pycom02g12230

gag-polypeptide of LTR copia-type

Design Primers CRISPR Design

Basic Information

Type: gene
Biological Identity
pyrus_communis
Chr2
OG0000258
Physical Location & Seq
Reverse (-)
8786381 .. 8787430
1050 bp
Loading structure...
UTR
Exon/CDS
Intron
pycom02g12230.1

Sequence Viewer

Length: 1050 bp
ATGGAACAATCGGGAACTAAACCTCATTCTGAGAAGCCTGAGAAATTTAAGGGCGGAGACTTCAAAAGATGGCAGCAAAAAATGTTGTTCTATTTGACAACCATGAATTTGGCTAATGTTCTGCGCGAGACTGTACCTACTGCAGATGGGGAAAATATTTTTTCTGCAGAAACTTTAACGGCTATAGATGCCTGGAATCATAATGATTTCCTCTGCAGAAACTATATTCTCAATGCATTAGATGATTCATTGTATGATGTTTATGTAGTATGCAAAACAACCAAGGAACTTTGGGAATCACTTGAGAAAAAATATAAAACCGAGGATGCTGGTTCGAAGAAATTTGTCGTGGGCAAATTTTTGGACTACAAAATGGTGGATTCCAAGTCCGTTGTTTCTCAAACTGAAGATCTCCAGAAAATCATCCATGACATTCATGTTGAAGGGATGATAATCAATGAGTCTTTCCAAGTGGCGTCCTTTATAGAAAAACTGTCACCTTCTTGGAAAGAGTTCAAGAATGATCTCAAGCACAAACGTAAGGAGATGACGTTTGAGGATCTCATTGTCAGGCTGAGAATAGAGGAAGATAACAGAAAGAATGAGAAGGGCTTGGTTTCGAGTATGGAAGCCAAGGCGAATGTTGTTGAAGGAAGTTCATCAAAGCAAAGGCCGAAGTTCCAGAAAACTAAGAAGAAGGAAAAACACTTTGTCCCTGGTGCGAAAGGCAAAGACTTCAAGAAAATCAAGGGAAGTTGCTGGGTTTGTGGAAAGCAAGGCCATAGGGCTCAAGAATGTCGTCATCGAAGGGATCAAGGTCCTGGAAATCAAGGCAACTACAACCGCGCAAACCTGATTGAAAACAATGTGGATGCCTTAGCTGCAATGATTTCTGAAATCAACCTTGTGTCTGATCACGCTGATTGGTGGATAGATACCGGTGCAACTCGCCATGTGTATACAGAAATATGTTCTCTTTGTACCAGAAAATCGAAGGAAATGAGCAGCTGTTTATGGGAAATGCATCTGCATCTGTTGTGGCTGGAATAG
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

350

Amino Acids

40.38

Weight (kDa)

8.59

Isoelectric Point (pI)

50.2

Instability Index
Protein Domains (Pfam)
Domain Name Pfam ID Position E-value Description
Retrotran_gag_2 PF14223 31 - 203 4.2e-27 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: 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)
AccI GTMKAC 1 cut(s) 959
AccII CGCG 2 cut(s) 126, 846
AciI CCGC 2 cut(s) 54, 844
AclWI GGATC 2 cut(s) 567, 819
AcsI RAATTY 4 cut(s) 44, 106, 341, 356
AcuI CTGAAG 1 cut(s) 426
AcyI GRCGYC 1 cut(s) 476
AfaI GTAC 2 cut(s) 135, 982
AgeI ACCGGT 1 cut(s) 938
AgsI TTSAA 6 cut(s) 64, 443, 517, 650, 739, 860
AjnI CCWGG 3 cut(s) 191, 715, 820
AluBI AGCT 2 cut(s) 881, 1008
AluI AGCT 2 cut(s) 881, 1008
Alw26I GTCTC 2 cut(s) 51, 122
AlwI GGATC 2 cut(s) 567, 819
AoxI GGCC 2 cut(s) 671, 778
ApeKI GCWGC 3 cut(s) 73, 881, 1005
ApoI RAATTY 4 cut(s) 44, 106, 341, 356
AsiGI ACCGGT 1 cut(s) 938
Asp700I GAANNNNTTC 1 cut(s) 512
AspLEI GCGC 2 cut(s) 126, 848
AspS9I GGNCC 1 cut(s) 818
AsuHPI GGTGA 1 cut(s) 489
AsuII TTCGAA 1 cut(s) 335
AvaII GGWCC 1 cut(s) 818
BanII GRGCYC 1 cut(s) 790
BbvI GCAGC 3 cut(s) 85, 868, 1017
BccI CCATC 2 cut(s) 63, 140
BceAI ACGGC 1 cut(s) 195
BciT130I CCWGG 3 cut(s) 193, 717, 822
BclI TGATCA 1 cut(s) 913
BcoDI GTCTC 2 cut(s) 51, 122
BfmI CTRYAG 4 cut(s) 141, 165, 183, 214
BglII AGATCT 1 cut(s) 409
BisI GCNGC 3 cut(s) 74, 882, 1006
BlsI GCNGC 3 cut(s) 75, 883, 1007
Bme1390I CCNGG 3 cut(s) 193, 717, 822
Bme18I GGWCC 1 cut(s) 818
BmgT120I GGNCC 1 cut(s) 818
BmrFI CCNGG 3 cut(s) 193, 717, 822
BmsI GCATC 5 cut(s) 178, 316, 862, 1033, 1039
BpmI CTGGAG 1 cut(s) 398
Bpu10I CCTNAGC 1 cut(s) 877
Bpu14I TTCGAA 1 cut(s) 335
BpuEI CTTGAG 3 cut(s) 323, 512, 774
BsaBI GATNNNNATC 1 cut(s) 452
BsaHI GRCGYC 1 cut(s) 476
BsaJI CCNNGG 4 cut(s) 282, 321, 633, 715
BsaWI WCCGGW 1 cut(s) 938
BsaXI ACNNNNNCTCC 2 cut(s) 536, 566
Bse118I RCCGGY 1 cut(s) 938
Bse3DI GCAATG 1 cut(s) 891
Bse8I GATNNNNATC 1 cut(s) 452
BseBI CCWGG 3 cut(s) 193, 717, 822
BseDI CCNNGG 4 cut(s) 282, 321, 633, 715
BseGI GGATG 4 cut(s) 331, 423, 453, 877
BseJI GATNNNNATC 1 cut(s) 452
BseMI GCAATG 1 cut(s) 891
BseMII CTCAG 3 cut(s) 21, 30, 566
BseXI GCAGC 3 cut(s) 85, 868, 1017
BseYI CCCAGC 1 cut(s) 759
Bsh1236I CGCG 2 cut(s) 126, 846
BshFI GGCC 2 cut(s) 673, 780
BshTI ACCGGT 1 cut(s) 938
BsiSI CCGG 1 cut(s) 939
BslFI GGGAC 1 cut(s) 698
BsmAI GTCTC 2 cut(s) 51, 122
BsmFI GGGAC 1 cut(s) 698
BsnI GGCC 2 cut(s) 673, 780
Bsp119I TTCGAA 1 cut(s) 335
Bsp1286I GDGCHC 1 cut(s) 790
Bsp143I GATC 5 cut(s) 409, 523, 559, 811, 913
BspACI CCGC 2 cut(s) 54, 844
BspANI GGCC 2 cut(s) 673, 780
BspCNI CTCAG 3 cut(s) 22, 31, 567
BspFNI CGCG 2 cut(s) 126, 846
BspMAI CTGCAG 3 cut(s) 145, 169, 218
BspPI GGATC 2 cut(s) 567, 819
BspT104I TTCGAA 1 cut(s) 335
BsrDI GCAATG 1 cut(s) 891
BsrFI RCCGGY 1 cut(s) 938
BssAI RCCGGY 1 cut(s) 938
BssECI CCNNGG 4 cut(s) 282, 321, 633, 715
BssMI GATC 5 cut(s) 409, 523, 559, 811, 913
BssNAI GTATAC 1 cut(s) 960
BssNI GRCGYC 1 cut(s) 476
BssT1I CCWWGG 2 cut(s) 282, 633
Bst1107I GTATAC 1 cut(s) 960
Bst2UI CCWGG 3 cut(s) 193, 717, 822
Bst4CI ACNGT 2 cut(s) 133, 495
BstACI GRCGYC 1 cut(s) 476
BstBI TTCGAA 1 cut(s) 335
BstDEI CTNAG 5 cut(s) 30, 39, 575, 690, 877
BstF5I GGATG 4 cut(s) 331, 423, 453, 877
BstFNI CGCG 2 cut(s) 126, 846
BstHHI GCGC 2 cut(s) 126, 848
BstKTI GATC 5 cut(s) 412, 526, 562, 814, 916
BstMAI GTCTC 2 cut(s) 51, 122
BstMBI GATC 5 cut(s) 409, 523, 559, 811, 913
BstMWI GCNNNNNNNGC 2 cut(s) 188, 881
BstNI CCWGG 3 cut(s) 193, 717, 822
BstSCI CCNGG 3 cut(s) 191, 715, 820
BstSFI CTRYAG 4 cut(s) 141, 165, 183, 214
BstUI CGCG 2 cut(s) 126, 846
BstV1I GCAGC 3 cut(s) 85, 868, 1017
BstX2I RGATCY 2 cut(s) 409, 559
BstXI CCANNNNNNTGG 1 cut(s) 109
BstYI RGATCY 2 cut(s) 409, 559
BstZ17I GTATAC 1 cut(s) 960
BsuRI GGCC 2 cut(s) 673, 780
BtsCI GGATG 4 cut(s) 331, 423, 453, 877
CfoI GCGC 2 cut(s) 126, 848
Cfr10I RCCGGY 1 cut(s) 938
Cfr13I GGNCC 1 cut(s) 818
CseI GACGC 1 cut(s) 465
Csp6I GTAC 2 cut(s) 134, 981
CspAI ACCGGT 1 cut(s) 938
CviAII CATG 4 cut(s) 103, 428, 437, 953
CviQI GTAC 2 cut(s) 134, 981
DdeI CTNAG 5 cut(s) 30, 39, 575, 690, 877
DpnI GATC 5 cut(s) 411, 525, 561, 813, 915
DpnII GATC 5 cut(s) 409, 523, 559, 811, 913
EciI GGCGGA 1 cut(s) 69
Eco130I CCWWGG 2 cut(s) 282, 633
Eco24I GRGCYC 1 cut(s) 790
Eco47I GGWCC 1 cut(s) 818
Eco57I CTGAAG 1 cut(s) 426
EcoO109I RGGNCCY 1 cut(s) 818
EcoRII CCWGG 3 cut(s) 191, 715, 820
EcoT14I CCWWGG 2 cut(s) 282, 633
EcoT22I ATGCAT 2 cut(s) 238, 1026
EcoT38I GRGCYC 1 cut(s) 790
ErhI CCWWGG 2 cut(s) 282, 633
FaeI CATG 4 cut(s) 106, 431, 440, 956
FaqI GGGAC 1 cut(s) 698
FatI CATG 4 cut(s) 102, 427, 436, 952
FbaI TGATCA 1 cut(s) 913
FblI GTMKAC 1 cut(s) 959
Fnu4HI GCNGC 3 cut(s) 74, 882, 1006
FokI GGATG 4 cut(s) 338, 410, 460, 884
FriOI GRGCYC 1 cut(s) 790
Fsp4HI GCNGC 3 cut(s) 74, 882, 1006
GlaI GCGC 2 cut(s) 125, 847
GluI GCNGC 3 cut(s) 74, 882, 1006
GsaI CCCAGC 1 cut(s) 763
GsuI CTGGAG 1 cut(s) 398
HaeIII GGCC 2 cut(s) 673, 780
HapII CCGG 1 cut(s) 939
HgaI GACGC 1 cut(s) 465
HhaI GCGC 2 cut(s) 126, 848
Hin1I GRCGYC 1 cut(s) 476
Hin1II CATG 4 cut(s) 106, 431, 440, 956
Hin6I GCGC 2 cut(s) 124, 846
HinP1I GCGC 2 cut(s) 124, 846
HinfI GANTC 5 cut(s) 196, 245, 296, 380, 461
HpaII CCGG 1 cut(s) 939
HphI GGTGA 1 cut(s) 489
Hpy166II GTNNAC 1 cut(s) 960
Hpy188I TCNGA 3 cut(s) 31, 895, 913
Hpy188III TCNNGA 6 cut(s) 12, 415, 517, 682, 739, 791
Hpy8I GTNNAC 1 cut(s) 960
HpyAV CCTTC 7 cut(s) 437, 510, 601, 644, 691, 801, 988
HpyCH4III ACNGT 2 cut(s) 133, 495
HpyCH4IV ACGT 2 cut(s) 538, 551
HpyCH4V TGCA 9 cut(s) 143, 167, 216, 236, 273, 884, 944, 1024, 1030
HpyF10VI GCNNNNNNNGC 2 cut(s) 188, 881
HpyF3I CTNAG 5 cut(s) 30, 39, 575, 690, 877
HpySE526I ACGT 2 cut(s) 538, 551
Hsp92I GRCGYC 1 cut(s) 476
Hsp92II CATG 4 cut(s) 106, 431, 440, 956
HspAI GCGC 2 cut(s) 124, 846
Ksp22I TGATCA 1 cut(s) 913
Kzo9I GATC 5 cut(s) 409, 523, 559, 811, 913
Lsp1109I GCAGC 3 cut(s) 85, 868, 1017
LweI GCATC 5 cut(s) 178, 316, 862, 1033, 1039
MaeII ACGT 2 cut(s) 538, 551
MaeIII GTNAC 1 cut(s) 495
MalI GATC 5 cut(s) 411, 525, 561, 813, 915
MboI GATC 5 cut(s) 409, 523, 559, 811, 913
MboII GAAGA 4 cut(s) 349, 419, 599, 706
MflI RGATCY 2 cut(s) 409, 559
MhlI GDGCHC 1 cut(s) 790
MluCI AATT 4 cut(s) 44, 106, 341, 356
MlyI GAGTC 1 cut(s) 470
MnlI CCTC 5 cut(s) 33, 221, 316, 550, 577
Mph1103I ATGCAT 2 cut(s) 238, 1026
MroXI GAANNNNTTC 1 cut(s) 512
MseI TTAA 2 cut(s) 48, 176
MspA1I CMGCKG 1 cut(s) 1008
MspI CCGG 1 cut(s) 939
MspR9I CCNGG 3 cut(s) 193, 717, 822
MvaI CCWGG 3 cut(s) 193, 717, 822
MvnI CGCG 2 cut(s) 126, 846
MwoI GCNNNNNNNGC 2 cut(s) 188, 881
NdeII GATC 5 cut(s) 409, 523, 559, 811, 913
NlaIII CATG 4 cut(s) 106, 431, 440, 956
NmuCI GTSAC 1 cut(s) 495
NsiI ATGCAT 2 cut(s) 238, 1026
NspV TTCGAA 1 cut(s) 335
PdmI GAANNNNTTC 1 cut(s) 512
PfeI GAWTC 4 cut(s) 196, 245, 296, 380
PfoI TCCNGGA 1 cut(s) 820
PinAI ACCGGT 1 cut(s) 938
PkrI GCNGC 3 cut(s) 75, 883, 1007
PleI GAGTC 1 cut(s) 469
PpsI GAGTC 1 cut(s) 469
PpuMI RGGWCCY 1 cut(s) 818
Psp5II RGGWCCY 1 cut(s) 818
Psp6I CCWGG 3 cut(s) 191, 715, 820
PspFI CCCAGC 1 cut(s) 759
PspGI CCWGG 3 cut(s) 191, 715, 820
PspPI GGNCC 1 cut(s) 818
PspPPI RGGWCCY 1 cut(s) 818
PstI CTGCAG 3 cut(s) 145, 169, 218
PsuI RGATCY 2 cut(s) 409, 559
PvuII CAGCTG 1 cut(s) 1008
RsaI GTAC 2 cut(s) 135, 982
RsaNI GTAC 2 cut(s) 134, 981
SaqAI TTAA 2 cut(s) 48, 176
SatI GCNGC 3 cut(s) 74, 882, 1006
Sau3AI GATC 5 cut(s) 409, 523, 559, 811, 913
Sau96I GGNCC 1 cut(s) 818
SchI GAGTC 1 cut(s) 470
ScrFI CCNGG 3 cut(s) 193, 717, 822
SduI GDGCHC 1 cut(s) 790
SfaNI GCATC 5 cut(s) 178, 316, 862, 1033, 1039
SfcI CTRYAG 4 cut(s) 141, 165, 183, 214
SfuI TTCGAA 1 cut(s) 335
SinI GGWCC 1 cut(s) 818
SmlI CTYRAG 3 cut(s) 302, 527, 789
SmoI CTYRAG 3 cut(s) 302, 527, 789
Sse9I AATT 4 cut(s) 44, 106, 341, 356
SsiI CCGC 2 cut(s) 54, 844
SspI AATATT 1 cut(s) 157
StyD4I CCNGG 3 cut(s) 191, 715, 820
StyI CCWWGG 2 cut(s) 282, 633
TaaI ACNGT 2 cut(s) 133, 495
TaiI ACGT 2 cut(s) 541, 554
TaqI TCGA 4 cut(s) 335, 620, 805, 992
TasI AATT 4 cut(s) 44, 106, 341, 356
TfiI GAWTC 4 cut(s) 196, 245, 296, 380
Tru1I TTAA 2 cut(s) 48, 176
Tru9I TTAA 2 cut(s) 48, 176
TseFI GTSAC 1 cut(s) 495
TseI GCWGC 3 cut(s) 73, 881, 1005
Tsp45I GTSAC 1 cut(s) 495
TspDTI ATGAA 4 cut(s) 119, 237, 425, 648
TspGWI ACGGA 1 cut(s) 379
VpaK11BI GGWCC 1 cut(s) 818
XapI RAATTY 4 cut(s) 44, 106, 341, 356
XmiI GTMKAC 1 cut(s) 959
XmnI GAANNNNTTC 1 cut(s) 512
Zsp2I ATGCAT 2 cut(s) 238, 1026
Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.