Rw3G010040

gag-polypeptide of LTR copia-type

Design Primers CRISPR Design

Basic Information

Type: gene
Biological Identity
rosa_wichuraiana
Chr3
OG0000154
Physical Location & Seq
Forward (+)
9623037 .. 9623978
942 bp
Loading structure...
UTR
Exon/CDS
Intron
Rw3G010040.1

Sequence Viewer

Length: 942 bp
ATGGCCAATGAAGGACAGAATTTTCTAAGCGTTCCCAAGTTTGAAGGTGACTATGATTACTGGAGTATGCTCATGGAGAACCTCCTCAGATCGAAAGAGTATTGGAGCATCATAGATCCGGGATACACAGAGCCTTCCTCCACAGTCGTGTTGACAGCAAGCCAAACCAAAACTCTAGAAGATCAGCGATTGAAAGACTTGAAGGCTAAGAACTATCATGTACAGTCCATCAACAAATCCATTCTGAAGACCATTACTCAGAAAGAAACTGCCAAGCGACTGTGGGACTCGATGAAGATCAAATATCAAGGTAATGAAAGAGTTCAGAGGGCTCAACTCCAAATTCTTCCAAGGGATTTTGAATTACTGGAGATGAAGCTCGAAGAATCAATAACCGACTACTTTGGCAGAGTGATGGTTGTAGCTAATGATATGAGAAACTGTGGAGAAGATATGCCGGATGTAAAGATTGTTGAAAAGATTCTGCGTACACTCACAGAAAAATTCAACTACATTGTGTGCTCAATCGAAGAATCAAAGGATATCGATCGTCTCACTGTTAATCAATTGCAAAGTTCCTTGCTTGTACACAAGCAAAAATTCAGAAAGGCTGGAGGAGATGAGCAAGCACTGAAGGTGTCATATGAGGACAGAACAGGAGGACGAGGGAGAGCACGAGGAGGCTTTAGAGGCAGTGGAGTTATGAGAGGCAGAGGCAGAGGTAGAGGTTTGAATAGAGCAACCATTGAGTGTTTTAAGTGCCATCAGTTGGGGCACTTTCAGTATGAGTGTCCAAAGTGGGAAAGGGCTGCCAATTATGTCGAGATAGATGAGGAGGAAGAGCTGCTTCTAATGGCTTTTGTGGAAGAGAACAAATCAAGTAGAGAAGGGGTGTGGTTCCTTGATTCAGGCTGCAGCAATCATATGACAGGGAACAAATAG
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

313

Amino Acids

36.18

Weight (kDa)

7.58

Isoelectric Point (pI)

43.52

Instability Index
Protein Domains (Pfam)
Domain Name Pfam ID Position E-value Description
Retrotran_gag_2 PF14223 25 - 202 8.7e-29 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)
AccB7I CCANNNNNTGG 1 cut(s) 769
AclWI GGATC 1 cut(s) 110
AcoI YGGCCR 1 cut(s) 3
AcsI RAATTY 4 cut(s) 19, 342, 503, 599
AcuI CTGAAG 2 cut(s) 266, 653
AfaI GTAC 3 cut(s) 222, 490, 588
AfiI CCNNNNNNNGG 1 cut(s) 769
AgsI TTSAA 7 cut(s) 44, 193, 202, 362, 476, 508, 733
AleI CACNNNNGTG 1 cut(s) 146
AluBI AGCT 3 cut(s) 379, 425, 844
AluI AGCT 3 cut(s) 379, 425, 844
Alw21I GWGCWC 2 cut(s) 524, 676
Alw26I GTCTC 1 cut(s) 557
AlwI GGATC 1 cut(s) 110
AoxI GGCC 1 cut(s) 3
ApeKI GCWGC 4 cut(s) 809, 844, 912, 915
ApoI RAATTY 4 cut(s) 19, 342, 503, 599
Asp700I GAANNNNTTC 2 cut(s) 321, 480
AsuC2I CCSGG 1 cut(s) 120
AsuHPI GGTGA 1 cut(s) 59
BaeGI GKGCMC 1 cut(s) 777
BalI TGGCCA 1 cut(s) 5
BanII GRGCYC 1 cut(s) 334
BauI CACGAG 1 cut(s) 675
BbsI GAAGAC 1 cut(s) 254
Bbv12I GWGCWC 2 cut(s) 524, 676
BbvI GCAGC 4 cut(s) 796, 831, 899, 927
BccI CCATC 3 cut(s) 236, 409, 771
BciVI GTATCC 1 cut(s) 116
BcnI CCSGG 1 cut(s) 120
BcoDI GTCTC 1 cut(s) 557
BfaI CTAG 1 cut(s) 176
BfmI CTRYAG 1 cut(s) 913
BfuI GTATCC 1 cut(s) 116
BisI GCNGC 4 cut(s) 810, 845, 913, 916
BlsI GCNGC 4 cut(s) 811, 846, 914, 917
Bme1390I CCNGG 1 cut(s) 120
BmiI GGNNCC 1 cut(s) 899
BmrFI CCNGG 1 cut(s) 120
BmsI GCATC 1 cut(s) 117
BpiI GAAGAC 1 cut(s) 254
BplI GAGNNNNNCTC 2 cut(s) 122, 154
BpmI CTGGAG 3 cut(s) 82, 389, 633
BpuMI CCSGG 1 cut(s) 120
Bsa29I ATCGAT 1 cut(s) 546
BsaBI GATNNNNATC 2 cut(s) 296, 546
BsaJI CCNNGG 1 cut(s) 350
Bsc4I CCNNNNNNNGG 1 cut(s) 769
Bse1I ACTGG 2 cut(s) 65, 372
Bse8I GATNNNNATC 2 cut(s) 296, 546
BseCI ATCGAT 1 cut(s) 546
BseDI CCNNGG 1 cut(s) 350
BseGI GGATG 1 cut(s) 466
BseJI GATNNNNATC 2 cut(s) 296, 546
BseLI CCNNNNNNNGG 1 cut(s) 769
BseMII CTCAG 2 cut(s) 100, 272
BseNI ACTGG 2 cut(s) 65, 372
BseRI GAGGAG 4 cut(s) 74, 630, 693, 848
BseSI GKGCMC 1 cut(s) 777
BseXI GCAGC 4 cut(s) 796, 831, 899, 927
Bsh1285I CGRYCG 1 cut(s) 550
BshFI GGCC 1 cut(s) 5
BshVI ATCGAT 1 cut(s) 546
BsiEI CGRYCG 1 cut(s) 550
BsiHKAI GWGCWC 2 cut(s) 524, 676
BsiSI CCGG 2 cut(s) 119, 458
BslFI GGGAC 1 cut(s) 299
BslI CCNNNNNNNGG 1 cut(s) 769
BsmAI GTCTC 1 cut(s) 557
BsmBI CGTCTC 1 cut(s) 557
BsmFI GGGAC 1 cut(s) 299
BsnI GGCC 1 cut(s) 5
Bsp1286I GDGCHC 4 cut(s) 334, 524, 676, 777
Bsp1407I TGTACA 2 cut(s) 220, 586
Bsp143I GATC 5 cut(s) 89, 115, 181, 297, 547
BspANI GGCC 1 cut(s) 5
BspCNI CTCAG 2 cut(s) 99, 271
BspDI ATCGAT 1 cut(s) 546
BspLI GGNNCC 1 cut(s) 899
BspMAI CTGCAG 1 cut(s) 917
BspPI GGATC 1 cut(s) 110
BspQI GCTCTTC 1 cut(s) 834
BsrGI TGTACA 2 cut(s) 220, 586
BsrI ACTGG 2 cut(s) 65, 372
BssECI CCNNGG 1 cut(s) 350
BssMI GATC 5 cut(s) 89, 115, 181, 297, 547
BssSI CACGAG 1 cut(s) 675
BssT1I CCWWGG 1 cut(s) 350
Bst2BI CACGAG 1 cut(s) 675
Bst4CI ACNGT 5 cut(s) 145, 225, 282, 443, 559
Bst6I CTCTTC 2 cut(s) 834, 861
BstAUI TGTACA 2 cut(s) 220, 586
BstC8I GCNNGC 2 cut(s) 160, 627
BstDEI CTNAG 4 cut(s) 26, 86, 207, 258
BstF5I GGATG 1 cut(s) 466
BstKTI GATC 5 cut(s) 92, 118, 184, 300, 550
BstMAI GTCTC 1 cut(s) 557
BstMBI GATC 5 cut(s) 89, 115, 181, 297, 547
BstMCI CGRYCG 1 cut(s) 550
BstMWI GCNNNNNNNGC 1 cut(s) 690
BstSCI CCNGG 1 cut(s) 118
BstSFI CTRYAG 1 cut(s) 913
BstSLI GKGCMC 1 cut(s) 777
BstV1I GCAGC 4 cut(s) 796, 831, 899, 927
BstV2I GAAGAC 1 cut(s) 254
BstX2I RGATCY 1 cut(s) 115
BstYI RGATCY 1 cut(s) 115
Bsu15I ATCGAT 1 cut(s) 546
BsuI GTATCC 1 cut(s) 116
BsuRI GGCC 1 cut(s) 5
BsuTUI ATCGAT 1 cut(s) 546
BtsCI GGATG 1 cut(s) 466
BtsI GCAGTG 1 cut(s) 700
BtsIMutI CAGTG 3 cut(s) 555, 629, 700
Cac8I GCNNGC 2 cut(s) 160, 627
ClaI ATCGAT 1 cut(s) 546
Csp6I GTAC 3 cut(s) 221, 489, 587
CviAII CATG 2 cut(s) 73, 218
CviQI GTAC 3 cut(s) 221, 489, 587
DdeI CTNAG 4 cut(s) 26, 86, 207, 258
DpnI GATC 5 cut(s) 91, 117, 183, 299, 549
DpnII GATC 5 cut(s) 89, 115, 181, 297, 547
EaeI YGGCCR 1 cut(s) 3
Eam1104I CTCTTC 2 cut(s) 834, 861
EarI CTCTTC 2 cut(s) 834, 861
Eco130I CCWWGG 1 cut(s) 350
Eco24I GRGCYC 1 cut(s) 334
Eco32I GATATC 1 cut(s) 544
Eco57I CTGAAG 2 cut(s) 266, 653
EcoRV GATATC 1 cut(s) 544
EcoT14I CCWWGG 1 cut(s) 350
EcoT38I GRGCYC 1 cut(s) 334
ErhI CCWWGG 1 cut(s) 350
Esp3I CGTCTC 1 cut(s) 557
FaeI CATG 2 cut(s) 76, 221
FalI AAGNNNNNCTT 2 cut(s) 831, 863
FaqI GGGAC 1 cut(s) 299
FatI CATG 2 cut(s) 72, 217
FauNDI CATATG 2 cut(s) 643, 924
Fnu4HI GCNGC 4 cut(s) 810, 845, 913, 916
FokI GGATG 1 cut(s) 473
FriOI GRGCYC 1 cut(s) 334
Fsp4HI GCNGC 4 cut(s) 810, 845, 913, 916
FspBI CTAG 1 cut(s) 176
GluI GCNGC 4 cut(s) 810, 845, 913, 916
GsuI CTGGAG 3 cut(s) 82, 389, 633
HaeIII GGCC 1 cut(s) 5
HapII CCGG 2 cut(s) 119, 458
Hin1II CATG 2 cut(s) 76, 221
HincII GTYRAC 1 cut(s) 153
HindII GTYRAC 1 cut(s) 153
HinfI GANTC 5 cut(s) 287, 386, 481, 533, 905
HpaII CCGG 2 cut(s) 119, 458
HphI GGTGA 1 cut(s) 59
Hpy166II GTNNAC 3 cut(s) 153, 491, 589
Hpy188I TCNGA 5 cut(s) 89, 246, 261, 327, 605
Hpy188III TCNNGA 2 cut(s) 176, 823
Hpy8I GTNNAC 3 cut(s) 153, 491, 589
HpyAV CCTTC 6 cut(s) 5, 38, 144, 196, 628, 881
HpyCH4III ACNGT 5 cut(s) 145, 225, 282, 443, 559
HpyCH4V TGCA 2 cut(s) 571, 915
HpyF10VI GCNNNNNNNGC 1 cut(s) 690
HpyF3I CTNAG 4 cut(s) 26, 86, 207, 258
Hsp92II CATG 2 cut(s) 76, 221
Kzo9I GATC 5 cut(s) 89, 115, 181, 297, 547
LguI GCTCTTC 1 cut(s) 834
LmnI GCTCC 1 cut(s) 105
LpnPI CCDG 8 cut(s) 46, 132, 353, 471, 597, 642, 894, 915
Lsp1109I GCAGC 4 cut(s) 796, 831, 899, 927
LweI GCATC 1 cut(s) 117
MaeI CTAG 1 cut(s) 176
MaeIII GTNAC 1 cut(s) 47
MalI GATC 5 cut(s) 91, 117, 183, 299, 549
MboI GATC 5 cut(s) 89, 115, 181, 297, 547
MboII GAAGA 9 cut(s) 191, 259, 307, 338, 395, 461, 542, 851, 878
MfeI CAATTG 1 cut(s) 566
MflI RGATCY 1 cut(s) 115
MhlI GDGCHC 4 cut(s) 334, 524, 676, 777
MlsI TGGCCA 1 cut(s) 5
MluCI AATT 7 cut(s) 19, 342, 362, 503, 566, 599, 814
MluNI TGGCCA 1 cut(s) 5
MlyI GAGTC 1 cut(s) 281
Mox20I TGGCCA 1 cut(s) 5
MroXI GAANNNNTTC 2 cut(s) 321, 480
MscI TGGCCA 1 cut(s) 5
MseI TTAA 2 cut(s) 561, 756
MslI CAYNNNNRTG 1 cut(s) 146
Msp20I TGGCCA 1 cut(s) 5
MspI CCGG 2 cut(s) 119, 458
MspR9I CCNGG 1 cut(s) 120
MunI CAATTG 1 cut(s) 566
MwoI GCNNNNNNNGC 1 cut(s) 690
NciI CCSGG 1 cut(s) 120
NdeI CATATG 2 cut(s) 643, 924
NdeII GATC 5 cut(s) 89, 115, 181, 297, 547
NlaIII CATG 2 cut(s) 76, 221
NlaIV GGNNCC 1 cut(s) 899
NmuCI GTSAC 1 cut(s) 47
OliI CACNNNNGTG 1 cut(s) 146
PciSI GCTCTTC 1 cut(s) 834
PdmI GAANNNNTTC 2 cut(s) 321, 480
PfeI GAWTC 4 cut(s) 386, 481, 533, 905
PflMI CCANNNNNTGG 1 cut(s) 769
PfoI TCCNGGA 1 cut(s) 118
PkrI GCNGC 4 cut(s) 811, 846, 914, 917
Ple19I CGATCG 1 cut(s) 550
PleI GAGTC 1 cut(s) 281
PpsI GAGTC 1 cut(s) 281
PspN4I GGNNCC 1 cut(s) 899
PstI CTGCAG 1 cut(s) 917
PsuI RGATCY 1 cut(s) 115
PvuI CGATCG 1 cut(s) 550
RsaI GTAC 3 cut(s) 222, 490, 588
RsaNI GTAC 3 cut(s) 221, 489, 587
RseI CAYNNNNRTG 1 cut(s) 146
SapI GCTCTTC 1 cut(s) 834
SaqAI TTAA 2 cut(s) 561, 756
SatI GCNGC 4 cut(s) 810, 845, 913, 916
Sau3AI GATC 5 cut(s) 89, 115, 181, 297, 547
SchI GAGTC 1 cut(s) 281
ScrFI CCNGG 1 cut(s) 120
SduI GDGCHC 4 cut(s) 334, 524, 676, 777
SetI ASST 9 cut(s) 49, 84, 313, 381, 427, 639, 724, 730, 846
SfaNI GCATC 1 cut(s) 117
SfcI CTRYAG 1 cut(s) 913
SmiMI CAYNNNNRTG 1 cut(s) 146
Sse9I AATT 7 cut(s) 19, 342, 362, 503, 566, 599, 814
SspMI CTAG 1 cut(s) 176
StyD4I CCNGG 1 cut(s) 118
StyI CCWWGG 1 cut(s) 350
TaaI ACNGT 5 cut(s) 145, 225, 282, 443, 559
TaqI TCGA 6 cut(s) 92, 290, 381, 528, 546, 822
TasI AATT 7 cut(s) 19, 342, 362, 503, 566, 599, 814
TatI WGTACW 2 cut(s) 220, 586
TfiI GAWTC 4 cut(s) 386, 481, 533, 905
Tru1I TTAA 2 cut(s) 561, 756
Tru9I TTAA 2 cut(s) 561, 756
TscAI CASTG 3 cut(s) 562, 636, 700
TseFI GTSAC 1 cut(s) 47
TseI GCWGC 4 cut(s) 809, 844, 912, 915
Tsp45I GTSAC 1 cut(s) 47
TspDTI ATGAA 4 cut(s) 24, 308, 330, 389
TspRI CASTG 3 cut(s) 562, 636, 700
Van91I CCANNNNNTGG 1 cut(s) 769
XapI RAATTY 4 cut(s) 19, 342, 503, 599
XbaI TCTAGA 1 cut(s) 175
XmnI GAANNNNTTC 2 cut(s) 321, 480
XspI CTAG 1 cut(s) 176
Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.