Rw6G026290

gag-polypeptide of LTR copia-type

Design Primers CRISPR Design

Basic Information

Type: gene
Biological Identity
rosa_wichuraiana
Chr6
OG0000154
Physical Location & Seq
Forward (+)
49665570 .. 49666583
1014 bp
Loading structure...
UTR
Exon/CDS
Intron
Rw6G026290.1

Sequence Viewer

Length: 1014 bp
ATGGCAGGGGAAGGGAGCAATAGCAATTTTGCTCCACCTAGTATTCCCAAGTTTGATGGAGACTATGATCACTGGAGCATGCTAATGGAGAATCTCTTGCGATCGAAGGAGTATTGGAGCCTTGTTGAGACTGGCTACACAGATCCTGCTGAGGGAGAAGTCATGACAGCTGCGCAAAGGAAGACATTGGAAGAATTAAAGCTGAAGGATTTCAAGGTCAAGAATTACCTCTTCCAGTCCATCGATAAATCGATTCTGAAAACCATCATTCAGAAGGACACGTCCAAACATTTGTGGGATTCAATGAAGCGTAAATATCAAGGGAATAAGAGGGTGCAGCGATCTCAACTCCAAACTCTTCGTAGAGAATTTGAGATCCTGGAGATGAAGAGTGGTGAATCAGTCACAGATTACTTCTCAAGGGTGATGATGGTGGCTAATGACATGAGGAATTATGGAGAAAATATGCAGGACGTGAAAATTGTTGAGAAAATCTTACGTACTCTCACAGATAAGTTTAACTATATTGTTTGCTCAATAGAAGAGTCGAAAGATATCAACCATCTTTCTGTAGATGAGTTGCAGAGCTCTCTGCTTGTCCATGAACAGAAGTTTAGAAAAGGCAACAGTGATGAACAAGTTTTGAAAGTCACAAGTGTTGAGAGGCTTGGACCAAACAGGGAAGAAGATGGATTCAAAGGAAGAGGCAGAGGACGTGGGGTTTTCAGAAGCAGAGGAAGAGGGCGAGGTAGACAAAGCTTCAACAAGGCTGTAGTTGAATGCTTTAAATGCCACAAACTAGGGCATTTTCAATATGAATGCCCTAGTTGGGAGAAGCGAGTGAATTATGCAGAGCTTGAGGAGGAAGATGAACTCTTGCTGATGGCTCATGTGGAGAGGAATGACTCCAAGCGTGAAGATGTGTGGTTTCTAGATAGTGGTTGCAGCAATCATATGTGCTGCAACAAGGATTGGTTCACTAACATTGATGAGGAATTTAGGCACTCTGTGTAA
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

337

Amino Acids

39.52

Weight (kDa)

6.54

Isoelectric Point (pI)

46.88

Instability Index
Protein Domains (Pfam)
Domain Name Pfam ID Position E-value Description
Retrotran_gag_2 PF14223 29 - 208 2.1e-30 gag-polypeptide of LTR copia-type
Pol_BBD PF22936 309 - 332 1.6e-08 Pol polyprotein, beta-barrel domain
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)
Acc16I TGCGCA 1 cut(s) 174
AccI GTMKAC 1 cut(s) 751
AclWI GGATC 2 cut(s) 137, 370
AcsI RAATTY 2 cut(s) 368, 995
AcuI CTGAAG 1 cut(s) 224
AdeI CACNNNGTG 1 cut(s) 1009
AfaI GTAC 1 cut(s) 502
AfiI CCNNNNNNNGG 2 cut(s) 152, 829
AflIII ACRYGT 1 cut(s) 279
AgsI TTSAA 7 cut(s) 214, 303, 646, 697, 763, 779, 812
AjiI CACGTC 3 cut(s) 282, 475, 716
AjnI CCWGG 1 cut(s) 378
AluBI AGCT 5 cut(s) 170, 202, 588, 759, 856
AluI AGCT 5 cut(s) 170, 202, 588, 759, 856
Alw21I GWGCWC 1 cut(s) 590
Alw26I GTCTC 2 cut(s) 54, 122
AlwI GGATC 2 cut(s) 137, 370
AlwNI CAGNNNCTG 1 cut(s) 146
ApeKI GCWGC 4 cut(s) 170, 337, 945, 960
ApoI RAATTY 2 cut(s) 368, 995
Asp700I GAANNNNTTC 1 cut(s) 209
AspLEI GCGC 1 cut(s) 175
AspS9I GGNCC 1 cut(s) 671
AsuHPI GGTGA 2 cut(s) 407, 436
AvaII GGWCC 1 cut(s) 671
BanII GRGCYC 1 cut(s) 590
BbsI GAAGAC 1 cut(s) 188
Bbv12I GWGCWC 1 cut(s) 590
BbvCI CCTCAGC 1 cut(s) 150
BbvI GCAGC 4 cut(s) 157, 349, 947, 957
BccI CCATC 7 cut(s) 50, 248, 272, 424, 570, 683, 877
BciT130I CCWGG 1 cut(s) 380
BclI TGATCA 1 cut(s) 67
BcoDI GTCTC 2 cut(s) 54, 122
BfaI CTAG 4 cut(s) 39, 800, 825, 932
BfmI CTRYAG 2 cut(s) 570, 771
BisI GCNGC 4 cut(s) 171, 338, 946, 961
BlsI GCNGC 4 cut(s) 172, 339, 947, 962
Bme1390I CCNGG 1 cut(s) 380
Bme18I GGWCC 1 cut(s) 671
BmgBI CACGTC 3 cut(s) 282, 475, 716
BmgT120I GGNCC 1 cut(s) 671
BmiI GGNNCC 1 cut(s) 119
BmrFI CCNGG 1 cut(s) 380
BpiI GAAGAC 1 cut(s) 188
BpmI CTGGAG 2 cut(s) 94, 401
Bpu10I CCTNAGC 1 cut(s) 150
BpuEI CTTGAG 2 cut(s) 403, 878
Bsa29I ATCGAT 2 cut(s) 243, 251
BsaAI YACGTR 1 cut(s) 500
Bsc4I CCNNNNNNNGG 2 cut(s) 152, 829
Bse1I ACTGG 3 cut(s) 77, 136, 235
BseBI CCWGG 1 cut(s) 380
BseCI ATCGAT 2 cut(s) 243, 251
BseLI CCNNNNNNNGG 2 cut(s) 152, 829
BseMII CTCAG 1 cut(s) 141
BseNI ACTGG 3 cut(s) 77, 136, 235
BseRI GAGGAG 1 cut(s) 875
BseXI GCAGC 4 cut(s) 157, 349, 947, 957
BsgI GTGCAG 1 cut(s) 356
Bsh1285I CGRYCG 1 cut(s) 104
BshVI ATCGAT 2 cut(s) 243, 251
BsiEI CGRYCG 1 cut(s) 104
BsiHKAI GWGCWC 1 cut(s) 590
BslI CCNNNNNNNGG 2 cut(s) 152, 829
BsmAI GTCTC 2 cut(s) 54, 122
BsmI GAATGC 2 cut(s) 785, 824
Bsp1286I GDGCHC 1 cut(s) 590
Bsp143I GATC 5 cut(s) 67, 101, 142, 341, 375
BspCNI CTCAG 1 cut(s) 142
BspDI ATCGAT 2 cut(s) 243, 251
BspHI TCATGA 1 cut(s) 162
BspLI GGNNCC 1 cut(s) 119
BspPI GGATC 2 cut(s) 137, 370
BsrI ACTGG 3 cut(s) 77, 136, 235
BssMI GATC 5 cut(s) 67, 101, 142, 341, 375
Bst2UI CCWGG 1 cut(s) 380
Bst4CI ACNGT 1 cut(s) 629
Bst6I CTCTTC 6 cut(s) 236, 363, 383, 537, 697, 733
BstBAI YACGTR 1 cut(s) 500
BstC8I GCNNGC 1 cut(s) 80
BstDEI CTNAG 1 cut(s) 150
BstHHI GCGC 1 cut(s) 175
BstKTI GATC 5 cut(s) 70, 104, 145, 344, 378
BstMAI GTCTC 2 cut(s) 54, 122
BstMBI GATC 5 cut(s) 67, 101, 142, 341, 375
BstMCI CGRYCG 1 cut(s) 104
BstMWI GCNNNNNNNGC 1 cut(s) 789
BstNI CCWGG 1 cut(s) 380
BstNSI RCATGY 1 cut(s) 82
BstSCI CCNGG 1 cut(s) 378
BstSFI CTRYAG 2 cut(s) 570, 771
BstSNI TACGTA 1 cut(s) 500
BstV1I GCAGC 4 cut(s) 157, 349, 947, 957
BstV2I GAAGAC 1 cut(s) 188
BstX2I RGATCY 2 cut(s) 142, 375
BstYI RGATCY 2 cut(s) 142, 375
Bsu15I ATCGAT 2 cut(s) 243, 251
BsuTUI ATCGAT 2 cut(s) 243, 251
BtrI CACGTC 3 cut(s) 282, 475, 716
BtsIMutI CAGTG 2 cut(s) 70, 634
Cac8I GCNNGC 1 cut(s) 80
CaiI CAGNNNCTG 1 cut(s) 146
CciI TCATGA 1 cut(s) 162
CfoI GCGC 1 cut(s) 175
Cfr13I GGNCC 1 cut(s) 671
ClaI ATCGAT 2 cut(s) 243, 251
Csp6I GTAC 1 cut(s) 501
CviAII CATG 5 cut(s) 79, 163, 445, 602, 890
CviQI GTAC 1 cut(s) 501
DdeI CTNAG 1 cut(s) 150
DpnI GATC 5 cut(s) 69, 103, 144, 343, 377
DpnII GATC 5 cut(s) 67, 101, 142, 341, 375
DraI TTTAAA 1 cut(s) 787
DraIII CACNNNGTG 1 cut(s) 1009
Eam1104I CTCTTC 6 cut(s) 236, 363, 383, 537, 697, 733
EarI CTCTTC 6 cut(s) 236, 363, 383, 537, 697, 733
Ecl136II GAGCTC 1 cut(s) 588
Eco105I TACGTA 1 cut(s) 500
Eco24I GRGCYC 1 cut(s) 590
Eco32I GATATC 1 cut(s) 556
Eco47I GGWCC 1 cut(s) 671
Eco53kI GAGCTC 1 cut(s) 588
Eco57I CTGAAG 1 cut(s) 224
EcoICRI GAGCTC 1 cut(s) 588
EcoRII CCWGG 1 cut(s) 378
EcoRV GATATC 1 cut(s) 556
EcoT38I GRGCYC 1 cut(s) 590
FaeI CATG 5 cut(s) 82, 166, 448, 605, 893
FatI CATG 5 cut(s) 78, 162, 444, 601, 889
FauNDI CATATG 1 cut(s) 954
FbaI TGATCA 1 cut(s) 67
FblI GTMKAC 1 cut(s) 751
Fnu4HI GCNGC 4 cut(s) 171, 338, 946, 961
FriOI GRGCYC 1 cut(s) 590
Fsp4HI GCNGC 4 cut(s) 171, 338, 946, 961
FspBI CTAG 4 cut(s) 39, 800, 825, 932
FspI TGCGCA 1 cut(s) 174
GlaI GCGC 1 cut(s) 174
GluI GCNGC 4 cut(s) 171, 338, 946, 961
GsuI CTGGAG 2 cut(s) 94, 401
HhaI GCGC 1 cut(s) 175
Hin1II CATG 5 cut(s) 82, 166, 448, 605, 893
Hin6I GCGC 1 cut(s) 173
HinP1I GCGC 1 cut(s) 173
HindIII AAGCTT 1 cut(s) 757
HinfI GANTC 7 cut(s) 91, 253, 299, 398, 545, 693, 905
HphI GGTGA 2 cut(s) 407, 436
Hpy166II GTNNAC 2 cut(s) 752, 978
Hpy188I TCNGA 3 cut(s) 258, 273, 728
Hpy188III TCNNGA 3 cut(s) 163, 220, 932
Hpy8I GTNNAC 2 cut(s) 752, 978
HpyAV CCTTC 4 cut(s) 5, 100, 199, 268
HpyCH4III ACNGT 1 cut(s) 629
HpyCH4IV ACGT 4 cut(s) 281, 474, 499, 715
HpyCH4V TGCA 6 cut(s) 337, 469, 583, 851, 945, 963
HpyF10VI GCNNNNNNNGC 1 cut(s) 789
HpyF3I CTNAG 1 cut(s) 150
HpySE526I ACGT 4 cut(s) 281, 474, 499, 715
Hsp92II CATG 5 cut(s) 82, 166, 448, 605, 893
HspAI GCGC 1 cut(s) 173
Ksp22I TGATCA 1 cut(s) 67
Kzo9I GATC 5 cut(s) 67, 101, 142, 341, 375
LmnI GCTCC 4 cut(s) 15, 37, 75, 117
LpnPI CCDG 8 cut(s) 58, 117, 159, 248, 365, 392, 455, 664
Lsp1109I GCAGC 4 cut(s) 157, 349, 947, 957
MaeI CTAG 4 cut(s) 39, 800, 825, 932
MaeII ACGT 4 cut(s) 281, 474, 499, 715
MaeIII GTNAC 2 cut(s) 403, 649
MalI GATC 5 cut(s) 69, 103, 144, 343, 377
MboI GATC 5 cut(s) 67, 101, 142, 341, 375
MflI RGATCY 2 cut(s) 142, 375
MhlI GDGCHC 1 cut(s) 590
MluCI AATT 8 cut(s) 25, 194, 223, 368, 451, 480, 844, 995
MlyI GAGTC 2 cut(s) 554, 899
MroXI GAANNNNTTC 1 cut(s) 209
MseI TTAA 3 cut(s) 197, 519, 786
MslI CAYNNNNRTG 1 cut(s) 83
MspA1I CMGCKG 1 cut(s) 170
MspR9I CCNGG 1 cut(s) 380
Mva1269I GAATGC 2 cut(s) 785, 824
MvaI CCWGG 1 cut(s) 380
MwoI GCNNNNNNNGC 1 cut(s) 789
NdeI CATATG 1 cut(s) 954
NdeII GATC 5 cut(s) 67, 101, 142, 341, 375
NlaIII CATG 5 cut(s) 82, 166, 448, 605, 893
NlaIV GGNNCC 1 cut(s) 119
NmuCI GTSAC 2 cut(s) 403, 649
NsbI TGCGCA 1 cut(s) 174
NspI RCATGY 1 cut(s) 82
PaeI GCATGC 1 cut(s) 82
PagI TCATGA 1 cut(s) 162
PctI GAATGC 2 cut(s) 785, 824
PdmI GAANNNNTTC 1 cut(s) 209
PfeI GAWTC 5 cut(s) 91, 253, 299, 398, 693
PfoI TCCNGGA 1 cut(s) 378
PkrI GCNGC 4 cut(s) 172, 339, 947, 962
Ple19I CGATCG 1 cut(s) 104
PleI GAGTC 2 cut(s) 553, 899
PpsI GAGTC 2 cut(s) 553, 899
Ppu21I YACGTR 1 cut(s) 500
Psp124BI GAGCTC 1 cut(s) 590
Psp6I CCWGG 1 cut(s) 378
PspGI CCWGG 1 cut(s) 378
PspN4I GGNNCC 1 cut(s) 119
PspPI GGNCC 1 cut(s) 671
PstNI CAGNNNCTG 1 cut(s) 146
PsuI RGATCY 2 cut(s) 142, 375
PvuI CGATCG 1 cut(s) 104
PvuII CAGCTG 1 cut(s) 170
RsaI GTAC 1 cut(s) 502
RsaNI GTAC 1 cut(s) 501
RseI CAYNNNNRTG 1 cut(s) 83
SacI GAGCTC 1 cut(s) 590
SaqAI TTAA 3 cut(s) 197, 519, 786
SatI GCNGC 4 cut(s) 171, 338, 946, 961
Sau3AI GATC 5 cut(s) 67, 101, 142, 341, 375
Sau96I GGNCC 1 cut(s) 671
SchI GAGTC 2 cut(s) 554, 899
ScrFI CCNGG 1 cut(s) 380
SduI GDGCHC 1 cut(s) 590
SfcI CTRYAG 2 cut(s) 570, 771
SinI GGWCC 1 cut(s) 671
SmiMI CAYNNNNRTG 1 cut(s) 83
SmlI CTYRAG 2 cut(s) 418, 857
SmoI CTYRAG 2 cut(s) 418, 857
SnaBI TACGTA 1 cut(s) 500
SphI GCATGC 1 cut(s) 82
Sse9I AATT 8 cut(s) 25, 194, 223, 368, 451, 480, 844, 995
SspMI CTAG 4 cut(s) 39, 800, 825, 932
SstI GAGCTC 1 cut(s) 590
StyD4I CCNGG 1 cut(s) 378
TaaI ACNGT 1 cut(s) 629
TaiI ACGT 4 cut(s) 284, 477, 502, 718
TaqI TCGA 4 cut(s) 104, 243, 251, 548
TasI AATT 8 cut(s) 25, 194, 223, 368, 451, 480, 844, 995
TfiI GAWTC 5 cut(s) 91, 253, 299, 398, 693
Tru1I TTAA 3 cut(s) 197, 519, 786
Tru9I TTAA 3 cut(s) 197, 519, 786
TscAI CASTG 2 cut(s) 77, 634
TseFI GTSAC 2 cut(s) 403, 649
TseI GCWGC 4 cut(s) 170, 337, 945, 960
Tsp45I GTSAC 2 cut(s) 403, 649
TspDTI ATGAA 6 cut(s) 320, 401, 618, 648, 831, 885
TspRI CASTG 2 cut(s) 77, 634
VpaK11BI GGWCC 1 cut(s) 671
XapI RAATTY 2 cut(s) 368, 995
XbaI TCTAGA 1 cut(s) 931
XceI RCATGY 1 cut(s) 82
XmiI GTMKAC 1 cut(s) 751
XmnI GAANNNNTTC 1 cut(s) 209
XspI CTAG 4 cut(s) 39, 800, 825, 932
Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.