pycom16g20010

gag-polypeptide of LTR copia-type

Design Primers CRISPR Design

Basic Information

Type: gene
Biological Identity
pyrus_communis
Chr16
OG0021274
Physical Location & Seq
Reverse (-)
17485246 .. 17487543
2298 bp
Loading structure...
UTR
Exon/CDS
Intron
N/A

Sequence Viewer

Length: 1449 bp
ATGGTTGCTTTGCTCTTGAGCGCTGAAAGCCGTATGGACGACTATAGCCCTACTTTCAGTCCTGATCACACCACTACAGCTCTCTTTGCCCCTTCTGGCTCCACTCCCAATCCTGGTCGTGGAACCATACTTCACCGAGGAAATGGTCGTACATCCTCATTCCGTCGTGGTGGTTTTCAAGGTCGTGGCTTTTTTCAAGGTCGCGGTGCTGGTAATCCTTTTGTTGGCCGTTGTGGTGGTTCAAACAGTGGTTTGTTTCATGGTGGATCCGGTCGTGGCTCGTTTCAGAATCGAAGACTTCTTCCTACACCAAATGCTGGTCTTCGTCGCTCTTCCTATCTTCCCAACCATGCTGCGGATGCTCCCTCTTCCTCTAATATTTGTAACTATTGTGGTGATCATCGTCATTCTACCGCAAATTGTTTCAAGTCTCCTTTTTCCGAAGGCCGCTATCCACAATCTCATGCTATGATGGCTGCCTCTCCTGTGGTTAATGCACGGTCCCCTACATGGTATACCGACAGTGGCGCATCGTCACACATCACCAATGATTTAGCTAATTTGAGCCTCTCCACAGAATATATTAGCCAAGACCAAGTCGCGGTTGGTAATGGTGCAGGTTTGTCTATAAAGCATATTGGTTCCGGTTTCGTGTCTCAATTTCCTTTAAATTCTGTGTTGCATTGTCCTTCTGCTTCTGCTAATCTACTAAGCGTTCATCGCTTTTGTTGTGATAATCATTGCTACTTCATTTTCACTCTTACTGATTTCTTTGTGAAGGATCTATCCACGGGGAAGACGCTTTTCCACGGCAAGAGTGAGAATGGATTGTATCTGTTTCGTGGCTATCGCTGTTATGATATGTCAAATGGACGAGTTTATTTGTCACGTCATGTGGTTTTTGATGAGGAAACTTTTCCATTCGACAACCCTACACAATTCTCCTCAGTCTTGCCGTCAGAAGCTTACTCTCCCGTGGTTATCACTCCTTCTCCCTTACCACCTCTCCCTCAGGTACCTTCATTATCTCATATTTCTATTCCTCATACTCTAACATCCTCTTCTAGTGCAGCACCTCTCTTCCCCTTGCAACCTTCCTCAAGTTCACCATTGTCTACACCTTCACTTTCCTCGCCACCTCATTCTCAACCTGCTCCTGATAGCTCTGACAGTTTGATTTCCATTAATGAGGCTCCTCCACCTTCCTCCGCTTCTGCTCCCCATCCCATGCTCACTCGGTCTAAATCTGGCATTCGAAAACCAAACCCCAAATATGCTTTATTGACATCATTACAAGCTCCTGATTCTGAACCAACCTCGTTTCGCGAGGCAAATCAATTATCTCATTGGCGTGATGCAATGACATTGGAGTTTAAGGCCTTGAAAGCTGCTGGTACATGGGAGTTGGTACCTTCTTCAACTGCTACTCATGTTCTTCCTTGCAAGTAG
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 Retrotran_gag_3

Protein Analysis

483

Amino Acids

51.72

Weight (kDa)

8.88

Isoelectric Point (pI)

56.15

Instability Index
Protein Domains (Pfam)
Domain Name Pfam ID Position E-value Description
Pol_BBD PF22936 171 - 242 4.7e-10 Pol polyprotein, beta-barrel domain
SH3_retrovirus PF25597 281 - 311 1.9e-08 Retroviral polymerase SH3-like 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: OG0021274)

Species Orthologous Gene IDs
pyrus_communis pycom11g04700 pycom13g12090 pycom14g19030 pycom16g20010
rosa_wichuraiana Rw6G007970

Restriction Enzyme Sites

1 / 10
Enzyme Recognition Site Cut Count Positions (bp)
Acc36I ACCTGC 2 cut(s) 608, 1159
Acc65I GGTACC 2 cut(s) 1015, 1408
AccB1I GGYRCC 2 cut(s) 1015, 1408
AccB7I CCANNNNNTGG 1 cut(s) 317
AccI GTMKAC 2 cut(s) 515, 1115
AccII CGCG 3 cut(s) 204, 602, 1326
AciI CCGC 6 cut(s) 204, 356, 414, 448, 602, 1209
AclWI GGATC 3 cut(s) 261, 274, 789
AcoI YGGCCR 1 cut(s) 226
AcsI RAATTY 1 cut(s) 670
AfaI GTAC 4 cut(s) 151, 1017, 1396, 1410
AfeI AGCGCT 1 cut(s) 22
AfiI CCNNNNNNNGG 7 cut(s) 113, 119, 224, 317, 355, 510, 601
AgsI TTSAA 6 cut(s) 179, 197, 243, 427, 1384, 1419
AjiI CACGTC 1 cut(s) 890
AjnI CCWGG 1 cut(s) 112
AluBI AGCT 6 cut(s) 80, 557, 965, 1164, 1298, 1388
AluI AGCT 6 cut(s) 80, 557, 965, 1164, 1298, 1388
Alw26I GTCTC 2 cut(s) 435, 660
AlwI GGATC 3 cut(s) 261, 274, 789
Aor51HI AGCGCT 1 cut(s) 22
AoxI GGCC 3 cut(s) 226, 445, 1377
ApeKI GCWGC 4 cut(s) 353, 476, 1070, 1388
ApoI RAATTY 1 cut(s) 670
AseI ATTAAT 1 cut(s) 1185
Asp700I GAANNNNTTC 1 cut(s) 915
Asp718I GGTACC 2 cut(s) 1015, 1408
AspLEI GCGC 2 cut(s) 23, 530
AspS9I GGNCC 1 cut(s) 501
AsuHPI GGTGA 4 cut(s) 125, 407, 535, 1098
AsuII TTCGAA 1 cut(s) 1255
AvaII GGWCC 1 cut(s) 501
AxyI CCTNAGG 1 cut(s) 1011
BamHI GGATCC 1 cut(s) 266
BanI GGYRCC 2 cut(s) 1015, 1408
BbsI GAAGAC 3 cut(s) 301, 314, 803
BbvI GCAGC 4 cut(s) 340, 463, 1082, 1375
BccI CCATC 2 cut(s) 466, 1230
BceAI ACGGC 4 cut(s) 15, 213, 826, 940
BciT130I CCWGG 1 cut(s) 114
BclI TGATCA 2 cut(s) 64, 397
BcoDI GTCTC 2 cut(s) 435, 660
BfaI CTAG 1 cut(s) 1065
BfmI CTRYAG 2 cut(s) 43, 75
BfoI RGCGCY 1 cut(s) 24
BfuAI ACCTGC 2 cut(s) 608, 1159
BisI GCNGC 5 cut(s) 354, 448, 477, 1071, 1389
BlsI GCNGC 5 cut(s) 355, 449, 478, 1072, 1390
Bme1390I CCNGG 1 cut(s) 114
Bme18I GGWCC 1 cut(s) 501
BmgBI CACGTC 1 cut(s) 890
BmgT120I GGNCC 1 cut(s) 501
BmiI GGNNCC 8 cut(s) 100, 124, 268, 503, 643, 1017, 1194, 1410
BmrFI CCNGG 1 cut(s) 114
BmsI GCATC 3 cut(s) 349, 539, 1345
BpiI GAAGAC 3 cut(s) 301, 314, 803
Bpu14I TTCGAA 1 cut(s) 1255
BpuEI CTTGAG 2 cut(s) 37, 1084
BsaJI CCNNGG 4 cut(s) 136, 789, 808, 975
BsaWI WCCGGW 2 cut(s) 269, 644
BsaXI ACNNNNNCTCC 4 cut(s) 976, 990, 1006, 1020
Bsc4I CCNNNNNNNGG 7 cut(s) 113, 119, 224, 317, 355, 510, 601
Bse21I CCTNAGG 1 cut(s) 1011
Bse3DI GCAATG 2 cut(s) 739, 1365
BseBI CCWGG 1 cut(s) 114
BseDI CCNNGG 4 cut(s) 136, 789, 808, 975
BseGI GGATG 4 cut(s) 152, 364, 1055, 1222
BseLI CCNNNNNNNGG 7 cut(s) 113, 119, 224, 317, 355, 510, 601
BseMI GCAATG 2 cut(s) 739, 1365
BseMII CTCAG 2 cut(s) 960, 1025
BseRI GAGGAG 2 cut(s) 934, 1185
BseXI GCAGC 4 cut(s) 340, 463, 1082, 1375
BsgI GTGCAG 2 cut(s) 636, 1089
Bsh1236I CGCG 3 cut(s) 204, 602, 1326
Bsh1285I CGRYCG 1 cut(s) 274
BshFI GGCC 3 cut(s) 228, 447, 1379
BshNI GGYRCC 2 cut(s) 1015, 1408
BsiEI CGRYCG 1 cut(s) 274
BsiSI CCGG 2 cut(s) 270, 645
BslFI GGGAC 1 cut(s) 487
BslI CCNNNNNNNGG 7 cut(s) 113, 119, 224, 317, 355, 510, 601
BsmAI GTCTC 2 cut(s) 435, 660
BsmFI GGGAC 1 cut(s) 487
BsmI GAATGC 1 cut(s) 1251
BsnI GGCC 3 cut(s) 228, 447, 1379
Bsp119I TTCGAA 1 cut(s) 1255
Bsp143I GATC 4 cut(s) 64, 266, 397, 781
Bsp68I TCGCGA 1 cut(s) 1326
BspACI CCGC 6 cut(s) 204, 356, 414, 448, 602, 1209
BspANI GGCC 3 cut(s) 228, 447, 1379
BspCNI CTCAG 2 cut(s) 959, 1024
BspFNI CGCG 3 cut(s) 204, 602, 1326
BspLI GGNNCC 8 cut(s) 100, 124, 268, 503, 643, 1017, 1194, 1410
BspMI ACCTGC 2 cut(s) 608, 1159
BspPI GGATC 3 cut(s) 261, 274, 789
BspQI GCTCTTC 1 cut(s) 337
BspT104I TTCGAA 1 cut(s) 1255
BspT107I GGYRCC 2 cut(s) 1015, 1408
BsrDI GCAATG 2 cut(s) 739, 1365
BssECI CCNNGG 4 cut(s) 136, 789, 808, 975
BssMI GATC 4 cut(s) 64, 266, 397, 781
BssNAI GTATAC 1 cut(s) 516
Bst1107I GTATAC 1 cut(s) 516
Bst2UI CCWGG 1 cut(s) 114
Bst4CI ACNGT 4 cut(s) 248, 501, 524, 1172
Bst6I CTCTTC 4 cut(s) 337, 373, 1066, 1085
BstBI TTCGAA 1 cut(s) 1255
BstDEI CTNAG 3 cut(s) 710, 946, 1011
BstDSI CCRYGG 3 cut(s) 789, 808, 975
BstF5I GGATG 4 cut(s) 152, 364, 1055, 1222
BstFNI CGCG 3 cut(s) 204, 602, 1326
BstH2I RGCGCY 1 cut(s) 24
BstHHI GCGC 2 cut(s) 23, 530
BstKTI GATC 4 cut(s) 67, 269, 400, 784
BstMAI GTCTC 2 cut(s) 435, 660
BstMBI GATC 4 cut(s) 64, 266, 397, 781
BstMCI CGRYCG 1 cut(s) 274
BstMWI GCNNNNNNNGC 6 cut(s) 27, 86, 359, 473, 720, 1385
BstNI CCWGG 1 cut(s) 114
BstSCI CCNGG 1 cut(s) 112
BstSFI CTRYAG 2 cut(s) 43, 75
BstUI CGCG 3 cut(s) 204, 602, 1326
BstV1I GCAGC 4 cut(s) 340, 463, 1082, 1375
BstV2I GAAGAC 3 cut(s) 301, 314, 803
BstX2I RGATCY 2 cut(s) 266, 781
BstYI RGATCY 2 cut(s) 266, 781
BstZ17I GTATAC 1 cut(s) 516
Bsu36I CCTNAGG 1 cut(s) 1011
BsuRI GGCC 3 cut(s) 228, 447, 1379
BtgI CCRYGG 3 cut(s) 789, 808, 975
BtgZI GCGATG 1 cut(s) 704
BtrI CACGTC 1 cut(s) 890
BtsCI GGATG 4 cut(s) 152, 364, 1055, 1222
BtsIMutI CAGTG 2 cut(s) 253, 529
BtuMI TCGCGA 1 cut(s) 1326
BveI ACCTGC 2 cut(s) 608, 1159
CfoI GCGC 2 cut(s) 23, 530
Cfr13I GGNCC 1 cut(s) 501
CseI GACGC 1 cut(s) 808
Csp6I GTAC 4 cut(s) 150, 1016, 1395, 1409
CviAII CATG 8 cut(s) 260, 350, 464, 510, 893, 1228, 1398, 1430
CviQI GTAC 4 cut(s) 150, 1016, 1395, 1409
DdeI CTNAG 3 cut(s) 710, 946, 1011
DpnI GATC 4 cut(s) 66, 268, 399, 783
DpnII GATC 4 cut(s) 64, 266, 397, 781
DraI TTTAAA 1 cut(s) 669
EaeI YGGCCR 1 cut(s) 226
Eam1104I CTCTTC 4 cut(s) 337, 373, 1066, 1085
EarI CTCTTC 4 cut(s) 337, 373, 1066, 1085
Eco147I AGGCCT 1 cut(s) 1379
Eco47I GGWCC 1 cut(s) 501
Eco47III AGCGCT 1 cut(s) 22
Eco81I CCTNAGG 1 cut(s) 1011
EcoRII CCWGG 1 cut(s) 112
FaeI CATG 8 cut(s) 263, 353, 467, 513, 896, 1231, 1401, 1433
FaqI GGGAC 1 cut(s) 487
FatI CATG 8 cut(s) 259, 349, 463, 509, 892, 1227, 1397, 1429
FbaI TGATCA 2 cut(s) 64, 397
FblI GTMKAC 2 cut(s) 515, 1115
Fnu4HI GCNGC 5 cut(s) 354, 448, 477, 1071, 1389
FokI GGATG 4 cut(s) 139, 371, 1042, 1209
Fsp4HI GCNGC 5 cut(s) 354, 448, 477, 1071, 1389
FspBI CTAG 1 cut(s) 1065
GlaI GCGC 2 cut(s) 22, 529
GluI GCNGC 5 cut(s) 354, 448, 477, 1071, 1389
HaeII RGCGCY 1 cut(s) 24
HaeIII GGCC 3 cut(s) 228, 447, 1379
HapII CCGG 2 cut(s) 270, 645
HgaI GACGC 1 cut(s) 808
HhaI GCGC 2 cut(s) 23, 530
Hin1II CATG 8 cut(s) 263, 353, 467, 513, 896, 1231, 1401, 1433
Hin6I GCGC 2 cut(s) 21, 528
HinP1I GCGC 2 cut(s) 21, 528
HindIII AAGCTT 1 cut(s) 963
HinfI GANTC 2 cut(s) 289, 1304
HpaII CCGG 2 cut(s) 270, 645
HphI GGTGA 4 cut(s) 125, 407, 535, 1098
Hpy166II GTNNAC 3 cut(s) 516, 1106, 1116
Hpy188I TCNGA 5 cut(s) 288, 442, 961, 1168, 1309
Hpy188III TCNNGA 5 cut(s) 16, 62, 1157, 1301, 1325
Hpy8I GTNNAC 3 cut(s) 516, 1106, 1116
Hpy99I CGWCG 2 cut(s) 168, 330
HpyCH4III ACNGT 4 cut(s) 248, 501, 524, 1172
HpyCH4IV ACGT 1 cut(s) 889
HpyCH4V TGCA 7 cut(s) 497, 617, 682, 1070, 1090, 1358, 1443
HpyF10VI GCNNNNNNNGC 6 cut(s) 27, 86, 359, 473, 720, 1385
HpyF3I CTNAG 3 cut(s) 710, 946, 1011
HpySE526I ACGT 1 cut(s) 889
Hsp92II CATG 8 cut(s) 263, 353, 467, 513, 896, 1231, 1401, 1433
HspAI GCGC 2 cut(s) 21, 528
KpnI GGTACC 2 cut(s) 1019, 1412
Ksp22I TGATCA 2 cut(s) 64, 397
Kzo9I GATC 4 cut(s) 64, 266, 397, 781
LguI GCTCTTC 1 cut(s) 337
LmnI GCTCC 6 cut(s) 104, 367, 1159, 1198, 1222, 1303
Lsp1109I GCAGC 4 cut(s) 340, 463, 1082, 1375
LweI GCATC 3 cut(s) 349, 539, 1345
MaeI CTAG 1 cut(s) 1065
MaeII ACGT 1 cut(s) 889
MaeIII GTNAC 3 cut(s) 383, 534, 885
MalI GATC 4 cut(s) 66, 268, 399, 783
MboI GATC 4 cut(s) 64, 266, 397, 781
MflI RGATCY 2 cut(s) 266, 781
MluCI AATT 6 cut(s) 418, 559, 659, 670, 938, 1337
MroXI GAANNNNTTC 1 cut(s) 915
MseI TTAA 4 cut(s) 492, 668, 1185, 1374
MslI CAYNNNNRTG 1 cut(s) 1350
MspI CCGG 2 cut(s) 270, 645
MspR9I CCNGG 1 cut(s) 114
Mva1269I GAATGC 1 cut(s) 1251
MvaI CCWGG 1 cut(s) 114
MvnI CGCG 3 cut(s) 204, 602, 1326
MwoI GCNNNNNNNGC 6 cut(s) 27, 86, 359, 473, 720, 1385
NdeII GATC 4 cut(s) 64, 266, 397, 781
NlaIII CATG 8 cut(s) 263, 353, 467, 513, 896, 1231, 1401, 1433
NlaIV GGNNCC 8 cut(s) 100, 124, 268, 503, 643, 1017, 1194, 1410
NmuCI GTSAC 2 cut(s) 534, 885
NruI TCGCGA 1 cut(s) 1326
NspV TTCGAA 1 cut(s) 1255
PceI AGGCCT 1 cut(s) 1379
PciSI GCTCTTC 1 cut(s) 337
PctI GAATGC 1 cut(s) 1251
PdmI GAANNNNTTC 1 cut(s) 915
PfeI GAWTC 2 cut(s) 289, 1304
PflFI GACNNNGTC 1 cut(s) 596
PflMI CCANNNNNTGG 1 cut(s) 317
PkrI GCNGC 5 cut(s) 355, 449, 478, 1072, 1390
PshBI ATTAAT 1 cut(s) 1185
Psp6I CCWGG 1 cut(s) 112
PspGI CCWGG 1 cut(s) 112
PspN4I GGNNCC 8 cut(s) 100, 124, 268, 503, 643, 1017, 1194, 1410
PspPI GGNCC 1 cut(s) 501
PsuI RGATCY 2 cut(s) 266, 781
PsyI GACNNNGTC 1 cut(s) 596
RruI TCGCGA 1 cut(s) 1326
RsaI GTAC 4 cut(s) 151, 1017, 1396, 1410
RsaNI GTAC 4 cut(s) 150, 1016, 1395, 1409
RseI CAYNNNNRTG 1 cut(s) 1350
SapI GCTCTTC 1 cut(s) 337
SaqAI TTAA 4 cut(s) 492, 668, 1185, 1374
SatI GCNGC 5 cut(s) 354, 448, 477, 1071, 1389
Sau3AI GATC 4 cut(s) 64, 266, 397, 781
Sau96I GGNCC 1 cut(s) 501
ScrFI CCNGG 1 cut(s) 114
SfaNI GCATC 3 cut(s) 349, 539, 1345
SfcI CTRYAG 2 cut(s) 43, 75
SfuI TTCGAA 1 cut(s) 1255
SinI GGWCC 1 cut(s) 501
SmiMI CAYNNNNRTG 1 cut(s) 1350
SmlI CTYRAG 2 cut(s) 16, 1099
SmoI CTYRAG 2 cut(s) 16, 1099
Sse9I AATT 6 cut(s) 418, 559, 659, 670, 938, 1337
SseBI AGGCCT 1 cut(s) 1379
SsiI CCGC 6 cut(s) 204, 356, 414, 448, 602, 1209
SspI AATATT 1 cut(s) 379
SspMI CTAG 1 cut(s) 1065
StuI AGGCCT 1 cut(s) 1379
StyD4I CCNGG 1 cut(s) 112
TaaI ACNGT 4 cut(s) 248, 501, 524, 1172
TaiI ACGT 1 cut(s) 892
TaqI TCGA 3 cut(s) 292, 924, 1255
TaqII GACCGA 1 cut(s) 1227
TasI AATT 6 cut(s) 418, 559, 659, 670, 938, 1337
TauI GCSGC 1 cut(s) 450
TfiI GAWTC 2 cut(s) 289, 1304
Tru1I TTAA 4 cut(s) 492, 668, 1185, 1374
Tru9I TTAA 4 cut(s) 492, 668, 1185, 1374
TscAI CASTG 2 cut(s) 253, 529
TseFI GTSAC 2 cut(s) 534, 885
TseI GCWGC 4 cut(s) 353, 476, 1070, 1388
Tsp45I GTSAC 2 cut(s) 534, 885
TspDTI ATGAA 4 cut(s) 248, 707, 739, 1011
TspGWI ACGGA 1 cut(s) 152
TspRI CASTG 2 cut(s) 253, 529
Tth111I GACNNNGTC 1 cut(s) 596
Van91I CCANNNNNTGG 1 cut(s) 317
VpaK11BI GGWCC 1 cut(s) 501
VspI ATTAAT 1 cut(s) 1185
XapI RAATTY 1 cut(s) 670
XcmI CCANNNNNNNNNTGG 1 cut(s) 602
XmiI GTMKAC 2 cut(s) 515, 1115
XmnI GAANNNNTTC 1 cut(s) 915
XspI CTAG 1 cut(s) 1065
Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.