Rw5G046620

gag-polypeptide of LTR copia-type

Design Primers CRISPR Design

Basic Information

Type: gene
Biological Identity
rosa_wichuraiana
Chr5
OG0000154
Physical Location & Seq
Forward (+)
80882407 .. 80883078
672 bp
Loading structure...
UTR
Exon/CDS
Intron
Rw5G046620.1

Sequence Viewer

Length: 672 bp
ATGGCATCCGACAACAACAACTATGTGCAACCAGCAATTCCACGCTTTGATGGTCACTATGACCATTGGAGCATGCTTATGGAGAATTTTCTGAGGTCCAAGGAGTATTGGAACATCATTGAAACCGGAATTGCTGAACCAGCCGCTGCTGGAGAAGTGTTGACGGCTGCACAGAAAAGGGTGCAGGAAGAGCAGCAGTTGAAGGATCTCAAGGCGAAAAATTACTTGTTTCAAGCAATTGATCGCACAATTTTGGAGACTATTCTTCAAAAGGACACATCCAAGCAAATTTGGGATTCAATGAGAAAGAAGTATCAAGGATCAGCCAAAGTGAAGCGTGCACAGCTTCAAGCCCTCCGCAAAGATTTTGAGACTCTTCAAATGAAGACGGGAGAGTCAGTCAATGATTACTTCTCAAGAGTCATGGCTATTGCAAACAAGATGCGAATCCATGGTGACAAGCTGGGAGATGTCACCATTATTGAAAAAATTCTTCGATCGATGCATACAAAATTTGACTATGTTGTATGTTCGATTGAGGAATCACATGACATTGATGAAGTTTCGATTGATGAGCTGCAAAGTTCGTTGTTGGTTCATGAGCAGAGAATTAATCAAGGGGCTACAACGGAGGAGCAAACATATAGATGTCAGATTTCACTTTTTGCGTGA
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

223

Amino Acids

25.83

Weight (kDa)

5.91

Isoelectric Point (pI)

56.55

Instability Index
Protein Domains (Pfam)
Domain Name Pfam ID Position E-value Description
Retrotran_gag_2 PF14223 27 - 205 1.8e-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
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)
AasI GACNNNNNNGTC 1 cut(s) 394
AciI CCGC 2 cut(s) 144, 358
AclWI GGATC 2 cut(s) 213, 328
AcsI RAATTY 4 cut(s) 85, 288, 489, 512
AgsI TTSAA 8 cut(s) 122, 202, 233, 269, 300, 350, 380, 485
AluBI AGCT 3 cut(s) 346, 463, 577
AluI AGCT 3 cut(s) 346, 463, 577
Alw21I GWGCWC 1 cut(s) 343
Alw26I GTCTC 2 cut(s) 251, 365
Alw44I GTGCAC 1 cut(s) 339
AlwI GGATC 2 cut(s) 213, 328
AlwNI CAGNNNCTG 1 cut(s) 146
ApaLI GTGCAC 1 cut(s) 339
ApeKI GCWGC 4 cut(s) 146, 167, 193, 577
ApoI RAATTY 4 cut(s) 85, 288, 489, 512
AseI ATTAAT 1 cut(s) 612
Asp700I GAANNNNTTC 1 cut(s) 489
AspS9I GGNCC 1 cut(s) 96
AsuHPI GGTGA 2 cut(s) 466, 467
AvaII GGWCC 1 cut(s) 96
BaeGI GKGCMC 1 cut(s) 343
BbsI GAAGAC 1 cut(s) 392
Bbv12I GWGCWC 1 cut(s) 343
BbvI GCAGC 4 cut(s) 133, 154, 205, 564
BccI CCATC 1 cut(s) 44
BceAI ACGGC 1 cut(s) 180
BcoDI GTCTC 2 cut(s) 251, 365
BisI GCNGC 5 cut(s) 144, 147, 168, 194, 578
BlsI GCNGC 5 cut(s) 145, 148, 169, 195, 579
Bme18I GGWCC 1 cut(s) 96
BmgT120I GGNCC 1 cut(s) 96
BmsI GCATC 3 cut(s) 14, 432, 492
BpiI GAAGAC 1 cut(s) 392
BpmI CTGGAG 1 cut(s) 171
BpuEI CTTGAG 2 cut(s) 194, 400
Bsa29I ATCGAT 1 cut(s) 500
BsaBI GATNNNNATC 1 cut(s) 446
BsaJI CCNNGG 2 cut(s) 99, 451
BsaWI WCCGGW 1 cut(s) 125
BsaXI ACNNNNNCTCC 2 cut(s) 384, 414
Bse8I GATNNNNATC 1 cut(s) 446
BseCI ATCGAT 1 cut(s) 500
BseDI CCNNGG 2 cut(s) 99, 451
BseGI GGATG 2 cut(s) 5, 278
BseJI GATNNNNATC 1 cut(s) 446
BseMII CTCAG 1 cut(s) 83
BseRI GAGGAG 1 cut(s) 647
BseSI GKGCMC 1 cut(s) 343
BseXI GCAGC 4 cut(s) 133, 154, 205, 564
BseYI CCCAGC 1 cut(s) 463
BsgI GTGCAG 2 cut(s) 153, 203
Bsh1285I CGRYCG 1 cut(s) 500
BshVI ATCGAT 1 cut(s) 500
BsiEI CGRYCG 1 cut(s) 500
BsiHKAI GWGCWC 1 cut(s) 343
BsiSI CCGG 1 cut(s) 126
BsmAI GTCTC 2 cut(s) 251, 365
Bsp1286I GDGCHC 1 cut(s) 343
Bsp143I GATC 4 cut(s) 205, 241, 320, 497
Bsp19I CCATGG 1 cut(s) 451
BspACI CCGC 2 cut(s) 144, 358
BspCNI CTCAG 1 cut(s) 84
BspDI ATCGAT 1 cut(s) 500
BspHI TCATGA 1 cut(s) 598
BspPI GGATC 2 cut(s) 213, 328
BspQI GCTCTTC 1 cut(s) 183
BssECI CCNNGG 2 cut(s) 99, 451
BssMI GATC 4 cut(s) 205, 241, 320, 497
BssT1I CCWWGG 2 cut(s) 99, 451
Bst6I CTCTTC 2 cut(s) 183, 381
BstC8I GCNNGC 2 cut(s) 74, 339
BstDEI CTNAG 1 cut(s) 92
BstDSI CCRYGG 1 cut(s) 451
BstF5I GGATG 2 cut(s) 5, 278
BstKTI GATC 4 cut(s) 208, 244, 323, 500
BstMAI GTCTC 2 cut(s) 251, 365
BstMBI GATC 4 cut(s) 205, 241, 320, 497
BstMCI CGRYCG 1 cut(s) 500
BstMWI GCNNNNNNNGC 3 cut(s) 140, 190, 343
BstNSI RCATGY 1 cut(s) 76
BstSLI GKGCMC 1 cut(s) 343
BstV1I GCAGC 4 cut(s) 133, 154, 205, 564
BstV2I GAAGAC 1 cut(s) 392
BstX2I RGATCY 1 cut(s) 205
BstYI RGATCY 1 cut(s) 205
Bsu15I ATCGAT 1 cut(s) 500
BsuTUI ATCGAT 1 cut(s) 500
BtgI CCRYGG 1 cut(s) 451
BtsCI GGATG 2 cut(s) 5, 278
Cac8I GCNNGC 2 cut(s) 74, 339
CaiI CAGNNNCTG 1 cut(s) 146
CciI TCATGA 1 cut(s) 598
Cfr13I GGNCC 1 cut(s) 96
ClaI ATCGAT 1 cut(s) 500
CviAII CATG 5 cut(s) 73, 424, 452, 548, 599
CviJI RGCY 9 cut(s) 143, 167, 326, 346, 353, 428, 463, 577, 623
CviKI_1 RGCY 9 cut(s) 143, 167, 326, 346, 353, 428, 463, 577, 623
DdeI CTNAG 1 cut(s) 92
DpnI GATC 4 cut(s) 207, 243, 322, 499
DpnII GATC 4 cut(s) 205, 241, 320, 497
DrdI GACNNNNNNGTC 1 cut(s) 394
DseDI GACNNNNNNGTC 1 cut(s) 394
Eam1104I CTCTTC 2 cut(s) 183, 381
EarI CTCTTC 2 cut(s) 183, 381
Eco130I CCWWGG 2 cut(s) 99, 451
Eco47I GGWCC 1 cut(s) 96
EcoT14I CCWWGG 2 cut(s) 99, 451
EcoT22I ATGCAT 1 cut(s) 507
ErhI CCWWGG 2 cut(s) 99, 451
FaeI CATG 5 cut(s) 76, 427, 455, 551, 602
FatI CATG 5 cut(s) 72, 423, 451, 547, 598
Fnu4HI GCNGC 5 cut(s) 144, 147, 168, 194, 578
FokI GGATG 1 cut(s) 265
Fsp4HI GCNGC 5 cut(s) 144, 147, 168, 194, 578
GluI GCNGC 5 cut(s) 144, 147, 168, 194, 578
GsaI CCCAGC 1 cut(s) 467
GsuI CTGGAG 1 cut(s) 171
HapII CCGG 1 cut(s) 126
Hin1II CATG 5 cut(s) 76, 427, 455, 551, 602
HincII GTYRAC 1 cut(s) 162
HindII GTYRAC 1 cut(s) 162
HinfI GANTC 6 cut(s) 296, 373, 395, 420, 447, 542
HpaII CCGG 1 cut(s) 126
HphI GGTGA 2 cut(s) 466, 467
Hpy166II GTNNAC 2 cut(s) 162, 341
Hpy188I TCNGA 3 cut(s) 10, 93, 654
Hpy188III TCNNGA 2 cut(s) 417, 599
Hpy8I GTNNAC 2 cut(s) 162, 341
HpyAV CCTTC 1 cut(s) 196
HpyCH4V TGCA 7 cut(s) 28, 170, 184, 341, 434, 505, 580
HpyF10VI GCNNNNNNNGC 3 cut(s) 140, 190, 343
HpyF3I CTNAG 1 cut(s) 92
Hsp92II CATG 5 cut(s) 76, 427, 455, 551, 602
Kzo9I GATC 4 cut(s) 205, 241, 320, 497
LguI GCTCTTC 1 cut(s) 183
LmnI GCTCC 2 cut(s) 69, 634
LpnPI CCDG 6 cut(s) 45, 135, 139, 153, 170, 449
Lsp1109I GCAGC 4 cut(s) 133, 154, 205, 564
LweI GCATC 3 cut(s) 14, 432, 492
MaeIII GTNAC 3 cut(s) 53, 455, 472
MalI GATC 4 cut(s) 207, 243, 322, 499
MboI GATC 4 cut(s) 205, 241, 320, 497
MboII GAAGA 5 cut(s) 200, 257, 368, 397, 485
MfeI CAATTG 1 cut(s) 237
MflI RGATCY 1 cut(s) 205
MhlI GDGCHC 1 cut(s) 343
MlyI GAGTC 3 cut(s) 367, 404, 429
MmeI TCCRAC 1 cut(s) 33
MnlI CCTC 4 cut(s) 87, 365, 532, 625
Mph1103I ATGCAT 1 cut(s) 507
MroXI GAANNNNTTC 1 cut(s) 489
MseI TTAA 1 cut(s) 612
MslI CAYNNNNRTG 2 cut(s) 77, 646
MspA1I CMGCKG 1 cut(s) 146
MspI CCGG 1 cut(s) 126
MunI CAATTG 1 cut(s) 237
MwoI GCNNNNNNNGC 3 cut(s) 140, 190, 343
NcoI CCATGG 1 cut(s) 451
NdeII GATC 4 cut(s) 205, 241, 320, 497
NlaIII CATG 5 cut(s) 76, 427, 455, 551, 602
NmuCI GTSAC 3 cut(s) 53, 455, 472
NsiI ATGCAT 1 cut(s) 507
NspI RCATGY 1 cut(s) 76
PaeI GCATGC 1 cut(s) 76
PagI TCATGA 1 cut(s) 598
PciSI GCTCTTC 1 cut(s) 183
PdmI GAANNNNTTC 1 cut(s) 489
PfeI GAWTC 3 cut(s) 296, 447, 542
PkrI GCNGC 5 cut(s) 145, 148, 169, 195, 579
Ple19I CGATCG 1 cut(s) 500
PleI GAGTC 3 cut(s) 367, 403, 428
PpsI GAGTC 3 cut(s) 367, 403, 428
PshBI ATTAAT 1 cut(s) 612
PspFI CCCAGC 1 cut(s) 463
PspPI GGNCC 1 cut(s) 96
PstNI CAGNNNCTG 1 cut(s) 146
PsuI RGATCY 1 cut(s) 205
PvuI CGATCG 1 cut(s) 500
RseI CAYNNNNRTG 2 cut(s) 77, 646
SapI GCTCTTC 1 cut(s) 183
SaqAI TTAA 1 cut(s) 612
SatI GCNGC 5 cut(s) 144, 147, 168, 194, 578
Sau3AI GATC 4 cut(s) 205, 241, 320, 497
Sau96I GGNCC 1 cut(s) 96
SchI GAGTC 3 cut(s) 367, 404, 429
SduI GDGCHC 1 cut(s) 343
SetI ASST 4 cut(s) 98, 348, 465, 579
SfaNI GCATC 3 cut(s) 14, 432, 492
SinI GGWCC 1 cut(s) 96
SmiMI CAYNNNNRTG 2 cut(s) 77, 646
SmlI CTYRAG 2 cut(s) 209, 415
SmoI CTYRAG 2 cut(s) 209, 415
SphI GCATGC 1 cut(s) 76
SsiI CCGC 2 cut(s) 144, 358
StyI CCWWGG 2 cut(s) 99, 451
TaqI TCGA 4 cut(s) 496, 500, 533, 566
TauI GCSGC 1 cut(s) 146
TfiI GAWTC 3 cut(s) 296, 447, 542
Tru1I TTAA 1 cut(s) 612
Tru9I TTAA 1 cut(s) 612
TseFI GTSAC 3 cut(s) 53, 455, 472
TseI GCWGC 4 cut(s) 146, 167, 193, 577
Tsp45I GTSAC 3 cut(s) 53, 455, 472
TspDTI ATGAA 3 cut(s) 398, 573, 587
TspGWI ACGGA 1 cut(s) 644
VneI GTGCAC 1 cut(s) 339
VpaK11BI GGWCC 1 cut(s) 96
VspI ATTAAT 1 cut(s) 612
XapI RAATTY 4 cut(s) 85, 288, 489, 512
XceI RCATGY 1 cut(s) 76
XmnI GAANNNNTTC 1 cut(s) 489
Zsp2I ATGCAT 1 cut(s) 507
Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.