Rw7G017250

gag-polypeptide of LTR copia-type

Design Primers CRISPR Design

Basic Information

Type: gene
Biological Identity
rosa_wichuraiana
Chr7
OG0000154
Physical Location & Seq
Forward (+)
17961653 .. 17963916
2264 bp
Loading structure...
UTR
Exon/CDS
Intron
Rw7G017250.1

Sequence Viewer

Length: 687 bp
ATGCAAACCAATGAGTATTGGAATCTGGTAGATGAGGGAATTCCGGCAGCGACTGAGGCGCAGCGGAAAACAGTGGATGAAGCAAAGCTCAAAGATTTGAAGGTCAAGAACTTTCTATTCCAAGCAATTGACAGAGAGATCATGGAGACTATTCTTGACAAAGGAACATCCAAAGCCATCTGGGATTCAATGAAACAAAAGTATCAGGGCTCAACAAAGGTGAGAAGGGCACAGCTGCAGGCTTTAAGAAGGGAGTTCGAGCTGCTAGGTATGAAGGAGGGAGAGAAGGTGGACAGCTATGTCTCAAGAACCCTAACTGTGGTGAACAAAATGAAGGTACATGGAGAGCAAATGGAGCAGAATGTGGTGGTTGAAAAAATCCTGAGGTCCATGACATTCAAATATAACTATGTTGTATGTTCGATAGAGGAGTCAAATGATCTCACCACCATGAGTATCGATGAGCTCCACGGGAGTTTGCTGGTTCATGAGCAGCGAATGCAGGGGTATCAGGAAGACGAACAGGTGTTGAAAATTGCAAATGAAGGGAGATTTGGAGGCAGAGGTGAGCAGAAGTTCGGAGGAAGAGCTCGTGGGAGCTTTCGTGGAAGAGGTAGAGGCAGAGGAAGAGGTTACACCAAAGACCTCGTAGAATGCTTTAAGTGCCACAAACTAGGGCATTTTTAG
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

228

Amino Acids

26.27

Weight (kDa)

9.12

Isoelectric Point (pI)

30.46

Instability Index
Protein Domains (Pfam)
Domain Name Pfam ID Position E-value Description
Retrotran_gag_2 PF14223 3 - 169 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)
AasI GACNNNNNNGTC 1 cut(s) 299
AciI CCGC 1 cut(s) 64
AcsI RAATTY 1 cut(s) 39
AfaI GTAC 1 cut(s) 339
AfiI CCNNNNNNNGG 1 cut(s) 319
AgsI TTSAA 5 cut(s) 100, 189, 374, 400, 532
AjuI GAANNNNNNNTTGG 2 cut(s) 537, 569
AluBI AGCT 7 cut(s) 88, 235, 262, 297, 466, 590, 600
AluI AGCT 7 cut(s) 88, 235, 262, 297, 466, 590, 600
Alw21I GWGCWC 2 cut(s) 468, 592
Alw26I GTCTC 2 cut(s) 140, 307
AlwNI CAGNNNCTG 1 cut(s) 53
ApeKI GCWGC 5 cut(s) 47, 61, 235, 262, 493
ApoI RAATTY 1 cut(s) 39
AspLEI GCGC 1 cut(s) 61
AspS9I GGNCC 1 cut(s) 387
AsuHPI GGTGA 4 cut(s) 232, 334, 436, 578
AvaII GGWCC 1 cut(s) 387
AxyI CCTNAGG 1 cut(s) 383
BaeGI GKGCMC 1 cut(s) 232
BaeI ACNNNNGTAYC 2 cut(s) 185, 218
BanII GRGCYC 3 cut(s) 212, 468, 592
BauI CACGAG 1 cut(s) 591
BbsI GAAGAC 1 cut(s) 522
Bbv12I GWGCWC 2 cut(s) 468, 592
BbvI GCAGC 5 cut(s) 59, 73, 222, 249, 505
BccI CCATC 1 cut(s) 185
BcoDI GTCTC 2 cut(s) 140, 307
BfaI CTAG 2 cut(s) 266, 674
BfmI CTRYAG 1 cut(s) 236
BisI GCNGC 5 cut(s) 48, 62, 236, 263, 494
BlsI GCNGC 5 cut(s) 49, 63, 237, 264, 495
Bme18I GGWCC 1 cut(s) 387
BmgT120I GGNCC 1 cut(s) 387
BpiI GAAGAC 1 cut(s) 522
BpuEI CTTGAG 1 cut(s) 289
Bsa29I ATCGAT 1 cut(s) 459
BsaJI CCNNGG 1 cut(s) 469
BsaXI ACNNNNNCTCC 4 cut(s) 273, 303, 589, 619
Bsc4I CCNNNNNNNGG 1 cut(s) 319
Bse21I CCTNAGG 1 cut(s) 383
BseCI ATCGAT 1 cut(s) 459
BseDI CCNNGG 1 cut(s) 469
BseGI GGATG 2 cut(s) 82, 167
BseLI CCNNNNNNNGG 1 cut(s) 319
BseMII CTCAG 2 cut(s) 45, 374
BseRI GAGGAG 1 cut(s) 443
BseSI GKGCMC 1 cut(s) 232
BseXI GCAGC 5 cut(s) 59, 73, 222, 249, 505
BshVI ATCGAT 1 cut(s) 459
BsiHKAI GWGCWC 2 cut(s) 468, 592
BsiSI CCGG 1 cut(s) 44
BslI CCNNNNNNNGG 1 cut(s) 319
BsmAI GTCTC 2 cut(s) 140, 307
BsmI GAATGC 2 cut(s) 504, 659
Bsp1286I GDGCHC 4 cut(s) 212, 232, 468, 592
Bsp143I GATC 2 cut(s) 138, 439
BspACI CCGC 1 cut(s) 64
BspCNI CTCAG 2 cut(s) 46, 375
BspDI ATCGAT 1 cut(s) 459
BspHI TCATGA 1 cut(s) 487
BspMAI CTGCAG 1 cut(s) 240
BspQI GCTCTTC 1 cut(s) 580
BssECI CCNNGG 1 cut(s) 469
BssMI GATC 2 cut(s) 138, 439
BssSI CACGAG 1 cut(s) 591
Bst2BI CACGAG 1 cut(s) 591
Bst4CI ACNGT 2 cut(s) 73, 319
Bst6I CTCTTC 3 cut(s) 580, 604, 622
BstAPI GCANNNNNTGC 1 cut(s) 499
BstC8I GCNNGC 1 cut(s) 240
BstDEI CTNAG 2 cut(s) 54, 383
BstDSI CCRYGG 1 cut(s) 469
BstF5I GGATG 2 cut(s) 82, 167
BstHHI GCGC 1 cut(s) 61
BstKTI GATC 2 cut(s) 141, 442
BstMAI GTCTC 2 cut(s) 140, 307
BstMBI GATC 2 cut(s) 138, 439
BstMWI GCNNNNNNNGC 4 cut(s) 56, 355, 499, 663
BstSFI CTRYAG 1 cut(s) 236
BstSLI GKGCMC 1 cut(s) 232
BstV1I GCAGC 5 cut(s) 59, 73, 222, 249, 505
BstV2I GAAGAC 1 cut(s) 522
Bsu15I ATCGAT 1 cut(s) 459
Bsu36I CCTNAGG 1 cut(s) 383
BsuTUI ATCGAT 1 cut(s) 459
BtgI CCRYGG 1 cut(s) 469
BtsCI GGATG 2 cut(s) 82, 167
BtsIMutI CAGTG 1 cut(s) 78
Cac8I GCNNGC 1 cut(s) 240
CaiI CAGNNNCTG 1 cut(s) 53
CciI TCATGA 1 cut(s) 487
CfoI GCGC 1 cut(s) 61
Cfr13I GGNCC 1 cut(s) 387
ClaI ATCGAT 1 cut(s) 459
Csp6I GTAC 1 cut(s) 338
CviAII CATG 5 cut(s) 142, 341, 391, 451, 488
CviQI GTAC 1 cut(s) 338
DdeI CTNAG 2 cut(s) 54, 383
DpnI GATC 2 cut(s) 140, 441
DpnII GATC 2 cut(s) 138, 439
DrdI GACNNNNNNGTC 1 cut(s) 299
DseDI GACNNNNNNGTC 1 cut(s) 299
Eam1104I CTCTTC 3 cut(s) 580, 604, 622
EarI CTCTTC 3 cut(s) 580, 604, 622
Ecl136II GAGCTC 2 cut(s) 466, 590
Eco24I GRGCYC 3 cut(s) 212, 468, 592
Eco47I GGWCC 1 cut(s) 387
Eco53kI GAGCTC 2 cut(s) 466, 590
Eco81I CCTNAGG 1 cut(s) 383
EcoICRI GAGCTC 2 cut(s) 466, 590
EcoRI GAATTC 1 cut(s) 39
EcoT38I GRGCYC 3 cut(s) 212, 468, 592
FaeI CATG 5 cut(s) 145, 344, 394, 454, 491
FatI CATG 5 cut(s) 141, 340, 390, 450, 487
Fnu4HI GCNGC 5 cut(s) 48, 62, 236, 263, 494
FokI GGATG 2 cut(s) 89, 154
FriOI GRGCYC 3 cut(s) 212, 468, 592
Fsp4HI GCNGC 5 cut(s) 48, 62, 236, 263, 494
FspBI CTAG 2 cut(s) 266, 674
GlaI GCGC 1 cut(s) 60
GluI GCNGC 5 cut(s) 48, 62, 236, 263, 494
HapII CCGG 1 cut(s) 44
HhaI GCGC 1 cut(s) 61
Hin1II CATG 5 cut(s) 145, 344, 394, 454, 491
Hin6I GCGC 1 cut(s) 59
HinP1I GCGC 1 cut(s) 59
HinfI GANTC 3 cut(s) 22, 185, 431
HpaII CCGG 1 cut(s) 44
HphI GGTGA 4 cut(s) 232, 334, 436, 578
Hpy166II GTNNAC 2 cut(s) 292, 325
Hpy188I TCNGA 1 cut(s) 581
Hpy188III TCNNGA 6 cut(s) 106, 155, 306, 382, 488, 512
Hpy8I GTNNAC 2 cut(s) 292, 325
HpyAV CCTTC 7 cut(s) 94, 219, 243, 268, 280, 328, 539
HpyCH4III ACNGT 2 cut(s) 73, 319
HpyCH4V TGCA 4 cut(s) 4, 238, 502, 539
HpyF10VI GCNNNNNNNGC 4 cut(s) 56, 355, 499, 663
HpyF3I CTNAG 2 cut(s) 54, 383
Hsp92II CATG 5 cut(s) 145, 344, 394, 454, 491
HspAI GCGC 1 cut(s) 59
Kzo9I GATC 2 cut(s) 138, 439
LguI GCTCTTC 1 cut(s) 580
LmnI GCTCC 3 cut(s) 355, 471, 597
Lsp1109I GCAGC 5 cut(s) 59, 73, 222, 249, 505
MaeI CTAG 2 cut(s) 266, 674
MaeIII GTNAC 1 cut(s) 632
MalI GATC 2 cut(s) 140, 441
MboI GATC 2 cut(s) 138, 439
MboII GAAGA 4 cut(s) 527, 597, 621, 639
MfeI CAATTG 1 cut(s) 126
MhlI GDGCHC 4 cut(s) 212, 232, 468, 592
MluCI AATT 3 cut(s) 39, 126, 534
MlyI GAGTC 1 cut(s) 440
MseI TTAA 2 cut(s) 245, 660
MslI CAYNNNNRTG 1 cut(s) 449
MspA1I CMGCKG 2 cut(s) 64, 235
MspI CCGG 1 cut(s) 44
MunI CAATTG 1 cut(s) 126
Mva1269I GAATGC 2 cut(s) 504, 659
MwoI GCNNNNNNNGC 4 cut(s) 56, 355, 499, 663
NdeII GATC 2 cut(s) 138, 439
NlaIII CATG 5 cut(s) 145, 344, 394, 454, 491
PagI TCATGA 1 cut(s) 487
PciSI GCTCTTC 1 cut(s) 580
PctI GAATGC 2 cut(s) 504, 659
PfeI GAWTC 2 cut(s) 22, 185
PkrI GCNGC 5 cut(s) 49, 63, 237, 264, 495
PleI GAGTC 1 cut(s) 439
PpsI GAGTC 1 cut(s) 439
Psp124BI GAGCTC 2 cut(s) 468, 592
PspPI GGNCC 1 cut(s) 387
PstI CTGCAG 1 cut(s) 240
PstNI CAGNNNCTG 1 cut(s) 53
PvuII CAGCTG 1 cut(s) 235
RsaI GTAC 1 cut(s) 339
RsaNI GTAC 1 cut(s) 338
RseI CAYNNNNRTG 1 cut(s) 449
SacI GAGCTC 2 cut(s) 468, 592
SapI GCTCTTC 1 cut(s) 580
SaqAI TTAA 2 cut(s) 245, 660
SatI GCNGC 5 cut(s) 48, 62, 236, 263, 494
Sau3AI GATC 2 cut(s) 138, 439
Sau96I GGNCC 1 cut(s) 387
SchI GAGTC 1 cut(s) 440
SduI GDGCHC 4 cut(s) 212, 232, 468, 592
SfcI CTRYAG 1 cut(s) 236
SinI GGWCC 1 cut(s) 387
SmiMI CAYNNNNRTG 1 cut(s) 449
SmlI CTYRAG 1 cut(s) 304
SmoI CTYRAG 1 cut(s) 304
Sse9I AATT 3 cut(s) 39, 126, 534
SsiI CCGC 1 cut(s) 64
SspMI CTAG 2 cut(s) 266, 674
SstI GAGCTC 2 cut(s) 468, 592
TaaI ACNGT 2 cut(s) 73, 319
TaqI TCGA 3 cut(s) 258, 422, 459
TasI AATT 3 cut(s) 39, 126, 534
TfiI GAWTC 2 cut(s) 22, 185
Tru1I TTAA 2 cut(s) 245, 660
Tru9I TTAA 2 cut(s) 245, 660
TscAI CASTG 1 cut(s) 78
TseI GCWGC 5 cut(s) 47, 61, 235, 262, 493
TspDTI ATGAA 6 cut(s) 93, 206, 287, 347, 476, 558
TspRI CASTG 1 cut(s) 78
VpaK11BI GGWCC 1 cut(s) 387
XapI RAATTY 1 cut(s) 39
XspI CTAG 2 cut(s) 266, 674
Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.