pycom16g17230

gag-polypeptide of LTR copia-type

Design Primers CRISPR Design

Basic Information

Type: gene
Biological Identity
pyrus_communis
Chr16
OG0000258
Physical Location & Seq
Reverse (-)
13295923 .. 13296714
792 bp
Loading structure...
UTR
Exon/CDS
Intron
pycom16g17230.2

Sequence Viewer

Length: 654 bp
ATGGAACAATCGGGAACTAAACCTCATTCTGAGAAGCCTGAGAAATTTAAGGGCGGAGACTTCAAAAGATGGCAGCAGAAAATGCTGTTTTATTTGACAACCTTCAATTTGGCTAATGGTCTGCGCGAGACTGCACCTACTGTAGATGGAGAAAATATTTTTTCTGCAGAAACTTTAACGGCTATAAATGCCTGGAATCATAATGATTTCCTCTGCAGAAACTATATTCTCAATGCATTAGATGATTCATTGTATGATGTCTATGTAGTATGCAAAACAGCCAAGGAACTTTGGGAATCACTTGAGAAAAAATATAAAACTGAGGATGCTGGTTTGAAGAAATTTGTCGTGGGCAAATTTTTGGACTACAAAATGGTGGATTCTAAGTCCGTTGTCTCTCAAACTGAAGATCTCCAGAAAATCATCCATGACATTCATATTGAAGGGATGGTGATCAATGAGTCTTTCCAAGTGGCGTCCTTTATAGAAAAATTGCCACCTTCTTGGAAAGAGTTCAAGAATTATCTCAAGCACAAACGTAAAGAGATGACCCTTGAGGATCTCATTGTAAGGCTGAGAATAGAGGAAGATAACAGAAAGAATGAGAAGGGCCTGGTTTCGAGTATAGAAGCCAAGCAAGGCCATAGGGCTTAA
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

218

Amino Acids

25.26

Weight (kDa)

7.02

Isoelectric Point (pI)

55.84

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
iTOL Interactive Tree Of Life · Most popular EvolView Flexible annotations MEGA Desktop phylogenetics suite FigTree Desktop tree editor

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)
AccII CGCG 1 cut(s) 126
AciI CCGC 1 cut(s) 54
AclWI GGATC 1 cut(s) 567
AcsI RAATTY 3 cut(s) 44, 341, 356
AcuI CTGAAG 1 cut(s) 426
AcyI GRCGYC 1 cut(s) 476
AgsI TTSAA 5 cut(s) 64, 106, 337, 443, 517
AjnI CCWGG 2 cut(s) 191, 612
Alw26I GTCTC 3 cut(s) 51, 122, 400
AlwI GGATC 1 cut(s) 567
AoxI GGCC 2 cut(s) 610, 640
ApeKI GCWGC 1 cut(s) 73
ApoI RAATTY 3 cut(s) 44, 341, 356
Asp700I GAANNNNTTC 1 cut(s) 512
AspLEI GCGC 1 cut(s) 126
AspS9I GGNCC 1 cut(s) 610
AsuHPI GGTGA 1 cut(s) 463
BbvI GCAGC 1 cut(s) 85
BccI CCATC 3 cut(s) 63, 140, 442
BceAI ACGGC 1 cut(s) 195
BciT130I CCWGG 2 cut(s) 193, 614
BclI TGATCA 1 cut(s) 453
BcoDI GTCTC 3 cut(s) 51, 122, 400
BfmI CTRYAG 3 cut(s) 141, 165, 214
BglII AGATCT 1 cut(s) 409
BisI GCNGC 1 cut(s) 74
BlsI GCNGC 1 cut(s) 75
Bme1390I CCNGG 2 cut(s) 193, 614
BmgT120I GGNCC 1 cut(s) 610
BmrFI CCNGG 2 cut(s) 193, 614
BmsI GCATC 1 cut(s) 316
BpmI CTGGAG 1 cut(s) 398
BpuEI CTTGAG 3 cut(s) 323, 512, 575
BsaBI GATNNNNATC 1 cut(s) 452
BsaHI GRCGYC 1 cut(s) 476
BsaJI CCNNGG 1 cut(s) 282
Bse8I GATNNNNATC 1 cut(s) 452
BseBI CCWGG 2 cut(s) 193, 614
BseDI CCNNGG 1 cut(s) 282
BseGI GGATG 3 cut(s) 331, 423, 453
BseJI GATNNNNATC 1 cut(s) 452
BseMII CTCAG 4 cut(s) 21, 30, 312, 566
BseXI GCAGC 1 cut(s) 85
BsgI GTGCAG 1 cut(s) 117
Bsh1236I CGCG 1 cut(s) 126
BshFI GGCC 2 cut(s) 612, 642
BsmAI GTCTC 3 cut(s) 51, 122, 400
BsnI GGCC 2 cut(s) 612, 642
Bsp143I GATC 3 cut(s) 409, 453, 559
BspACI CCGC 1 cut(s) 54
BspANI GGCC 2 cut(s) 612, 642
BspCNI CTCAG 4 cut(s) 22, 31, 313, 567
BspFNI CGCG 1 cut(s) 126
BspMAI CTGCAG 2 cut(s) 169, 218
BspPI GGATC 1 cut(s) 567
BssECI CCNNGG 1 cut(s) 282
BssMI GATC 3 cut(s) 409, 453, 559
BssNI GRCGYC 1 cut(s) 476
BssT1I CCWWGG 1 cut(s) 282
Bst2UI CCWGG 2 cut(s) 193, 614
Bst4CI ACNGT 1 cut(s) 142
BstACI GRCGYC 1 cut(s) 476
BstAPI GCANNNNNTGC 1 cut(s) 82
BstDEI CTNAG 5 cut(s) 30, 39, 321, 384, 575
BstF5I GGATG 3 cut(s) 331, 423, 453
BstFNI CGCG 1 cut(s) 126
BstHHI GCGC 1 cut(s) 126
BstKTI GATC 3 cut(s) 412, 456, 562
BstMAI GTCTC 3 cut(s) 51, 122, 400
BstMBI GATC 3 cut(s) 409, 453, 559
BstMWI GCNNNNNNNGC 2 cut(s) 82, 188
BstNI CCWGG 2 cut(s) 193, 614
BstSCI CCNGG 2 cut(s) 191, 612
BstSFI CTRYAG 3 cut(s) 141, 165, 214
BstUI CGCG 1 cut(s) 126
BstV1I GCAGC 1 cut(s) 85
BstX2I RGATCY 2 cut(s) 409, 559
BstXI CCANNNNNNTGG 1 cut(s) 504
BstYI RGATCY 2 cut(s) 409, 559
BsuRI GGCC 2 cut(s) 612, 642
BtsCI GGATG 3 cut(s) 331, 423, 453
CfoI GCGC 1 cut(s) 126
Cfr13I GGNCC 1 cut(s) 610
CseI GACGC 1 cut(s) 465
CviAII CATG 1 cut(s) 428
CviJI RGCY 9 cut(s) 37, 113, 182, 281, 574, 612, 632, 642, 650
CviKI_1 RGCY 9 cut(s) 37, 113, 182, 281, 574, 612, 632, 642, 650
DdeI CTNAG 5 cut(s) 30, 39, 321, 384, 575
DpnI GATC 3 cut(s) 411, 455, 561
DpnII GATC 3 cut(s) 409, 453, 559
EciI GGCGGA 1 cut(s) 69
Eco130I CCWWGG 1 cut(s) 282
Eco57I CTGAAG 1 cut(s) 426
EcoO109I RGGNCCY 1 cut(s) 610
EcoRII CCWGG 2 cut(s) 191, 612
EcoT14I CCWWGG 1 cut(s) 282
EcoT22I ATGCAT 1 cut(s) 238
ErhI CCWWGG 1 cut(s) 282
FaeI CATG 1 cut(s) 431
FatI CATG 1 cut(s) 427
FbaI TGATCA 1 cut(s) 453
Fnu4HI GCNGC 1 cut(s) 74
FokI GGATG 3 cut(s) 338, 410, 460
Fsp4HI GCNGC 1 cut(s) 74
GlaI GCGC 1 cut(s) 125
GluI GCNGC 1 cut(s) 74
GsuI CTGGAG 1 cut(s) 398
HaeIII GGCC 2 cut(s) 612, 642
HgaI GACGC 1 cut(s) 465
HhaI GCGC 1 cut(s) 126
Hin1I GRCGYC 1 cut(s) 476
Hin1II CATG 1 cut(s) 431
Hin6I GCGC 1 cut(s) 124
HinP1I GCGC 1 cut(s) 124
HinfI GANTC 5 cut(s) 196, 245, 296, 380, 461
HphI GGTGA 1 cut(s) 463
Hpy188I TCNGA 1 cut(s) 31
Hpy188III TCNNGA 3 cut(s) 12, 415, 517
HpyAV CCTTC 4 cut(s) 112, 437, 510, 601
HpyCH4III ACNGT 1 cut(s) 142
HpyCH4IV ACGT 1 cut(s) 538
HpyCH4V TGCA 5 cut(s) 134, 167, 216, 236, 273
HpyF10VI GCNNNNNNNGC 2 cut(s) 82, 188
HpyF3I CTNAG 5 cut(s) 30, 39, 321, 384, 575
HpySE526I ACGT 1 cut(s) 538
Hsp92I GRCGYC 1 cut(s) 476
Hsp92II CATG 1 cut(s) 431
HspAI GCGC 1 cut(s) 124
Ksp22I TGATCA 1 cut(s) 453
Kzo9I GATC 3 cut(s) 409, 453, 559
LpnPI CCDG 7 cut(s) 51, 178, 205, 315, 428, 599, 626
Lsp1109I GCAGC 1 cut(s) 85
LweI GCATC 1 cut(s) 316
MaeII ACGT 1 cut(s) 538
MalI GATC 3 cut(s) 411, 455, 561
MboI GATC 3 cut(s) 409, 453, 559
MboII GAAGA 3 cut(s) 349, 419, 599
MflI RGATCY 2 cut(s) 409, 559
MluCI AATT 6 cut(s) 44, 106, 341, 356, 491, 520
MlyI GAGTC 1 cut(s) 470
MnlI CCTC 5 cut(s) 33, 221, 316, 550, 577
Mph1103I ATGCAT 1 cut(s) 238
MroXI GAANNNNTTC 1 cut(s) 512
MseI TTAA 3 cut(s) 48, 176, 652
MspR9I CCNGG 2 cut(s) 193, 614
MvaI CCWGG 2 cut(s) 193, 614
MvnI CGCG 1 cut(s) 126
MwoI GCNNNNNNNGC 2 cut(s) 82, 188
NdeII GATC 3 cut(s) 409, 453, 559
NlaIII CATG 1 cut(s) 431
NsiI ATGCAT 1 cut(s) 238
PdmI GAANNNNTTC 1 cut(s) 512
PfeI GAWTC 4 cut(s) 196, 245, 296, 380
PkrI GCNGC 1 cut(s) 75
PleI GAGTC 1 cut(s) 469
PpsI GAGTC 1 cut(s) 469
Psp6I CCWGG 2 cut(s) 191, 612
PspGI CCWGG 2 cut(s) 191, 612
PspPI GGNCC 1 cut(s) 610
PstI CTGCAG 2 cut(s) 169, 218
PsuI RGATCY 2 cut(s) 409, 559
SaqAI TTAA 3 cut(s) 48, 176, 652
SatI GCNGC 1 cut(s) 74
Sau3AI GATC 3 cut(s) 409, 453, 559
Sau96I GGNCC 1 cut(s) 610
SchI GAGTC 1 cut(s) 470
ScrFI CCNGG 2 cut(s) 193, 614
SetI ASST 5 cut(s) 25, 104, 139, 502, 541
SfaNI GCATC 1 cut(s) 316
SfcI CTRYAG 3 cut(s) 141, 165, 214
SmlI CTYRAG 3 cut(s) 302, 527, 554
SmoI CTYRAG 3 cut(s) 302, 527, 554
Sse9I AATT 6 cut(s) 44, 106, 341, 356, 491, 520
SsiI CCGC 1 cut(s) 54
SspI AATATT 1 cut(s) 157
StyD4I CCNGG 2 cut(s) 191, 612
StyI CCWWGG 1 cut(s) 282
TaaI ACNGT 1 cut(s) 142
TaiI ACGT 1 cut(s) 541
TaqI TCGA 1 cut(s) 620
TasI AATT 6 cut(s) 44, 106, 341, 356, 491, 520
TfiI GAWTC 4 cut(s) 196, 245, 296, 380
Tru1I TTAA 3 cut(s) 48, 176, 652
Tru9I TTAA 3 cut(s) 48, 176, 652
TseI GCWGC 1 cut(s) 73
TspDTI ATGAA 2 cut(s) 237, 425
TspGWI ACGGA 1 cut(s) 379
XapI RAATTY 3 cut(s) 44, 341, 356
XmnI GAANNNNTTC 1 cut(s) 512
Zsp2I ATGCAT 1 cut(s) 238
Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.