccI CCATC 2 cut(s) 44, 268
BcoDI GTCTC 2 cut(s) 116, 182
BcuI ACTAGT 1 cut(s) 161
BfaI CTAG 1 cut(s) 162
BfuAI ACCTGC 1 cut(s) 148
BglII AGATCT 1 cut(s) 486
BisI GCNGC 2 cut(s) 6, 332
BlsI GCNGC 2 cut(s) 7, 333
BmgT120I GGNCC 1 cut(s) 678
BmsI GCATC 4 cut(s) 45, 411, 774, 820
BpiI GAAGAC 1 cut(s) 260
BpmI CTGGAG 1 cut(s) 168
BsaJI CCNNGG 4 cut(s) 180, 313, 622, 681
BsaXI ACNNNNNCTCC 2 cut(s) 381, 411
Bsc4I CCNNNNNNNGG 1 cut(s) 146
Bse1I ACTGG 1 cut(s) 151
BseDI CCNNGG 4 cut(s) 180, 313, 622, 681
BseGI GGATG 2 cut(s) 36, 784
BseLI CCNNNNNNNGG 1 cut(s) 146
BseMII CTCAG 4 cut(s) 278, 495, 578, 861
BseNI ACTGG 1 cut(s) 151
BseRI GAGGAG 2 cut(s) 200, 551
BseSI GKGCMC 1 cut(s) 169
BseXI GCAGC 2 cut(s) 17, 343
BsgI GTGCAG 1 cut(s) 350
Bsh1285I CGRYCG 1 cut(s) 534
BshFI GGCC 2 cut(s) 621, 680
BsiEI CGRYCG 1 cut(s) 534
BsiHKAI GWGCWC 3 cut(s) 169, 340, 857
BslI CCNNNNNNNGG 1 cut(s) 146
BsmAI GTCTC 2 cut(s) 116, 182
BsmBI CGTCTC 1 cut(s) 116
BsmI GAATGC 1 cut(s) 695
BsnI GGCC 2 cut(s) 621, 680
Bsp1286I GDGCHC 3 cut(s) 169, 340, 857
Bsp143I GATC 4 cut(s) 202, 474, 486, 531
BspANI GGCC 2 cut(s) 621, 680
BspCNI CTCAG 4 cut(s) 277, 496, 579, 860
BspMI ACCTGC 1 cut(s) 148
BspPI GGATC 1 cut(s) 210
BsrI ACTGG 1 cut(s) 151
BssECI CCNNGG 4 cut(s) 180, 313, 622, 681
BssMI GATC 4 cut(s) 202, 474, 486, 531
BssT1I CCWWGG 2 cut(s) 180, 313
Bst4CI ACNGT 1 cut(s) 685
Bst6I CTCTTC 4 cut(s) 610, 640, 652, 768
BstAPI GCANNNNNTGC 1 cut(s) 140
BstC8I GCNNGC 1 cut(s) 336
BstDEI CTNAG 5 cut(s) 213, 264, 504, 587, 847
BstDSI CCRYGG 1 cut(s) 681
BstF5I GGATG 2 cut(s) 36, 784
BstHHI GCGC 2 cut(s) 28, 495
BstKTI GATC 4 cut(s) 205, 477, 489, 534
BstMAI GTCTC 2 cut(s) 116, 182
BstMBI GATC 4 cut(s) 202, 474, 486, 531
BstMCI CGRYCG 1 cut(s) 534
BstMWI GCNNNNNNNGC 3 cut(s) 140, 699, 758
BstNSI RCATGY 2 cut(s) 76, 463
BstSLI GKGCMC 1 cut(s) 169
BstV1I GCAGC 2 cut(s) 17, 343
BstV2I GAAGAC 1 cut(s) 260
BstX2I RGATCY 2 cut(s) 202, 486
BstXI CCANNNNNNTGG 1 cut(s) 710
BstYI RGATCY 2 cut(s) 202, 486
BsuRI GGCC 2 cut(s) 621, 680
BtgI CCRYGG 1 cut(s) 681
BtsCI GGATG 2 cut(s) 36, 784
BtsIMutI CAGTG 1 cut(s) 584
BveI ACCTGC 1 cut(s) 148
Cac8I GCNNGC 1 cut(s) 336
CaiI CAGNNNCTG 1 cut(s) 140
CfoI GCGC 2 cut(s) 28, 495
Cfr13I GGNCC 1 cut(s) 678
Csp6I GTAC 1 cut(s) 310
CviAII CATG 4 cut(s) 73, 298, 460, 812
CviJI RGCY 6 cut(s) 196, 212, 621, 680, 752, 766
CviKI_1 RGCY 6 cut(s) 196, 212, 621, 680, 752, 766
CviQI GTAC 1 cut(s) 310
DdeI CTNAG 5 cut(s) 213, 264, 504, 587, 847
DpnI GATC 4 cut(s) 204, 476, 488, 533
DpnII GATC 4 cut(s) 202, 474, 486, 531
Eam1104I CTCTTC 4 cut(s) 610, 640, 652, 768
EarI CTCTTC 4 cut(s) 610, 640, 652, 768
Eco130I CCWWGG 2 cut(s) 180, 313
Eco57I CTGAAG 1 cut(s) 227
EcoT14I CCWWGG 2 cut(s) 180, 313
ErhI CCWWGG 2 cut(s) 180, 313
Esp3I CGTCTC 1 cut(s) 116
FaeI CATG 4 cut(s) 76, 301, 463, 815
FatI CATG 4 cut(s) 72, 297, 459, 811
FauNDI CATATG 1 cut(s) 864
Fnu4HI GCNGC 2 cut(s) 6, 332
FokI GGATG 2 cut(s) 23, 791
Fsp4HI GCNGC 2 cut(s) 6, 332
FspBI CTAG 1 cut(s) 162
FspI TGCGCA 2 cut(s) 27, 494
GlaI GCGC 2 cut(s) 27, 494
GluI GCNGC 2 cut(s) 6, 332
GsuI CTGGAG 1 cut(s) 168
HaeIII GGCC 2 cut(s) 621, 680
HhaI GCGC 2 cut(s) 28, 495
Hin1II CATG 4 cut(s) 76, 301, 463, 815
Hin6I GCGC 2 cut(s) 26, 493
HinP1I GCGC 2 cut(s) 26, 493
HinfI GANTC 7 cut(s) 11, 85, 293, 392, 445, 539, 845
HphI GGTGA 2 cut(s) 283, 430
Hpy166II GTNNAC 1 cut(s) 167
Hpy188I TCNGA 2 cut(s) 207, 267
Hpy188III TCNNGA 1 cut(s) 842
Hpy8I GTNNAC 1 cut(s) 167
HpyAV CCTTC 5 cut(s) 202, 262, 295, 362, 563
HpyCH4III ACNGT 1 cut(s) 685
HpyCH4IV ACGT 1 cut(s) 94
HpyCH4V TGCA 5 cut(s) 36, 134, 167, 331, 413
HpyF10VI GCNNNNNNNGC 3 cut(s) 140, 699, 758
HpyF3I CTNAG 5 cut(s) 213, 264, 504, 587, 847
HpySE526I ACGT 1 cut(s) 94
Hsp92II CATG 4 cut(s) 76, 301, 463, 815
HspAI GCGC 2 cut(s) 26, 493
Kzo9I GATC 4 cut(s) 202, 474, 486, 531
LmnI GCTCC 1 cut(s) 860
LpnPI CCDG 5 cut(s) 132, 153, 343, 410, 834
Lsp1109I GCAGC 2 cut(s) 17, 343
LweI GCATC 4 cut(s) 45, 411, 774, 820
MaeI CTAG 1 cut(s) 162
MaeII ACGT 1 cut(s) 94
MaeIII GTNAC 2 cut(s) 17, 397
MalI GATC 4 cut(s) 204, 476, 488, 533
MboI GATC 4 cut(s) 202, 474, 486, 531
MboII GAAGA 8 cut(s) 265, 484, 496, 627, 639, 657, 669, 785
MfeI CAATTG 1 cut(s) 258
MflI RGATCY 2 cut(s) 202, 486
MhlI GDGCHC 3 cut(s) 169, 340, 857
MluCI AATT 6 cut(s) 217, 258, 361, 634, 754, 806
MlyI GAGTC 3 cut(s) 20, 548, 839
MmeI TCCRAC 2 cut(s) 354, 589
MseI TTAA 2 cut(s) 158, 672
MslI CAYNNNNRTG 2 cut(s) 77, 867
MunI CAATTG 1 cut(s) 258
Mva1269I GAATGC 1 cut(s) 695
MwoI GCNNNNNNNGC 3 cut(s) 140, 699, 758
NdeI CATATG 1 cut(s) 864
NdeII GATC 4 cut(s) 202, 474, 486, 531
NlaIII CATG 4 cut(s) 76, 301, 463, 815
NmeAIII GCCGAG 1 cut(s) 647
NmuCI GTSAC 1 cut(s) 397
NsbI TGCGCA 2 cut(s) 27, 494
NspI RCATGY 2 cut(s) 76, 463
PctI GAATGC 1 cut(s) 695
PfeI GAWTC 4 cut(s) 85, 293, 392, 445
PkrI GCNGC 2 cut(s) 7, 333
Ple19I CGATCG 1 cut(s) 534
PleI GAGTC 3 cut(s) 19, 547, 839
PpsI GAGTC 3 cut(s) 19, 547, 839
PspPI GGNCC 1 cut(s) 678
PstNI CAGNNNCTG 1 cut(s) 140
PsuI RGATCY 2 cut(s) 202, 486
PvuI CGATCG 1 cut(s) 534
RsaI GTAC 1 cut(s) 311
RsaNI GTAC 1 cut(s) 310
RseI CAYNNNNRTG 2 cut(s) 77, 867
SaqAI TTAA 2 cut(s) 158, 672
SatI GCNGC 2 cut(s) 6, 332
Sau3AI GATC 4 cut(s) 202, 474, 486, 531
Sau96I GGNCC 1 cut(s) 678
SchI GAGTC 3 cut(s) 20, 548, 839
SduI GDGCHC 3 cut(s) 169, 340, 857
SfaNI GCATC 4 cut(s) 45, 411, 774, 820
SmiMI CAYNNNNRTG 2 cut(s) 77, 867
SpeI ACTAGT 1 cut(s) 161
Sse9I AATT 6 cut(s) 217, 258, 361, 634, 754, 806
SspMI CTAG 1 cut(s) 162
StyI CCWWGG 2 cut(s) 180, 313
TaaI ACNGT 1 cut(s) 685
TaiI ACGT 1 cut(s) 97
TaqI TCGA 2 cut(s) 530, 534
TasI AATT 6 cut(s) 217, 258, 361, 634, 754, 806
TfiI GAWTC 4 cut(s) 85, 293, 392, 445
Tru1I TTAA 2 cut(s) 158, 672
Tru9I TTAA 2 cut(s) 158, 672
TscAI CASTG 1 cut(s) 591
TseFI GTSAC 1 cut(s) 397
TseI GCWGC 2 cut(s) 5, 331
Tsp45I GTSAC 1 cut(s) 397
TspDTI ATGAA 6 cut(s) 266, 314, 395, 582, 741, 786
TspGWI ACGGA 1 cut(s) 838
TspRI CASTG 1 cut(s) 591
VneI GTGCAC 1 cut(s) 165
XapI RAATTY 1 cut(s) 361
XceI RCATGY 2 cut(s) 76, 463
XspI CTAG 1 cut(s) 162
Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.