pycom15g25800

gag-polypeptide of LTR copia-type

Design Primers CRISPR Design

Basic Information

Type: gene
Biological Identity
pyrus_communis
Chr15
OG0000258
Physical Location & Seq
Reverse (-)
20458583 .. 20459359
777 bp
Loading structure...
UTR
Exon/CDS
Intron
pycom15g25800.1

Sequence Viewer

Length: 777 bp
ATGCTGTTTTATTTGACAACCTTGAATTTGGCTAATGTTCTGCGCGAGACTGTACCTACTGCAGATGGAGAAAATATTTTTTCTGCAGAAACTTTAACGGCTATAGATGCCTGGAATCATAATGATTTCCTCTATAGAAACTATATTCTCAATGCATTAGATGATTCATTGTATGATGTCTATGTAGTATGCAAAATAGCCAAGGAACTTTGGGAATCACTTGAGAAAAAATATAAAACTGAGGATGCTGGTTCGAAGAAATTTGTCGTGGGCAAATTTTTGGACTACAAAATGGTGGATTCCAAGTCCGTTGTCTCTCAAACTGAAGATCTCCAGAAAATCATCCATGACATTCATGTTGAAGGGATGGTGATCAATGAGTCTTTCCAAGTGGCGTCCTTTATAGAAAAATTGCCACCTTCTTGGAAAGAGTTCAAGAATTATCTCAAGTATAAACGTAAAGAGATGACCCTTGAGGATCTCATTGTAAGGCTGAGAATAGAGGAAGATAACAGAAAGAATGAGAAGGGTCTGGTTTCGAGTATGGAAGCCAAGGCGAATGTTGTTGAAGGAAGTTCATCAAAGCAAAGGCCGAAGTTCCAGAAAACTAAGAAGAAGGAAAAACACTTTATCCCTGGTGCGAAAGGCAAAGACTTCAAGAAAATCAAGGGAAGTTGCTGGGTTTATGGAAAGCAAGGCCATAGGGCTCAAGAATGTCGCCATCGAAGATCGATCAAGGTCTTGGAAATCAAGGCAACAACAACCGCGCTAACCTGA
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

259

Amino Acids

29.87

Weight (kDa)

9.27

Isoelectric Point (pI)

42.67

Instability Index
Protein Domains (Pfam)
Domain Name Pfam ID Position E-value Description
Retrotran_gag_2 PF14223 25 - 176 2.8e-26 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)
AccII CGCG 2 cut(s) 45, 767
AciI CCGC 1 cut(s) 765
AclWI GGATC 1 cut(s) 486
AcsI RAATTY 3 cut(s) 25, 260, 275
AcuI CTGAAG 1 cut(s) 345
AcyI GRCGYC 1 cut(s) 395
AfaI GTAC 1 cut(s) 54
AgsI TTSAA 5 cut(s) 25, 362, 436, 569, 658
AjnI CCWGG 2 cut(s) 110, 634
Alw26I GTCTC 2 cut(s) 41, 319
AlwI GGATC 1 cut(s) 486
AoxI GGCC 2 cut(s) 590, 697
ApoI RAATTY 3 cut(s) 25, 260, 275
Asp700I GAANNNNTTC 1 cut(s) 431
AspLEI GCGC 2 cut(s) 45, 769
AsuHPI GGTGA 1 cut(s) 382
AsuII TTCGAA 1 cut(s) 254
BanII GRGCYC 1 cut(s) 709
BccI CCATC 3 cut(s) 59, 361, 729
BceAI ACGGC 1 cut(s) 114
BciT130I CCWGG 2 cut(s) 112, 636
BclI TGATCA 1 cut(s) 372
BcoDI GTCTC 2 cut(s) 41, 319
BfmI CTRYAG 4 cut(s) 60, 84, 102, 133
BglII AGATCT 1 cut(s) 328
Bme1390I CCNGG 2 cut(s) 112, 636
BmrFI CCNGG 2 cut(s) 112, 636
BmsI GCATC 2 cut(s) 97, 235
BpmI CTGGAG 1 cut(s) 317
Bpu14I TTCGAA 1 cut(s) 254
BpuEI CTTGAG 4 cut(s) 242, 431, 494, 693
Bsa29I ATCGAT 1 cut(s) 731
BsaBI GATNNNNATC 1 cut(s) 371
BsaHI GRCGYC 1 cut(s) 395
BsaJI CCNNGG 3 cut(s) 201, 552, 634
Bse8I GATNNNNATC 1 cut(s) 371
BseBI CCWGG 2 cut(s) 112, 636
BseCI ATCGAT 1 cut(s) 731
BseDI CCNNGG 3 cut(s) 201, 552, 634
BseGI GGATG 3 cut(s) 250, 342, 372
BseJI GATNNNNATC 1 cut(s) 371
BseMII CTCAG 2 cut(s) 231, 485
BseYI CCCAGC 1 cut(s) 678
Bsh1236I CGCG 2 cut(s) 45, 767
BshFI GGCC 2 cut(s) 592, 699
BshVI ATCGAT 1 cut(s) 731
BsmAI GTCTC 2 cut(s) 41, 319
BsnI GGCC 2 cut(s) 592, 699
Bsp119I TTCGAA 1 cut(s) 254
Bsp1286I GDGCHC 1 cut(s) 709
Bsp143I GATC 5 cut(s) 328, 372, 478, 728, 732
BspACI CCGC 1 cut(s) 765
BspANI GGCC 2 cut(s) 592, 699
BspCNI CTCAG 2 cut(s) 232, 486
BspDI ATCGAT 1 cut(s) 731
BspFNI CGCG 2 cut(s) 45, 767
BspMAI CTGCAG 2 cut(s) 64, 88
BspPI GGATC 1 cut(s) 486
BspT104I TTCGAA 1 cut(s) 254
BssECI CCNNGG 3 cut(s) 201, 552, 634
BssMI GATC 5 cut(s) 328, 372, 478, 728, 732
BssNI GRCGYC 1 cut(s) 395
BssT1I CCWWGG 2 cut(s) 201, 552
Bst2UI CCWGG 2 cut(s) 112, 636
Bst4CI ACNGT 1 cut(s) 52
BstACI GRCGYC 1 cut(s) 395
BstBI TTCGAA 1 cut(s) 254
BstDEI CTNAG 3 cut(s) 240, 494, 609
BstF5I GGATG 3 cut(s) 250, 342, 372
BstFNI CGCG 2 cut(s) 45, 767
BstHHI GCGC 2 cut(s) 45, 769
BstKTI GATC 5 cut(s) 331, 375, 481, 731, 735
BstMAI GTCTC 2 cut(s) 41, 319
BstMBI GATC 5 cut(s) 328, 372, 478, 728, 732
BstMWI GCNNNNNNNGC 1 cut(s) 107
BstNI CCWGG 2 cut(s) 112, 636
BstSCI CCNGG 2 cut(s) 110, 634
BstSFI CTRYAG 4 cut(s) 60, 84, 102, 133
BstUI CGCG 2 cut(s) 45, 767
BstX2I RGATCY 2 cut(s) 328, 478
BstXI CCANNNNNNTGG 1 cut(s) 423
BstYI RGATCY 2 cut(s) 328, 478
Bsu15I ATCGAT 1 cut(s) 731
BsuRI GGCC 2 cut(s) 592, 699
BsuTUI ATCGAT 1 cut(s) 731
BtsCI GGATG 3 cut(s) 250, 342, 372
CfoI GCGC 2 cut(s) 45, 769
ClaI ATCGAT 1 cut(s) 731
CseI GACGC 1 cut(s) 384
Csp6I GTAC 1 cut(s) 53
CviAII CATG 2 cut(s) 347, 356
CviJI RGCY 8 cut(s) 32, 101, 200, 493, 551, 592, 699, 707
CviKI_1 RGCY 8 cut(s) 32, 101, 200, 493, 551, 592, 699, 707
CviQI GTAC 1 cut(s) 53
DdeI CTNAG 3 cut(s) 240, 494, 609
DpnI GATC 5 cut(s) 330, 374, 480, 730, 734
DpnII GATC 5 cut(s) 328, 372, 478, 728, 732
Eco130I CCWWGG 2 cut(s) 201, 552
Eco24I GRGCYC 1 cut(s) 709
Eco57I CTGAAG 1 cut(s) 345
EcoRII CCWGG 2 cut(s) 110, 634
EcoT14I CCWWGG 2 cut(s) 201, 552
EcoT22I ATGCAT 1 cut(s) 157
EcoT38I GRGCYC 1 cut(s) 709
ErhI CCWWGG 2 cut(s) 201, 552
FaeI CATG 2 cut(s) 350, 359
FatI CATG 2 cut(s) 346, 355
FbaI TGATCA 1 cut(s) 372
FokI GGATG 3 cut(s) 257, 329, 379
FriOI GRGCYC 1 cut(s) 709
GlaI GCGC 2 cut(s) 44, 768
GsaI CCCAGC 1 cut(s) 682
GsuI CTGGAG 1 cut(s) 317
HaeIII GGCC 2 cut(s) 592, 699
HgaI GACGC 1 cut(s) 384
HhaI GCGC 2 cut(s) 45, 769
Hin1I GRCGYC 1 cut(s) 395
Hin1II CATG 2 cut(s) 350, 359
Hin6I GCGC 2 cut(s) 43, 767
HinP1I GCGC 2 cut(s) 43, 767
HinfI GANTC 5 cut(s) 115, 164, 215, 299, 380
HphI GGTGA 1 cut(s) 382
Hpy188III TCNNGA 5 cut(s) 334, 436, 601, 658, 710
HpyAV CCTTC 5 cut(s) 356, 429, 520, 563, 610
HpyCH4III ACNGT 1 cut(s) 52
HpyCH4IV ACGT 1 cut(s) 457
HpyCH4V TGCA 4 cut(s) 62, 86, 155, 192
HpyF10VI GCNNNNNNNGC 1 cut(s) 107
HpyF3I CTNAG 3 cut(s) 240, 494, 609
HpySE526I ACGT 1 cut(s) 457
Hsp92I GRCGYC 1 cut(s) 395
Hsp92II CATG 2 cut(s) 350, 359
HspAI GCGC 2 cut(s) 43, 767
Ksp22I TGATCA 1 cut(s) 372
Kzo9I GATC 5 cut(s) 328, 372, 478, 728, 732
LpnPI CCDG 9 cut(s) 97, 124, 234, 347, 518, 614, 621, 648, 664
LweI GCATC 2 cut(s) 97, 235
MaeII ACGT 1 cut(s) 457
MalI GATC 5 cut(s) 330, 374, 480, 730, 734
MboI GATC 5 cut(s) 328, 372, 478, 728, 732
MboII GAAGA 5 cut(s) 268, 338, 518, 625, 738
MflI RGATCY 2 cut(s) 328, 478
MhlI GDGCHC 1 cut(s) 709
MluCI AATT 5 cut(s) 25, 260, 275, 410, 439
MlyI GAGTC 1 cut(s) 389
MnlI CCTC 4 cut(s) 140, 235, 469, 496
Mph1103I ATGCAT 1 cut(s) 157
MroXI GAANNNNTTC 1 cut(s) 431
MseI TTAA 1 cut(s) 95
MspR9I CCNGG 2 cut(s) 112, 636
MvaI CCWGG 2 cut(s) 112, 636
MvnI CGCG 2 cut(s) 45, 767
MwoI GCNNNNNNNGC 1 cut(s) 107
NdeII GATC 5 cut(s) 328, 372, 478, 728, 732
NlaIII CATG 2 cut(s) 350, 359
NsiI ATGCAT 1 cut(s) 157
NspV TTCGAA 1 cut(s) 254
PdmI GAANNNNTTC 1 cut(s) 431
PfeI GAWTC 4 cut(s) 115, 164, 215, 299
PleI GAGTC 1 cut(s) 388
PpsI GAGTC 1 cut(s) 388
Psp6I CCWGG 2 cut(s) 110, 634
PspFI CCCAGC 1 cut(s) 678
PspGI CCWGG 2 cut(s) 110, 634
PstI CTGCAG 2 cut(s) 64, 88
PsuI RGATCY 2 cut(s) 328, 478
RsaI GTAC 1 cut(s) 54
RsaNI GTAC 1 cut(s) 53
SaqAI TTAA 1 cut(s) 95
Sau3AI GATC 5 cut(s) 328, 372, 478, 728, 732
SchI GAGTC 1 cut(s) 389
ScrFI CCNGG 2 cut(s) 112, 636
SduI GDGCHC 1 cut(s) 709
SetI ASST 6 cut(s) 23, 58, 421, 460, 741, 776
SfaNI GCATC 2 cut(s) 97, 235
SfcI CTRYAG 4 cut(s) 60, 84, 102, 133
SfuI TTCGAA 1 cut(s) 254
SmlI CTYRAG 4 cut(s) 221, 446, 473, 708
SmoI CTYRAG 4 cut(s) 221, 446, 473, 708
Sse9I AATT 5 cut(s) 25, 260, 275, 410, 439
SsiI CCGC 1 cut(s) 765
SspI AATATT 1 cut(s) 76
StyD4I CCNGG 2 cut(s) 110, 634
StyI CCWWGG 2 cut(s) 201, 552
TaaI ACNGT 1 cut(s) 52
TaiI ACGT 1 cut(s) 460
TaqI TCGA 4 cut(s) 254, 539, 724, 731
TasI AATT 5 cut(s) 25, 260, 275, 410, 439
TfiI GAWTC 4 cut(s) 115, 164, 215, 299
Tru1I TTAA 1 cut(s) 95
Tru9I TTAA 1 cut(s) 95
TspDTI ATGAA 3 cut(s) 156, 344, 567
TspGWI ACGGA 1 cut(s) 298
XapI RAATTY 3 cut(s) 25, 260, 275
XmnI GAANNNNTTC 1 cut(s) 431
Zsp2I ATGCAT 1 cut(s) 157
Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.