pycom16g16210

gag-polypeptide of LTR copia-type

Design Primers CRISPR Design

Basic Information

Type: gene
Biological Identity
pyrus_communis
Chr16
OG0000258
Physical Location & Seq
Forward (+)
12154778 .. 12155937
1160 bp
Loading structure...
UTR
Exon/CDS
Intron
pycom16g16210.2

Sequence Viewer

Length: 759 bp
ATGGTGGATTCCAAGTCCATTATCTCTCAAACTGAAGATTTCCAGAAAATCATCCATGACATTCATGTTGAAGGGATGGTGATCAATGAGTCCTTTCAAGTGGCGTCCTTTATAGAAAAACTGTCATCTTCTTGGAAAGAGTTCAAGAATTATCTCAAGCACAAACGTAAGGAGATGACCCTTGAGGATCTCATTGTAAGGCTAAGAATTGAGGAAGATAACAGAAAAAATGAGAAGAGCCTGGTTTTGAGTATGGGAGCCAAGGCTAATGTTGTTGAAGGAAGTTCATCAAAGCAAAGGCCAAAATTCCAGAAAACTAAGAAGAAGGAAAAACACTTTGTCCCTGGTGCGAAAGGCAAAGACTTCAAGAAAATCAAGGGAAGTTGCTGGGTTTGTGGAAAGCAAGGCCAAAGGGCTCAAGAATGTCGCCATCGAATGGATCAAGGTCCTAGAAATCAAGGCAACAACAACCGCGCGAACCTGATTAAAAACAATGTTGATGCCTTGGCTGCAATGATTTCTGAAGTCAACATTGTATCTGACCATGCTGATTGGTGGATAGATACCGGTGCGACTCGCCTTGTATGTGGTGACAGAAATATGTTCTCTACGTACCAGAAAATCGAGGGGAACGAGCAACTGTTTATGGGAAATGCATCTGTATCTATTGTGGCTGGAATAGGAAAATGTGTTTTGAAATTCACTTCTGGAAAGGAATTAACCCTCCTTGACGTCCTGCATGTCCCCGATATAATTTAG
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

253

Amino Acids

28.52

Weight (kDa)

9.34

Isoelectric Point (pI)

27.8

Instability Index
Protein Domains (Pfam)
No Pfam domains detected for this protein.
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)
AatII GACGTC 1 cut(s) 735
AccB7I CCANNNNNTGG 1 cut(s) 436
AccII CGCG 2 cut(s) 474, 476
AciI CCGC 1 cut(s) 472
AclWI GGATC 2 cut(s) 195, 447
AcsI RAATTY 2 cut(s) 305, 698
AcuI CTGAAG 2 cut(s) 54, 543
AcyI GRCGYC 2 cut(s) 104, 732
AfaI GTAC 1 cut(s) 614
AfiI CCNNNNNNNGG 1 cut(s) 436
AgeI ACCGGT 1 cut(s) 566
AgsI TTSAA 6 cut(s) 71, 98, 145, 278, 367, 697
AjnI CCWGG 2 cut(s) 240, 343
AlwI GGATC 2 cut(s) 195, 447
AoxI GGCC 2 cut(s) 299, 406
ApeKI GCWGC 1 cut(s) 509
ApoI RAATTY 2 cut(s) 305, 698
AsiGI ACCGGT 1 cut(s) 566
Asp700I GAANNNNTTC 1 cut(s) 140
AspLEI GCGC 1 cut(s) 476
AspS9I GGNCC 1 cut(s) 446
AsuHPI GGTGA 2 cut(s) 91, 602
AvaII GGWCC 1 cut(s) 446
BanII GRGCYC 1 cut(s) 418
BbvI GCAGC 1 cut(s) 496
BccI CCATC 2 cut(s) 70, 438
BciT130I CCWGG 2 cut(s) 242, 345
BclI TGATCA 1 cut(s) 81
BfaI CTAG 1 cut(s) 450
BisI GCNGC 1 cut(s) 510
BlsI GCNGC 1 cut(s) 511
Bme1390I CCNGG 2 cut(s) 242, 345
Bme18I GGWCC 1 cut(s) 446
BmgT120I GGNCC 1 cut(s) 446
BmiI GGNNCC 1 cut(s) 259
BmrFI CCNGG 2 cut(s) 242, 345
BmsI GCATC 2 cut(s) 490, 665
BpuEI CTTGAG 3 cut(s) 140, 203, 402
BsaAI YACGTR 1 cut(s) 612
BsaBI GATNNNNATC 1 cut(s) 80
BsaHI GRCGYC 2 cut(s) 104, 732
BsaJI CCNNGG 3 cut(s) 261, 343, 504
BsaWI WCCGGW 1 cut(s) 566
Bsc4I CCNNNNNNNGG 1 cut(s) 436
Bse118I RCCGGY 1 cut(s) 566
Bse3DI GCAATG 1 cut(s) 519
Bse8I GATNNNNATC 1 cut(s) 80
BseBI CCWGG 2 cut(s) 242, 345
BseDI CCNNGG 3 cut(s) 261, 343, 504
BseGI GGATG 2 cut(s) 51, 81
BseJI GATNNNNATC 1 cut(s) 80
BseLI CCNNNNNNNGG 1 cut(s) 436
BseMI GCAATG 1 cut(s) 519
BseXI GCAGC 1 cut(s) 496
BseYI CCCAGC 1 cut(s) 387
Bsh1236I CGCG 2 cut(s) 474, 476
BshFI GGCC 2 cut(s) 301, 408
BshTI ACCGGT 1 cut(s) 566
BsiSI CCGG 1 cut(s) 567
BslFI GGGAC 2 cut(s) 326, 728
BslI CCNNNNNNNGG 1 cut(s) 436
BsmFI GGGAC 2 cut(s) 326, 728
BsnI GGCC 2 cut(s) 301, 408
Bsp1286I GDGCHC 1 cut(s) 418
Bsp143I GATC 3 cut(s) 81, 187, 439
BspACI CCGC 1 cut(s) 472
BspANI GGCC 2 cut(s) 301, 408
BspFNI CGCG 2 cut(s) 474, 476
BspLI GGNNCC 1 cut(s) 259
BspPI GGATC 2 cut(s) 195, 447
BspQI GCTCTTC 1 cut(s) 230
BsrDI GCAATG 1 cut(s) 519
BsrFI RCCGGY 1 cut(s) 566
BssAI RCCGGY 1 cut(s) 566
BssECI CCNNGG 3 cut(s) 261, 343, 504
BssMI GATC 3 cut(s) 81, 187, 439
BssNI GRCGYC 2 cut(s) 104, 732
BssT1I CCWWGG 2 cut(s) 261, 504
Bst2UI CCWGG 2 cut(s) 242, 345
Bst4CI ACNGT 2 cut(s) 123, 642
Bst6I CTCTTC 1 cut(s) 230
BstACI GRCGYC 2 cut(s) 104, 732
BstBAI YACGTR 1 cut(s) 612
BstDEI CTNAG 2 cut(s) 203, 318
BstF5I GGATG 2 cut(s) 51, 81
BstFNI CGCG 2 cut(s) 474, 476
BstHHI GCGC 1 cut(s) 476
BstKTI GATC 3 cut(s) 84, 190, 442
BstMBI GATC 3 cut(s) 81, 187, 439
BstMWI GCNNNNNNNGC 1 cut(s) 509
BstNI CCWGG 2 cut(s) 242, 345
BstNSI RCATGY 1 cut(s) 743
BstSCI CCNGG 2 cut(s) 240, 343
BstSNI TACGTA 1 cut(s) 612
BstUI CGCG 2 cut(s) 474, 476
BstV1I GCAGC 1 cut(s) 496
BstX2I RGATCY 1 cut(s) 187
BstYI RGATCY 1 cut(s) 187
BsuRI GGCC 2 cut(s) 301, 408
BtsCI GGATG 2 cut(s) 51, 81
CfoI GCGC 1 cut(s) 476
Cfr10I RCCGGY 1 cut(s) 566
Cfr13I GGNCC 1 cut(s) 446
CseI GACGC 1 cut(s) 93
Csp6I GTAC 1 cut(s) 613
CspAI ACCGGT 1 cut(s) 566
CviAII CATG 4 cut(s) 56, 65, 545, 740
CviJI RGCY 9 cut(s) 202, 240, 260, 266, 301, 408, 416, 509, 674
CviKI_1 RGCY 9 cut(s) 202, 240, 260, 266, 301, 408, 416, 509, 674
CviQI GTAC 1 cut(s) 613
DdeI CTNAG 2 cut(s) 203, 318
DpnI GATC 3 cut(s) 83, 189, 441
DpnII GATC 3 cut(s) 81, 187, 439
Eam1104I CTCTTC 1 cut(s) 230
EarI CTCTTC 1 cut(s) 230
Eco105I TACGTA 1 cut(s) 612
Eco130I CCWWGG 2 cut(s) 261, 504
Eco24I GRGCYC 1 cut(s) 418
Eco47I GGWCC 1 cut(s) 446
Eco57I CTGAAG 2 cut(s) 54, 543
EcoO109I RGGNCCY 1 cut(s) 446
EcoRII CCWGG 2 cut(s) 240, 343
EcoT14I CCWWGG 2 cut(s) 261, 504
EcoT22I ATGCAT 1 cut(s) 658
EcoT38I GRGCYC 1 cut(s) 418
ErhI CCWWGG 2 cut(s) 261, 504
FaeI CATG 4 cut(s) 59, 68, 548, 743
FaqI GGGAC 2 cut(s) 326, 728
FatI CATG 4 cut(s) 55, 64, 544, 739
FbaI TGATCA 1 cut(s) 81
Fnu4HI GCNGC 1 cut(s) 510
FokI GGATG 2 cut(s) 38, 88
FriOI GRGCYC 1 cut(s) 418
Fsp4HI GCNGC 1 cut(s) 510
FspBI CTAG 1 cut(s) 450
GlaI GCGC 1 cut(s) 475
GluI GCNGC 1 cut(s) 510
GsaI CCCAGC 1 cut(s) 391
HaeIII GGCC 2 cut(s) 301, 408
HapII CCGG 1 cut(s) 567
HgaI GACGC 1 cut(s) 93
HhaI GCGC 1 cut(s) 476
Hin1I GRCGYC 2 cut(s) 104, 732
Hin1II CATG 4 cut(s) 59, 68, 548, 743
Hin6I GCGC 1 cut(s) 474
HinP1I GCGC 1 cut(s) 474
HincII GTYRAC 1 cut(s) 529
HindII GTYRAC 1 cut(s) 529
HinfI GANTC 3 cut(s) 8, 89, 574
HpaII CCGG 1 cut(s) 567
HphI GGTGA 2 cut(s) 91, 602
Hpy166II GTNNAC 1 cut(s) 529
Hpy188I TCNGA 2 cut(s) 523, 541
Hpy188III TCNNGA 6 cut(s) 43, 145, 310, 367, 419, 708
Hpy8I GTNNAC 1 cut(s) 529
HpyAV CCTTC 3 cut(s) 65, 272, 319
HpyCH4III ACNGT 2 cut(s) 123, 642
HpyCH4IV ACGT 3 cut(s) 166, 611, 732
HpyCH4V TGCA 3 cut(s) 512, 656, 739
HpyF10VI GCNNNNNNNGC 1 cut(s) 509
HpyF3I CTNAG 2 cut(s) 203, 318
HpySE526I ACGT 3 cut(s) 166, 611, 732
Hsp92I GRCGYC 2 cut(s) 104, 732
Hsp92II CATG 4 cut(s) 59, 68, 548, 743
HspAI GCGC 1 cut(s) 474
Ksp22I TGATCA 1 cut(s) 81
Kzo9I GATC 3 cut(s) 81, 187, 439
LguI GCTCTTC 1 cut(s) 230
LmnI GCTCC 1 cut(s) 257
Lsp1109I GCAGC 1 cut(s) 496
LweI GCATC 2 cut(s) 490, 665
MaeI CTAG 1 cut(s) 450
MaeII ACGT 3 cut(s) 166, 611, 732
MaeIII GTNAC 1 cut(s) 590
MalI GATC 3 cut(s) 83, 189, 441
MboI GATC 3 cut(s) 81, 187, 439
MboII GAAGA 5 cut(s) 47, 120, 227, 247, 334
MflI RGATCY 1 cut(s) 187
MhlI GDGCHC 1 cut(s) 418
MluCI AATT 6 cut(s) 148, 207, 305, 698, 716, 753
MlyI GAGTC 2 cut(s) 98, 568
MnlI CCTC 4 cut(s) 178, 205, 619, 734
Mph1103I ATGCAT 1 cut(s) 658
MroXI GAANNNNTTC 1 cut(s) 140
MseI TTAA 2 cut(s) 486, 719
MspI CCGG 1 cut(s) 567
MspR9I CCNGG 2 cut(s) 242, 345
MvaI CCWGG 2 cut(s) 242, 345
MvnI CGCG 2 cut(s) 474, 476
MwoI GCNNNNNNNGC 1 cut(s) 509
NdeII GATC 3 cut(s) 81, 187, 439
NlaIII CATG 4 cut(s) 59, 68, 548, 743
NlaIV GGNNCC 1 cut(s) 259
NmuCI GTSAC 1 cut(s) 590
NsiI ATGCAT 1 cut(s) 658
NspI RCATGY 1 cut(s) 743
PciSI GCTCTTC 1 cut(s) 230
PcsI WCGNNNNNNNCGW 1 cut(s) 630
PdmI GAANNNNTTC 1 cut(s) 140
PfeI GAWTC 1 cut(s) 8
PflMI CCANNNNNTGG 1 cut(s) 436
PinAI ACCGGT 1 cut(s) 566
PkrI GCNGC 1 cut(s) 511
PleI GAGTC 2 cut(s) 97, 568
PpsI GAGTC 2 cut(s) 97, 568
Ppu21I YACGTR 1 cut(s) 612
PpuMI RGGWCCY 1 cut(s) 446
Psp5II RGGWCCY 1 cut(s) 446
Psp6I CCWGG 2 cut(s) 240, 343
PspFI CCCAGC 1 cut(s) 387
PspGI CCWGG 2 cut(s) 240, 343
PspN4I GGNNCC 1 cut(s) 259
PspPI GGNCC 1 cut(s) 446
PspPPI RGGWCCY 1 cut(s) 446
PsuI RGATCY 1 cut(s) 187
RsaI GTAC 1 cut(s) 614
RsaNI GTAC 1 cut(s) 613
SapI GCTCTTC 1 cut(s) 230
SaqAI TTAA 2 cut(s) 486, 719
SatI GCNGC 1 cut(s) 510
Sau3AI GATC 3 cut(s) 81, 187, 439
Sau96I GGNCC 1 cut(s) 446
SchI GAGTC 2 cut(s) 98, 568
ScrFI CCNGG 2 cut(s) 242, 345
SduI GDGCHC 1 cut(s) 418
SetI ASST 5 cut(s) 169, 448, 483, 614, 735
SfaNI GCATC 2 cut(s) 490, 665
SinI GGWCC 1 cut(s) 446
SmlI CTYRAG 3 cut(s) 155, 182, 417
SmoI CTYRAG 3 cut(s) 155, 182, 417
SnaBI TACGTA 1 cut(s) 612
Sse9I AATT 6 cut(s) 148, 207, 305, 698, 716, 753
SsiI CCGC 1 cut(s) 472
SspMI CTAG 1 cut(s) 450
StyD4I CCNGG 2 cut(s) 240, 343
StyI CCWWGG 2 cut(s) 261, 504
TaaI ACNGT 2 cut(s) 123, 642
TaiI ACGT 3 cut(s) 169, 614, 735
TaqI TCGA 2 cut(s) 433, 624
TasI AATT 6 cut(s) 148, 207, 305, 698, 716, 753
TfiI GAWTC 1 cut(s) 8
Tru1I TTAA 2 cut(s) 486, 719
Tru9I TTAA 2 cut(s) 486, 719
TseFI GTSAC 1 cut(s) 590
TseI GCWGC 1 cut(s) 509
Tsp45I GTSAC 1 cut(s) 590
TspDTI ATGAA 2 cut(s) 53, 276
Van91I CCANNNNNTGG 1 cut(s) 436
VpaK11BI GGWCC 1 cut(s) 446
XapI RAATTY 2 cut(s) 305, 698
XceI RCATGY 1 cut(s) 743
XmnI GAANNNNTTC 1 cut(s) 140
XspI CTAG 1 cut(s) 450
ZraI GACGTC 1 cut(s) 733
Zsp2I ATGCAT 1 cut(s) 658
Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.