Rw6G036550

gag-polypeptide of LTR copia-type

Design Primers CRISPR Design

Basic Information

Type: gene
Biological Identity
rosa_wichuraiana
Chr6
OG0000154
Physical Location & Seq
Forward (+)
61033043 .. 61034017
975 bp
Loading structure...
UTR
Exon/CDS
Intron
Rw6G036550.1

Sequence Viewer

Length: 975 bp
ATGACGAGTGAAGGGAATTTCGTTCAACCAGCGATTCCTCGTTTTGATGGTCACTATGACCACTGGAGTATGTTAATGGAGAACTTCCTTAGATCGAAGGAATACTGGAGTTTAGTTGAAACTGGTTATGAGGAACCAGTAGATGGAGCACCTGTGACTGAGGCACAGCAGAAGAAGCTTGATGAGATAAAGTTGAAGGACCTGAAAGTAAAGAATTATCTGTTTCAGGCAATTGACAGAACAATTCTGGAGACCATATTGAAGAAGGATACGTCAAAGGAGATTTGGGATTCCATGAGGAGGAAGTACGCAGGGAATGCCAGAGTAAAGAGGTCAGTCCTTCAAGCTCTACGAAAGGACTTCGAAACCCTAGAGATGAAATCAGGTGAAACTATTACCGAGTACTTTTCTAGGGTTATGACTGTGGCTAACAAGATGCGTGTGTATGGAGAAGAGATAAAAGATGTGACTATTGTAGAGAAAATTCTTAGATCTTTAACTGACAGATTTAATTATATAGTCTGCTCAATTGAAGAATCTAAAGATGTTGACAAAATGTCCATTGATGAGTTACAAAGCTCCTTGATAGTTCATGAGCAAAAGTTTCATAGGCAGAGTGGTGAAGAACAGGCTCTCAAGGTGTCTTATGAGGAAAAGCTAAGTAGAAGAGGTCGTGGTAGAGCCACAGTCAGAGGCAGAGGCCGAGGGAGAGGGCGCCAACCATTCAACAAAGCTATTGTTGAATGTTACAGGTGCCACAAGCTCGGTCATTTCCAGTACGAGTGTCCTACATGGGGAAAAGAAGCAAATTATGCAGAGATGGATGAACAAGAAGAGTTGCTTCTGATGTCTTACGTTGAAATCAATGAGGCAAAAAGAGAAGATGCATGGTTTCTAGACTCGGGTTGCAGTAACCACATGTGTGGTGATGATCCTTGTTTTCTGAGTTGGATGATAGCTTCCGACAAATGGTGA
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

324

Amino Acids

37.96

Weight (kDa)

6.08

Isoelectric Point (pI)

51.2

Instability Index
Protein Domains (Pfam)
Domain Name Pfam ID Position E-value Description
Retrotran_gag_2 PF14223 26 - 205 3.6e-31 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)
AccB1I GGYRCC 2 cut(s) 714, 753
AccB7I CCANNNNNTGG 1 cut(s) 143
AclWI GGATC 1 cut(s) 926
AcsI RAATTY 2 cut(s) 16, 483
AcyI GRCGYC 1 cut(s) 715
AfaI GTAC 3 cut(s) 308, 404, 779
AfiI CCNNNNNNNGG 4 cut(s) 143, 300, 794, 969
AflIII ACRYGT 1 cut(s) 918
AgsI TTSAA 9 cut(s) 26, 119, 196, 262, 344, 533, 727, 743, 860
AhdI GACNNNNNGTC 1 cut(s) 556
AleI CACNNNNGTG 1 cut(s) 921
AluBI AGCT 7 cut(s) 178, 347, 579, 658, 734, 763, 959
AluI AGCT 7 cut(s) 178, 347, 579, 658, 734, 763, 959
Alw21I GWGCWC 1 cut(s) 151
Alw26I GTCTC 1 cut(s) 245
AlwI GGATC 1 cut(s) 926
Ama87I CYCGRG 1 cut(s) 901
AoxI GGCC 1 cut(s) 700
ApoI RAATTY 2 cut(s) 16, 483
AspLEI GCGC 1 cut(s) 717
AspS9I GGNCC 1 cut(s) 199
AsuHPI GGTGA 3 cut(s) 398, 632, 938
AsuII TTCGAA 1 cut(s) 363
AvaI CYCGRG 1 cut(s) 901
AvaII GGWCC 1 cut(s) 199
BanI GGYRCC 2 cut(s) 714, 753
Bbv12I GWGCWC 1 cut(s) 151
BccI CCATC 3 cut(s) 41, 137, 814
BciVI GTATCC 1 cut(s) 262
BcoDI GTCTC 1 cut(s) 245
BfaI CTAG 3 cut(s) 371, 411, 896
BfoI RGCGCY 1 cut(s) 718
BfuI GTATCC 1 cut(s) 262
BglII AGATCT 1 cut(s) 491
BmcAI AGTACT 1 cut(s) 404
Bme18I GGWCC 1 cut(s) 199
BmeRI GACNNNNNGTC 1 cut(s) 556
BmeT110I CYCGRG 1 cut(s) 901
BmgT120I GGNCC 1 cut(s) 199
BmiI GGNNCC 3 cut(s) 135, 716, 755
BmsI GCATC 2 cut(s) 426, 874
BpmI CTGGAG 3 cut(s) 85, 127, 269
Bpu14I TTCGAA 1 cut(s) 363
BpuEI CTTGAG 1 cut(s) 620
BsaHI GRCGYC 1 cut(s) 715
BsaI GGTCTC 1 cut(s) 245
BsaJI CCNNGG 1 cut(s) 703
BsaXI ACNNNNNCTCC 2 cut(s) 138, 168
Bsc4I CCNNNNNNNGG 4 cut(s) 143, 300, 794, 969
Bse1I ACTGG 5 cut(s) 68, 110, 127, 137, 775
BseDI CCNNGG 1 cut(s) 703
BseGI GGATG 2 cut(s) 829, 957
BseLI CCNNNNNNNGG 4 cut(s) 143, 300, 794, 969
BseMII CTCAG 2 cut(s) 150, 935
BseNI ACTGG 5 cut(s) 68, 110, 127, 137, 775
BseRI GAGGAG 1 cut(s) 313
BshFI GGCC 1 cut(s) 702
BshNI GGYRCC 2 cut(s) 714, 753
BsiHKAI GWGCWC 1 cut(s) 151
BsiHKCI CYCGRG 1 cut(s) 901
BslI CCNNNNNNNGG 4 cut(s) 143, 300, 794, 969
BsmAI GTCTC 1 cut(s) 245
BsmI GAATGC 1 cut(s) 322
BsnI GGCC 1 cut(s) 702
Bso31I GGTCTC 1 cut(s) 245
BsoBI CYCGRG 1 cut(s) 901
Bsp119I TTCGAA 1 cut(s) 363
Bsp1286I GDGCHC 1 cut(s) 151
Bsp143I GATC 3 cut(s) 92, 491, 931
BspANI GGCC 1 cut(s) 702
BspCNI CTCAG 2 cut(s) 151, 936
BspHI TCATGA 1 cut(s) 592
BspLI GGNNCC 3 cut(s) 135, 716, 755
BspPI GGATC 1 cut(s) 926
BspT104I TTCGAA 1 cut(s) 363
BspT107I GGYRCC 2 cut(s) 714, 753
BspTNI GGTCTC 1 cut(s) 245
BsrI ACTGG 5 cut(s) 68, 110, 127, 137, 775
BssECI CCNNGG 1 cut(s) 703
BssMI GATC 3 cut(s) 92, 491, 931
BssNI GRCGYC 1 cut(s) 715
Bst4CI ACNGT 2 cut(s) 424, 688
Bst6I CTCTTC 3 cut(s) 447, 661, 828
BstACI GRCGYC 1 cut(s) 715
BstAPI GCANNNNNTGC 2 cut(s) 317, 812
BstBI TTCGAA 1 cut(s) 363
BstDEI CTNAG 5 cut(s) 89, 159, 488, 659, 944
BstF5I GGATG 2 cut(s) 829, 957
BstH2I RGCGCY 1 cut(s) 718
BstHHI GCGC 1 cut(s) 717
BstKTI GATC 3 cut(s) 95, 494, 934
BstMAI GTCTC 1 cut(s) 245
BstMBI GATC 3 cut(s) 92, 491, 931
BstMWI GCNNNNNNNGC 3 cut(s) 175, 317, 812
BstNSI RCATGY 1 cut(s) 922
BstX2I RGATCY 1 cut(s) 491
BstXI CCANNNNNNTGG 1 cut(s) 923
BstYI RGATCY 1 cut(s) 491
BsuI GTATCC 1 cut(s) 262
BsuRI GGCC 1 cut(s) 702
BtsCI GGATG 2 cut(s) 829, 957
BtsIMutI CAGTG 1 cut(s) 61
CciI TCATGA 1 cut(s) 592
CfoI GCGC 1 cut(s) 717
Cfr13I GGNCC 1 cut(s) 199
Csp6I GTAC 3 cut(s) 307, 403, 778
CviAII CATG 5 cut(s) 295, 593, 792, 888, 919
CviQI GTAC 3 cut(s) 307, 403, 778
DdeI CTNAG 5 cut(s) 89, 159, 488, 659, 944
DinI GGCGCC 1 cut(s) 716
DpnI GATC 3 cut(s) 94, 493, 933
DpnII GATC 3 cut(s) 92, 491, 931
DriI GACNNNNNGTC 1 cut(s) 556
Eam1104I CTCTTC 3 cut(s) 447, 661, 828
Eam1105I GACNNNNNGTC 1 cut(s) 556
EarI CTCTTC 3 cut(s) 447, 661, 828
Eco31I GGTCTC 1 cut(s) 245
Eco47I GGWCC 1 cut(s) 199
Eco88I CYCGRG 1 cut(s) 901
EcoO109I RGGNCCY 1 cut(s) 199
EcoT22I ATGCAT 1 cut(s) 889
EgeI GGCGCC 1 cut(s) 716
EheI GGCGCC 1 cut(s) 716
FaeI CATG 5 cut(s) 298, 596, 795, 891, 922
FalI AAGNNNNNCTT 2 cut(s) 825, 857
FatI CATG 5 cut(s) 294, 592, 791, 887, 918
FokI GGATG 2 cut(s) 836, 964
FspBI CTAG 3 cut(s) 371, 411, 896
GlaI GCGC 1 cut(s) 716
GsuI CTGGAG 3 cut(s) 85, 127, 269
HaeII RGCGCY 1 cut(s) 718
HaeIII GGCC 1 cut(s) 702
HhaI GCGC 1 cut(s) 717
Hin1I GRCGYC 1 cut(s) 715
Hin1II CATG 5 cut(s) 298, 596, 795, 891, 922
Hin6I GCGC 1 cut(s) 715
HinP1I GCGC 1 cut(s) 715
HincII GTYRAC 1 cut(s) 550
HindII GTYRAC 1 cut(s) 550
HindIII AAGCTT 1 cut(s) 176
HinfI GANTC 4 cut(s) 34, 290, 536, 899
HphI GGTGA 3 cut(s) 398, 632, 938
Hpy166II GTNNAC 1 cut(s) 550
Hpy188I TCNGA 4 cut(s) 692, 846, 945, 964
Hpy188III TCNNGA 3 cut(s) 248, 593, 896
Hpy8I GTNNAC 1 cut(s) 550
HpyAV CCTTC 5 cut(s) 5, 91, 190, 259, 350
HpyCH4III ACNGT 2 cut(s) 424, 688
HpyCH4IV ACGT 2 cut(s) 272, 855
HpyCH4V TGCA 3 cut(s) 815, 887, 909
HpyF10VI GCNNNNNNNGC 3 cut(s) 175, 317, 812
HpyF3I CTNAG 5 cut(s) 89, 159, 488, 659, 944
HpySE526I ACGT 2 cut(s) 272, 855
Hsp92I GRCGYC 1 cut(s) 715
Hsp92II CATG 5 cut(s) 298, 596, 795, 891, 922
HspAI GCGC 1 cut(s) 715
KasI GGCGCC 1 cut(s) 714
Kzo9I GATC 3 cut(s) 92, 491, 931
LmnI GCTCC 2 cut(s) 146, 584
LweI GCATC 2 cut(s) 426, 874
MaeI CTAG 3 cut(s) 371, 411, 896
MaeII ACGT 2 cut(s) 272, 855
MaeIII GTNAC 6 cut(s) 50, 154, 466, 570, 746, 911
MalI GATC 3 cut(s) 94, 493, 933
MboI GATC 3 cut(s) 92, 491, 931
MboII GAAGA 8 cut(s) 184, 274, 464, 545, 635, 678, 845, 893
MfeI CAATTG 2 cut(s) 231, 528
MflI RGATCY 1 cut(s) 491
MhlI GDGCHC 1 cut(s) 151
MluCI AATT 8 cut(s) 16, 214, 231, 243, 483, 511, 528, 808
Mly113I GGCGCC 1 cut(s) 715
MlyI GAGTC 1 cut(s) 893
MmeI TCCRAC 1 cut(s) 929
Mph1103I ATGCAT 1 cut(s) 889
MseI TTAA 3 cut(s) 74, 497, 510
MslI CAYNNNNRTG 1 cut(s) 921
MunI CAATTG 2 cut(s) 231, 528
Mva1269I GAATGC 1 cut(s) 322
MwoI GCNNNNNNNGC 3 cut(s) 175, 317, 812
NarI GGCGCC 1 cut(s) 715
NdeII GATC 3 cut(s) 92, 491, 931
NlaIII CATG 5 cut(s) 298, 596, 795, 891, 922
NlaIV GGNNCC 3 cut(s) 135, 716, 755
NmeAIII GCCGAG 1 cut(s) 728
NmuCI GTSAC 3 cut(s) 50, 154, 466
NsiI ATGCAT 1 cut(s) 889
NspI RCATGY 1 cut(s) 922
NspV TTCGAA 1 cut(s) 363
OliI CACNNNNGTG 1 cut(s) 921
PagI TCATGA 1 cut(s) 592
PciI ACATGT 1 cut(s) 918
PctI GAATGC 1 cut(s) 322
PfeI GAWTC 3 cut(s) 34, 290, 536
PflMI CCANNNNNTGG 1 cut(s) 143
PleI GAGTC 1 cut(s) 893
PluTI GGCGCC 1 cut(s) 718
PpsI GAGTC 1 cut(s) 893
PpuMI RGGWCCY 1 cut(s) 199
PscI ACATGT 1 cut(s) 918
Psp5II RGGWCCY 1 cut(s) 199
PspN4I GGNNCC 3 cut(s) 135, 716, 755
PspPI GGNCC 1 cut(s) 199
PspPPI RGGWCCY 1 cut(s) 199
PsuI RGATCY 1 cut(s) 491
RsaI GTAC 3 cut(s) 308, 404, 779
RsaNI GTAC 3 cut(s) 307, 403, 778
RseI CAYNNNNRTG 1 cut(s) 921
SaqAI TTAA 3 cut(s) 74, 497, 510
Sau3AI GATC 3 cut(s) 92, 491, 931
Sau96I GGNCC 1 cut(s) 199
ScaI AGTACT 1 cut(s) 404
SchI GAGTC 1 cut(s) 893
SduI GDGCHC 1 cut(s) 151
SfaNI GCATC 2 cut(s) 426, 874
SfoI GGCGCC 1 cut(s) 716
SfuI TTCGAA 1 cut(s) 363
SinI GGWCC 1 cut(s) 199
SmiMI CAYNNNNRTG 1 cut(s) 921
SmlI CTYRAG 1 cut(s) 635
SmoI CTYRAG 1 cut(s) 635
Sse9I AATT 8 cut(s) 16, 214, 231, 243, 483, 511, 528, 808
SspDI GGCGCC 1 cut(s) 714
SspMI CTAG 3 cut(s) 371, 411, 896
TaaI ACNGT 2 cut(s) 424, 688
TaiI ACGT 2 cut(s) 275, 858
TaqI TCGA 2 cut(s) 95, 363
TaqII GACCGA 1 cut(s) 755
TasI AATT 8 cut(s) 16, 214, 231, 243, 483, 511, 528, 808
TatI WGTACW 1 cut(s) 402
TfiI GAWTC 3 cut(s) 34, 290, 536
Tru1I TTAA 3 cut(s) 74, 497, 510
Tru9I TTAA 3 cut(s) 74, 497, 510
TscAI CASTG 1 cut(s) 68
TseFI GTSAC 3 cut(s) 50, 154, 466
Tsp45I GTSAC 3 cut(s) 50, 154, 466
TspDTI ATGAA 4 cut(s) 392, 581, 596, 840
TspRI CASTG 1 cut(s) 68
Van91I CCANNNNNTGG 1 cut(s) 143
VpaK11BI GGWCC 1 cut(s) 199
XapI RAATTY 2 cut(s) 16, 483
XbaI TCTAGA 1 cut(s) 895
XceI RCATGY 1 cut(s) 922
XspI CTAG 3 cut(s) 371, 411, 896
ZrmI AGTACT 1 cut(s) 404
Zsp2I ATGCAT 1 cut(s) 889
Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.