Rw2G029550

gag-polypeptide of LTR copia-type

Design Primers CRISPR Design

Basic Information

Type: gene
Biological Identity
rosa_wichuraiana
Chr2
OG0000154
Physical Location & Seq
Reverse (-)
47937968 .. 47948784
10817 bp
Loading structure...
UTR
Exon/CDS
Intron
Rw2G029550.1

Sequence Viewer

Length: 840 bp
ATGCAGCCAGCAATCCCTAGATTCGACGGGCACTACGATCATTGGTCGATGCTAATGGAAAATTTCCTTCGATCGAATGAGTATTGGGGCCTGATAGAGAATGATTTGGGTTCAGCACCAAGCAGTTCGGAGGGGACTGAGGCACAATGCCAGCAGTATGAGGATAAAAAGCTTAAGGACCTGAAGGTCAAAAATTATTTGTTCCAGGCCATTGATCGTACCATTATGGAGACCATCCTCGTCAAAGACACAGCAAAACAAATTTGGGATTCGATGCGACAGAAGTATCAAGGGTCGACTAGGGTAAAGAGAGCTCAGTTACAAGCCCTAAGGAGAGAATTTGAGGTCCTGCAGATGAAGGAAGGAGAAGGAGTTGATGAGTATTTTGCACGCACCCTCACCATAGCTAACAAGATGAAGATCCACGGTGAGACCATGACTCAAGTTGTCATTATCGAAAAGATTATGAGGTCTATGGTTCCTAGATTCAATTATGTTGTGTGTTCCGTGGAAGAGTCGAATGATTTGGACAAGCTCACAATTGACGAGCTGCAGAACAGTCTGTTAGTGCATGAACAGAGGATGAAGGGGCATCATGGAAGTGAGGAACAGGCTCTGAAAGTTTCTTATGAGGACAGAGACACAGGTAGAGGAAGAGGACGTGGAACATTCAGAGGAAGGGGTCGAGGCCGAGGAAGACAACCCTTCAACAAGGCTATAGTGGAATGCTACCGGTGTCACAAACTAGGGCACTTTCAATATGAGTGCCCTAGCTGGGAAAGGAATGCAAATTACGCCGAGTTGGATGAAGAGAGTGATGCTGCTTATGTCACATGTTGA
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

279

Amino Acids

32.53

Weight (kDa)

6.47

Isoelectric Point (pI)

41.35

Instability Index
Protein Domains (Pfam)
Domain Name Pfam ID Position E-value Description
Retrotran_gag_2 PF14223 19 - 197 8.7e-28 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) 185
AccI GTMKAC 1 cut(s) 296
AclWI GGATC 1 cut(s) 415
AcsI RAATTY 3 cut(s) 61, 261, 338
AcuI CTGAAG 1 cut(s) 203
AfaI GTAC 1 cut(s) 220
AfiI CCNNNNNNNGG 1 cut(s) 775
AflII CTTAAG 1 cut(s) 173
AflIII ACRYGT 1 cut(s) 833
AgeI ACCGGT 1 cut(s) 732
AgsI TTSAA 3 cut(s) 490, 709, 758
AjiI CACGTC 1 cut(s) 662
AjnI CCWGG 1 cut(s) 204
AluBI AGCT 6 cut(s) 172, 314, 407, 535, 550, 774
AluI AGCT 6 cut(s) 172, 314, 407, 535, 550, 774
Alw21I GWGCWC 1 cut(s) 316
Alw26I GTCTC 3 cut(s) 224, 425, 633
AlwI GGATC 1 cut(s) 415
AlwNI CAGNNNCTG 1 cut(s) 616
AoxI GGCC 3 cut(s) 88, 207, 688
ApeKI GCWGC 3 cut(s) 4, 550, 821
ApoI RAATTY 3 cut(s) 61, 261, 338
AsiGI ACCGGT 1 cut(s) 732
AspS9I GGNCC 3 cut(s) 88, 178, 346
AsuHPI GGTGA 2 cut(s) 391, 440
AvaII GGWCC 2 cut(s) 178, 346
AxyI CCTNAGG 1 cut(s) 329
BaeGI GKGCMC 3 cut(s) 33, 753, 770
BaeI ACNNNNGTAYC 2 cut(s) 269, 302
BanII GRGCYC 1 cut(s) 316
BbsI GAAGAC 1 cut(s) 703
Bbv12I GWGCWC 1 cut(s) 316
BbvI GCAGC 3 cut(s) 16, 537, 808
BccI CCATC 1 cut(s) 242
BciT130I CCWGG 1 cut(s) 206
BcoDI GTCTC 3 cut(s) 224, 425, 633
BfaI CTAG 5 cut(s) 18, 300, 483, 746, 771
BfmI CTRYAG 3 cut(s) 350, 551, 717
BfrI CTTAAG 1 cut(s) 173
BisI GCNGC 3 cut(s) 5, 551, 822
BlsI GCNGC 3 cut(s) 6, 552, 823
Bme1390I CCNGG 1 cut(s) 206
Bme18I GGWCC 2 cut(s) 178, 346
BmgBI CACGTC 1 cut(s) 662
BmgT120I GGNCC 3 cut(s) 88, 178, 346
BmiI GGNNCC 2 cut(s) 89, 480
BmrFI CCNGG 1 cut(s) 206
BmsI GCATC 4 cut(s) 39, 264, 601, 808
BpiI GAAGAC 1 cut(s) 703
BpuEI CTTGAG 1 cut(s) 426
BsaBI GATNNNNATC 1 cut(s) 419
BsaI GGTCTC 2 cut(s) 224, 425
BsaJI CCNNGG 3 cut(s) 424, 507, 691
BsaWI WCCGGW 1 cut(s) 732
BsaXI ACNNNNNCTCC 2 cut(s) 357, 387
Bsc4I CCNNNNNNNGG 1 cut(s) 775
Bse118I RCCGGY 1 cut(s) 732
Bse21I CCTNAGG 1 cut(s) 329
Bse8I GATNNNNATC 1 cut(s) 419
BseBI CCWGG 1 cut(s) 206
BseDI CCNNGG 3 cut(s) 424, 507, 691
BseGI GGATG 3 cut(s) 234, 588, 811
BseJI GATNNNNATC 1 cut(s) 419
BseLI CCNNNNNNNGG 1 cut(s) 775
BseMII CTCAG 2 cut(s) 129, 329
BseSI GKGCMC 3 cut(s) 33, 753, 770
BseXI GCAGC 3 cut(s) 16, 537, 808
BseYI CCCAGC 1 cut(s) 774
Bsh1285I CGRYCG 1 cut(s) 74
BshFI GGCC 3 cut(s) 90, 209, 690
BshTI ACCGGT 1 cut(s) 732
BsiEI CGRYCG 1 cut(s) 74
BsiHKAI GWGCWC 1 cut(s) 316
BsiSI CCGG 1 cut(s) 733
BslFI GGGAC 1 cut(s) 148
BslI CCNNNNNNNGG 1 cut(s) 775
BsmAI GTCTC 3 cut(s) 224, 425, 633
BsmFI GGGAC 1 cut(s) 148
BsmI GAATGC 2 cut(s) 731, 790
BsnI GGCC 3 cut(s) 90, 209, 690
Bso31I GGTCTC 2 cut(s) 224, 425
Bsp1286I GDGCHC 4 cut(s) 33, 316, 753, 770
Bsp143I GATC 4 cut(s) 37, 71, 214, 420
BspANI GGCC 3 cut(s) 90, 209, 690
BspCNI CTCAG 2 cut(s) 130, 328
BspLI GGNNCC 2 cut(s) 89, 480
BspMAI CTGCAG 2 cut(s) 354, 555
BspPI GGATC 1 cut(s) 415
BspTI CTTAAG 1 cut(s) 173
BspTNI GGTCTC 2 cut(s) 224, 425
BsrFI RCCGGY 1 cut(s) 732
BssAI RCCGGY 1 cut(s) 732
BssECI CCNNGG 3 cut(s) 424, 507, 691
BssMI GATC 4 cut(s) 37, 71, 214, 420
Bst2UI CCWGG 1 cut(s) 206
Bst4CI ACNGT 2 cut(s) 428, 560
Bst6I CTCTTC 3 cut(s) 507, 649, 804
BstAFI CTTAAG 1 cut(s) 173
BstC8I GCNNGC 3 cut(s) 9, 152, 391
BstDEI CTNAG 3 cut(s) 138, 315, 329
BstDSI CCRYGG 2 cut(s) 424, 507
BstF5I GGATG 3 cut(s) 234, 588, 811
BstKTI GATC 4 cut(s) 40, 74, 217, 423
BstMAI GTCTC 3 cut(s) 224, 425, 633
BstMBI GATC 4 cut(s) 37, 71, 214, 420
BstMCI CGRYCG 1 cut(s) 74
BstMWI GCNNNNNNNGC 1 cut(s) 794
BstNI CCWGG 1 cut(s) 206
BstNSI RCATGY 1 cut(s) 837
BstSCI CCNGG 1 cut(s) 204
BstSFI CTRYAG 3 cut(s) 350, 551, 717
BstSLI GKGCMC 3 cut(s) 33, 753, 770
BstV1I GCAGC 3 cut(s) 16, 537, 808
BstV2I GAAGAC 1 cut(s) 703
BstX2I RGATCY 1 cut(s) 420
BstYI RGATCY 1 cut(s) 420
Bsu36I CCTNAGG 1 cut(s) 329
BsuRI GGCC 3 cut(s) 90, 209, 690
BtgI CCRYGG 2 cut(s) 424, 507
BtrI CACGTC 1 cut(s) 662
BtsCI GGATG 3 cut(s) 234, 588, 811
Cac8I GCNNGC 3 cut(s) 9, 152, 391
CaiI CAGNNNCTG 1 cut(s) 616
Cfr10I RCCGGY 1 cut(s) 732
Cfr13I GGNCC 3 cut(s) 88, 178, 346
Csp6I GTAC 1 cut(s) 219
CspAI ACCGGT 1 cut(s) 732
CviAII CATG 4 cut(s) 436, 572, 596, 834
CviQI GTAC 1 cut(s) 219
DdeI CTNAG 3 cut(s) 138, 315, 329
DpnI GATC 4 cut(s) 39, 73, 216, 422
DpnII GATC 4 cut(s) 37, 71, 214, 420
DrdI GACNNNNNNGTC 1 cut(s) 185
DseDI GACNNNNNNGTC 1 cut(s) 185
Eam1104I CTCTTC 3 cut(s) 507, 649, 804
EarI CTCTTC 3 cut(s) 507, 649, 804
Ecl136II GAGCTC 1 cut(s) 314
Eco24I GRGCYC 1 cut(s) 316
Eco31I GGTCTC 2 cut(s) 224, 425
Eco47I GGWCC 2 cut(s) 178, 346
Eco53kI GAGCTC 1 cut(s) 314
Eco57I CTGAAG 1 cut(s) 203
Eco81I CCTNAGG 1 cut(s) 329
EcoICRI GAGCTC 1 cut(s) 314
EcoO109I RGGNCCY 3 cut(s) 88, 178, 346
EcoRII CCWGG 1 cut(s) 204
EcoT38I GRGCYC 1 cut(s) 316
FaeI CATG 4 cut(s) 439, 575, 599, 837
FaqI GGGAC 1 cut(s) 148
FatI CATG 4 cut(s) 435, 571, 595, 833
FblI GTMKAC 1 cut(s) 296
Fnu4HI GCNGC 3 cut(s) 5, 551, 822
FokI GGATG 3 cut(s) 221, 595, 818
FriOI GRGCYC 1 cut(s) 316
Fsp4HI GCNGC 3 cut(s) 5, 551, 822
FspBI CTAG 5 cut(s) 18, 300, 483, 746, 771
GluI GCNGC 3 cut(s) 5, 551, 822
GsaI CCCAGC 1 cut(s) 778
HaeIII GGCC 3 cut(s) 90, 209, 690
HapII CCGG 1 cut(s) 733
Hin1II CATG 4 cut(s) 439, 575, 599, 837
HincII GTYRAC 1 cut(s) 297
HindII GTYRAC 1 cut(s) 297
HindIII AAGCTT 1 cut(s) 170
HinfI GANTC 5 cut(s) 21, 269, 439, 486, 515
HpaII CCGG 1 cut(s) 733
HphI GGTGA 2 cut(s) 391, 440
Hpy166II GTNNAC 1 cut(s) 297
Hpy188I TCNGA 3 cut(s) 130, 618, 674
Hpy8I GTNNAC 1 cut(s) 297
Hpy99I CGWCG 1 cut(s) 29
HpyAV CCTTC 8 cut(s) 77, 178, 352, 356, 362, 580, 672, 715
HpyCH4III ACNGT 2 cut(s) 428, 560
HpyCH4IV ACGT 1 cut(s) 661
HpyCH4V TGCA 6 cut(s) 4, 352, 389, 553, 571, 788
HpyF10VI GCNNNNNNNGC 1 cut(s) 794
HpyF3I CTNAG 3 cut(s) 138, 315, 329
HpySE526I ACGT 1 cut(s) 661
Hsp92II CATG 4 cut(s) 439, 575, 599, 837
Kzo9I GATC 4 cut(s) 37, 71, 214, 420
Lsp1109I GCAGC 3 cut(s) 16, 537, 808
LweI GCATC 4 cut(s) 39, 264, 601, 808
MaeI CTAG 5 cut(s) 18, 300, 483, 746, 771
MaeII ACGT 1 cut(s) 661
MaeIII GTNAC 3 cut(s) 318, 737, 829
MalI GATC 4 cut(s) 39, 73, 216, 422
MboI GATC 4 cut(s) 37, 71, 214, 420
MboII GAAGA 5 cut(s) 430, 524, 666, 708, 821
MfeI CAATTG 1 cut(s) 540
MflI RGATCY 1 cut(s) 420
MhlI GDGCHC 4 cut(s) 33, 316, 753, 770
MluCI AATT 7 cut(s) 61, 193, 261, 338, 490, 540, 790
MlyI GAGTC 2 cut(s) 433, 524
MmeI TCCRAC 1 cut(s) 783
MseI TTAA 1 cut(s) 174
MslI CAYNNNNRTG 1 cut(s) 600
MspCI CTTAAG 1 cut(s) 173
MspI CCGG 1 cut(s) 733
MspR9I CCNGG 1 cut(s) 206
MunI CAATTG 1 cut(s) 540
Mva1269I GAATGC 2 cut(s) 731, 790
MvaI CCWGG 1 cut(s) 206
MwoI GCNNNNNNNGC 1 cut(s) 794
NdeII GATC 4 cut(s) 37, 71, 214, 420
NlaIII CATG 4 cut(s) 439, 575, 599, 837
NlaIV GGNNCC 2 cut(s) 89, 480
NmeAIII GCCGAG 2 cut(s) 716, 823
NmuCI GTSAC 2 cut(s) 737, 829
NspI RCATGY 1 cut(s) 837
PciI ACATGT 1 cut(s) 833
PcsI WCGNNNNNNNCGW 1 cut(s) 33
PctI GAATGC 2 cut(s) 731, 790
PfeI GAWTC 3 cut(s) 21, 269, 486
PinAI ACCGGT 1 cut(s) 732
PkrI GCNGC 3 cut(s) 6, 552, 823
Ple19I CGATCG 1 cut(s) 74
PleI GAGTC 2 cut(s) 433, 523
PpsI GAGTC 2 cut(s) 433, 523
PpuMI RGGWCCY 2 cut(s) 178, 346
PscI ACATGT 1 cut(s) 833
Psp124BI GAGCTC 1 cut(s) 316
Psp5II RGGWCCY 2 cut(s) 178, 346
Psp6I CCWGG 1 cut(s) 204
PspFI CCCAGC 1 cut(s) 774
PspGI CCWGG 1 cut(s) 204
PspN4I GGNNCC 2 cut(s) 89, 480
PspPI GGNCC 3 cut(s) 88, 178, 346
PspPPI RGGWCCY 2 cut(s) 178, 346
PstI CTGCAG 2 cut(s) 354, 555
PstNI CAGNNNCTG 1 cut(s) 616
PsuI RGATCY 1 cut(s) 420
PvuI CGATCG 1 cut(s) 74
RsaI GTAC 1 cut(s) 220
RsaNI GTAC 1 cut(s) 219
RseI CAYNNNNRTG 1 cut(s) 600
SacI GAGCTC 1 cut(s) 316
SalI GTCGAC 1 cut(s) 295
SaqAI TTAA 1 cut(s) 174
SatI GCNGC 3 cut(s) 5, 551, 822
Sau3AI GATC 4 cut(s) 37, 71, 214, 420
Sau96I GGNCC 3 cut(s) 88, 178, 346
SchI GAGTC 2 cut(s) 433, 524
ScrFI CCNGG 1 cut(s) 206
SduI GDGCHC 4 cut(s) 33, 316, 753, 770
SfaNI GCATC 4 cut(s) 39, 264, 601, 808
SfcI CTRYAG 3 cut(s) 350, 551, 717
SinI GGWCC 2 cut(s) 178, 346
SmiMI CAYNNNNRTG 1 cut(s) 600
SmlI CTYRAG 2 cut(s) 173, 441
SmoI CTYRAG 2 cut(s) 173, 441
Sse9I AATT 7 cut(s) 61, 193, 261, 338, 490, 540, 790
SspMI CTAG 5 cut(s) 18, 300, 483, 746, 771
SstI GAGCTC 1 cut(s) 316
StyD4I CCNGG 1 cut(s) 204
TaaI ACNGT 2 cut(s) 428, 560
TaiI ACGT 1 cut(s) 664
TaqI TCGA 9 cut(s) 24, 47, 70, 74, 272, 296, 456, 518, 685
TasI AATT 7 cut(s) 61, 193, 261, 338, 490, 540, 790
TfiI GAWTC 3 cut(s) 21, 269, 486
Tru1I TTAA 1 cut(s) 174
Tru9I TTAA 1 cut(s) 174
TseFI GTSAC 2 cut(s) 737, 829
TseI GCWGC 3 cut(s) 4, 550, 821
Tsp45I GTSAC 2 cut(s) 737, 829
TspDTI ATGAA 5 cut(s) 371, 431, 588, 599, 822
TspGWI ACGGA 1 cut(s) 496
Vha464I CTTAAG 1 cut(s) 173
VpaK11BI GGWCC 2 cut(s) 178, 346
XapI RAATTY 3 cut(s) 61, 261, 338
XceI RCATGY 1 cut(s) 837
XmiI GTMKAC 1 cut(s) 296
XspI CTAG 5 cut(s) 18, 300, 483, 746, 771
Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.