Rw4G003350

gag-polypeptide of LTR copia-type

Design Primers CRISPR Design

Basic Information

Type: gene
Biological Identity
rosa_wichuraiana
Chr4
OG0000154
Physical Location & Seq
Reverse (-)
6705371 .. 6706618
1248 bp
Loading structure...
UTR
Exon/CDS
Intron
Rw4G003350.1

Sequence Viewer

Length: 1173 bp
ATGTCCAACGAAGGACAGAACTTGTTGAGTATTCCCAAGTTTGATGGAGACTATGAATATTGGAGCTTGCTCATGGAGAATCTCTTAAGGTCCAGGGAGTACTGGAACCTAATAGAGACGGGGTATAGAGAACCAGCTGAAGGAGAAGCTGTGACAGCGGGTCAGAGAAAAACTCTAGATGAGTTGAAGCTAAAGGATCTAAAGGTGAAGAATTACCTACTTCAATCCATTGACAAGAGTGTACTGAAGACCCTGCAACAGAGGGAAACATCCAAGCAGATATGGGACTGCATGAAGATCAGATACCAAGGAAATGCTAGGGTTCAGAGAGCACAACTTCAGATTCTTCGTAGGAATTTTGAAGTCTTGGAGATGAAGCTGGGAGAAACAGTAGATGATTACCTTGGAAGGGTAATAACAGTAGCCAATGAGATGAGAAATTACGGAGAAGACATGCCAGACGTAAAGATAGTTGAGAAGATCTTGAGAACGCTCACGGAGAGGTTCAATTACATAGTCTGCTCGATAGAAGAGTCTAAGGATATCAATGGACTCTCAGTTGATGAATTACGAAGTTCCTTGTTGGTACATGAACAAAAGTTTCGAAAGGATGGAGGTGATGAGGAAGCACTTAAAATCTCATATGAAGCAGGCAATCGAGGAAGAGGACGAGGAATTATGAGAGGCGGAGGGCATTTTCAATACGAGTGTCCTAGATGGGAGAAAGCAGCCAACTATGCCGAGCTAGATGAAGAAGAAGAATTGCTTCTAATGGCCTATGTTGAAAGCAACAATGCAAGTCGAGAAGGTGTGTGGTTTCTTGACTCTGGTTGTAGCAATCACATGACAGGGAATAAACAATGGTTTACTGAGCTAGATGAGAGCTTTAGACACTCAGTTAAGCTTGGAAATAGTATGAGAATGCCTGTAATGGGAAAGGGGAGTGTGAGATTGCAAATTGGAGATATGAAGCAAGTGGTGTCCGATGTGTATTACATTCCTGATCTGACAAACAATCTTTTTAGTATCGGACAATTACAGGAGAAGGGTCTAGCCATTTTGATTCGAGATGGAACTTGCAAGGTTTATCACAAGAGAAGAGGTCTTATCATGGAAACAAAGATGACAACTAATCGAATGTTTGTGGTGCTTGCCCTCGTAGCAAACCAATAG
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

390

Amino Acids

45.05

Weight (kDa)

6.11

Isoelectric Point (pI)

39.16

Instability Index
Protein Domains (Pfam)
Domain Name Pfam ID Position E-value Description
Retrotran_gag_2 PF14223 25 - 204 8.6e-29 gag-polypeptide of LTR copia-type
Pol_BBD PF22936 272 - 350 5.6e-29 Pol polyprotein, beta-barrel domain
Hydrophobicity Profile (Kyte-Doolittle)
AI Structure Prediction Report
Calculating structure properties...

Genomic Context

Gene Family Tree

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

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)
AciI CCGC 2 cut(s) 158, 687
AclWI GGATC 1 cut(s) 204
AcsI RAATTY 1 cut(s) 355
AcuI CTGAAG 3 cut(s) 159, 266, 323
AfaI GTAC 3 cut(s) 101, 243, 588
AfiI CCNNNNNNNGG 3 cut(s) 140, 409, 932
AflII CTTAAG 1 cut(s) 85
AgsI TTSAA 6 cut(s) 187, 224, 362, 508, 701, 785
AhdI GACNNNNNGTC 1 cut(s) 159
AjnI CCWGG 1 cut(s) 92
AluBI AGCT 9 cut(s) 66, 137, 149, 190, 379, 745, 874, 885, 904
AluI AGCT 9 cut(s) 66, 137, 149, 190, 379, 745, 874, 885, 904
Alw21I GWGCWC 1 cut(s) 334
Alw26I GTCTC 2 cut(s) 42, 110
AlwI GGATC 1 cut(s) 204
AoxI GGCC 1 cut(s) 774
ApeKI GCWGC 1 cut(s) 728
ApoI RAATTY 1 cut(s) 355
Asp700I GAANNNNTTC 1 cut(s) 765
AspS9I GGNCC 1 cut(s) 90
AsuHPI GGTGA 2 cut(s) 217, 629
AsuII TTCGAA 1 cut(s) 604
AvaII GGWCC 1 cut(s) 90
BarI GAAGNNNNNNTAC 2 cut(s) 287, 319
BbsI GAAGAC 2 cut(s) 254, 456
Bbv12I GWGCWC 1 cut(s) 334
BbvI GCAGC 1 cut(s) 740
BccI CCATC 4 cut(s) 38, 605, 711, 1064
BciT130I CCWGG 1 cut(s) 94
BcoDI GTCTC 2 cut(s) 42, 110
BfaI CTAG 6 cut(s) 176, 318, 714, 746, 875, 1052
BfrI CTTAAG 1 cut(s) 85
BglII AGATCT 1 cut(s) 480
BisI GCNGC 1 cut(s) 729
BlsI GCNGC 1 cut(s) 730
BmcAI AGTACT 1 cut(s) 101
Bme1390I CCNGG 1 cut(s) 94
Bme18I GGWCC 1 cut(s) 90
BmeRI GACNNNNNGTC 1 cut(s) 159
BmgT120I GGNCC 1 cut(s) 90
BmiI GGNNCC 1 cut(s) 107
BmrFI CCNGG 1 cut(s) 94
BpiI GAAGAC 2 cut(s) 254, 456
BplI GAGNNNNNCTC 2 cut(s) 157, 189
Bpu14I TTCGAA 1 cut(s) 604
BpuEI CTTGAG 1 cut(s) 505
BsaJI CCNNGG 3 cut(s) 93, 307, 403
BsaXI ACNNNNNCTCC 4 cut(s) 135, 165, 375, 405
Bsc4I CCNNNNNNNGG 3 cut(s) 140, 409, 932
Bse1I ACTGG 1 cut(s) 107
BseBI CCWGG 1 cut(s) 94
BseDI CCNNGG 3 cut(s) 93, 307, 403
BseGI GGATG 2 cut(s) 269, 616
BseLI CCNNNNNNNGG 3 cut(s) 140, 409, 932
BseMII CTCAG 3 cut(s) 570, 861, 909
BseNI ACTGG 1 cut(s) 107
BseXI GCAGC 1 cut(s) 740
BseYI CCCAGC 1 cut(s) 379
BshFI GGCC 1 cut(s) 776
BsiHKAI GWGCWC 1 cut(s) 334
BslFI GGGAC 1 cut(s) 299
BslI CCNNNNNNNGG 3 cut(s) 140, 409, 932
BsmAI GTCTC 2 cut(s) 42, 110
BsmBI CGTCTC 1 cut(s) 110
BsmFI GGGAC 1 cut(s) 299
BsmI GAATGC 1 cut(s) 927
BsnI GGCC 1 cut(s) 776
Bsp119I TTCGAA 1 cut(s) 604
Bsp1286I GDGCHC 1 cut(s) 334
Bsp143I GATC 4 cut(s) 196, 297, 480, 1003
BspACI CCGC 2 cut(s) 158, 687
BspANI GGCC 1 cut(s) 776
BspCNI CTCAG 3 cut(s) 569, 862, 908
BspLI GGNNCC 1 cut(s) 107
BspPI GGATC 1 cut(s) 204
BspT104I TTCGAA 1 cut(s) 604
BspTI CTTAAG 1 cut(s) 85
BsrI ACTGG 1 cut(s) 107
BssECI CCNNGG 3 cut(s) 93, 307, 403
BssMI GATC 4 cut(s) 196, 297, 480, 1003
BssT1I CCWWGG 2 cut(s) 307, 403
Bst2UI CCWGG 1 cut(s) 94
Bst4CI ACNGT 2 cut(s) 391, 421
Bst6I CTCTTC 3 cut(s) 525, 658, 1093
BstAFI CTTAAG 1 cut(s) 85
BstBI TTCGAA 1 cut(s) 604
BstC8I GCNNGC 3 cut(s) 68, 652, 1152
BstDEI CTNAG 4 cut(s) 537, 556, 870, 895
BstF5I GGATG 2 cut(s) 269, 616
BstKTI GATC 4 cut(s) 199, 300, 483, 1006
BstMAI GTCTC 2 cut(s) 42, 110
BstMBI GATC 4 cut(s) 196, 297, 480, 1003
BstMWI GCNNNNNNNGC 3 cut(s) 155, 737, 1160
BstNI CCWGG 1 cut(s) 94
BstNSI RCATGY 1 cut(s) 457
BstSCI CCNGG 1 cut(s) 92
BstV1I GCAGC 1 cut(s) 740
BstV2I GAAGAC 2 cut(s) 254, 456
BstX2I RGATCY 2 cut(s) 196, 480
BstYI RGATCY 2 cut(s) 196, 480
BsuRI GGCC 1 cut(s) 776
BtsCI GGATG 2 cut(s) 269, 616
Cac8I GCNNGC 3 cut(s) 68, 652, 1152
Cfr13I GGNCC 1 cut(s) 90
Csp6I GTAC 3 cut(s) 100, 242, 587
CviAII CATG 6 cut(s) 73, 292, 454, 590, 844, 1111
CviQI GTAC 3 cut(s) 100, 242, 587
DdeI CTNAG 4 cut(s) 537, 556, 870, 895
DpnI GATC 4 cut(s) 198, 299, 482, 1005
DpnII GATC 4 cut(s) 196, 297, 480, 1003
DriI GACNNNNNGTC 1 cut(s) 159
Eam1104I CTCTTC 3 cut(s) 525, 658, 1093
Eam1105I GACNNNNNGTC 1 cut(s) 159
EarI CTCTTC 3 cut(s) 525, 658, 1093
EciI GGCGGA 1 cut(s) 702
Eco130I CCWWGG 2 cut(s) 307, 403
Eco32I GATATC 1 cut(s) 544
Eco47I GGWCC 1 cut(s) 90
Eco57I CTGAAG 3 cut(s) 159, 266, 323
EcoRII CCWGG 1 cut(s) 92
EcoRV GATATC 1 cut(s) 544
EcoT14I CCWWGG 2 cut(s) 307, 403
ErhI CCWWGG 2 cut(s) 307, 403
Esp3I CGTCTC 1 cut(s) 110
FaeI CATG 6 cut(s) 76, 295, 457, 593, 847, 1114
FalI AAGNNNNNCTT 2 cut(s) 750, 782
FaqI GGGAC 1 cut(s) 299
FatI CATG 6 cut(s) 72, 291, 453, 589, 843, 1110
FauI CCCGC 1 cut(s) 151
FauNDI CATATG 1 cut(s) 643
Fnu4HI GCNGC 1 cut(s) 729
FokI GGATG 2 cut(s) 256, 623
Fsp4HI GCNGC 1 cut(s) 729
FspBI CTAG 6 cut(s) 176, 318, 714, 746, 875, 1052
GluI GCNGC 1 cut(s) 729
GsaI CCCAGC 1 cut(s) 383
HaeIII GGCC 1 cut(s) 776
Hin1II CATG 6 cut(s) 76, 295, 457, 593, 847, 1114
HindIII AAGCTT 1 cut(s) 902
HinfI GANTC 6 cut(s) 79, 343, 533, 552, 824, 1063
HphI GGTGA 2 cut(s) 217, 629
Hpy166II GTNNAC 2 cut(s) 242, 867
Hpy188I TCNGA 7 cut(s) 165, 302, 327, 342, 985, 1008, 1031
Hpy188III TCNNGA 6 cut(s) 176, 484, 803, 821, 1001, 1067
Hpy8I GTNNAC 2 cut(s) 242, 867
HpyAV CCTTC 5 cut(s) 5, 134, 402, 800, 1039
HpyCH4III ACNGT 2 cut(s) 391, 421
HpyCH4IV ACGT 1 cut(s) 462
HpyCH4V TGCA 5 cut(s) 256, 291, 797, 955, 1080
HpyF10VI GCNNNNNNNGC 3 cut(s) 155, 737, 1160
HpyF3I CTNAG 4 cut(s) 537, 556, 870, 895
HpySE526I ACGT 1 cut(s) 462
Hsp92II CATG 6 cut(s) 76, 295, 457, 593, 847, 1114
Kzo9I GATC 4 cut(s) 196, 297, 480, 1003
LmnI GCTCC 1 cut(s) 63
Lsp1109I GCAGC 1 cut(s) 740
MaeI CTAG 6 cut(s) 176, 318, 714, 746, 875, 1052
MaeII ACGT 1 cut(s) 462
MaeIII GTNAC 1 cut(s) 151
MalI GATC 4 cut(s) 198, 299, 482, 1005
MboI GATC 4 cut(s) 196, 297, 480, 1003
MflI RGATCY 2 cut(s) 196, 480
MhlI GDGCHC 1 cut(s) 334
MluCI AATT 9 cut(s) 211, 355, 439, 508, 566, 675, 761, 957, 1034
MlyI GAGTC 3 cut(s) 542, 546, 818
MmeI TCCRAC 1 cut(s) 30
MroXI GAANNNNTTC 1 cut(s) 765
MseI TTAA 3 cut(s) 86, 633, 900
MspA1I CMGCKG 2 cut(s) 137, 158
MspCI CTTAAG 1 cut(s) 85
MspR9I CCNGG 1 cut(s) 94
Mva1269I GAATGC 1 cut(s) 927
MvaI CCWGG 1 cut(s) 94
MwoI GCNNNNNNNGC 3 cut(s) 155, 737, 1160
NdeI CATATG 1 cut(s) 643
NdeII GATC 4 cut(s) 196, 297, 480, 1003
NlaIII CATG 6 cut(s) 76, 295, 457, 593, 847, 1114
NlaIV GGNNCC 1 cut(s) 107
NmeAIII GCCGAG 1 cut(s) 766
NmuCI GTSAC 1 cut(s) 151
NspI RCATGY 1 cut(s) 457
NspV TTCGAA 1 cut(s) 604
PctI GAATGC 1 cut(s) 927
PdmI GAANNNNTTC 1 cut(s) 765
PfeI GAWTC 3 cut(s) 79, 343, 1063
PkrI GCNGC 1 cut(s) 730
PleI GAGTC 3 cut(s) 541, 546, 818
PpsI GAGTC 3 cut(s) 541, 546, 818
Psp6I CCWGG 1 cut(s) 92
PspFI CCCAGC 1 cut(s) 379
PspGI CCWGG 1 cut(s) 92
PspN4I GGNNCC 1 cut(s) 107
PspPI GGNCC 1 cut(s) 90
PsuI RGATCY 2 cut(s) 196, 480
PvuII CAGCTG 1 cut(s) 137
RsaI GTAC 3 cut(s) 101, 243, 588
RsaNI GTAC 3 cut(s) 100, 242, 587
SaqAI TTAA 3 cut(s) 86, 633, 900
SatI GCNGC 1 cut(s) 729
Sau3AI GATC 4 cut(s) 196, 297, 480, 1003
Sau96I GGNCC 1 cut(s) 90
ScaI AGTACT 1 cut(s) 101
SchI GAGTC 3 cut(s) 542, 546, 818
ScrFI CCNGG 1 cut(s) 94
SduI GDGCHC 1 cut(s) 334
SfuI TTCGAA 1 cut(s) 604
SinI GGWCC 1 cut(s) 90
SmlI CTYRAG 2 cut(s) 85, 484
SmoI CTYRAG 2 cut(s) 85, 484
Sse9I AATT 9 cut(s) 211, 355, 439, 508, 566, 675, 761, 957, 1034
SsiI CCGC 2 cut(s) 158, 687
SspI AATATT 1 cut(s) 59
SspMI CTAG 6 cut(s) 176, 318, 714, 746, 875, 1052
StyD4I CCNGG 1 cut(s) 92
StyI CCWWGG 2 cut(s) 307, 403
TaaI ACNGT 2 cut(s) 391, 421
TaiI ACGT 1 cut(s) 465
TaqI TCGA 6 cut(s) 524, 604, 658, 802, 1066, 1135
TasI AATT 9 cut(s) 211, 355, 439, 508, 566, 675, 761, 957, 1034
TatI WGTACW 2 cut(s) 99, 241
TfiI GAWTC 3 cut(s) 79, 343, 1063
Tru1I TTAA 3 cut(s) 86, 633, 900
Tru9I TTAA 3 cut(s) 86, 633, 900
TseFI GTSAC 1 cut(s) 151
TseI GCWGC 1 cut(s) 728
Tsp45I GTSAC 1 cut(s) 151
TspDTI ATGAA 8 cut(s) 69, 308, 389, 579, 606, 660, 765, 983
TspGWI ACGGA 2 cut(s) 459, 512
Vha464I CTTAAG 1 cut(s) 85
VpaK11BI GGWCC 1 cut(s) 90
XapI RAATTY 1 cut(s) 355
XbaI TCTAGA 1 cut(s) 175
XceI RCATGY 1 cut(s) 457
XmnI GAANNNNTTC 1 cut(s) 765
XspI CTAG 6 cut(s) 176, 318, 714, 746, 875, 1052
ZrmI AGTACT 1 cut(s) 101
Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.