Rw6G028610

gag-polypeptide of LTR copia-type

Design Primers CRISPR Design

Basic Information

Type: gene
Biological Identity
rosa_wichuraiana
Chr6
OG0000154
Physical Location & Seq
Forward (+)
52695244 .. 52696842
1599 bp
Loading structure...
UTR
Exon/CDS
Intron
Rw6G028610.1

Sequence Viewer

Length: 960 bp
ATGAGAGGAAGCCAACGAATAATTGTATGTCAAATTGAGTATTGGAGTCTCATTGAGACAGGCTTTACTGAGCCTGCCACTGGAGAGGGGATGACGGCTGCACAGAGAAGGTCATTGGATGAGTTGAAGCTGAAAGATCTCAAGGTAAAGAATTACCTCTTTCAGGCAATTGACCGCGCAATTTTGGAGACCATTCTCCAAAAGGACACAGCGAAGCAGATATGGGACTCGCTAAAAAAGAAGTATGAAGGCAATGCAAGAGTGAAATGCTCCCAACTCCAAGCACTACGTCGAGAGTTTGAAACCCTTGAGATGAAGGTTGGTGAGTCTGTTTCAGATTATTTCTCAAGAGTTATGTCAGTGGCAAATAGGATGCGAACCCATGGCGAACAGATGCAAGATGTTACTGTGGTGGAGAAGATACTTCGCTCCTTGACTGACAAGTTCAACTACATAGTCTGCTCCATTGAAGAATCCAAAGACATTGATCAGTTATCAGTGGATGAGCTGCAGAGTTCGTTGCTCGTACATGAGCAAAAACTCAATCGAAATAACGGAGAGGTGCAAGCAGCCTTGAAAGTAGCAACAAATGGTGGTTTTCCAACAAGAGGAAGAGGTCGTGGGACTTGGAGAGGTAGAGGCAGAGGCTCTAGAGATGGCAGCGGTAGTAGGACCCGACATGATCTTCAATCCTACGATAGGACCAAACATGATCTTCACTCCTACGATCATCAGCCCTCAAATTCCCAAAGTAGAGGCAGGGGGCACTTTGATAAGTCCAAGGTTGAATGCTTCAGATGTCATGGGCTTGGTCACTTTCGTTCAGAGTGTTATGCGAAGCTTCACAAAGACAAGCAAAAGAATGGGGAGCAGTCCAATTTTGCAGAGAAAAAGGAAAAGGAAGAAGAGACACTTCTGATGGCATTGCATGTGAAGGAGGAGCCTGAAGCAAACACATAG
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

319

Amino Acids

36.62

Weight (kDa)

8.98

Isoelectric Point (pI)

47.08

Instability Index
Protein Domains (Pfam)
Domain Name Pfam ID Position E-value Description
Retrotran_gag_2 PF14223 12 - 185 2.1e-30 gag-polypeptide of LTR copia-type
Hydrophobicity Profile (Kyte-Doolittle)
AI Structure Prediction Report
Calculating structure properties...

Genomic Context

Gene Family Tree

Species Filter
Loading...
Style Settings
Image
Tree File
Tip: Beautify your tree with professional tools

Download the Full Tree (.nwk) file, then upload it to any of the following tools to customize colors, fonts, annotations, clades, and branch support.

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)
AccII CGCG 1 cut(s) 177
AciI CCGC 2 cut(s) 175, 663
AcsI RAATTY 1 cut(s) 742
AcuI CTGAAG 1 cut(s) 778
AfaI GTAC 1 cut(s) 528
AfiI CCNNNNNNNGG 4 cut(s) 80, 163, 608, 699
AgsI TTSAA 7 cut(s) 127, 302, 448, 470, 577, 689, 788
AluBI AGCT 3 cut(s) 130, 508, 841
AluI AGCT 3 cut(s) 130, 508, 841
Alw26I GTCTC 4 cut(s) 50, 53, 182, 902
ApeKI GCWGC 4 cut(s) 98, 508, 569, 660
ApoI RAATTY 1 cut(s) 742
AspLEI GCGC 1 cut(s) 179
AspS9I GGNCC 2 cut(s) 672, 702
AsuHPI GGTGA 1 cut(s) 335
AvaII GGWCC 2 cut(s) 672, 702
BaeGI GKGCMC 1 cut(s) 768
BbvI GCAGC 4 cut(s) 85, 495, 581, 672
BccI CCATC 2 cut(s) 650, 913
BceAI ACGGC 1 cut(s) 111
BclI TGATCA 1 cut(s) 487
BcoDI GTCTC 4 cut(s) 50, 53, 182, 902
BfaI CTAG 1 cut(s) 651
BfmI CTRYAG 1 cut(s) 509
BglII AGATCT 1 cut(s) 136
BisI GCNGC 4 cut(s) 99, 509, 570, 661
BlsI GCNGC 4 cut(s) 100, 510, 571, 662
Bme18I GGWCC 2 cut(s) 672, 702
BmgT120I GGNCC 2 cut(s) 672, 702
BmiI GGNNCC 2 cut(s) 674, 942
BmsI GCATC 2 cut(s) 363, 384
BpmI CTGGAG 1 cut(s) 102
BpuEI CTTGAG 3 cut(s) 125, 329, 331
BsaI GGTCTC 1 cut(s) 182
BsaJI CCNNGG 2 cut(s) 382, 780
Bsc4I CCNNNNNNNGG 4 cut(s) 80, 163, 608, 699
Bse1I ACTGG 1 cut(s) 85
Bse3DI GCAATG 2 cut(s) 259, 923
BseDI CCNNGG 2 cut(s) 382, 780
BseGI GGATG 4 cut(s) 96, 124, 378, 508
BseLI CCNNNNNNNGG 4 cut(s) 80, 163, 608, 699
BseMI GCAATG 2 cut(s) 259, 923
BseMII CTCAG 1 cut(s) 60
BseNI ACTGG 1 cut(s) 85
BseRI GAGGAG 1 cut(s) 953
BseSI GKGCMC 1 cut(s) 768
BseXI GCAGC 4 cut(s) 85, 495, 581, 672
BsgI GTGCAG 1 cut(s) 84
Bsh1236I CGCG 1 cut(s) 177
BslFI GGGAC 2 cut(s) 239, 637
BslI CCNNNNNNNGG 4 cut(s) 80, 163, 608, 699
BsmAI GTCTC 4 cut(s) 50, 53, 182, 902
BsmFI GGGAC 2 cut(s) 239, 637
BsmI GAATGC 1 cut(s) 794
Bso31I GGTCTC 1 cut(s) 182
Bsp1286I GDGCHC 1 cut(s) 768
Bsp143I GATC 5 cut(s) 136, 487, 682, 712, 727
Bsp19I CCATGG 1 cut(s) 382
BspACI CCGC 2 cut(s) 175, 663
BspCNI CTCAG 1 cut(s) 61
BspFNI CGCG 1 cut(s) 177
BspLI GGNNCC 2 cut(s) 674, 942
BspMAI CTGCAG 1 cut(s) 513
BspTNI GGTCTC 1 cut(s) 182
BsrDI GCAATG 2 cut(s) 259, 923
BsrI ACTGG 1 cut(s) 85
BssECI CCNNGG 2 cut(s) 382, 780
BssMI GATC 5 cut(s) 136, 487, 682, 712, 727
BssT1I CCWWGG 2 cut(s) 382, 780
Bst4CI ACNGT 1 cut(s) 409
Bst6I CTCTTC 2 cut(s) 607, 900
BstC8I GCNNGC 2 cut(s) 75, 567
BstDEI CTNAG 1 cut(s) 69
BstDSI CCRYGG 1 cut(s) 382
BstENI CCTNNNNNAGG 2 cut(s) 161, 697
BstF5I GGATG 4 cut(s) 96, 124, 378, 508
BstFNI CGCG 1 cut(s) 177
BstHHI GCGC 1 cut(s) 179
BstKTI GATC 5 cut(s) 139, 490, 685, 715, 730
BstMAI GTCTC 4 cut(s) 50, 53, 182, 902
BstMBI GATC 5 cut(s) 136, 487, 682, 712, 727
BstNSI RCATGY 1 cut(s) 932
BstSFI CTRYAG 1 cut(s) 509
BstSLI GKGCMC 1 cut(s) 768
BstUI CGCG 1 cut(s) 177
BstV1I GCAGC 4 cut(s) 85, 495, 581, 672
BstX2I RGATCY 1 cut(s) 136
BstYI RGATCY 1 cut(s) 136
BtgI CCRYGG 1 cut(s) 382
BtsCI GGATG 4 cut(s) 96, 124, 378, 508
BtsIMutI CAGTG 3 cut(s) 78, 366, 504
Cac8I GCNNGC 2 cut(s) 75, 567
CfoI GCGC 1 cut(s) 179
Cfr13I GGNCC 2 cut(s) 672, 702
Csp6I GTAC 1 cut(s) 527
CviAII CATG 6 cut(s) 383, 530, 680, 710, 803, 929
CviQI GTAC 1 cut(s) 527
DdeI CTNAG 1 cut(s) 69
DpnI GATC 5 cut(s) 138, 489, 684, 714, 729
DpnII GATC 5 cut(s) 136, 487, 682, 712, 727
Eam1104I CTCTTC 2 cut(s) 607, 900
EarI CTCTTC 2 cut(s) 607, 900
Eco130I CCWWGG 2 cut(s) 382, 780
Eco31I GGTCTC 1 cut(s) 182
Eco47I GGWCC 2 cut(s) 672, 702
Eco57I CTGAAG 1 cut(s) 778
EcoNI CCTNNNNNAGG 2 cut(s) 161, 697
EcoO109I RGGNCCY 1 cut(s) 672
EcoT14I CCWWGG 2 cut(s) 382, 780
ErhI CCWWGG 2 cut(s) 382, 780
FaeI CATG 6 cut(s) 386, 533, 683, 713, 806, 932
FalI AAGNNNNNCTT 2 cut(s) 897, 929
FaqI GGGAC 2 cut(s) 239, 637
FatI CATG 6 cut(s) 382, 529, 679, 709, 802, 928
FbaI TGATCA 1 cut(s) 487
Fnu4HI GCNGC 4 cut(s) 99, 509, 570, 661
FokI GGATG 4 cut(s) 103, 131, 385, 515
Fsp4HI GCNGC 4 cut(s) 99, 509, 570, 661
FspBI CTAG 1 cut(s) 651
GlaI GCGC 1 cut(s) 178
GluI GCNGC 4 cut(s) 99, 509, 570, 661
GsuI CTGGAG 1 cut(s) 102
HhaI GCGC 1 cut(s) 179
Hin1II CATG 6 cut(s) 386, 533, 683, 713, 806, 932
Hin6I GCGC 1 cut(s) 177
HinP1I GCGC 1 cut(s) 177
HindIII AAGCTT 1 cut(s) 839
HinfI GANTC 4 cut(s) 46, 227, 326, 473
HphI GGTGA 1 cut(s) 335
Hpy188I TCNGA 4 cut(s) 337, 797, 826, 918
Hpy188III TCNNGA 3 cut(s) 293, 348, 651
Hpy99I CGWCG 1 cut(s) 294
HpyAV CCTTC 4 cut(s) 102, 242, 310, 928
HpyCH4III ACNGT 1 cut(s) 409
HpyCH4IV ACGT 1 cut(s) 289
HpyCH4V TGCA 7 cut(s) 101, 257, 397, 511, 565, 884, 928
HpyF3I CTNAG 1 cut(s) 69
HpySE526I ACGT 1 cut(s) 289
Hsp92II CATG 6 cut(s) 386, 533, 683, 713, 806, 932
HspAI GCGC 1 cut(s) 177
Ksp22I TGATCA 1 cut(s) 487
Kzo9I GATC 5 cut(s) 136, 487, 682, 712, 727
LmnI GCTCC 5 cut(s) 275, 434, 467, 868, 940
LpnPI CCDG 5 cut(s) 45, 66, 87, 149, 745
Lsp1109I GCAGC 4 cut(s) 85, 495, 581, 672
LweI GCATC 2 cut(s) 363, 384
MaeI CTAG 1 cut(s) 651
MaeII ACGT 1 cut(s) 289
MaeIII GTNAC 2 cut(s) 403, 812
MalI GATC 5 cut(s) 138, 489, 684, 714, 729
MboI GATC 5 cut(s) 136, 487, 682, 712, 727
MboII GAAGA 7 cut(s) 430, 482, 624, 677, 707, 914, 917
MfeI CAATTG 1 cut(s) 168
MflI RGATCY 1 cut(s) 136
MhlI GDGCHC 1 cut(s) 768
MluCI AATT 7 cut(s) 21, 33, 151, 168, 180, 742, 877
MlyI GAGTC 3 cut(s) 55, 221, 335
MmeI TCCRAC 1 cut(s) 626
MspA1I CMGCKG 1 cut(s) 663
MunI CAATTG 1 cut(s) 168
Mva1269I GAATGC 1 cut(s) 794
MvnI CGCG 1 cut(s) 177
NcoI CCATGG 1 cut(s) 382
NdeII GATC 5 cut(s) 136, 487, 682, 712, 727
NlaIII CATG 6 cut(s) 386, 533, 683, 713, 806, 932
NlaIV GGNNCC 2 cut(s) 674, 942
NmuCI GTSAC 1 cut(s) 812
NspI RCATGY 1 cut(s) 932
PctI GAATGC 1 cut(s) 794
PfeI GAWTC 1 cut(s) 473
PkrI GCNGC 4 cut(s) 100, 510, 571, 662
PleI GAGTC 3 cut(s) 54, 221, 334
PpsI GAGTC 3 cut(s) 54, 221, 334
PpuMI RGGWCCY 1 cut(s) 672
Psp5II RGGWCCY 1 cut(s) 672
PspN4I GGNNCC 2 cut(s) 674, 942
PspPI GGNCC 2 cut(s) 672, 702
PspPPI RGGWCCY 1 cut(s) 672
PstI CTGCAG 1 cut(s) 513
PsuI RGATCY 1 cut(s) 136
RsaI GTAC 1 cut(s) 528
RsaNI GTAC 1 cut(s) 527
SatI GCNGC 4 cut(s) 99, 509, 570, 661
Sau3AI GATC 5 cut(s) 136, 487, 682, 712, 727
Sau96I GGNCC 2 cut(s) 672, 702
SchI GAGTC 3 cut(s) 55, 221, 335
SduI GDGCHC 1 cut(s) 768
SfaNI GCATC 2 cut(s) 363, 384
SfcI CTRYAG 1 cut(s) 509
SinI GGWCC 2 cut(s) 672, 702
SmlI CTYRAG 3 cut(s) 140, 308, 346
SmoI CTYRAG 3 cut(s) 140, 308, 346
Sse9I AATT 7 cut(s) 21, 33, 151, 168, 180, 742, 877
SsiI CCGC 2 cut(s) 175, 663
SspMI CTAG 1 cut(s) 651
StyI CCWWGG 2 cut(s) 382, 780
TaaI ACNGT 1 cut(s) 409
TaiI ACGT 1 cut(s) 292
TaqI TCGA 2 cut(s) 292, 547
TasI AATT 7 cut(s) 21, 33, 151, 168, 180, 742, 877
TfiI GAWTC 1 cut(s) 473
TscAI CASTG 3 cut(s) 85, 366, 504
TseFI GTSAC 1 cut(s) 812
TseI GCWGC 4 cut(s) 98, 508, 569, 660
Tsp45I GTSAC 1 cut(s) 812
TspDTI ATGAA 2 cut(s) 261, 329
TspGWI ACGGA 1 cut(s) 570
TspRI CASTG 3 cut(s) 85, 366, 504
VpaK11BI GGWCC 2 cut(s) 672, 702
XagI CCTNNNNNAGG 2 cut(s) 161, 697
XapI RAATTY 1 cut(s) 742
XbaI TCTAGA 1 cut(s) 650
XceI RCATGY 1 cut(s) 932
XspI CTAG 1 cut(s) 651
Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.