RchiOBHm_Chr2g0171331

gag-polypeptide of LTR copia-type

Design Primers CRISPR Design

Basic Information

Type: gene
Biological Identity
rosa_chinensis
2
OG0000258
Physical Location & Seq
Reverse (-)
85010839 .. 85012483
1645 bp
Loading structure...
UTR
Exon/CDS
Intron
PRQ53875

Sequence Viewer

Length: 1206 bp
ATGGATCAAGTATCAGTGAATGGTGTGAAAACTCATGTTGAGAAACCAGAAAAATTCAAGGGCGTGGACTTTAAACGCTGGCAACAAAAAATGTTGTTTTATCTAACAACATTGAACCTTGCTCATGTCGTGAAGGAAGAAGTTCCAAAGGCAGAAGGAGATGATGTGACTGCAGAACAATTGAATGCAATTGATGCCTGGAAACATTGTGAGTTTCTCTGCAGGAACTATATTCTCAATGGTCTGGATGATACTTTGTATGATGTATATAGGTCATACACCACTGCAAAGGAACTCTGGAATTCTTTGGAGAAAAAATACAAAGTTGATGACGCAGGTTCAAAGAAGTTCATTATTGGAAAATTTTTGAACTATAAGATGGTGGATAGCAAGACTGTTGTTAGTCAAGTTGATGAACTCCAGGTGATTATTCATGAACTTCATGCTGAAGGTATGGTGATTAATGAAAGCTTTCAAGTTGGTTCTGTTATAGAAAAATTACCACCTTCTTGGAAGGATTTCAAAGTGCATTTGAAGCACAAGAAGAGTGAAATGACCATGGAGGATCTGGTTTTGAAACTACGAGTTCAAGAAGACCACCTGAAAAGTGAGAAGCAACCCGATGGATTTGTCATCGAAGCCAAAGCAAATATGGTTGAGGGAGAAACTTCCAAACCAAAATTCAAAGGTCAGAAATTCAAAGGCAATAAACATGATGTCAAATATGCAACAAAGACCAAGAATTTCAAGAAAATTAAAGGTAGTTGCTGGGTGTGTGGAAAGCCTGGACACAAGGCACAAGAATGTCGCCACAAGAAAGATGCACCTGTTGCCTTTAGGAACAACAACAACAATAACAACCAAGCAAATGTGGCTGTGGCTATGGAGGATTTTGTGGCTGTTGTTTCTGAAGTTAACTTGGTGAATGACAATAAGGACTGGTGGATTGATACTGGTGCGACAAGGCACATTTGTGGAGATAGAAATCTGTTTACCACCTATCAACCACTTAATGGTGAGGAGCAATTGTTCATGGGAAATGCATCTGCATCAAGTGTTGCTGGAAAGGGTAATGTGGTTTTGACATTCACTTCTGGGAAAAAACTCACTCTAACTGAGGTGCTACATGTTCCTGAAATTAGGAAGAATCTTGTGTCTGGGTTACCTGGCAGAGGGGCTCTTCAAACTCAATCTGTATGTATATGA
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

401

Amino Acids

45.36

Weight (kDa)

8.87

Isoelectric Point (pI)

32.34

Instability Index
Protein Domains (Pfam)
Domain Name Pfam ID Position E-value Description
Retrotran_gag_2 PF14223 31 - 204 1.4e-29 gag-polypeptide of LTR copia-type
Pol_BBD PF22936 314 - 386 2.6e-23 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) 1013
AclWI GGATC 2 cut(s) 12, 573
AcsI RAATTY 6 cut(s) 53, 301, 362, 680, 695, 742
AcuI CTGAAG 2 cut(s) 468, 930
AfiI CCNNNNNNNGG 2 cut(s) 1013, 1172
AflIII ACRYGT 1 cut(s) 1126
AjnI CCWGG 4 cut(s) 197, 420, 784, 1165
AjuI GAANNNNNNNTTGG 2 cut(s) 665, 697
AleI CACNNNNGTG 1 cut(s) 972
AloI GAACNNNNNNTCC 2 cut(s) 1013, 1045
AluBI AGCT 1 cut(s) 471
AluI AGCT 1 cut(s) 471
AlwI GGATC 2 cut(s) 12, 573
ApoI RAATTY 6 cut(s) 53, 301, 362, 680, 695, 742
AseI ATTAAT 1 cut(s) 462
Asp700I GAANNNNTTC 3 cut(s) 141, 471, 518
AsuHPI GGTGA 4 cut(s) 436, 469, 934, 1028
BanII GRGCYC 1 cut(s) 1180
BbsI GAAGAC 1 cut(s) 600
BccI CCATC 2 cut(s) 373, 617
BciT130I CCWGG 4 cut(s) 199, 422, 786, 1167
BfmI CTRYAG 2 cut(s) 171, 220
BfuAI ACCTGC 1 cut(s) 326
Bme1390I CCNGG 4 cut(s) 199, 422, 786, 1167
BmrFI CCNGG 4 cut(s) 199, 422, 786, 1167
BmsI GCATC 4 cut(s) 184, 811, 1052, 1058
BpiI GAAGAC 1 cut(s) 600
BpmI CTGGAG 1 cut(s) 404
BsaBI GATNNNNATC 1 cut(s) 984
BsaJI CCNNGG 1 cut(s) 558
BsaXI ACNNNNNCTCC 4 cut(s) 150, 180, 1013, 1043
Bsc4I CCNNNNNNNGG 2 cut(s) 1013, 1172
Bse1I ACTGG 2 cut(s) 944, 958
Bse8I GATNNNNATC 1 cut(s) 984
BseBI CCWGG 4 cut(s) 199, 422, 786, 1167
BseDI CCNNGG 1 cut(s) 558
BseGI GGATG 1 cut(s) 253
BseJI GATNNNNATC 1 cut(s) 984
BseLI CCNNNNNNNGG 2 cut(s) 1013, 1172
BseMII CTCAG 1 cut(s) 1107
BseNI ACTGG 2 cut(s) 944, 958
BseRI GAGGAG 1 cut(s) 1034
BseYI CCCAGC 1 cut(s) 768
BslI CCNNNNNNNGG 2 cut(s) 1013, 1172
BsmI GAATGC 1 cut(s) 190
Bsp1286I GDGCHC 1 cut(s) 1180
Bsp143I GATC 2 cut(s) 4, 565
Bsp19I CCATGG 1 cut(s) 558
BspCNI CTCAG 1 cut(s) 1108
BspHI TCATGA 1 cut(s) 433
BspMAI CTGCAG 2 cut(s) 175, 224
BspMI ACCTGC 1 cut(s) 326
BspPI GGATC 2 cut(s) 12, 573
BspQI GCTCTTC 1 cut(s) 1185
BsrI ACTGG 2 cut(s) 944, 958
BssECI CCNNGG 1 cut(s) 558
BssMI GATC 2 cut(s) 4, 565
BssT1I CCWWGG 1 cut(s) 558
Bst2UI CCWGG 4 cut(s) 199, 422, 786, 1167
Bst4CI ACNGT 1 cut(s) 397
Bst6I CTCTTC 2 cut(s) 539, 1185
BstAPI GCANNNNNTGC 2 cut(s) 194, 830
BstC8I GCNNGC 1 cut(s) 80
BstDEI CTNAG 1 cut(s) 1116
BstDSI CCRYGG 1 cut(s) 558
BstEII GGTNACC 1 cut(s) 1161
BstENI CCTNNNNNAGG 1 cut(s) 1170
BstF5I GGATG 1 cut(s) 253
BstKTI GATC 2 cut(s) 7, 568
BstMBI GATC 2 cut(s) 4, 565
BstMWI GCNNNNNNNGC 4 cut(s) 194, 535, 830, 872
BstNI CCWGG 4 cut(s) 199, 422, 786, 1167
BstNSI RCATGY 1 cut(s) 1130
BstPI GGTNACC 1 cut(s) 1161
BstSCI CCNGG 4 cut(s) 197, 420, 784, 1165
BstSFI CTRYAG 2 cut(s) 171, 220
BstV2I GAAGAC 1 cut(s) 600
BstX2I RGATCY 1 cut(s) 565
BstXI CCANNNNNNTGG 1 cut(s) 510
BstYI RGATCY 1 cut(s) 565
BtgI CCRYGG 1 cut(s) 558
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
CseI GACGC 1 cut(s) 341
CviAII CATG 8 cut(s) 35, 125, 434, 443, 559, 713, 1033, 1127
CviJI RGCY 7 cut(s) 471, 641, 784, 875, 881, 899, 1178
CviKI_1 RGCY 7 cut(s) 471, 641, 784, 875, 881, 899, 1178
DdeI CTNAG 1 cut(s) 1116
DpnI GATC 2 cut(s) 6, 567
DpnII GATC 2 cut(s) 4, 565
DraI TTTAAA 1 cut(s) 73
Eam1104I CTCTTC 2 cut(s) 539, 1185
EarI CTCTTC 2 cut(s) 539, 1185
Eco130I CCWWGG 1 cut(s) 558
Eco24I GRGCYC 1 cut(s) 1180
Eco57I CTGAAG 2 cut(s) 468, 930
Eco91I GGTNACC 1 cut(s) 1161
EcoNI CCTNNNNNAGG 1 cut(s) 1170
EcoO65I GGTNACC 1 cut(s) 1161
EcoRI GAATTC 1 cut(s) 301
EcoRII CCWGG 4 cut(s) 197, 420, 784, 1165
EcoT14I CCWWGG 1 cut(s) 558
EcoT22I ATGCAT 1 cut(s) 1045
EcoT38I GRGCYC 1 cut(s) 1180
ErhI CCWWGG 1 cut(s) 558
FaeI CATG 8 cut(s) 38, 128, 437, 446, 562, 716, 1036, 1130
FatI CATG 8 cut(s) 34, 124, 433, 442, 558, 712, 1032, 1126
FokI GGATG 1 cut(s) 260
FriOI GRGCYC 1 cut(s) 1180
GsaI CCCAGC 1 cut(s) 772
GsuI CTGGAG 1 cut(s) 404
HgaI GACGC 1 cut(s) 341
Hin1II CATG 8 cut(s) 38, 128, 437, 446, 562, 716, 1036, 1130
HincII GTYRAC 1 cut(s) 916
HindII GTYRAC 1 cut(s) 916
HindIII AAGCTT 1 cut(s) 469
HinfI GANTC 1 cut(s) 1147
HpaI GTTAAC 1 cut(s) 916
HphI GGTGA 4 cut(s) 436, 469, 934, 1028
Hpy166II GTNNAC 3 cut(s) 67, 916, 993
Hpy188I TCNGA 2 cut(s) 693, 910
Hpy188III TCNNGA 7 cut(s) 130, 245, 298, 434, 590, 748, 1133
Hpy8I GTNNAC 3 cut(s) 67, 916, 993
HpyAV CCTTC 5 cut(s) 127, 149, 443, 508, 516
HpyCH4III ACNGT 1 cut(s) 397
HpyCH4V TGCA 9 cut(s) 173, 188, 222, 287, 529, 728, 824, 1043, 1049
HpyF10VI GCNNNNNNNGC 4 cut(s) 194, 535, 830, 872
HpyF3I CTNAG 1 cut(s) 1116
Hsp92II CATG 8 cut(s) 38, 128, 437, 446, 562, 716, 1036, 1130
KspAI GTTAAC 1 cut(s) 916
Kzo9I GATC 2 cut(s) 4, 565
LguI GCTCTTC 1 cut(s) 1185
LmnI GCTCC 1 cut(s) 1021
LweI GCATC 4 cut(s) 184, 811, 1052, 1058
MaeIII GTNAC 2 cut(s) 166, 1161
MalI GATC 2 cut(s) 6, 567
MboI GATC 2 cut(s) 4, 565
MboII GAAGA 5 cut(s) 149, 556, 605, 1156, 1172
MfeI CAATTG 3 cut(s) 179, 189, 1025
MflI RGATCY 1 cut(s) 565
MhlI GDGCHC 1 cut(s) 1180
MnlI CCTC 6 cut(s) 556, 652, 880, 1012, 1111, 1166
Mph1103I ATGCAT 1 cut(s) 1045
MroXI GAANNNNTTC 3 cut(s) 141, 471, 518
MseI TTAA 5 cut(s) 72, 462, 756, 915, 1011
MslI CAYNNNNRTG 2 cut(s) 802, 972
MspR9I CCNGG 4 cut(s) 199, 422, 786, 1167
MunI CAATTG 3 cut(s) 179, 189, 1025
Mva1269I GAATGC 1 cut(s) 190
MvaI CCWGG 4 cut(s) 199, 422, 786, 1167
MwoI GCNNNNNNNGC 4 cut(s) 194, 535, 830, 872
NcoI CCATGG 1 cut(s) 558
NdeII GATC 2 cut(s) 4, 565
NlaIII CATG 8 cut(s) 38, 128, 437, 446, 562, 716, 1036, 1130
NmuCI GTSAC 1 cut(s) 166
NsiI ATGCAT 1 cut(s) 1045
NspI RCATGY 1 cut(s) 1130
OliI CACNNNNGTG 1 cut(s) 972
PagI TCATGA 1 cut(s) 433
PciI ACATGT 1 cut(s) 1126
PciSI GCTCTTC 1 cut(s) 1185
PctI GAATGC 1 cut(s) 190
PdmI GAANNNNTTC 3 cut(s) 141, 471, 518
PfeI GAWTC 1 cut(s) 1147
PflMI CCANNNNNTGG 1 cut(s) 1013
PscI ACATGT 1 cut(s) 1126
PshBI ATTAAT 1 cut(s) 462
Psp6I CCWGG 4 cut(s) 197, 420, 784, 1165
PspEI GGTNACC 1 cut(s) 1161
PspFI CCCAGC 1 cut(s) 768
PspGI CCWGG 4 cut(s) 197, 420, 784, 1165
PstI CTGCAG 2 cut(s) 175, 224
PsuI RGATCY 1 cut(s) 565
RseI CAYNNNNRTG 2 cut(s) 802, 972
SapI GCTCTTC 1 cut(s) 1185
SaqAI TTAA 5 cut(s) 72, 462, 756, 915, 1011
Sau3AI GATC 2 cut(s) 4, 565
ScrFI CCNGG 4 cut(s) 199, 422, 786, 1167
SduI GDGCHC 1 cut(s) 1180
SfaNI GCATC 4 cut(s) 184, 811, 1052, 1058
SfcI CTRYAG 2 cut(s) 171, 220
SmiMI CAYNNNNRTG 2 cut(s) 802, 972
StyD4I CCNGG 4 cut(s) 197, 420, 784, 1165
StyI CCWWGG 1 cut(s) 558
TaaI ACNGT 1 cut(s) 397
TaqI TCGA 1 cut(s) 636
TfiI GAWTC 1 cut(s) 1147
Tru1I TTAA 5 cut(s) 72, 462, 756, 915, 1011
Tru9I TTAA 5 cut(s) 72, 462, 756, 915, 1011
TscAI CASTG 2 cut(s) 21, 289
TseFI GTSAC 1 cut(s) 166
Tsp45I GTSAC 1 cut(s) 166
TspDTI ATGAA 7 cut(s) 340, 422, 429, 431, 450, 480, 1021
TspRI CASTG 2 cut(s) 21, 289
Van91I CCANNNNNTGG 1 cut(s) 1013
VspI ATTAAT 1 cut(s) 462
XagI CCTNNNNNAGG 1 cut(s) 1170
XapI RAATTY 6 cut(s) 53, 301, 362, 680, 695, 742
XceI RCATGY 1 cut(s) 1130
XcmI CCANNNNNNNNNTGG 2 cut(s) 565, 649
XmnI GAANNNNTTC 3 cut(s) 141, 471, 518
Zsp2I ATGCAT 1 cut(s) 1045
Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.