Rw4G009270

gag-polypeptide of LTR copia-type

Design Primers CRISPR Design

Basic Information

Type: gene
Biological Identity
rosa_wichuraiana
Chr4
OG0000258
Physical Location & Seq
Forward (+)
20761176 .. 20763179
2004 bp
Loading structure...
UTR
Exon/CDS
Intron
Rw4G009270.1

Sequence Viewer

Length: 1260 bp
ATGGATCAAGTATCAGTGAATGGTGTGAAAACTCATGTTGAGAAACCAGAAAAATTCAAGGGCGTGGACTTTAAACGCTGGCAACAAAAAATGTTGTTTTATCTAACAACATTGAACCTTGCTCATGTCGTGAAGGAAGAAGTTTCAAAAGCAGAAGGAGATGATGTGACTGCAGAACAATTGAATGCAATTGATGCCTGGAAACATTGTGAGTTTCTCTGTAGGAACTATGTTCTCAATGGTCTGGATGACACTTTGTATGATGTATATAGGTCATACACCACTGCAAAGGAACTCTGGAATTCTTTGGAGAAAAAATACAAAGTTGATGACGCAGGTTCAAAGAAGTTCAGTATTGGAAAATTTTTGAACTATAAGATGGTGGATAGCAAGACTGTTGTTAGTCAAGTTGATGAACTCCAGGTGATTATTCATGAACTTCATGCTGAAGTTGGTTCTGTTATAGAAAAATTACCACCTTCTTGGAAGGATTTCAAAGTGCATTTGAAGCACAAGAAGAGTGAAATGACCATGGAGGATCTGGTTTTGAAACTACGAGTTCAAGAAGACCACCTGAAAAGTGAGAAGCAACCCGATGGATCTATCATCGAAGCCAAAGCAAATATGGTTGAGGGAGAAACTTCCAAACCAAAATTCAAAGGCAATAAACATGATGTCAAATATGCAACAAAGACCAAGAATTTCAAGAAAATTAAAGGTAGTTGCTGGGTGTGTGGAAAGCCTGGACACAAGGCACAAGAATGTCGCCACAAGAAAGATGCACCTGTTGCCTTTAGGAACAACAACAACAACAACAACAACCAAGCAAATGTGGTTGTGGCTATGGAGGATTTTGTGGCTGTTGTTTCTGAAGTCAACTTGGTGAATGACAATAAGGACTGGTGGATTGATACCGGTGCGACAAGGCACATTTGTGGAGATAGAAATCTGTTTACCACCTATCAACCACTTAATGGTGAGGAGCAATTGTTCATGGGAAATGCATCTGCATCAAGTGTTGCTGGAAAGGGTAATGTGGTTTTGACATTCACTTCTGGGAAAAAACTCACTCTAACTGAGGTGCTACATGTTCCTGAAATTAGGAAGAATCTTGTGTCTGGTCCTTTGTTGAGCAACAAAGGATTTAAACTTGTTTTTGAATCTGACAAGTTTGTTCTCACTAAGGGAGGAACTTTTGTAGGAAAGGGTTACCTGGCAGAGGGGCTCTTCAAACTCAATCTATATAATGCCTTCGTATAA
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

419

Amino Acids

47.34

Weight (kDa)

8.95

Isoelectric Point (pI)

27.91

Instability Index
Protein Domains (Pfam)
Domain Name Pfam ID Position E-value Description
Retrotran_gag_2 PF14223 31 - 195 1.1e-19 gag-polypeptide of LTR copia-type
Pol_BBD PF22936 301 - 382 6.4e-25 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) 326
AccB7I CCANNNNNTGG 1 cut(s) 974
AclWI GGATC 3 cut(s) 12, 546, 607
AcsI RAATTY 5 cut(s) 53, 301, 362, 653, 700
AcuI CTGAAG 2 cut(s) 468, 891
AfiI CCNNNNNNNGG 2 cut(s) 974, 1219
AflIII ACRYGT 1 cut(s) 1087
AgeI ACCGGT 1 cut(s) 914
AjnI CCWGG 4 cut(s) 197, 420, 742, 1212
AjuI GAANNNNNNNTTGG 2 cut(s) 638, 670
AleI CACNNNNGTG 1 cut(s) 933
AloI GAACNNNNNNTCC 2 cut(s) 974, 1006
AlwI GGATC 3 cut(s) 12, 546, 607
ApoI RAATTY 5 cut(s) 53, 301, 362, 653, 700
AsiGI ACCGGT 1 cut(s) 914
Asp700I GAANNNNTTC 1 cut(s) 491
AspS9I GGNCC 1 cut(s) 1121
AsuHPI GGTGA 3 cut(s) 436, 895, 989
AvaII GGWCC 1 cut(s) 1121
BanII GRGCYC 1 cut(s) 1227
BbsI GAAGAC 1 cut(s) 573
BccI CCATC 2 cut(s) 373, 590
BciT130I CCWGG 4 cut(s) 199, 422, 744, 1214
BfmI CTRYAG 2 cut(s) 171, 220
BfuAI ACCTGC 1 cut(s) 326
Bme1390I CCNGG 4 cut(s) 199, 422, 744, 1214
Bme18I GGWCC 1 cut(s) 1121
BmgT120I GGNCC 1 cut(s) 1121
BmrFI CCNGG 4 cut(s) 199, 422, 744, 1214
BmsI GCATC 4 cut(s) 184, 769, 1013, 1019
BpiI GAAGAC 1 cut(s) 573
BpmI CTGGAG 1 cut(s) 404
BsaBI GATNNNNATC 1 cut(s) 945
BsaJI CCNNGG 1 cut(s) 531
BsaWI WCCGGW 1 cut(s) 914
BsaXI ACNNNNNCTCC 4 cut(s) 150, 180, 974, 1004
Bsc4I CCNNNNNNNGG 2 cut(s) 974, 1219
Bse118I RCCGGY 1 cut(s) 914
Bse1I ACTGG 1 cut(s) 905
Bse8I GATNNNNATC 1 cut(s) 945
BseBI CCWGG 4 cut(s) 199, 422, 744, 1214
BseDI CCNNGG 1 cut(s) 531
BseGI GGATG 1 cut(s) 253
BseJI GATNNNNATC 1 cut(s) 945
BseLI CCNNNNNNNGG 2 cut(s) 974, 1219
BseMII CTCAG 1 cut(s) 1068
BseNI ACTGG 1 cut(s) 905
BseRI GAGGAG 1 cut(s) 995
BseYI CCCAGC 1 cut(s) 726
BshTI ACCGGT 1 cut(s) 914
BsiSI CCGG 1 cut(s) 915
BslI CCNNNNNNNGG 2 cut(s) 974, 1219
BsmI GAATGC 1 cut(s) 190
Bsp1286I GDGCHC 1 cut(s) 1227
Bsp143I GATC 3 cut(s) 4, 538, 599
Bsp19I CCATGG 1 cut(s) 531
BspCNI CTCAG 1 cut(s) 1069
BspHI TCATGA 1 cut(s) 433
BspMAI CTGCAG 1 cut(s) 175
BspMI ACCTGC 1 cut(s) 326
BspPI GGATC 3 cut(s) 12, 546, 607
BspQI GCTCTTC 1 cut(s) 1232
BsrFI RCCGGY 1 cut(s) 914
BsrI ACTGG 1 cut(s) 905
BssAI RCCGGY 1 cut(s) 914
BssECI CCNNGG 1 cut(s) 531
BssMI GATC 3 cut(s) 4, 538, 599
BssT1I CCWWGG 1 cut(s) 531
Bst2UI CCWGG 4 cut(s) 199, 422, 744, 1214
Bst4CI ACNGT 1 cut(s) 397
Bst6I CTCTTC 2 cut(s) 512, 1232
BstAPI GCANNNNNTGC 2 cut(s) 194, 788
BstC8I GCNNGC 1 cut(s) 80
BstDEI CTNAG 2 cut(s) 1077, 1182
BstDSI CCRYGG 1 cut(s) 531
BstEII GGTNACC 1 cut(s) 1208
BstENI CCTNNNNNAGG 1 cut(s) 1217
BstF5I GGATG 1 cut(s) 253
BstKTI GATC 3 cut(s) 7, 541, 602
BstMBI GATC 3 cut(s) 4, 538, 599
BstMWI GCNNNNNNNGC 3 cut(s) 194, 508, 788
BstNI CCWGG 4 cut(s) 199, 422, 744, 1214
BstNSI RCATGY 1 cut(s) 1091
BstPI GGTNACC 1 cut(s) 1208
BstSCI CCNGG 4 cut(s) 197, 420, 742, 1212
BstSFI CTRYAG 2 cut(s) 171, 220
BstV2I GAAGAC 1 cut(s) 573
BstX2I RGATCY 2 cut(s) 538, 599
BstXI CCANNNNNNTGG 1 cut(s) 483
BstYI RGATCY 2 cut(s) 538, 599
BtgI CCRYGG 1 cut(s) 531
BtsCI GGATG 1 cut(s) 253
BtsI GCAGTG 1 cut(s) 282
BtsIMutI CAGTG 2 cut(s) 21, 282
BveI ACCTGC 1 cut(s) 326
Cac8I GCNNGC 1 cut(s) 80
CciI TCATGA 1 cut(s) 433
Cfr10I RCCGGY 1 cut(s) 914
Cfr13I GGNCC 1 cut(s) 1121
CseI GACGC 1 cut(s) 341
CspAI ACCGGT 1 cut(s) 914
CviAII CATG 8 cut(s) 35, 125, 434, 443, 532, 671, 994, 1088
CviJI RGCY 5 cut(s) 614, 742, 842, 860, 1225
CviKI_1 RGCY 5 cut(s) 614, 742, 842, 860, 1225
DdeI CTNAG 2 cut(s) 1077, 1182
DpnI GATC 3 cut(s) 6, 540, 601
DpnII GATC 3 cut(s) 4, 538, 599
DraI TTTAAA 2 cut(s) 73, 1147
Eam1104I CTCTTC 2 cut(s) 512, 1232
EarI CTCTTC 2 cut(s) 512, 1232
Eco130I CCWWGG 1 cut(s) 531
Eco24I GRGCYC 1 cut(s) 1227
Eco47I GGWCC 1 cut(s) 1121
Eco57I CTGAAG 2 cut(s) 468, 891
Eco91I GGTNACC 1 cut(s) 1208
EcoNI CCTNNNNNAGG 1 cut(s) 1217
EcoO65I GGTNACC 1 cut(s) 1208
EcoRI GAATTC 1 cut(s) 301
EcoRII CCWGG 4 cut(s) 197, 420, 742, 1212
EcoT14I CCWWGG 1 cut(s) 531
EcoT22I ATGCAT 1 cut(s) 1006
EcoT38I GRGCYC 1 cut(s) 1227
ErhI CCWWGG 1 cut(s) 531
FaeI CATG 8 cut(s) 38, 128, 437, 446, 535, 674, 997, 1091
FatI CATG 8 cut(s) 34, 124, 433, 442, 531, 670, 993, 1087
FokI GGATG 1 cut(s) 260
FriOI GRGCYC 1 cut(s) 1227
GsaI CCCAGC 1 cut(s) 730
GsuI CTGGAG 1 cut(s) 404
HapII CCGG 1 cut(s) 915
HgaI GACGC 1 cut(s) 341
Hin1II CATG 8 cut(s) 38, 128, 437, 446, 535, 674, 997, 1091
HincII GTYRAC 1 cut(s) 877
HindII GTYRAC 1 cut(s) 877
HinfI GANTC 2 cut(s) 1108, 1160
HpaII CCGG 1 cut(s) 915
HphI GGTGA 3 cut(s) 436, 895, 989
Hpy166II GTNNAC 3 cut(s) 67, 877, 954
Hpy188I TCNGA 2 cut(s) 871, 1165
Hpy188III TCNNGA 7 cut(s) 130, 245, 298, 434, 563, 706, 1094
Hpy8I GTNNAC 3 cut(s) 67, 877, 954
HpyAV CCTTC 4 cut(s) 127, 149, 481, 489
HpyCH4III ACNGT 1 cut(s) 397
HpyCH4V TGCA 8 cut(s) 173, 188, 287, 502, 686, 782, 1004, 1010
HpyF10VI GCNNNNNNNGC 3 cut(s) 194, 508, 788
HpyF3I CTNAG 2 cut(s) 1077, 1182
Hsp92II CATG 8 cut(s) 38, 128, 437, 446, 535, 674, 997, 1091
Kzo9I GATC 3 cut(s) 4, 538, 599
LguI GCTCTTC 1 cut(s) 1232
LmnI GCTCC 1 cut(s) 982
LweI GCATC 4 cut(s) 184, 769, 1013, 1019
MaeIII GTNAC 2 cut(s) 166, 1208
MalI GATC 3 cut(s) 6, 540, 601
MboI GATC 3 cut(s) 4, 538, 599
MboII GAAGA 5 cut(s) 149, 529, 578, 1117, 1219
MfeI CAATTG 3 cut(s) 179, 189, 986
MflI RGATCY 2 cut(s) 538, 599
MhlI GDGCHC 1 cut(s) 1227
MnlI CCTC 7 cut(s) 529, 625, 841, 973, 1072, 1181, 1213
Mph1103I ATGCAT 1 cut(s) 1006
MroXI GAANNNNTTC 1 cut(s) 491
MseI TTAA 4 cut(s) 72, 714, 972, 1146
MslI CAYNNNNRTG 2 cut(s) 760, 933
MspI CCGG 1 cut(s) 915
MspR9I CCNGG 4 cut(s) 199, 422, 744, 1214
MunI CAATTG 3 cut(s) 179, 189, 986
Mva1269I GAATGC 1 cut(s) 190
MvaI CCWGG 4 cut(s) 199, 422, 744, 1214
MwoI GCNNNNNNNGC 3 cut(s) 194, 508, 788
NcoI CCATGG 1 cut(s) 531
NdeII GATC 3 cut(s) 4, 538, 599
NlaIII CATG 8 cut(s) 38, 128, 437, 446, 535, 674, 997, 1091
NmuCI GTSAC 1 cut(s) 166
NsiI ATGCAT 1 cut(s) 1006
NspI RCATGY 1 cut(s) 1091
OliI CACNNNNGTG 1 cut(s) 933
PagI TCATGA 1 cut(s) 433
PciI ACATGT 1 cut(s) 1087
PciSI GCTCTTC 1 cut(s) 1232
PctI GAATGC 1 cut(s) 190
PdmI GAANNNNTTC 1 cut(s) 491
PfeI GAWTC 2 cut(s) 1108, 1160
PflMI CCANNNNNTGG 1 cut(s) 974
PinAI ACCGGT 1 cut(s) 914
PscI ACATGT 1 cut(s) 1087
Psp6I CCWGG 4 cut(s) 197, 420, 742, 1212
PspEI GGTNACC 1 cut(s) 1208
PspFI CCCAGC 1 cut(s) 726
PspGI CCWGG 4 cut(s) 197, 420, 742, 1212
PspPI GGNCC 1 cut(s) 1121
PstI CTGCAG 1 cut(s) 175
PsuI RGATCY 2 cut(s) 538, 599
RseI CAYNNNNRTG 2 cut(s) 760, 933
SapI GCTCTTC 1 cut(s) 1232
SaqAI TTAA 4 cut(s) 72, 714, 972, 1146
Sau3AI GATC 3 cut(s) 4, 538, 599
Sau96I GGNCC 1 cut(s) 1121
ScrFI CCNGG 4 cut(s) 199, 422, 744, 1214
SduI GDGCHC 1 cut(s) 1227
SfaNI GCATC 4 cut(s) 184, 769, 1013, 1019
SfcI CTRYAG 2 cut(s) 171, 220
SinI GGWCC 1 cut(s) 1121
SmiMI CAYNNNNRTG 2 cut(s) 760, 933
StyD4I CCNGG 4 cut(s) 197, 420, 742, 1212
StyI CCWWGG 1 cut(s) 531
TaaI ACNGT 1 cut(s) 397
TaqI TCGA 1 cut(s) 609
TfiI GAWTC 2 cut(s) 1108, 1160
Tru1I TTAA 4 cut(s) 72, 714, 972, 1146
Tru9I TTAA 4 cut(s) 72, 714, 972, 1146
TscAI CASTG 2 cut(s) 21, 289
TseFI GTSAC 1 cut(s) 166
Tsp45I GTSAC 1 cut(s) 166
TspDTI ATGAA 5 cut(s) 422, 429, 431, 450, 982
TspRI CASTG 2 cut(s) 21, 289
Van91I CCANNNNNTGG 1 cut(s) 974
VpaK11BI GGWCC 1 cut(s) 1121
XagI CCTNNNNNAGG 1 cut(s) 1217
XapI RAATTY 5 cut(s) 53, 301, 362, 653, 700
XceI RCATGY 1 cut(s) 1091
XcmI CCANNNNNNNNNTGG 2 cut(s) 538, 622
XmnI GAANNNNTTC 1 cut(s) 491
Zsp2I ATGCAT 1 cut(s) 1006
Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.