pycom11g21580

gag-polypeptide of LTR copia-type

Design Primers CRISPR Design

Basic Information

Type: gene
Biological Identity
pyrus_communis
Chr11
OG0000258
Physical Location & Seq
Forward (+)
24687116 .. 24687892
777 bp
Loading structure...
UTR
Exon/CDS
Intron
pycom11g21580.1

Sequence Viewer

Length: 639 bp
ATGGAACAATCGGGAACTAAATCTCATTCTGAGAAGCCTGAGAAATTTAAGGGTGGAGACTTCAAAAGATGGCAGCAGAAGATGCTGTTTTATTTGACAACTTTGAATTTGGCTAATGTTCTGCGCGAGACTGTACCTACTGCAGATGGAGAAAATATTTTTTTTGCAGAAACTTTAACGGCTATAGATGCCTGGAATCATAATGATTTCCTCTGCAGAAACTATATTCTCAATGCATTAGATGATTCATTGTATGATGTCTATGTAGTATGCAAAACAGCCAAGGAACTTTGGGAATCACTTGAGAAAAAATATAAAACTGAAGATGCTGGTTCGAAGAAATTTGTCGTGGGCAAATTTTTGGACTACAAAATGGTGGATTCCAAGTCCGTTGTCTCTCAAATTAAAGATCTCCAGAAAATCATCCATGACATTCATGTTGAAGGGATGGTGATCAATGAGTCTTTCCAAGTGGCGTCCTTTATAGAAAAACTGCCACCTTCTTGGAAAGAGTTCAAGAATTATCTCAAACACAAACGTAAAGAGATGACCCTTGAGGATCTCATTGTAAGGTTGAGAATAGAGGAATATAACAGAAAGAATGAGAAGGGCCTGGTTTCGAGTATGGAAGCCAAGTAA
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

213

Amino Acids

24.8

Weight (kDa)

7.7

Isoelectric Point (pI)

47.66

Instability Index
Protein Domains (Pfam)
Domain Name Pfam ID Position E-value Description
Retrotran_gag_2 PF14223 52 - 203 4.3e-30 gag-polypeptide of LTR copia-type
Hydrophobicity Profile (Kyte-Doolittle)
AI Structure Prediction Report
Calculating structure properties...

Genomic Context

Gene Family Tree

Species Filter
Loading...
Style Settings
Image
Tree File
Tip: Beautify your tree with professional tools

Download the Full Tree (.nwk) file, then upload it to any of the following tools to customize colors, fonts, annotations, clades, and branch support.

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
AclWI GGATC 1 cut(s) 567
AcsI RAATTY 4 cut(s) 44, 106, 341, 356
AcuI CTGAAG 1 cut(s) 342
AcyI GRCGYC 1 cut(s) 476
AfaI GTAC 1 cut(s) 135
AgsI TTSAA 4 cut(s) 64, 106, 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 1 cut(s) 610
ApeKI GCWGC 1 cut(s) 73
ApoI RAATTY 4 cut(s) 44, 106, 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
AsuII TTCGAA 1 cut(s) 335
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, 183, 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 3 cut(s) 72, 178, 316
BpmI CTGGAG 1 cut(s) 398
Bpu14I TTCGAA 1 cut(s) 335
BpuEI CTTGAG 2 cut(s) 323, 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 2 cut(s) 423, 453
BseJI GATNNNNATC 1 cut(s) 452
BseMII CTCAG 2 cut(s) 21, 30
BseXI GCAGC 1 cut(s) 85
Bsh1236I CGCG 1 cut(s) 126
BshFI GGCC 1 cut(s) 612
BsmAI GTCTC 3 cut(s) 51, 122, 400
BsnI GGCC 1 cut(s) 612
Bsp119I TTCGAA 1 cut(s) 335
Bsp143I GATC 3 cut(s) 409, 453, 559
BspANI GGCC 1 cut(s) 612
BspCNI CTCAG 2 cut(s) 22, 31
BspFNI CGCG 1 cut(s) 126
BspMAI CTGCAG 2 cut(s) 145, 218
BspPI GGATC 1 cut(s) 567
BspT104I TTCGAA 1 cut(s) 335
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) 133
BstACI GRCGYC 1 cut(s) 476
BstAPI GCANNNNNTGC 1 cut(s) 82
BstBI TTCGAA 1 cut(s) 335
BstDEI CTNAG 2 cut(s) 30, 39
BstF5I GGATG 2 cut(s) 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, 183, 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 1 cut(s) 612
BtsCI GGATG 2 cut(s) 423, 453
CfoI GCGC 1 cut(s) 126
Cfr13I GGNCC 1 cut(s) 610
CseI GACGC 1 cut(s) 465
Csp6I GTAC 1 cut(s) 134
CviAII CATG 2 cut(s) 428, 437
CviJI RGCY 6 cut(s) 37, 113, 182, 281, 612, 632
CviKI_1 RGCY 6 cut(s) 37, 113, 182, 281, 612, 632
CviQI GTAC 1 cut(s) 134
DdeI CTNAG 2 cut(s) 30, 39
DpnI GATC 3 cut(s) 411, 455, 561
DpnII GATC 3 cut(s) 409, 453, 559
Eco130I CCWWGG 1 cut(s) 282
Eco57I CTGAAG 1 cut(s) 342
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 2 cut(s) 431, 440
FatI CATG 2 cut(s) 427, 436
FbaI TGATCA 1 cut(s) 453
Fnu4HI GCNGC 1 cut(s) 74
FokI GGATG 2 cut(s) 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 1 cut(s) 612
HgaI GACGC 1 cut(s) 465
HhaI GCGC 1 cut(s) 126
Hin1I GRCGYC 1 cut(s) 476
Hin1II CATG 2 cut(s) 431, 440
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 3 cut(s) 437, 510, 601
HpyCH4III ACNGT 1 cut(s) 133
HpyCH4IV ACGT 1 cut(s) 538
HpyCH4V TGCA 5 cut(s) 143, 167, 216, 236, 273
HpyF10VI GCNNNNNNNGC 2 cut(s) 82, 188
HpyF3I CTNAG 2 cut(s) 30, 39
HpySE526I ACGT 1 cut(s) 538
Hsp92I GRCGYC 1 cut(s) 476
Hsp92II CATG 2 cut(s) 431, 440
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 3 cut(s) 72, 178, 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) 91, 335, 349
MflI RGATCY 2 cut(s) 409, 559
MluCI AATT 6 cut(s) 44, 106, 341, 356, 402, 520
MlyI GAGTC 1 cut(s) 470
MnlI CCTC 3 cut(s) 221, 550, 577
Mph1103I ATGCAT 1 cut(s) 238
MroXI GAANNNNTTC 1 cut(s) 512
MseI TTAA 3 cut(s) 48, 176, 405
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 2 cut(s) 431, 440
NsiI ATGCAT 1 cut(s) 238
NspV TTCGAA 1 cut(s) 335
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) 145, 218
PsuI RGATCY 2 cut(s) 409, 559
RsaI GTAC 1 cut(s) 135
RsaNI GTAC 1 cut(s) 134
SaqAI TTAA 3 cut(s) 48, 176, 405
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 4 cut(s) 139, 502, 541, 575
SfaNI GCATC 3 cut(s) 72, 178, 316
SfcI CTRYAG 3 cut(s) 141, 183, 214
SfuI TTCGAA 1 cut(s) 335
SmlI CTYRAG 2 cut(s) 302, 554
SmoI CTYRAG 2 cut(s) 302, 554
Sse9I AATT 6 cut(s) 44, 106, 341, 356, 402, 520
SspI AATATT 1 cut(s) 157
StyD4I CCNGG 2 cut(s) 191, 612
StyI CCWWGG 1 cut(s) 282
TaaI ACNGT 1 cut(s) 133
TaiI ACGT 1 cut(s) 541
TaqI TCGA 2 cut(s) 335, 620
TasI AATT 6 cut(s) 44, 106, 341, 356, 402, 520
TfiI GAWTC 4 cut(s) 196, 245, 296, 380
Tru1I TTAA 3 cut(s) 48, 176, 405
Tru9I TTAA 3 cut(s) 48, 176, 405
TseI GCWGC 1 cut(s) 73
TspDTI ATGAA 2 cut(s) 237, 425
TspGWI ACGGA 1 cut(s) 379
XapI RAATTY 4 cut(s) 44, 106, 341, 356
XmnI GAANNNNTTC 1 cut(s) 512
Zsp2I ATGCAT 1 cut(s) 238
Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.