pycom04g04480

gag-polypeptide of LTR copia-type

Design Primers CRISPR Design

Basic Information

Type: gene
Biological Identity
pyrus_communis
Chr4
OG0000258
Physical Location & Seq
Forward (+)
4065872 .. 4066778
907 bp
Loading structure...
UTR
Exon/CDS
Intron
pycom04g04480.1

Sequence Viewer

Length: 720 bp
ATGGTGATCAATGAGTCTTTCCAAGTGACGTCCTTTATAGAAAAACTGCCACCTTCTTGGAAAGAGTTCAAGAATTATCTCAAGCACAAACGTAAGAAGATGACCCTTGAGGATCTCATTGTTAGGCTAAGAATAGAGGAAGATAACAGAAAGAATGAGAAGGGCCTGGTTTCAAGTATGGAAGCCAAGCAAGGCCATAGGGCTCAAGAATGTCGCCATCGAATGGATCAATGTCCTAGAAATCAAGGCAACAACAACCGTGCGAACCTGATTGAAAACAATGTGGATGCCTTGGCTGCAATGATTTCTGAAATCAACCTTGTATCTGATCACGTTGATTGGTGGATAGATACTGGTGCAACTCGCCATGTGTGCGGTGACAGAAATATGTTCTCTTCGTACCAGAAAATCGAGGGAAACGAGCAGCTGTTTATGGGAAATGCATATGCATCTGTTGTGGCTGGAATAGGGAAATGTGTTCTGAAATTCACTTTTGGAAAGGAATTAACCCTCCTTGACGTGCTGCATGTCCCCGATATAAGGAAGAATCTTGTTTCTGGTCCTATCCTTAGTAATAAAGGATTCAAACTAGTTTTTGAGTCCAATAAGTTTGTACTAACTAAAGGGGGAATGTTTGTAGGGAAGGGTTACCTTGCTGATGGATTATTCAAACTAAATGTACTTGTTAATGTTATGAATGAAATAAATAATGATATGTAA
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

240

Amino Acids

27.21

Weight (kDa)

8.96

Isoelectric Point (pI)

31.75

Instability Index
Protein Domains (Pfam)
Domain Name Pfam ID Position E-value Description
Pol_BBD PF22936 114 - 195 1.9e-22 Pol polyprotein, beta-barrel domain
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)
AatII GACGTC 1 cut(s) 32
AccB7I CCANNNNNTGG 1 cut(s) 223
AciI CCGC 1 cut(s) 375
AclWI GGATC 2 cut(s) 120, 234
AcsI RAATTY 1 cut(s) 485
AcyI GRCGYC 1 cut(s) 29
AfaI GTAC 3 cut(s) 401, 615, 681
AfiI CCNNNNNNNGG 2 cut(s) 223, 540
AgsI TTSAA 5 cut(s) 70, 174, 275, 586, 670
AhlI ACTAGT 1 cut(s) 589
AjiI CACGTC 1 cut(s) 520
AjnI CCWGG 1 cut(s) 165
AluBI AGCT 1 cut(s) 427
AluI AGCT 1 cut(s) 427
AlwI GGATC 2 cut(s) 120, 234
AoxI GGCC 2 cut(s) 163, 193
ApeKI GCWGC 3 cut(s) 296, 424, 523
ApoI RAATTY 1 cut(s) 485
Asp700I GAANNNNTTC 1 cut(s) 65
AspS9I GGNCC 2 cut(s) 163, 560
AsuHPI GGTGA 2 cut(s) 16, 389
AvaII GGWCC 1 cut(s) 560
BanII GRGCYC 1 cut(s) 205
BbvI GCAGC 3 cut(s) 283, 436, 510
BccI CCATC 2 cut(s) 225, 653
BciT130I CCWGG 1 cut(s) 167
BclI TGATCA 2 cut(s) 6, 328
BcuI ACTAGT 1 cut(s) 589
BfaI CTAG 2 cut(s) 237, 590
BisI GCNGC 3 cut(s) 297, 425, 524
BlsI GCNGC 3 cut(s) 298, 426, 525
Bme1390I CCNGG 1 cut(s) 167
Bme18I GGWCC 1 cut(s) 560
BmgBI CACGTC 1 cut(s) 520
BmgT120I GGNCC 2 cut(s) 163, 560
BmrFI CCNGG 1 cut(s) 167
BmsI GCATC 2 cut(s) 277, 458
BpuEI CTTGAG 3 cut(s) 65, 128, 189
BsaHI GRCGYC 1 cut(s) 29
BsaJI CCNNGG 1 cut(s) 291
Bsc4I CCNNNNNNNGG 2 cut(s) 223, 540
Bse1I ACTGG 1 cut(s) 358
Bse3DI GCAATG 1 cut(s) 306
BseBI CCWGG 1 cut(s) 167
BseDI CCNNGG 1 cut(s) 291
BseGI GGATG 1 cut(s) 292
BseLI CCNNNNNNNGG 2 cut(s) 223, 540
BseMI GCAATG 1 cut(s) 306
BseNI ACTGG 1 cut(s) 358
BseXI GCAGC 3 cut(s) 283, 436, 510
BshFI GGCC 2 cut(s) 165, 195
BslFI GGGAC 1 cut(s) 515
BslI CCNNNNNNNGG 2 cut(s) 223, 540
BsmFI GGGAC 1 cut(s) 515
BsnI GGCC 2 cut(s) 165, 195
Bsp1286I GDGCHC 1 cut(s) 205
Bsp143I GATC 4 cut(s) 6, 112, 226, 328
BspACI CCGC 1 cut(s) 375
BspANI GGCC 2 cut(s) 165, 195
BspPI GGATC 2 cut(s) 120, 234
BsrDI GCAATG 1 cut(s) 306
BsrI ACTGG 1 cut(s) 358
BssECI CCNNGG 1 cut(s) 291
BssMI GATC 4 cut(s) 6, 112, 226, 328
BssNI GRCGYC 1 cut(s) 29
BssT1I CCWWGG 1 cut(s) 291
Bst2UI CCWGG 1 cut(s) 167
Bst4CI ACNGT 1 cut(s) 260
Bst6I CTCTTC 1 cut(s) 400
BstACI GRCGYC 1 cut(s) 29
BstDEI CTNAG 2 cut(s) 128, 569
BstEII GGTNACC 1 cut(s) 647
BstF5I GGATG 1 cut(s) 292
BstKTI GATC 4 cut(s) 9, 115, 229, 331
BstMBI GATC 4 cut(s) 6, 112, 226, 328
BstMWI GCNNNNNNNGC 2 cut(s) 296, 372
BstNI CCWGG 1 cut(s) 167
BstNSI RCATGY 1 cut(s) 530
BstPI GGTNACC 1 cut(s) 647
BstSCI CCNGG 1 cut(s) 165
BstV1I GCAGC 3 cut(s) 283, 436, 510
BstX2I RGATCY 1 cut(s) 112
BstXI CCANNNNNNTGG 1 cut(s) 57
BstYI RGATCY 1 cut(s) 112
BsuRI GGCC 2 cut(s) 165, 195
BtrI CACGTC 1 cut(s) 520
BtsCI GGATG 1 cut(s) 292
Cfr13I GGNCC 2 cut(s) 163, 560
Csp6I GTAC 3 cut(s) 400, 614, 680
CviAII CATG 2 cut(s) 368, 527
CviJI RGCY 8 cut(s) 127, 165, 185, 195, 203, 296, 427, 461
CviKI_1 RGCY 8 cut(s) 127, 165, 185, 195, 203, 296, 427, 461
CviQI GTAC 3 cut(s) 400, 614, 680
DdeI CTNAG 2 cut(s) 128, 569
DpnI GATC 4 cut(s) 8, 114, 228, 330
DpnII GATC 4 cut(s) 6, 112, 226, 328
Eam1104I CTCTTC 1 cut(s) 400
EarI CTCTTC 1 cut(s) 400
Eco130I CCWWGG 1 cut(s) 291
Eco24I GRGCYC 1 cut(s) 205
Eco47I GGWCC 1 cut(s) 560
Eco91I GGTNACC 1 cut(s) 647
EcoO109I RGGNCCY 1 cut(s) 163
EcoO65I GGTNACC 1 cut(s) 647
EcoRII CCWGG 1 cut(s) 165
EcoT14I CCWWGG 1 cut(s) 291
EcoT22I ATGCAT 2 cut(s) 445, 451
EcoT38I GRGCYC 1 cut(s) 205
ErhI CCWWGG 1 cut(s) 291
FaeI CATG 2 cut(s) 371, 530
FaqI GGGAC 1 cut(s) 515
FatI CATG 2 cut(s) 367, 526
FauNDI CATATG 1 cut(s) 445
FbaI TGATCA 2 cut(s) 6, 328
Fnu4HI GCNGC 3 cut(s) 297, 425, 524
FokI GGATG 1 cut(s) 299
FriOI GRGCYC 1 cut(s) 205
Fsp4HI GCNGC 3 cut(s) 297, 425, 524
FspBI CTAG 2 cut(s) 237, 590
GluI GCNGC 3 cut(s) 297, 425, 524
HaeIII GGCC 2 cut(s) 165, 195
Hin1I GRCGYC 1 cut(s) 29
Hin1II CATG 2 cut(s) 371, 530
HinfI GANTC 4 cut(s) 14, 547, 582, 599
HphI GGTGA 2 cut(s) 16, 389
Hpy188I TCNGA 3 cut(s) 310, 328, 483
Hpy188III TCNNGA 2 cut(s) 70, 206
HpyAV CCTTC 3 cut(s) 63, 154, 637
HpyCH4III ACNGT 1 cut(s) 260
HpyCH4IV ACGT 4 cut(s) 29, 91, 333, 519
HpyCH4V TGCA 5 cut(s) 299, 359, 443, 449, 526
HpyF10VI GCNNNNNNNGC 2 cut(s) 296, 372
HpyF3I CTNAG 2 cut(s) 128, 569
HpySE526I ACGT 4 cut(s) 29, 91, 333, 519
Hsp92I GRCGYC 1 cut(s) 29
Hsp92II CATG 2 cut(s) 371, 530
Ksp22I TGATCA 2 cut(s) 6, 328
Kzo9I GATC 4 cut(s) 6, 112, 226, 328
LpnPI CCDG 7 cut(s) 152, 179, 281, 339, 416, 447, 543
Lsp1109I GCAGC 3 cut(s) 283, 436, 510
LweI GCATC 2 cut(s) 277, 458
MaeI CTAG 2 cut(s) 237, 590
MaeII ACGT 4 cut(s) 29, 91, 333, 519
MaeIII GTNAC 3 cut(s) 25, 377, 647
MalI GATC 4 cut(s) 8, 114, 228, 330
MboI GATC 4 cut(s) 6, 112, 226, 328
MboII GAAGA 4 cut(s) 109, 152, 387, 556
MflI RGATCY 1 cut(s) 112
MhlI GDGCHC 1 cut(s) 205
MluCI AATT 3 cut(s) 73, 485, 503
MlyI GAGTC 2 cut(s) 23, 608
MnlI CCTC 4 cut(s) 103, 130, 406, 521
Mph1103I ATGCAT 2 cut(s) 445, 451
MroXI GAANNNNTTC 1 cut(s) 65
MseI TTAA 2 cut(s) 506, 687
MspA1I CMGCKG 1 cut(s) 427
MspR9I CCNGG 1 cut(s) 167
MvaI CCWGG 1 cut(s) 167
MwoI GCNNNNNNNGC 2 cut(s) 296, 372
NdeI CATATG 1 cut(s) 445
NdeII GATC 4 cut(s) 6, 112, 226, 328
NlaIII CATG 2 cut(s) 371, 530
NmuCI GTSAC 2 cut(s) 25, 377
NsiI ATGCAT 2 cut(s) 445, 451
NspI RCATGY 1 cut(s) 530
PcsI WCGNNNNNNNCGW 1 cut(s) 417
PdmI GAANNNNTTC 1 cut(s) 65
PfeI GAWTC 2 cut(s) 547, 582
PflMI CCANNNNNTGG 1 cut(s) 223
PkrI GCNGC 3 cut(s) 298, 426, 525
PleI GAGTC 2 cut(s) 22, 607
PpsI GAGTC 2 cut(s) 22, 607
Psp6I CCWGG 1 cut(s) 165
PspEI GGTNACC 1 cut(s) 647
PspGI CCWGG 1 cut(s) 165
PspPI GGNCC 2 cut(s) 163, 560
PsuI RGATCY 1 cut(s) 112
PvuII CAGCTG 1 cut(s) 427
RsaI GTAC 3 cut(s) 401, 615, 681
RsaNI GTAC 3 cut(s) 400, 614, 680
SaqAI TTAA 2 cut(s) 506, 687
SatI GCNGC 3 cut(s) 297, 425, 524
Sau3AI GATC 4 cut(s) 6, 112, 226, 328
Sau96I GGNCC 2 cut(s) 163, 560
SchI GAGTC 2 cut(s) 23, 608
ScrFI CCNGG 1 cut(s) 167
SduI GDGCHC 1 cut(s) 205
SetI ASST 9 cut(s) 32, 55, 94, 270, 321, 336, 429, 522, 654
SfaNI GCATC 2 cut(s) 277, 458
SinI GGWCC 1 cut(s) 560
SmlI CTYRAG 3 cut(s) 80, 107, 204
SmoI CTYRAG 3 cut(s) 80, 107, 204
SpeI ACTAGT 1 cut(s) 589
Sse9I AATT 3 cut(s) 73, 485, 503
SsiI CCGC 1 cut(s) 375
SspMI CTAG 2 cut(s) 237, 590
StyD4I CCNGG 1 cut(s) 165
StyI CCWWGG 1 cut(s) 291
TaaI ACNGT 1 cut(s) 260
TaiI ACGT 4 cut(s) 32, 94, 336, 522
TaqI TCGA 2 cut(s) 220, 411
TasI AATT 3 cut(s) 73, 485, 503
TatI WGTACW 2 cut(s) 613, 679
TfiI GAWTC 2 cut(s) 547, 582
Tru1I TTAA 2 cut(s) 506, 687
Tru9I TTAA 2 cut(s) 506, 687
TseFI GTSAC 2 cut(s) 25, 377
TseI GCWGC 3 cut(s) 296, 424, 523
Tsp45I GTSAC 2 cut(s) 25, 377
TspDTI ATGAA 2 cut(s) 710, 714
Van91I CCANNNNNTGG 1 cut(s) 223
VpaK11BI GGWCC 1 cut(s) 560
XapI RAATTY 1 cut(s) 485
XceI RCATGY 1 cut(s) 530
XmnI GAANNNNTTC 1 cut(s) 65
XspI CTAG 2 cut(s) 237, 590
ZraI GACGTC 1 cut(s) 30
Zsp2I ATGCAT 2 cut(s) 445, 451
Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.