Rw2G025840

gag-polypeptide of LTR copia-type

Design Primers CRISPR Design

Basic Information

Type: gene
Biological Identity
rosa_wichuraiana
Chr2
OG0000258
Physical Location & Seq
Reverse (-)
39281158 .. 39282494
1337 bp
Loading structure...
UTR
Exon/CDS
Intron
Rw2G025840.1

Sequence Viewer

Length: 1266 bp
ATGAACGGTGACAATTCAAATGTTAAAAGGGATGATATGGGACAAAGCGAGGCAAATCCTATATCTGTGGTGATATCAGACTCCTCTAAACATGGAGAGAAACCTGCGAAGTTCAATGGAACAGACTTCAAGAGGTGGCAACAAAAGATGCTCTTCTACCTGACAACCTTGAGTTTGACAAAATTTCTGAAGGAAGATGCCTCTGCCAGTGGCTCATCTGTGGAGGCTGCTGCGGCTGCAGATGCTTGGCATCATTCTGATTTTCTGTGCAAAAATTACATCCTCAATGGATTGGACAATGCATTATACAATGTCTATAGTCCAATGAAAACTGCTAAGGCCTTATGGGAGTCTCTTGACAAGAAATATAAGACCGAGGACGCTGGAAAGAAGAAATATATCATTGGGCGTTTTCTTGATTACAAGATGATAGACTCCAAATCAGTCATGAGTGAAAAAATGGATATGACTGAAGCTTTACAAGTTGGTTGTGTGATTGAAAAATTACCTCCATCTTGGAAAGAGTTTAAGAATTATCTCAAGCATAAGCGCAAGGAAATGGACCTTGAAGGTTTGACTGTGAGGCTAAGGGTTGAGGAAGACAACCGTATTGCTGACAAGAAAAATGGAATTAATTCCATGGCAGCAAATGCTCATAGAAAATATTCTGGTGAAGGCAAAGAGCAAGAGAATACAAAGAAGCATCGTAATTTCAAAGGAAAATGTTTCAATTGTAACAAGCCTGGGCATAGAGCTTCTGATTGTCGCAGCCGTAAAGGAAAGAAAAACAATTACAAGAAATATAAAGGCAAGGCCAAGGAGGTTCATATAGCCGAAGAGGACAAACTCTCATGTGGAATATCTGATATCAATTTGTCAGCTGTGATCTCTGAAGTAAATATGATGACCAGCAGTGATGATTGGTGGGTAGACACTGGGGCTACACGCCACATTTGTTTTGACAAGAAGATGTTTGCTACATATGAAGCAGTGGAACACGGAGAGCAGCTCTTTATGGGAAATTCCTCTACTTCAGGGGTTGAAGGACAAGGAAATGTGACACTCAAGTTGACATCTGGAAAGGTACTCACTCTAACAGAAGTACTTCATGTTCCTGATATTAGAAAAAACTTGGTTTCTGGATCGCTGCTCAGTAAGAATGGTTTCAAGTTGGTTTTTGAGGCTGACAAGTTTATGTTAACTAAGAATGGAATGTATGTGGGGAAAGGTTATCTCAGTCATGGCCTCTTCAAAATACAAGGATGA
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

421

Amino Acids

47.37

Weight (kDa)

9.25

Isoelectric Point (pI)

28.23

Instability Index
Protein Domains (Pfam)
Domain Name Pfam ID Position E-value Description
Retrotran_gag_2 PF14223 50 - 206 7.7e-15 gag-polypeptide of LTR copia-type
zf-CCHC PF00098 240 - 256 3.5e-06 Zinc knuckle
Pol_BBD PF22936 308 - 389 1.7e-24 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: OG0000258)

Species Orthologous Gene IDs
arabidopsis_thaliana AT4G00980
fragaria_vesca FvH4_1g25682 FvH4_2g13961 FvH4_2g20162 FvH4_2g24753 FvH4_3g12191 FvH4_3g12632 FvH4_3g16171 FvH4_4g05871 FvH4_4g05873 FvH4_4g10121 FvH4_4g15488 FvH4_4g23911 FvH4_4g27782 FvH4_5g08912 FvH4_5g23001 FvH4_5g24552 FvH4_5g32801 FvH4_5g32802 FvH4_6g05093 FvH4_6g19722 FvH4_6g20391 FvH4_6g33792 FvH4_7g01381 FvH4_7g16761 FvH4_7g16761 FvH4_7g16761
malus_domestica MD01G1082500.v1.1 MD15G1436400.v1.1
prunus_persica Prupe.2G021400_v2.0.a1 Prupe.2G052400_v2.0.a1 Prupe.2G065000_v2.0.a1 Prupe.2G187700_v2.0.a1 Prupe.2G187800_v2.0.a1 Prupe.2G189900_v2.0.a1 Prupe.2G191300_v2.0.a1 Prupe.2G191700_v2.0.a1 Prupe.4G265600_v2.0.a1 Prupe.7G014200_v2.0.a1 Prupe.7G039000_v2.0.a1
pyrus_communis pycom01g05590 pycom01g05910 pycom02g12230 pycom02g25840 pycom03g15580 pycom04g04480 pycom05g09230 pycom05g23350 pycom05g23360 pycom07g08380 pycom09g01980 pycom09g01990 pycom11g18190 pycom11g18200 pycom11g21580 pycom13g04160 pycom15g25800 pycom16g16210 pycom16g17230 pycom16g24560 pycom16g25700 pycom17g11020
rosa_chinensis RchiOBHm_Chr1g0359981 RchiOBHm_Chr2g0151961 RchiOBHm_Chr2g0171331 RchiOBHm_Chr5g0081471 RchiOBHm_Chr6g0283031 RchiOBHm_Chr7g0197111 RchiOBHm_Chr7g0222601
rosa_laevigata RLG00000027843 RLG00000027845 RLG00000030065
rosa_multiflora Rmu_sc0000381.1_g000031 Rmu_sc0001179.1_g000035 Rmu_sc0001616.1_g000046 Rmu_sc0001851.1_g000032 Rmu_sc0002152.1_g000013 Rmu_sc0004031.1_g000015 Rmu_sc0004645.1_g000003 Rmu_sc0007393.1_g000001 Rmu_sc0008949.1_g000003 Rmu_sc0009799.1_g000011 Rmu_sc0011614.1_g000001 Rmu_sc0011699.1_g000009 Rmu_sc0019280.1_g000001 Rmu_sc0023984.1_g000001 Rmu_ssc0000050.1_g000036
rosa_roxburghii Rroxscaffold_1G00022650 Rroxscaffold_1G00033480 Rroxscaffold_3G00270250 Rroxscaffold_4G00296600 Rroxscaffold_4G00296760 Rroxscaffold_6G00409840
rosa_rugosa Rorug01G0273800 Rorug01G0273900 Rorug01G0274000
rosa_samantha Rh1AG287300 Rh1AG288100 Rh1BG253000 Rh1BG253500 Rh1BG399800 Rh1CG270400 Rh1CG271000 Rh1DG282000 Rh1DG282500 Rh4DG126500 Rh5DG194600 Rh5DG461100
rosa_wichuraiana Rw0G009130 Rw1G002590 Rw1G008490 Rw1G012210 Rw1G014290 Rw1G014490 Rw1G025510 Rw2G025840 Rw2G026170 Rw2G036510 Rw3G003050 Rw4G009270 Rw5G002350 Rw5G013930 Rw5G019500 Rw5G025890 Rw5G029960 Rw5G032360 Rw6G009890 Rw6G015670 Rw6G015860 Rw7G010030 Rw7G032600 Rw7G032770

Restriction Enzyme Sites

1 / 10
Enzyme Recognition Site Cut Count Positions (bp)
Acc36I ACCTGC 1 cut(s) 112
AccI GTMKAC 1 cut(s) 930
AciI CCGC 1 cut(s) 233
AclWI GGATC 1 cut(s) 1150
AcsI RAATTY 2 cut(s) 182, 1021
AcuI CTGAAG 4 cut(s) 209, 492, 912, 1017
AfaI GTAC 2 cut(s) 1086, 1104
AjnI CCWGG 1 cut(s) 742
AluBI AGCT 4 cut(s) 476, 755, 881, 1009
AluI AGCT 4 cut(s) 476, 755, 881, 1009
Alw26I GTCTC 1 cut(s) 357
AlwI GGATC 1 cut(s) 1150
AoxI GGCC 3 cut(s) 339, 813, 1243
ApeKI GCWGC 7 cut(s) 227, 230, 236, 644, 768, 1006, 1147
ApoI RAATTY 2 cut(s) 182, 1021
AseI ATTAAT 1 cut(s) 633
Asp700I GAANNNNTTC 4 cut(s) 634, 664, 1104, 1163
AspLEI GCGC 1 cut(s) 552
AspS9I GGNCC 1 cut(s) 562
AsuHPI GGTGA 3 cut(s) 20, 82, 683
AvaII GGWCC 1 cut(s) 562
BbsI GAAGAC 1 cut(s) 606
BbvI GCAGC 7 cut(s) 214, 217, 223, 656, 780, 1018, 1134
BccI CCATC 1 cut(s) 520
BceAI ACGGC 1 cut(s) 756
BciT130I CCWGG 1 cut(s) 744
BcoDI GTCTC 1 cut(s) 357
BfmI CTRYAG 2 cut(s) 237, 316
BfuAI ACCTGC 1 cut(s) 112
BisI GCNGC 8 cut(s) 228, 231, 234, 237, 645, 769, 1007, 1148
BlsI GCNGC 8 cut(s) 229, 232, 235, 238, 646, 770, 1008, 1149
BmcAI AGTACT 1 cut(s) 1104
Bme1390I CCNGG 1 cut(s) 744
Bme18I GGWCC 1 cut(s) 562
BmgT120I GGNCC 1 cut(s) 562
BmrFI CCNGG 1 cut(s) 744
BmrI ACTGGG 1 cut(s) 945
BmsI GCATC 5 cut(s) 138, 187, 232, 259, 712
BmuI ACTGGG 1 cut(s) 945
BpiI GAAGAC 1 cut(s) 606
BplI GAGNNNNNCTC 2 cut(s) 993, 1025
Bpu10I CCTNAGC 2 cut(s) 336, 587
BpuEI CTTGAG 3 cut(s) 190, 524, 1049
BsaJI CCNNGG 4 cut(s) 375, 639, 743, 816
Bse1I ACTGG 2 cut(s) 207, 940
BseBI CCWGG 1 cut(s) 744
BseDI CCNNGG 4 cut(s) 375, 639, 743, 816
BseGI GGATG 2 cut(s) 37, 279
BseMII CTCAG 2 cut(s) 1165, 1249
BseNI ACTGG 2 cut(s) 207, 940
BseRI GAGGAG 1 cut(s) 73
BseXI GCAGC 7 cut(s) 214, 217, 223, 656, 780, 1018, 1134
BshFI GGCC 3 cut(s) 341, 815, 1245
BslFI GGGAC 1 cut(s) 54
BsmAI GTCTC 1 cut(s) 357
BsmFI GGGAC 1 cut(s) 54
BsnI GGCC 3 cut(s) 341, 815, 1245
Bsp143I GATC 2 cut(s) 885, 1142
Bsp19I CCATGG 1 cut(s) 639
BspACI CCGC 1 cut(s) 233
BspANI GGCC 3 cut(s) 341, 815, 1245
BspCNI CTCAG 2 cut(s) 1164, 1248
BspHI TCATGA 1 cut(s) 447
BspMAI CTGCAG 1 cut(s) 241
BspMI ACCTGC 1 cut(s) 112
BspPI GGATC 1 cut(s) 1150
BspQI GCTCTTC 1 cut(s) 158
BsrI ACTGG 2 cut(s) 207, 940
BssECI CCNNGG 4 cut(s) 375, 639, 743, 816
BssMI GATC 2 cut(s) 885, 1142
BssT1I CCWWGG 2 cut(s) 639, 816
Bst2UI CCWGG 1 cut(s) 744
Bst4CI ACNGT 3 cut(s) 8, 580, 608
Bst6I CTCTTC 3 cut(s) 158, 831, 1253
BstAPI GCANNNNNTGC 1 cut(s) 650
BstDEI CTNAG 5 cut(s) 336, 587, 1151, 1203, 1235
BstDSI CCRYGG 1 cut(s) 639
BstF5I GGATG 2 cut(s) 37, 279
BstHHI GCGC 1 cut(s) 552
BstKTI GATC 2 cut(s) 888, 1145
BstMAI GTCTC 1 cut(s) 357
BstMBI GATC 2 cut(s) 885, 1142
BstMWI GCNNNNNNNGC 4 cut(s) 233, 236, 242, 650
BstNI CCWGG 1 cut(s) 744
BstSCI CCNGG 1 cut(s) 742
BstSFI CTRYAG 2 cut(s) 237, 316
BstV1I GCAGC 7 cut(s) 214, 217, 223, 656, 780, 1018, 1134
BstV2I GAAGAC 1 cut(s) 606
BsuRI GGCC 3 cut(s) 341, 815, 1245
BtgI CCRYGG 1 cut(s) 639
BtsCI GGATG 2 cut(s) 37, 279
BtsI GCAGTG 2 cut(s) 919, 996
BtsIMutI CAGTG 4 cut(s) 214, 919, 933, 996
BveI ACCTGC 1 cut(s) 112
CciI TCATGA 1 cut(s) 447
CfoI GCGC 1 cut(s) 552
Cfr13I GGNCC 1 cut(s) 562
CseI GACGC 1 cut(s) 389
Csp6I GTAC 2 cut(s) 1085, 1103
CviAII CATG 6 cut(s) 92, 448, 640, 852, 1109, 1241
CviQI GTAC 2 cut(s) 1085, 1103
DdeI CTNAG 5 cut(s) 336, 587, 1151, 1203, 1235
DpnI GATC 2 cut(s) 887, 1144
DpnII GATC 2 cut(s) 885, 1142
Eam1104I CTCTTC 3 cut(s) 158, 831, 1253
EarI CTCTTC 3 cut(s) 158, 831, 1253
Eco130I CCWWGG 2 cut(s) 639, 816
Eco147I AGGCCT 1 cut(s) 341
Eco32I GATATC 2 cut(s) 75, 868
Eco47I GGWCC 1 cut(s) 562
Eco57I CTGAAG 4 cut(s) 209, 492, 912, 1017
EcoRII CCWGG 1 cut(s) 742
EcoRV GATATC 2 cut(s) 75, 868
EcoT14I CCWWGG 2 cut(s) 639, 816
EcoT22I ATGCAT 1 cut(s) 304
ErhI CCWWGG 2 cut(s) 639, 816
FaeI CATG 6 cut(s) 95, 451, 643, 855, 1112, 1244
FalI AAGNNNNNCTT 2 cut(s) 137, 169
FaqI GGGAC 1 cut(s) 54
FatI CATG 6 cut(s) 91, 447, 639, 851, 1108, 1240
FauNDI CATATG 1 cut(s) 982
FblI GTMKAC 1 cut(s) 930
Fnu4HI GCNGC 8 cut(s) 228, 231, 234, 237, 645, 769, 1007, 1148
FokI GGATG 2 cut(s) 44, 266
Fsp4HI GCNGC 8 cut(s) 228, 231, 234, 237, 645, 769, 1007, 1148
GlaI GCGC 1 cut(s) 551
GluI GCNGC 8 cut(s) 228, 231, 234, 237, 645, 769, 1007, 1148
HaeIII GGCC 3 cut(s) 341, 815, 1245
HgaI GACGC 1 cut(s) 389
HhaI GCGC 1 cut(s) 552
Hin1II CATG 6 cut(s) 95, 451, 643, 855, 1112, 1244
Hin6I GCGC 1 cut(s) 550
HinP1I GCGC 1 cut(s) 550
HincII GTYRAC 2 cut(s) 1071, 1200
HindII GTYRAC 2 cut(s) 1071, 1200
HindIII AAGCTT 1 cut(s) 474
HinfI GANTC 3 cut(s) 80, 350, 434
HpaI GTTAAC 1 cut(s) 1200
HphI GGTGA 3 cut(s) 20, 82, 683
Hpy166II GTNNAC 3 cut(s) 931, 1071, 1200
Hpy188I TCNGA 6 cut(s) 79, 189, 259, 760, 865, 892
Hpy188III TCNNGA 7 cut(s) 130, 356, 416, 448, 1077, 1115, 1140
Hpy8I GTNNAC 3 cut(s) 931, 1071, 1200
HpyAV CCTTC 4 cut(s) 184, 563, 668, 1037
HpyCH4III ACNGT 3 cut(s) 8, 580, 608
HpyCH4V TGCA 3 cut(s) 239, 270, 302
HpyF10VI GCNNNNNNNGC 4 cut(s) 233, 236, 242, 650
HpyF3I CTNAG 5 cut(s) 336, 587, 1151, 1203, 1235
Hsp92II CATG 6 cut(s) 95, 451, 643, 855, 1112, 1244
HspAI GCGC 1 cut(s) 550
KspAI GTTAAC 1 cut(s) 1200
Kzo9I GATC 2 cut(s) 885, 1142
LguI GCTCTTC 1 cut(s) 158
Lsp1109I GCAGC 7 cut(s) 214, 217, 223, 656, 780, 1018, 1134
LweI GCATC 5 cut(s) 138, 187, 232, 259, 712
MaeIII GTNAC 3 cut(s) 8, 734, 1057
MalI GATC 2 cut(s) 887, 1144
MboI GATC 2 cut(s) 885, 1142
MboII GAAGA 7 cut(s) 145, 206, 403, 611, 848, 979, 1240
MfeI CAATTG 1 cut(s) 730
MlyI GAGTC 3 cut(s) 74, 359, 428
Mph1103I ATGCAT 1 cut(s) 304
MroXI GAANNNNTTC 4 cut(s) 634, 664, 1104, 1163
MseI TTAA 4 cut(s) 24, 528, 633, 1199
MspA1I CMGCKG 1 cut(s) 881
MspR9I CCNGG 1 cut(s) 744
MunI CAATTG 1 cut(s) 730
MvaI CCWGG 1 cut(s) 744
MwoI GCNNNNNNNGC 4 cut(s) 233, 236, 242, 650
NcoI CCATGG 1 cut(s) 639
NdeI CATATG 1 cut(s) 982
NdeII GATC 2 cut(s) 885, 1142
NlaIII CATG 6 cut(s) 95, 451, 643, 855, 1112, 1244
NmuCI GTSAC 2 cut(s) 8, 1057
NsiI ATGCAT 1 cut(s) 304
PagI TCATGA 1 cut(s) 447
PceI AGGCCT 1 cut(s) 341
PciSI GCTCTTC 1 cut(s) 158
PdmI GAANNNNTTC 4 cut(s) 634, 664, 1104, 1163
PkrI GCNGC 8 cut(s) 229, 232, 235, 238, 646, 770, 1008, 1149
PleI GAGTC 3 cut(s) 74, 358, 428
PpsI GAGTC 3 cut(s) 74, 358, 428
PshBI ATTAAT 1 cut(s) 633
Psp6I CCWGG 1 cut(s) 742
PspGI CCWGG 1 cut(s) 742
PspPI GGNCC 1 cut(s) 562
PsrI GAACNNNNNNTAC 2 cut(s) 1095, 1127
PstI CTGCAG 1 cut(s) 241
PvuII CAGCTG 1 cut(s) 881
RsaI GTAC 2 cut(s) 1086, 1104
RsaNI GTAC 2 cut(s) 1085, 1103
SapI GCTCTTC 1 cut(s) 158
SaqAI TTAA 4 cut(s) 24, 528, 633, 1199
SatI GCNGC 8 cut(s) 228, 231, 234, 237, 645, 769, 1007, 1148
Sau3AI GATC 2 cut(s) 885, 1142
Sau96I GGNCC 1 cut(s) 562
ScaI AGTACT 1 cut(s) 1104
SchI GAGTC 3 cut(s) 74, 359, 428
ScrFI CCNGG 1 cut(s) 744
SfaNI GCATC 5 cut(s) 138, 187, 232, 259, 712
SfcI CTRYAG 2 cut(s) 237, 316
SinI GGWCC 1 cut(s) 562
SmlI CTYRAG 3 cut(s) 169, 539, 1064
SmoI CTYRAG 3 cut(s) 169, 539, 1064
SseBI AGGCCT 1 cut(s) 341
SsiI CCGC 1 cut(s) 233
SspI AATATT 1 cut(s) 665
StuI AGGCCT 1 cut(s) 341
StyD4I CCNGG 1 cut(s) 742
StyI CCWWGG 2 cut(s) 639, 816
TaaI ACNGT 3 cut(s) 8, 580, 608
TaqII GACCGA 1 cut(s) 389
TatI WGTACW 1 cut(s) 1102
TauI GCSGC 1 cut(s) 236
Tru1I TTAA 4 cut(s) 24, 528, 633, 1199
Tru9I TTAA 4 cut(s) 24, 528, 633, 1199
TscAI CASTG 4 cut(s) 214, 919, 940, 996
TseFI GTSAC 2 cut(s) 8, 1057
TseI GCWGC 7 cut(s) 227, 230, 236, 644, 768, 1006, 1147
Tsp45I GTSAC 2 cut(s) 8, 1057
TspDTI ATGAA 5 cut(s) 17, 341, 815, 999, 1097
TspGWI ACGGA 1 cut(s) 1014
TspRI CASTG 4 cut(s) 214, 919, 940, 996
VpaK11BI GGWCC 1 cut(s) 562
VspI ATTAAT 1 cut(s) 633
XapI RAATTY 2 cut(s) 182, 1021
XmiI GTMKAC 1 cut(s) 930
XmnI GAANNNNTTC 4 cut(s) 634, 664, 1104, 1163
ZrmI AGTACT 1 cut(s) 1104
Zsp2I ATGCAT 1 cut(s) 304
Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.