Rw3G025140

gag-polypeptide of LTR copia-type

Design Primers CRISPR Design

Basic Information

Type: gene
Biological Identity
rosa_wichuraiana
Chr3
OG0000154
Physical Location & Seq
Forward (+)
33047639 .. 33052235
4597 bp
Loading structure...
UTR
Exon/CDS
Intron
Rw3G025140.1

Sequence Viewer

Length: 864 bp
ATGGCAACAGACAACAATTTTGTGCAGCCTGCAATCCCTCGCTTTGATGATCACTATGACCATTGGAGCATGCTAATGGAGAATTTCCTAAGATCCAAGGAGTATAGGAGTCTTATGGAAACCAGATTCGTCGAACTGGAAAGTGGAGCAGCAGTGACAAAAGCACAACAAAGGAAACTAGATGAGTTGAGGCTGAAGGATTTAAAGAAGAAGTACAAGGGCTCAATGAAAGTCAAGCGTTCTCAGCTTCAAGCTTTACCCAGGGAATTTGAGACTCTCCAAATGAAGCAGGAAGAGTCCGTGAATGAGTACTTCTCAAGAACAATGGCAATTGCAAACAAGATGAGGCTGCAAGGTGATTCAATGATTGATGTCACCATAGTTGAGAAGATTCTTCGATCAATGACACCAAAGTTTGACTATATCGTATGTTCAATTGAAGAATCAAACGATGTAGATGAACTTTCCATTGATGAGCTGCAGAGTTCCTTGTTGGTACATGACCAGAAGCTGAATAGAAGCAGTACTACAACTGAAGAACAAGCATTGAAAGTAGGGGTGGGTTCGCGAAACCGAAAACAGAAAAAAACCGAATGTCACAAGATTGGTCACTTTCGATCTAAATGCTTCACCAAGTTGCCTGGTAACAAAGAAAAGGAAGAGAAGTCTAATTTTGCTGAGAAGAATGAACAAGAAACACTCTTGATGGAGTTTCATATCAAGGAGAATGAGTTTGCACCAGACATATGGTATCTAGACACAGGCTGCAGCAATCATATGTCTTACAAGTTGTTCAACCCTATCACAAAGAGGATAATCATTAGTCGAGATGTTGTTTTCGATGAGGAGCACACATGGAATTGA
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

287

Amino Acids

33.78

Weight (kDa)

6.73

Isoelectric Point (pI)

55.83

Instability Index
Protein Domains (Pfam)
Domain Name Pfam ID Position E-value Description
Retrotran_gag_2 PF14223 67 - 175 1.5e-15 gag-polypeptide of LTR copia-type
SH3_retrovirus PF25597 257 - 286 1.8e-08 Retroviral polymerase SH3-like 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
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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)
AccII CGCG 1 cut(s) 568
AclWI GGATC 1 cut(s) 87
AcsI RAATTY 2 cut(s) 82, 266
AcuI CTGAAG 2 cut(s) 215, 555
AfaI GTAC 4 cut(s) 215, 311, 498, 526
AgsI TTSAA 6 cut(s) 251, 363, 435, 440, 550, 796
AjnI CCWGG 2 cut(s) 260, 640
AluBI AGCT 4 cut(s) 247, 254, 478, 511
AluI AGCT 4 cut(s) 247, 254, 478, 511
Alw21I GWGCWC 1 cut(s) 852
Alw26I GTCTC 1 cut(s) 266
AlwI GGATC 1 cut(s) 87
AlwNI CAGNNNCTG 1 cut(s) 511
ApeKI GCWGC 6 cut(s) 25, 149, 349, 478, 765, 768
ApoI RAATTY 2 cut(s) 82, 266
ArsI GACNNNNNNTTYG 1 cut(s) 34
AsuHPI GGTGA 3 cut(s) 367, 368, 622
BanII GRGCYC 1 cut(s) 224
BarI GAAGNNNNNNTAC 2 cut(s) 511, 543
Bbv12I GWGCWC 1 cut(s) 852
BbvI GCAGC 6 cut(s) 37, 161, 336, 465, 752, 780
BccI CCATC 1 cut(s) 700
BcgI CGANNNNNNTGC 2 cut(s) 606, 640
BciT130I CCWGG 2 cut(s) 262, 642
BclI TGATCA 1 cut(s) 49
BcoDI GTCTC 1 cut(s) 266
BfaI CTAG 2 cut(s) 179, 755
BfmI CTRYAG 2 cut(s) 479, 766
BisI GCNGC 6 cut(s) 26, 150, 350, 479, 766, 769
BlsI GCNGC 6 cut(s) 27, 151, 351, 480, 767, 770
BmcAI AGTACT 2 cut(s) 311, 526
Bme1390I CCNGG 2 cut(s) 262, 642
BmrFI CCNGG 2 cut(s) 262, 642
BplI GAGNNNNNCTC 2 cut(s) 299, 331
BpuEI CTTGAG 1 cut(s) 301
BsaJI CCNNGG 3 cut(s) 96, 260, 261
BsaXI ACNNNNNCTCC 4 cut(s) 138, 168, 716, 746
Bse1I ACTGG 1 cut(s) 141
BseBI CCWGG 2 cut(s) 262, 642
BseDI CCNNGG 3 cut(s) 96, 260, 261
BseMII CTCAG 2 cut(s) 257, 669
BseNI ACTGG 1 cut(s) 141
BseRI GAGGAG 1 cut(s) 860
BseXI GCAGC 6 cut(s) 37, 161, 336, 465, 752, 780
BsgI GTGCAG 1 cut(s) 44
Bsh1236I CGCG 1 cut(s) 568
BsiHKAI GWGCWC 1 cut(s) 852
BsmAI GTCTC 1 cut(s) 266
Bsp1286I GDGCHC 2 cut(s) 224, 852
Bsp143I GATC 4 cut(s) 49, 92, 398, 617
Bsp68I TCGCGA 1 cut(s) 568
BspCNI CTCAG 2 cut(s) 256, 670
BspFNI CGCG 1 cut(s) 568
BspMAI CTGCAG 2 cut(s) 483, 770
BspPI GGATC 1 cut(s) 87
BsrI ACTGG 1 cut(s) 141
BssECI CCNNGG 3 cut(s) 96, 260, 261
BssMI GATC 4 cut(s) 49, 92, 398, 617
BssT1I CCWWGG 1 cut(s) 96
Bst2UI CCWGG 2 cut(s) 262, 642
Bst6I CTCTTC 2 cut(s) 288, 654
BstC8I GCNNGC 2 cut(s) 30, 71
BstDEI CTNAG 3 cut(s) 89, 243, 678
BstFNI CGCG 1 cut(s) 568
BstKTI GATC 4 cut(s) 52, 95, 401, 620
BstMAI GTCTC 1 cut(s) 266
BstMBI GATC 4 cut(s) 49, 92, 398, 617
BstMWI GCNNNNNNNGC 1 cut(s) 244
BstNI CCWGG 2 cut(s) 262, 642
BstNSI RCATGY 1 cut(s) 73
BstSCI CCNGG 2 cut(s) 260, 640
BstSFI CTRYAG 2 cut(s) 479, 766
BstUI CGCG 1 cut(s) 568
BstV1I GCAGC 6 cut(s) 37, 161, 336, 465, 752, 780
BstX2I RGATCY 1 cut(s) 92
BstXI CCANNNNNNTGG 1 cut(s) 747
BstYI RGATCY 1 cut(s) 92
BtsI GCAGTG 1 cut(s) 159
BtsIMutI CAGTG 1 cut(s) 159
BtuMI TCGCGA 1 cut(s) 568
Cac8I GCNNGC 2 cut(s) 30, 71
CaiI CAGNNNCTG 1 cut(s) 511
Csp6I GTAC 4 cut(s) 214, 310, 497, 525
CviAII CATG 3 cut(s) 70, 500, 855
CviJI RGCY 9 cut(s) 28, 193, 222, 247, 254, 349, 478, 511, 765
CviKI_1 RGCY 9 cut(s) 28, 193, 222, 247, 254, 349, 478, 511, 765
CviQI GTAC 4 cut(s) 214, 310, 497, 525
DdeI CTNAG 3 cut(s) 89, 243, 678
DpnI GATC 4 cut(s) 51, 94, 400, 619
DpnII GATC 4 cut(s) 49, 92, 398, 617
DraI TTTAAA 1 cut(s) 204
Eam1104I CTCTTC 2 cut(s) 288, 654
EarI CTCTTC 2 cut(s) 288, 654
Eco130I CCWWGG 1 cut(s) 96
Eco24I GRGCYC 1 cut(s) 224
Eco57I CTGAAG 2 cut(s) 215, 555
EcoRII CCWGG 2 cut(s) 260, 640
EcoT14I CCWWGG 1 cut(s) 96
EcoT38I GRGCYC 1 cut(s) 224
ErhI CCWWGG 1 cut(s) 96
FaeI CATG 3 cut(s) 73, 503, 858
FatI CATG 3 cut(s) 69, 499, 854
FauNDI CATATG 2 cut(s) 746, 777
FbaI TGATCA 1 cut(s) 49
Fnu4HI GCNGC 6 cut(s) 26, 150, 350, 479, 766, 769
FriOI GRGCYC 1 cut(s) 224
Fsp4HI GCNGC 6 cut(s) 26, 150, 350, 479, 766, 769
FspBI CTAG 2 cut(s) 179, 755
GluI GCNGC 6 cut(s) 26, 150, 350, 479, 766, 769
Hin1II CATG 3 cut(s) 73, 503, 858
HindIII AAGCTT 1 cut(s) 252
HinfI GANTC 7 cut(s) 109, 126, 274, 296, 359, 391, 443
HphI GGTGA 3 cut(s) 367, 368, 622
Hpy188III TCNNGA 5 cut(s) 318, 567, 703, 755, 827
Hpy99I CGWCG 1 cut(s) 134
HpyAV CCTTC 1 cut(s) 190
HpyCH4V TGCA 7 cut(s) 25, 32, 335, 352, 481, 737, 768
HpyF10VI GCNNNNNNNGC 1 cut(s) 244
HpyF3I CTNAG 3 cut(s) 89, 243, 678
Hsp92II CATG 3 cut(s) 73, 503, 858
Ksp22I TGATCA 1 cut(s) 49
Kzo9I GATC 4 cut(s) 49, 92, 398, 617
LmnI GCTCC 3 cut(s) 66, 146, 847
Lsp1109I GCAGC 6 cut(s) 37, 161, 336, 465, 752, 780
MaeI CTAG 2 cut(s) 179, 755
MaeIII GTNAC 5 cut(s) 154, 373, 596, 608, 644
MalI GATC 4 cut(s) 51, 94, 400, 619
MboI GATC 4 cut(s) 49, 92, 398, 617
MboII GAAGA 8 cut(s) 220, 305, 386, 400, 452, 548, 671, 694
MfeI CAATTG 2 cut(s) 330, 435
MflI RGATCY 1 cut(s) 92
MhlI GDGCHC 2 cut(s) 224, 852
MluCI AATT 7 cut(s) 16, 82, 266, 330, 435, 670, 859
MlyI GAGTC 3 cut(s) 118, 268, 305
MnlI CCTC 5 cut(s) 48, 183, 339, 804, 838
MseI TTAA 1 cut(s) 203
MslI CAYNNNNRTG 1 cut(s) 74
MspR9I CCNGG 2 cut(s) 262, 642
MunI CAATTG 2 cut(s) 330, 435
MvaI CCWGG 2 cut(s) 262, 642
MvnI CGCG 1 cut(s) 568
MwoI GCNNNNNNNGC 1 cut(s) 244
NdeI CATATG 2 cut(s) 746, 777
NdeII GATC 4 cut(s) 49, 92, 398, 617
NlaIII CATG 3 cut(s) 73, 503, 858
NmuCI GTSAC 4 cut(s) 154, 373, 596, 608
NruI TCGCGA 1 cut(s) 568
NspI RCATGY 1 cut(s) 73
PaeI GCATGC 1 cut(s) 73
PasI CCCWGGG 1 cut(s) 261
PfeI GAWTC 4 cut(s) 126, 359, 391, 443
PkrI GCNGC 6 cut(s) 27, 151, 351, 480, 767, 770
PleI GAGTC 3 cut(s) 117, 268, 304
PpsI GAGTC 3 cut(s) 117, 268, 304
Psp6I CCWGG 2 cut(s) 260, 640
PspGI CCWGG 2 cut(s) 260, 640
PstI CTGCAG 2 cut(s) 483, 770
PstNI CAGNNNCTG 1 cut(s) 511
PsuI RGATCY 1 cut(s) 92
RruI TCGCGA 1 cut(s) 568
RsaI GTAC 4 cut(s) 215, 311, 498, 526
RsaNI GTAC 4 cut(s) 214, 310, 497, 525
RseI CAYNNNNRTG 1 cut(s) 74
SaqAI TTAA 1 cut(s) 203
SatI GCNGC 6 cut(s) 26, 150, 350, 479, 766, 769
Sau3AI GATC 4 cut(s) 49, 92, 398, 617
ScaI AGTACT 2 cut(s) 311, 526
SchI GAGTC 3 cut(s) 118, 268, 305
ScrFI CCNGG 2 cut(s) 262, 642
SduI GDGCHC 2 cut(s) 224, 852
SetI ASST 5 cut(s) 249, 256, 358, 480, 513
SfcI CTRYAG 2 cut(s) 479, 766
SmiMI CAYNNNNRTG 1 cut(s) 74
SmlI CTYRAG 1 cut(s) 316
SmoI CTYRAG 1 cut(s) 316
SphI GCATGC 1 cut(s) 73
Sse9I AATT 7 cut(s) 16, 82, 266, 330, 435, 670, 859
SspMI CTAG 2 cut(s) 179, 755
StyD4I CCNGG 2 cut(s) 260, 640
StyI CCWWGG 1 cut(s) 96
TaqI TCGA 5 cut(s) 132, 397, 616, 826, 840
TasI AATT 7 cut(s) 16, 82, 266, 330, 435, 670, 859
TatI WGTACW 3 cut(s) 213, 309, 524
TfiI GAWTC 4 cut(s) 126, 359, 391, 443
Tru1I TTAA 1 cut(s) 203
Tru9I TTAA 1 cut(s) 203
TscAI CASTG 1 cut(s) 159
TseFI GTSAC 4 cut(s) 154, 373, 596, 608
TseI GCWGC 6 cut(s) 25, 149, 349, 478, 765, 768
Tsp45I GTSAC 4 cut(s) 154, 373, 596, 608
TspDTI ATGAA 5 cut(s) 242, 299, 474, 702, 704
TspGWI ACGGA 1 cut(s) 289
TspRI CASTG 1 cut(s) 159
XapI RAATTY 2 cut(s) 82, 266
XbaI TCTAGA 1 cut(s) 754
XceI RCATGY 1 cut(s) 73
XspI CTAG 2 cut(s) 179, 755
ZrmI AGTACT 2 cut(s) 311, 526
Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.