Rw4G034500

gag-polypeptide of LTR copia-type

Design Primers CRISPR Design

Basic Information

Type: gene
Biological Identity
rosa_wichuraiana
Chr4
OG0000154
Physical Location & Seq
Reverse (-)
61543841 .. 61544860
1020 bp
Loading structure...
UTR
Exon/CDS
Intron
Rw4G034500.1

Sequence Viewer

Length: 1020 bp
ATGGCAGAGGCCAACTTTGTGCAGCCAACGATACCACGGTTCGATGGTCATTATGACCACTGGGCCATGCTCATGGAGAACTTCCTTCGTTGGAAGGAGTATTGGCATATGGTGGAGATTAGTATTCCAGCAGCTGTAGCAGAAGGAGGTGAGGCGACAGAGGCTCAACGAAAGTTAAGAGAAGATGCAAAACTAAAGGACTTGAAGGTCAAAAACTACTTGTTCCAGGCCATCAACAGAACCATCATGGAGACCATCTTGAATAAGGAGACAGCAAAAGGAATTTGGGACTCGATGAGACAGAAATATCAAGTCTCAACGAAGGTTAAGAGAGCTCAATTGCAAGCGCTTAGAAGGGAGTTTGAAGTTCTTGGCATGAAAGAGGGTGAGAAAGTGAATGATTACTTTGCTCGTACACTTACAGTGGCAAACAAGATGAAGGCACATGGGGAGAGAATGGAAGAATTGGTGATTGTGGAAAAGATCTTGAGATCCATGACTCGTAAATATGATTATGTGGTGTGCTCGATTGAGGAGTCCAACGATCTTACAACTATGACGATCGATGAGCTTCAAAGTAGCCTCTTGGTACATGAGCAACGTATGCATGCACATGATGGTAGTGATGAGCAAGTTTTGAAGATAACACATGAAGACACCTTTAGTACAAGAGGTAGAGGCCGTGGAATGTTCAGAGGAAGGGGAAGAGGTCGAGGAAGGAAAGGAATCAATAAAGTTCTAATGGAATGTTATAAATGTCATAAACTAGGTCACTTTCAATATGAGTGCCCTAGTTGGGGAAAAACAGCAAACTATGTTGAACTTGAAGAGGAGGAGGAGCTCTTGCTGATGGCCTATGTGGAGGTGAATAATTTGAAGCGAGAAGATGTGTGGTTCCTGGACAGTGGATGCAGTAACCATATGTGTGGCAACAGAAAATGGTTCTCCAACCTCGATGAAACCTTCAAGAACTCTGTGAAGCTTGGCAACAACACTAGAATGGCAGTAACAGGGAAATGA
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

339

Amino Acids

39.55

Weight (kDa)

8.38

Isoelectric Point (pI)

39.41

Instability Index
Protein Domains (Pfam)
Domain Name Pfam ID Position E-value Description
Retrotran_gag_2 PF14223 25 - 204 7.1e-27 gag-polypeptide of LTR copia-type
Pol_BBD PF22936 298 - 339 3e-14 Pol polyprotein, beta-barrel domain
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)
AanI TTATAA 1 cut(s) 753
AasI GACNNNNNNGTC 1 cut(s) 206
AclWI GGATC 1 cut(s) 486
AcsI RAATTY 1 cut(s) 282
AfaI GTAC 3 cut(s) 415, 591, 667
AfeI AGCGCT 1 cut(s) 348
AfiI CCNNNNNNNGG 2 cut(s) 796, 797
AjnI CCWGG 2 cut(s) 225, 897
AluBI AGCT 5 cut(s) 134, 335, 571, 841, 982
AluI AGCT 5 cut(s) 134, 335, 571, 841, 982
Alw21I GWGCWC 3 cut(s) 337, 527, 843
Alw26I GTCTC 4 cut(s) 245, 263, 292, 319
AlwI GGATC 1 cut(s) 486
AlwNI CAGNNNCTG 1 cut(s) 134
Aor51HI AGCGCT 1 cut(s) 348
AoxI GGCC 5 cut(s) 9, 63, 228, 679, 852
ApeKI GCWGC 2 cut(s) 22, 131
ApoI RAATTY 1 cut(s) 282
AspLEI GCGC 1 cut(s) 349
AspS9I GGNCC 1 cut(s) 63
AsuHPI GGTGA 4 cut(s) 161, 398, 481, 877
BaeGI GKGCMC 1 cut(s) 791
BaeI ACNNNNGTAYC 2 cut(s) 23, 56
BanII GRGCYC 2 cut(s) 337, 843
BbsI GAAGAC 1 cut(s) 660
Bbv12I GWGCWC 3 cut(s) 337, 527, 843
BbvI GCAGC 2 cut(s) 34, 143
BccI CCATC 6 cut(s) 38, 239, 251, 263, 611, 844
BceAI ACGGC 1 cut(s) 666
BciT130I CCWGG 2 cut(s) 227, 899
BcoDI GTCTC 4 cut(s) 245, 263, 292, 319
BfaI CTAG 3 cut(s) 767, 792, 996
BfmI CTRYAG 1 cut(s) 135
BfoI RGCGCY 1 cut(s) 350
BglII AGATCT 1 cut(s) 483
BisI GCNGC 2 cut(s) 23, 132
BlsI GCNGC 2 cut(s) 24, 133
Bme1390I CCNGG 2 cut(s) 227, 899
BmgT120I GGNCC 1 cut(s) 63
BmiI GGNNCC 1 cut(s) 896
BmrFI CCNGG 2 cut(s) 227, 899
BmrI ACTGGG 1 cut(s) 70
BmsI GCATC 2 cut(s) 175, 899
BmuI ACTGGG 1 cut(s) 70
BpiI GAAGAC 1 cut(s) 660
BpuEI CTTGAG 1 cut(s) 508
Bsa29I ATCGAT 1 cut(s) 564
BsaI GGTCTC 1 cut(s) 245
BsaJI CCNNGG 2 cut(s) 35, 682
Bsc4I CCNNNNNNNGG 2 cut(s) 796, 797
Bse1I ACTGG 1 cut(s) 65
BseBI CCWGG 2 cut(s) 227, 899
BseCI ATCGAT 1 cut(s) 564
BseDI CCNNGG 2 cut(s) 35, 682
BseGI GGATG 1 cut(s) 914
BseLI CCNNNNNNNGG 2 cut(s) 796, 797
BseNI ACTGG 1 cut(s) 65
BseRI GAGGAG 4 cut(s) 548, 845, 848, 851
BseSI GKGCMC 1 cut(s) 791
BseXI GCAGC 2 cut(s) 34, 143
BsgI GTGCAG 1 cut(s) 41
Bsh1285I CGRYCG 1 cut(s) 564
BshFI GGCC 5 cut(s) 11, 65, 230, 681, 854
BshVI ATCGAT 1 cut(s) 564
BsiEI CGRYCG 1 cut(s) 564
BsiHKAI GWGCWC 3 cut(s) 337, 527, 843
BslFI GGGAC 1 cut(s) 302
BslI CCNNNNNNNGG 2 cut(s) 796, 797
BsmAI GTCTC 4 cut(s) 245, 263, 292, 319
BsmFI GGGAC 1 cut(s) 302
BsnI GGCC 5 cut(s) 11, 65, 230, 681, 854
Bso31I GGTCTC 1 cut(s) 245
Bsp1286I GDGCHC 4 cut(s) 337, 527, 791, 843
Bsp143I GATC 4 cut(s) 483, 491, 544, 561
BspANI GGCC 5 cut(s) 11, 65, 230, 681, 854
BspDI ATCGAT 1 cut(s) 564
BspLI GGNNCC 1 cut(s) 896
BspPI GGATC 1 cut(s) 486
BspTNI GGTCTC 1 cut(s) 245
BsrI ACTGG 1 cut(s) 65
BssECI CCNNGG 2 cut(s) 35, 682
BssMI GATC 4 cut(s) 483, 491, 544, 561
Bst2UI CCWGG 2 cut(s) 227, 899
Bst4CI ACNGT 3 cut(s) 39, 424, 905
Bst6I CTCTTC 2 cut(s) 700, 822
BstAPI GCANNNNNTGC 1 cut(s) 604
BstC8I GCNNGC 2 cut(s) 345, 609
BstDEI CTNAG 1 cut(s) 350
BstDSI CCRYGG 2 cut(s) 35, 682
BstF5I GGATG 1 cut(s) 914
BstH2I RGCGCY 1 cut(s) 350
BstHHI GCGC 1 cut(s) 349
BstKTI GATC 4 cut(s) 486, 494, 547, 564
BstMAI GTCTC 4 cut(s) 245, 263, 292, 319
BstMBI GATC 4 cut(s) 483, 491, 544, 561
BstMCI CGRYCG 1 cut(s) 564
BstMWI GCNNNNNNNGC 3 cut(s) 137, 161, 604
BstNI CCWGG 2 cut(s) 227, 899
BstNSI RCATGY 1 cut(s) 611
BstSCI CCNGG 2 cut(s) 225, 897
BstSFI CTRYAG 1 cut(s) 135
BstSLI GKGCMC 1 cut(s) 791
BstV1I GCAGC 2 cut(s) 34, 143
BstV2I GAAGAC 1 cut(s) 660
BstX2I RGATCY 2 cut(s) 483, 491
BstXI CCANNNNNNTGG 2 cut(s) 73, 926
BstYI RGATCY 2 cut(s) 483, 491
Bsu15I ATCGAT 1 cut(s) 564
BsuRI GGCC 5 cut(s) 11, 65, 230, 681, 854
BsuTUI ATCGAT 1 cut(s) 564
BtgI CCRYGG 2 cut(s) 35, 682
BtsCI GGATG 1 cut(s) 914
BtsIMutI CAGTG 3 cut(s) 58, 429, 910
Cac8I GCNNGC 2 cut(s) 345, 609
CaiI CAGNNNCTG 1 cut(s) 134
CfoI GCGC 1 cut(s) 349
Cfr13I GGNCC 1 cut(s) 63
ClaI ATCGAT 1 cut(s) 564
Csp6I GTAC 3 cut(s) 414, 590, 666
CviQI GTAC 3 cut(s) 414, 590, 666
DdeI CTNAG 1 cut(s) 350
DpnI GATC 4 cut(s) 485, 493, 546, 563
DpnII GATC 4 cut(s) 483, 491, 544, 561
DrdI GACNNNNNNGTC 1 cut(s) 206
DseDI GACNNNNNNGTC 1 cut(s) 206
Eam1104I CTCTTC 2 cut(s) 700, 822
EarI CTCTTC 2 cut(s) 700, 822
Ecl136II GAGCTC 2 cut(s) 335, 841
Eco24I GRGCYC 2 cut(s) 337, 843
Eco31I GGTCTC 1 cut(s) 245
Eco47III AGCGCT 1 cut(s) 348
Eco53kI GAGCTC 2 cut(s) 335, 841
EcoICRI GAGCTC 2 cut(s) 335, 841
EcoRII CCWGG 2 cut(s) 225, 897
EcoT22I ATGCAT 1 cut(s) 609
EcoT38I GRGCYC 2 cut(s) 337, 843
FaqI GGGAC 1 cut(s) 302
FauNDI CATATG 2 cut(s) 108, 921
Fnu4HI GCNGC 2 cut(s) 23, 132
FokI GGATG 1 cut(s) 921
FriOI GRGCYC 2 cut(s) 337, 843
Fsp4HI GCNGC 2 cut(s) 23, 132
FspBI CTAG 3 cut(s) 767, 792, 996
GlaI GCGC 1 cut(s) 348
GluI GCNGC 2 cut(s) 23, 132
HaeII RGCGCY 1 cut(s) 350
HaeIII GGCC 5 cut(s) 11, 65, 230, 681, 854
HhaI GCGC 1 cut(s) 349
Hin6I GCGC 1 cut(s) 347
HinP1I GCGC 1 cut(s) 347
HindIII AAGCTT 1 cut(s) 980
HinfI GANTC 4 cut(s) 290, 499, 536, 726
HphI GGTGA 4 cut(s) 161, 398, 481, 877
Hpy166II GTNNAC 1 cut(s) 416
Hpy188I TCNGA 1 cut(s) 695
Hpy188III TCNNGA 3 cut(s) 259, 487, 967
Hpy8I GTNNAC 1 cut(s) 416
HpyCH4III ACNGT 3 cut(s) 39, 424, 905
HpyCH4IV ACGT 1 cut(s) 601
HpyCH4V TGCA 6 cut(s) 22, 188, 343, 607, 611, 912
HpyF10VI GCNNNNNNNGC 3 cut(s) 137, 161, 604
HpyF3I CTNAG 1 cut(s) 350
HpySE526I ACGT 1 cut(s) 601
HspAI GCGC 1 cut(s) 347
Kzo9I GATC 4 cut(s) 483, 491, 544, 561
LmnI GCTCC 1 cut(s) 838
LpnPI CCDG 7 cut(s) 46, 141, 212, 239, 884, 911, 996
Lsp1109I GCAGC 2 cut(s) 34, 143
LweI GCATC 2 cut(s) 175, 899
MaeI CTAG 3 cut(s) 767, 792, 996
MaeII ACGT 1 cut(s) 601
MaeIII GTNAC 3 cut(s) 770, 914, 1006
MalI GATC 4 cut(s) 485, 493, 546, 563
MboI GATC 4 cut(s) 483, 491, 544, 561
MboII GAAGA 7 cut(s) 194, 473, 652, 665, 717, 839, 896
MfeI CAATTG 1 cut(s) 338
MflI RGATCY 2 cut(s) 483, 491
MhlI GDGCHC 4 cut(s) 337, 527, 791, 843
MluCI AATT 4 cut(s) 282, 338, 464, 871
MlyI GAGTC 3 cut(s) 284, 493, 545
MmeI TCCRAC 3 cut(s) 71, 564, 972
Mph1103I ATGCAT 1 cut(s) 609
MseI TTAA 2 cut(s) 176, 327
MslI CAYNNNNRTG 4 cut(s) 71, 612, 924, 998
MspA1I CMGCKG 1 cut(s) 134
MspR9I CCNGG 2 cut(s) 227, 899
MunI CAATTG 1 cut(s) 338
MvaI CCWGG 2 cut(s) 227, 899
MwoI GCNNNNNNNGC 3 cut(s) 137, 161, 604
NdeI CATATG 2 cut(s) 108, 921
NdeII GATC 4 cut(s) 483, 491, 544, 561
NlaIV GGNNCC 1 cut(s) 896
NmuCI GTSAC 1 cut(s) 770
NsiI ATGCAT 1 cut(s) 609
NspI RCATGY 1 cut(s) 611
PaeI GCATGC 1 cut(s) 611
PfeI GAWTC 1 cut(s) 726
PfoI TCCNGGA 1 cut(s) 897
PkrI GCNGC 2 cut(s) 24, 133
Ple19I CGATCG 1 cut(s) 564
PleI GAGTC 3 cut(s) 284, 493, 544
PpsI GAGTC 3 cut(s) 284, 493, 544
PsiI TTATAA 1 cut(s) 753
Psp124BI GAGCTC 2 cut(s) 337, 843
Psp6I CCWGG 2 cut(s) 225, 897
PspGI CCWGG 2 cut(s) 225, 897
PspN4I GGNNCC 1 cut(s) 896
PspPI GGNCC 1 cut(s) 63
PstNI CAGNNNCTG 1 cut(s) 134
PsuI RGATCY 2 cut(s) 483, 491
PvuI CGATCG 1 cut(s) 564
PvuII CAGCTG 1 cut(s) 134
RsaI GTAC 3 cut(s) 415, 591, 667
RsaNI GTAC 3 cut(s) 414, 590, 666
RseI CAYNNNNRTG 4 cut(s) 71, 612, 924, 998
SacI GAGCTC 2 cut(s) 337, 843
SaqAI TTAA 2 cut(s) 176, 327
SatI GCNGC 2 cut(s) 23, 132
Sau3AI GATC 4 cut(s) 483, 491, 544, 561
Sau96I GGNCC 1 cut(s) 63
SchI GAGTC 3 cut(s) 284, 493, 545
ScrFI CCNGG 2 cut(s) 227, 899
SduI GDGCHC 4 cut(s) 337, 527, 791, 843
SfaNI GCATC 2 cut(s) 175, 899
SfcI CTRYAG 1 cut(s) 135
SmiMI CAYNNNNRTG 4 cut(s) 71, 612, 924, 998
SmlI CTYRAG 1 cut(s) 487
SmoI CTYRAG 1 cut(s) 487
SphI GCATGC 1 cut(s) 611
Sse9I AATT 4 cut(s) 282, 338, 464, 871
SspMI CTAG 3 cut(s) 767, 792, 996
SstI GAGCTC 2 cut(s) 337, 843
StyD4I CCNGG 2 cut(s) 225, 897
TaaI ACNGT 3 cut(s) 39, 424, 905
TaiI ACGT 1 cut(s) 604
TaqI TCGA 6 cut(s) 42, 293, 527, 564, 712, 954
TasI AATT 4 cut(s) 282, 338, 464, 871
TatI WGTACW 1 cut(s) 665
TfiI GAWTC 1 cut(s) 726
Tru1I TTAA 2 cut(s) 176, 327
Tru9I TTAA 2 cut(s) 176, 327
TscAI CASTG 3 cut(s) 65, 429, 910
TseFI GTSAC 1 cut(s) 770
TseI GCWGC 2 cut(s) 22, 131
Tsp45I GTSAC 1 cut(s) 770
TspDTI ATGAA 4 cut(s) 392, 452, 666, 972
TspRI CASTG 3 cut(s) 65, 429, 910
XapI RAATTY 1 cut(s) 282
XceI RCATGY 1 cut(s) 611
XspI CTAG 3 cut(s) 767, 792, 996
Zsp2I ATGCAT 1 cut(s) 609
Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.