Rw6G026310

gag-polypeptide of LTR copia-type

Design Primers CRISPR Design

Basic Information

Type: gene
Biological Identity
rosa_wichuraiana
Chr6
OG0000106
Physical Location & Seq
Reverse (-)
49675899 .. 49676602
704 bp
Loading structure...
UTR
Exon/CDS
Intron
Rw6G026310.1

Sequence Viewer

Length: 663 bp
ATGGCTAGTTCAAGCAACTCATCAGAAATTAGAGTTCCAATCTTCAATGGTGAGAACTTCGACTTTTGGATGATCAAGATGAGAACCATGTTCATCTCACATGAACTATGGAGTTATGCGGATGAAGGCTATATAGTTCCAGAAACTGAAAATATGTCTAATGCTCAGAAAGTGGAGCTAAAGACAAACATAAAGAAAGATGCAAAAGCTCTAGGAATACTGCAAAACTCAATCTCAGATGAGATCTTTCCAAGAATCTCAAAGGAAGAAACAGCCAAAGCAGCTTGGGATGTTCTGCTGCTTGAGTTCAAAGGCTCAAAACAGGTCAGAGCTGTTAAACTTCTATCCTTGAGAAGAGATTTTGAGTATACTAGAATGACTGAAACTGAGCTGCTAAATGATTATAGTACTAGACTGACTGATATAGTAAACCAAATGAAAACCTATGCTGATCTAAAAAGAAAAGATGATGCTATAATCTATATTATAGATGGGACTAAGGATATTGAAACTTTTGGTGTACAAGATGTGATGGGGACACTTAAGGCTTTTGATCAAAGGTTAATGAGTCATGATGAACCATCTGAAAAAGCTTTTGAAACACTGAGTCTTAGCTCAAATCAGAAAAATGATGAGCCATGCATCTACTTCTTATTGAAATAA
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
DUF4219 Retrotran_gag_2 gag_pre-integrs rve zf-CCHC

Protein Analysis

220

Amino Acids

25.41

Weight (kDa)

5.07

Isoelectric Point (pI)

39.37

Instability Index
Protein Domains (Pfam)
Domain Name Pfam ID Position E-value Description
Retrotran_gag_2 PF14223 27 - 151 5.1e-20 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: OG0000106)

Species Orthologous Gene IDs
arabidopsis_thaliana AT3G20980 AT3G21000
fragaria_vesca FvH4_1g15931 FvH4_1g15931 FvH4_1g18381 FvH4_1g18382 FvH4_1g22571 FvH4_1g24950 FvH4_1g29372 FvH4_2g03582 FvH4_2g09851 FvH4_2g13112 FvH4_2g20843 FvH4_2g22701 FvH4_2g22702 FvH4_2g23403 FvH4_2g40201 FvH4_3g03542 FvH4_3g03543 FvH4_3g04761 FvH4_3g10464 FvH4_3g12741 FvH4_3g15781 FvH4_3g30981 FvH4_4g00985 FvH4_4g07035 FvH4_4g08192 FvH4_4g08211 FvH4_4g08553 FvH4_4g14242 FvH4_4g14243 FvH4_4g14641 FvH4_4g14843 FvH4_4g14844 FvH4_4g15061 FvH4_4g16281 FvH4_4g19152 FvH4_4g26451 FvH4_5g06442 FvH4_5g22521 FvH4_5g24301 FvH4_5g38641 FvH4_6g02393 FvH4_6g12782 FvH4_6g13871 FvH4_6g19391 FvH4_6g20105 FvH4_6g21292 FvH4_6g23581 FvH4_6g29153 FvH4_6g29691 FvH4_6g30871 FvH4_6g33351 FvH4_6g37042 FvH4_6g38781 FvH4_6g40340 FvH4_7g11221 FvH4_7g23352 FvH4_7g23352 FvH4_7g31212 FvH4_7g32172 FvH4_7g32173 FvH4_7g33701
malus_domestica MD03G1006900.v1.1 MD04G1039100.v1.1 MD04G1239100.v1.1 MD05G1048700.v1.1 MD08G1001800.v1.1 MD09G1165800.v1.1 MD11G1065200.v1.1 MD11G1138200.v1.1 MD14G1033300.v1.1 MD14G1173900.v1.1 MD15G1218200.v1.1 MD16G1034000.v1.1
prunus_persica Prupe.1G219500_v2.0.a1 Prupe.2G169400_v2.0.a1 Prupe.4G109700_v2.0.a1 Prupe.7G022000_v2.0.a1
pyrus_communis pycom01g02000 pycom02g13350 pycom03g01010 pycom04g05000 pycom04g06100 pycom05g05580 pycom05g09950 pycom05g13280 pycom05g26610 pycom06g05940 pycom06g07760 pycom07g06120 pycom07g24780 pycom08g08820 pycom09g03600 pycom09g07200 pycom10g01280 pycom10g06730 pycom10g08410 pycom10g25520 pycom11g00470 pycom11g05250 pycom11g25180 pycom12g08050 pycom13g14760 pycom13g28170 pycom15g14310 pycom15g19880 pycom15g24230 pycom15g33640 pycom16g02150 pycom16g16240 pycom16g20050 pycom16g21090 pycom17g06100
rosa_chinensis RchiOBHm_Chr1g0322161 RchiOBHm_Chr1g0326341 RchiOBHm_Chr1g0357701 RchiOBHm_Chr1g0379861 RchiOBHm_Chr1g0383421 RchiOBHm_Chr2g0093981 RchiOBHm_Chr2g0139051 RchiOBHm_Chr2g0145501 RchiOBHm_Chr3g0450971 RchiOBHm_Chr3g0451441 RchiOBHm_Chr3g0457411 RchiOBHm_Chr4g0436261 RchiOBHm_Chr5g0051431 RchiOBHm_Chr5g0064031 RchiOBHm_Chr5g0073141 RchiOBHm_Chr5g0080061 RchiOBHm_Chr7g0200561 RchiOBHm_Chr7g0235911
rosa_laevigata RLG00000000145 RLG00000000429 RLG00000020339 RLG00000035212
rosa_multiflora Rmu_co7977988.1_g000001 Rmu_co8037866.1_g000001 Rmu_co8243895.1_g000001 Rmu_co8363787.1_g000001 Rmu_co8381003.1_g000001 Rmu_sc0000263.1_g000006 Rmu_sc0000349.1_g000002 Rmu_sc0000455.1_g000031 Rmu_sc0000936.1_g000022 Rmu_sc0001035.1_g000023 Rmu_sc0001169.1_g000019 Rmu_sc0001250.1_g000026 Rmu_sc0002200.1_g000051 Rmu_sc0002230.1_g000027 Rmu_sc0002591.1_g000039 Rmu_sc0003182.1_g000003 Rmu_sc0003441.1_g000068 Rmu_sc0003722.1_g000018 Rmu_sc0003764.1_g000007 Rmu_sc0006014.1_g000016 Rmu_sc0012582.1_g000002 Rmu_sc0013519.1_g000002 Rmu_sc0014550.1_g000005 Rmu_sc0014857.1_g000007 Rmu_sc0019855.1_g000001 Rmu_sc0030839.1_g000001 Rmu_sc0031308.1_g000001
rosa_roxburghii Rroxscaffold_1G00011290 Rroxscaffold_1G00041340 Rroxscaffold_1G00053780 Rroxscaffold_1G00059130 Rroxscaffold_1G00061580 Rroxscaffold_2G00080940 Rroxscaffold_2G00109540 Rroxscaffold_3G00228400 Rroxscaffold_3G00237710 Rroxscaffold_4G00285210 Rroxscaffold_4G00299600 Rroxscaffold_4G00324940 Rroxscaffold_4G00330580 Rroxscaffold_5G00333000 Rroxscaffold_5G00347920 Rroxscaffold_5G00375310 Rroxscaffold_6G00394760 Rroxscaffold_6G00406260 Rroxscaffold_7G00165690 Rroxscaffold_7G00187680
rosa_rugosa Rorug01G0050200 Rorug02G0273800 Rorug06G0490600 Rorug06G0490600 Rorug06G0490700
rosa_samantha Rh1AG348400 Rh5AG222600 Rh6DG000500 Rh6DG194500 Rh7BG452700
rosa_wichuraiana Rw0G003060 Rw0G010530 Rw0G012970 Rw0G022560 Rw0G023390 Rw1G001270 Rw1G001530 Rw1G006070 Rw1G008210 Rw1G022090 Rw1G023320 Rw2G003790 Rw2G004140 Rw2G005280 Rw2G006460 Rw2G019620 Rw2G019840 Rw2G022530 Rw2G023280 Rw2G024990 Rw2G042380 Rw2G051390 Rw3G001640 Rw3G016720 Rw3G017100 Rw3G020890 Rw3G020900 Rw3G021100 Rw4G004820 Rw4G014950 Rw4G030920 Rw4G031400 Rw5G008500 Rw5G017950 Rw5G020170 Rw5G030160 Rw5G033050 Rw5G034640 Rw5G043920 Rw6G005060 Rw6G005540 Rw6G006720 Rw6G008460 Rw6G008670 Rw6G014780 Rw6G019100 Rw6G019350 Rw6G026310 Rw7G016810 Rw7G019180 Rw7G022890 Rw7G025880 Rw7G026390 Rw7G028340 Rw7G034850 Rw7G035170 Rw7G035420 Rw7G037990 Rw7G041560

Restriction Enzyme Sites

1 / 10
Enzyme Recognition Site Cut Count Positions (bp)
AccI GTMKAC 1 cut(s) 368
AciI CCGC 1 cut(s) 119
AfaI GTAC 2 cut(s) 409, 522
AflII CTTAAG 1 cut(s) 542
AgsI TTSAA 6 cut(s) 12, 46, 310, 509, 599, 658
AluBI AGCT 7 cut(s) 178, 209, 284, 332, 391, 593, 615
AluI AGCT 7 cut(s) 178, 209, 284, 332, 391, 593, 615
AlwNI CAGNNNCTG 1 cut(s) 146
ApeKI GCWGC 3 cut(s) 281, 298, 391
AsuHPI GGTGA 1 cut(s) 62
BbvI GCAGC 3 cut(s) 285, 293, 378
BccI CCATC 3 cut(s) 485, 526, 589
BclI TGATCA 2 cut(s) 72, 553
BfaI CTAG 4 cut(s) 6, 212, 372, 411
BfrI CTTAAG 1 cut(s) 542
BglII AGATCT 1 cut(s) 243
BisI GCNGC 3 cut(s) 282, 299, 392
BlsI GCNGC 3 cut(s) 283, 300, 393
BmcAI AGTACT 1 cut(s) 409
BmsI GCATC 3 cut(s) 190, 460, 651
BpuEI CTTGAG 2 cut(s) 323, 370
BseGI GGATG 3 cut(s) 75, 127, 295
BseMII CTCAG 4 cut(s) 179, 249, 378, 596
BseXI GCAGC 3 cut(s) 285, 293, 378
BslFI GGGAC 2 cut(s) 508, 550
BsmFI GGGAC 2 cut(s) 508, 550
Bsp1407I TGTACA 1 cut(s) 520
Bsp143I GATC 4 cut(s) 72, 243, 451, 553
BspACI CCGC 1 cut(s) 119
BspCNI CTCAG 4 cut(s) 178, 248, 379, 597
BspHI TCATGA 1 cut(s) 571
BspTI CTTAAG 1 cut(s) 542
BsrGI TGTACA 1 cut(s) 520
BssMI GATC 4 cut(s) 72, 243, 451, 553
BssNAI GTATAC 1 cut(s) 369
Bst1107I GTATAC 1 cut(s) 369
Bst6I CTCTTC 1 cut(s) 349
BstAFI CTTAAG 1 cut(s) 542
BstAUI TGTACA 1 cut(s) 520
BstDEI CTNAG 6 cut(s) 165, 235, 387, 498, 605, 611
BstF5I GGATG 3 cut(s) 75, 127, 295
BstKTI GATC 4 cut(s) 75, 246, 454, 556
BstMBI GATC 4 cut(s) 72, 243, 451, 553
BstMWI GCNNNNNNNGC 1 cut(s) 281
BstV1I GCAGC 3 cut(s) 285, 293, 378
BstX2I RGATCY 1 cut(s) 243
BstYI RGATCY 1 cut(s) 243
BstZ17I GTATAC 1 cut(s) 369
BtsCI GGATG 3 cut(s) 75, 127, 295
BtsIMutI CAGTG 1 cut(s) 602
CaiI CAGNNNCTG 1 cut(s) 146
CciI TCATGA 1 cut(s) 571
Csp6I GTAC 2 cut(s) 408, 521
CviAII CATG 4 cut(s) 88, 101, 572, 639
CviQI GTAC 2 cut(s) 408, 521
DdeI CTNAG 6 cut(s) 165, 235, 387, 498, 605, 611
DpnI GATC 4 cut(s) 74, 245, 453, 555
DpnII GATC 4 cut(s) 72, 243, 451, 553
Eam1104I CTCTTC 1 cut(s) 349
EarI CTCTTC 1 cut(s) 349
EcoT22I ATGCAT 1 cut(s) 644
FaeI CATG 4 cut(s) 91, 104, 575, 642
FaqI GGGAC 2 cut(s) 508, 550
FatI CATG 4 cut(s) 87, 100, 571, 638
FbaI TGATCA 2 cut(s) 72, 553
FblI GTMKAC 1 cut(s) 368
Fnu4HI GCNGC 3 cut(s) 282, 299, 392
FokI GGATG 3 cut(s) 82, 134, 302
Fsp4HI GCNGC 3 cut(s) 282, 299, 392
FspBI CTAG 4 cut(s) 6, 212, 372, 411
GluI GCNGC 3 cut(s) 282, 299, 392
Hin1II CATG 4 cut(s) 91, 104, 575, 642
HindIII AAGCTT 1 cut(s) 591
HinfI GANTC 3 cut(s) 255, 568, 607
HphI GGTGA 1 cut(s) 62
Hpy166II GTNNAC 3 cut(s) 369, 430, 521
Hpy188I TCNGA 6 cut(s) 25, 168, 238, 329, 586, 624
Hpy188III TCNNGA 3 cut(s) 76, 140, 572
Hpy8I GTNNAC 3 cut(s) 369, 430, 521
HpyAV CCTTC 1 cut(s) 119
HpyCH4V TGCA 3 cut(s) 203, 223, 642
HpyF10VI GCNNNNNNNGC 1 cut(s) 281
HpyF3I CTNAG 6 cut(s) 165, 235, 387, 498, 605, 611
Hsp92II CATG 4 cut(s) 91, 104, 575, 642
Ksp22I TGATCA 2 cut(s) 72, 553
Kzo9I GATC 4 cut(s) 72, 243, 451, 553
LmnI GCTCC 1 cut(s) 175
LpnPI CCDG 2 cut(s) 153, 308
Lsp1109I GCAGC 3 cut(s) 285, 293, 378
LweI GCATC 3 cut(s) 190, 460, 651
MaeI CTAG 4 cut(s) 6, 212, 372, 411
MalI GATC 4 cut(s) 74, 245, 453, 555
MboI GATC 4 cut(s) 72, 243, 451, 553
MboII GAAGA 3 cut(s) 34, 278, 366
MflI RGATCY 1 cut(s) 243
MluCI AATT 1 cut(s) 27
MlyI GAGTC 2 cut(s) 577, 616
Mph1103I ATGCAT 1 cut(s) 644
MseI TTAA 3 cut(s) 336, 543, 563
MspCI CTTAAG 1 cut(s) 542
MwoI GCNNNNNNNGC 1 cut(s) 281
NdeII GATC 4 cut(s) 72, 243, 451, 553
NlaIII CATG 4 cut(s) 91, 104, 575, 642
NsiI ATGCAT 1 cut(s) 644
PagI TCATGA 1 cut(s) 571
PfeI GAWTC 1 cut(s) 255
PkrI GCNGC 3 cut(s) 283, 300, 393
PleI GAGTC 2 cut(s) 576, 615
PpsI GAGTC 2 cut(s) 576, 615
PstNI CAGNNNCTG 1 cut(s) 146
PsuI RGATCY 1 cut(s) 243
RsaI GTAC 2 cut(s) 409, 522
RsaNI GTAC 2 cut(s) 408, 521
SaqAI TTAA 3 cut(s) 336, 543, 563
SatI GCNGC 3 cut(s) 282, 299, 392
Sau3AI GATC 4 cut(s) 72, 243, 451, 553
ScaI AGTACT 1 cut(s) 409
SchI GAGTC 2 cut(s) 577, 616
SfaNI GCATC 3 cut(s) 190, 460, 651
SmlI CTYRAG 3 cut(s) 302, 349, 542
SmoI CTYRAG 3 cut(s) 302, 349, 542
Sse9I AATT 1 cut(s) 27
SsiI CCGC 1 cut(s) 119
SspMI CTAG 4 cut(s) 6, 212, 372, 411
TaqI TCGA 1 cut(s) 60
TasI AATT 1 cut(s) 27
TatI WGTACW 2 cut(s) 407, 520
TfiI GAWTC 1 cut(s) 255
Tru1I TTAA 3 cut(s) 336, 543, 563
Tru9I TTAA 3 cut(s) 336, 543, 563
TscAI CASTG 1 cut(s) 609
TseI GCWGC 3 cut(s) 281, 298, 391
TspDTI ATGAA 5 cut(s) 82, 117, 138, 452, 591
TspRI CASTG 1 cut(s) 609
Vha464I CTTAAG 1 cut(s) 542
XmiI GTMKAC 1 cut(s) 368
XspI CTAG 4 cut(s) 6, 212, 372, 411
ZrmI AGTACT 1 cut(s) 409
Zsp2I ATGCAT 1 cut(s) 644
Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.