RchiOBHm_Chr2g0151961

gag-polypeptide of LTR copia-type

Design Primers CRISPR Design

Basic Information

Type: gene
Biological Identity
rosa_chinensis
2
OG0000258
Physical Location & Seq
Forward (+)
69446057 .. 69448017
1961 bp
Loading structure...
UTR
Exon/CDS
Intron
PRQ52113

Sequence Viewer

Length: 1095 bp
ATGGATCAAGTATCAGTGAATGGTGTGAAAACTCATGTTGAGAAACCAGAAAAATTCAAGGGCGTGGACTTTAAACGCTGGCAACAAAAAATGTTGTTTTATCTAACAACATTGAACCTTGCTCATGTCGTGAAGGAAGAAGTTCCAAAGGCAGAAGGAGATGATGTGACTGCAGAACAATTGAATGCAATTGATGCCTGGAAACATTGTGAGTTTCTCTGCAGGAACTATATTCTCAATGGTCTGGATGATACTTTGTATGATGTATATAGGTCATACATCACTGCAAAGGAACTCTGGAATTCTTTGGAGAAAAAATACAAAGTTGATGACGCAGGTTCAAAGAAGTTCATTATTGGAAAATTTTTGAACTATAAGATGGTGGATAGCAAGACTGTTGTTAGTCAAGTTGATGAACTCCAAGTGATTATTCATGAACTTCATGATGAAGGTATGGTGATTAATGAAAGCTTTCAAGTTGGTTCTGTTATAGAAAAATTACCACCTTCTTGGAAGGATTTCAAAGTGCATTTGAAGCACAAGAAGAGTGAAATGACCATGGAGGATCTGGTTTTGAAACTACGAGTTCAAGAAGACCACCTGAAAAGTGAGAAGCAACCCGATGGATCTATCATCGAAGCCAAAGCAAATATGGTTGAGGGAGAAACTTCCAAACCAAAATTCAAAGGTCAGAAATTCAAAGGCAATAAACATGATGTCAAATATGCAACAAAGACCAAGAATTTCAAGAAAATTAAAGGTAGTTGCTGGGTGTGTGGAAAGCCTGGACACAAGGCACAAGAATGTCGCCACAAGAAAGATGCACCTGCTGCCATTAGGAACAACAACAACAACAACCAAGCAAATGTGGCTGTGGCTATGGAGGATTTTGTGGCTGTTGTTTCTGAAGTCAACTTGGTGAATGACAATAAGGACTGGTGGATTGATACTGGTGCGACAAGGCACATTTGTGGAGATAGAAATCTGTTTACCACCTATCAACCACTTAATGGTGAGGAGCAATTGTTCATGGGAAATGCATCTGCATCAAGTGTTGCTGGAAAGGGAAGAATCTTGTGTCTGGTCCTTTGTTGA
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

364

Amino Acids

41.41

Weight (kDa)

8.56

Isoelectric Point (pI)

32.24

Instability Index
Protein Domains (Pfam)
Domain Name Pfam ID Position E-value Description
Retrotran_gag_2 PF14223 31 - 204 1.1e-28 gag-polypeptide of LTR copia-type
Pol_BBD PF22936 313 - 359 5.7e-11 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)
AarI CACCTGC 1 cut(s) 835
Acc36I ACCTGC 2 cut(s) 326, 835
AccB7I CCANNNNNTGG 1 cut(s) 1010
AclWI GGATC 3 cut(s) 12, 573, 634
AcsI RAATTY 6 cut(s) 53, 301, 362, 680, 695, 742
AcuI CTGAAG 1 cut(s) 927
AfiI CCNNNNNNNGG 1 cut(s) 1010
AjnI CCWGG 2 cut(s) 197, 784
AjuI GAANNNNNNNTTGG 4 cut(s) 414, 446, 665, 697
AleI CACNNNNGTG 1 cut(s) 969
AloI GAACNNNNNNTCC 2 cut(s) 1010, 1042
AluBI AGCT 1 cut(s) 471
AluI AGCT 1 cut(s) 471
AlwI GGATC 3 cut(s) 12, 573, 634
ApeKI GCWGC 1 cut(s) 830
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
AspS9I GGNCC 1 cut(s) 1084
AsuHPI GGTGA 3 cut(s) 469, 931, 1025
AvaII GGWCC 1 cut(s) 1084
BbsI GAAGAC 1 cut(s) 600
BbvI GCAGC 1 cut(s) 817
BccI CCATC 2 cut(s) 373, 617
BciT130I CCWGG 2 cut(s) 199, 786
BfmI CTRYAG 2 cut(s) 171, 220
BfuAI ACCTGC 2 cut(s) 326, 835
BisI GCNGC 1 cut(s) 831
BlsI GCNGC 1 cut(s) 832
Bme1390I CCNGG 2 cut(s) 199, 786
Bme18I GGWCC 1 cut(s) 1084
BmgT120I GGNCC 1 cut(s) 1084
BmrFI CCNGG 2 cut(s) 199, 786
BmsI GCATC 4 cut(s) 184, 811, 1049, 1055
BpiI GAAGAC 1 cut(s) 600
BsaBI GATNNNNATC 1 cut(s) 981
BsaJI CCNNGG 1 cut(s) 558
BsaXI ACNNNNNCTCC 4 cut(s) 150, 180, 1010, 1040
Bsc4I CCNNNNNNNGG 1 cut(s) 1010
Bse1I ACTGG 2 cut(s) 941, 955
Bse8I GATNNNNATC 1 cut(s) 981
BseBI CCWGG 2 cut(s) 199, 786
BseDI CCNNGG 1 cut(s) 558
BseGI GGATG 1 cut(s) 253
BseJI GATNNNNATC 1 cut(s) 981
BseLI CCNNNNNNNGG 1 cut(s) 1010
BseNI ACTGG 2 cut(s) 941, 955
BseRI GAGGAG 1 cut(s) 1031
BseXI GCAGC 1 cut(s) 817
BseYI CCCAGC 1 cut(s) 768
BslI CCNNNNNNNGG 1 cut(s) 1010
BsmI GAATGC 1 cut(s) 190
Bsp143I GATC 3 cut(s) 4, 565, 626
Bsp19I CCATGG 1 cut(s) 558
BspHI TCATGA 2 cut(s) 433, 442
BspMAI CTGCAG 2 cut(s) 175, 224
BspMI ACCTGC 2 cut(s) 326, 835
BspPI GGATC 3 cut(s) 12, 573, 634
BsrI ACTGG 2 cut(s) 941, 955
BssECI CCNNGG 1 cut(s) 558
BssMI GATC 3 cut(s) 4, 565, 626
BssT1I CCWWGG 1 cut(s) 558
Bst2UI CCWGG 2 cut(s) 199, 786
Bst4CI ACNGT 1 cut(s) 397
Bst6I CTCTTC 1 cut(s) 539
BstAPI GCANNNNNTGC 2 cut(s) 194, 830
BstC8I GCNNGC 1 cut(s) 80
BstDSI CCRYGG 1 cut(s) 558
BstF5I GGATG 1 cut(s) 253
BstKTI GATC 3 cut(s) 7, 568, 629
BstMBI GATC 3 cut(s) 4, 565, 626
BstMWI GCNNNNNNNGC 4 cut(s) 194, 535, 830, 869
BstNI CCWGG 2 cut(s) 199, 786
BstSCI CCNGG 2 cut(s) 197, 784
BstSFI CTRYAG 2 cut(s) 171, 220
BstV1I GCAGC 1 cut(s) 817
BstV2I GAAGAC 1 cut(s) 600
BstX2I RGATCY 2 cut(s) 565, 626
BstXI CCANNNNNNTGG 1 cut(s) 510
BstYI RGATCY 2 cut(s) 565, 626
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 2 cut(s) 326, 835
Cac8I GCNNGC 1 cut(s) 80
CciI TCATGA 2 cut(s) 433, 442
Cfr13I GGNCC 1 cut(s) 1084
CseI GACGC 1 cut(s) 341
CviAII CATG 7 cut(s) 35, 125, 434, 443, 559, 713, 1030
CviJI RGCY 6 cut(s) 471, 641, 784, 872, 878, 896
CviKI_1 RGCY 6 cut(s) 471, 641, 784, 872, 878, 896
DpnI GATC 3 cut(s) 6, 567, 628
DpnII GATC 3 cut(s) 4, 565, 626
DraI TTTAAA 1 cut(s) 73
Eam1104I CTCTTC 1 cut(s) 539
EarI CTCTTC 1 cut(s) 539
Eco130I CCWWGG 1 cut(s) 558
Eco47I GGWCC 1 cut(s) 1084
Eco57I CTGAAG 1 cut(s) 927
EcoRI GAATTC 1 cut(s) 301
EcoRII CCWGG 2 cut(s) 197, 784
EcoT14I CCWWGG 1 cut(s) 558
EcoT22I ATGCAT 1 cut(s) 1042
ErhI CCWWGG 1 cut(s) 558
FaeI CATG 7 cut(s) 38, 128, 437, 446, 562, 716, 1033
FatI CATG 7 cut(s) 34, 124, 433, 442, 558, 712, 1029
Fnu4HI GCNGC 1 cut(s) 831
FokI GGATG 1 cut(s) 260
Fsp4HI GCNGC 1 cut(s) 831
GluI GCNGC 1 cut(s) 831
GsaI CCCAGC 1 cut(s) 772
HgaI GACGC 1 cut(s) 341
Hin1II CATG 7 cut(s) 38, 128, 437, 446, 562, 716, 1033
HincII GTYRAC 1 cut(s) 913
HindII GTYRAC 1 cut(s) 913
HindIII AAGCTT 1 cut(s) 469
HinfI GANTC 1 cut(s) 1071
HphI GGTGA 3 cut(s) 469, 931, 1025
Hpy166II GTNNAC 3 cut(s) 67, 913, 990
Hpy188I TCNGA 2 cut(s) 693, 907
Hpy188III TCNNGA 7 cut(s) 130, 245, 298, 434, 443, 590, 748
Hpy8I GTNNAC 3 cut(s) 67, 913, 990
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, 1040, 1046
HpyF10VI GCNNNNNNNGC 4 cut(s) 194, 535, 830, 869
Hsp92II CATG 7 cut(s) 38, 128, 437, 446, 562, 716, 1033
Kzo9I GATC 3 cut(s) 4, 565, 626
LmnI GCTCC 1 cut(s) 1018
Lsp1109I GCAGC 1 cut(s) 817
LweI GCATC 4 cut(s) 184, 811, 1049, 1055
MaeIII GTNAC 1 cut(s) 166
MalI GATC 3 cut(s) 6, 567, 628
MboI GATC 3 cut(s) 4, 565, 626
MboII GAAGA 4 cut(s) 149, 556, 605, 1080
MfeI CAATTG 3 cut(s) 179, 189, 1022
MflI RGATCY 2 cut(s) 565, 626
MnlI CCTC 4 cut(s) 556, 652, 877, 1009
Mph1103I ATGCAT 1 cut(s) 1042
MroXI GAANNNNTTC 3 cut(s) 141, 471, 518
MseI TTAA 4 cut(s) 72, 462, 756, 1008
MslI CAYNNNNRTG 2 cut(s) 802, 969
MspR9I CCNGG 2 cut(s) 199, 786
MunI CAATTG 3 cut(s) 179, 189, 1022
Mva1269I GAATGC 1 cut(s) 190
MvaI CCWGG 2 cut(s) 199, 786
MwoI GCNNNNNNNGC 4 cut(s) 194, 535, 830, 869
NcoI CCATGG 1 cut(s) 558
NdeII GATC 3 cut(s) 4, 565, 626
NlaIII CATG 7 cut(s) 38, 128, 437, 446, 562, 716, 1033
NmuCI GTSAC 1 cut(s) 166
NsiI ATGCAT 1 cut(s) 1042
OliI CACNNNNGTG 1 cut(s) 969
PagI TCATGA 2 cut(s) 433, 442
PaqCI CACCTGC 1 cut(s) 835
PctI GAATGC 1 cut(s) 190
PdmI GAANNNNTTC 3 cut(s) 141, 471, 518
PfeI GAWTC 1 cut(s) 1071
PflMI CCANNNNNTGG 1 cut(s) 1010
PkrI GCNGC 1 cut(s) 832
PshBI ATTAAT 1 cut(s) 462
Psp6I CCWGG 2 cut(s) 197, 784
PspFI CCCAGC 1 cut(s) 768
PspGI CCWGG 2 cut(s) 197, 784
PspPI GGNCC 1 cut(s) 1084
PstI CTGCAG 2 cut(s) 175, 224
PsuI RGATCY 2 cut(s) 565, 626
RseI CAYNNNNRTG 2 cut(s) 802, 969
SaqAI TTAA 4 cut(s) 72, 462, 756, 1008
SatI GCNGC 1 cut(s) 831
Sau3AI GATC 3 cut(s) 4, 565, 626
Sau96I GGNCC 1 cut(s) 1084
ScrFI CCNGG 2 cut(s) 199, 786
SfaNI GCATC 4 cut(s) 184, 811, 1049, 1055
SfcI CTRYAG 2 cut(s) 171, 220
SinI GGWCC 1 cut(s) 1084
SmiMI CAYNNNNRTG 2 cut(s) 802, 969
StyD4I CCNGG 2 cut(s) 197, 784
StyI CCWWGG 1 cut(s) 558
TaaI ACNGT 1 cut(s) 397
TaqI TCGA 1 cut(s) 636
TfiI GAWTC 1 cut(s) 1071
Tru1I TTAA 4 cut(s) 72, 462, 756, 1008
Tru9I TTAA 4 cut(s) 72, 462, 756, 1008
TscAI CASTG 2 cut(s) 21, 289
TseFI GTSAC 1 cut(s) 166
TseI GCWGC 1 cut(s) 830
Tsp45I GTSAC 1 cut(s) 166
TspDTI ATGAA 8 cut(s) 340, 422, 429, 431, 450, 462, 480, 1018
TspRI CASTG 2 cut(s) 21, 289
Van91I CCANNNNNTGG 1 cut(s) 1010
VpaK11BI GGWCC 1 cut(s) 1084
VspI ATTAAT 1 cut(s) 462
XapI RAATTY 6 cut(s) 53, 301, 362, 680, 695, 742
XcmI CCANNNNNNNNNTGG 2 cut(s) 565, 649
XmnI GAANNNNTTC 3 cut(s) 141, 471, 518
Zsp2I ATGCAT 1 cut(s) 1042
Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.