pycom13g24110

gag-polypeptide of LTR copia-type

Design Primers CRISPR Design

Basic Information

Type: gene
Biological Identity
pyrus_communis
Chr13
OG0000562
Physical Location & Seq
Forward (+)
21352598 .. 21353612
1015 bp
Loading structure...
UTR
Exon/CDS
Intron
pycom13g24110.1

Sequence Viewer

Length: 708 bp
ATGAATATATGTGTGTCTCTCTATATATATATATATATATATTGTAGATGTGATGTAAGAGCCGACCTCGGCCGGCATGTGTTGAATATGAAGAAACAAAATTTTACTAGCCAGATATTAATTAATATAATACTTCATCTTCTCCCATACCAATTTGATAGTTACTTGAGTATTTGTGGGATCGTCCGTCAATATAAGATCAGCTATCATGTTACGCATTGTTTAACCAGAATAGCTTTGAAATTAACTCTTCTATTAGAAAAAGTGTACCATGTGGAGTGGGCTGTTTTCTGCCTTCTTCTACATTTCAAGGGATGTGTATCTAGTAGTTGTTTACTTTTGGTTGTTAGCTTTTTAGGCTTAAATCAAGGAGGGATAGGGAGTTTGTTCCTTCTCTTCGACATACATATATTGGTTAGGTCTTATGGTATCAGAGCAATGACCCTAACCGGCCTGTCTATGTGTACTCTCTTGAGAGCTTTTTTGAGCTTTTTTTGTTCTTCAAACATGGATGAAGAAAGTTCAGTACATGGCGAAGGAGATAGCTTTCATGCTGCTCCATCATCACCTCGCTCAAACGTTGATGAGTTTAACTATCTTCCTTGGGAGAAAGCAGTCACTTTTGCTTTGGGAGGACGATCAAAGCTTGGCTATGTCAATGGTGCTATTCCAATGCCTGAGAAGTCCTCACTAGATTACAATGCTTAG
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 Retrotran_gag_3

Protein Analysis

236

Amino Acids

26.52

Weight (kDa)

8.3

Isoelectric Point (pI)

40.58

Instability Index
Protein Domains (Pfam)
Domain Name Pfam ID Position E-value Description
Retrotran_gag_3 PF14244 194 - 226 2.3e-08 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: OG0000562)

Species Orthologous Gene IDs
fragaria_vesca FvH4_2g17331 FvH4_3g36541
malus_domestica MD07G1078600.v1.1 MD10G1237700.v1.1 MD10G1333400.v1.1 MD11G1102200.v1.1 MD13G1138400.v1.1 MD14G1033400.v1.1 MD15G1053300.v1.1
prunus_persica Prupe.1G465400_v2.0.a1 Prupe.3G136000_v2.0.a1 Prupe.7G119900_v2.0.a1
pyrus_communis pycom01g04630 pycom03g13050 pycom04g21190 pycom05g04910 pycom05g05510 pycom08g15850 pycom09g15040 pycom1094g00010 pycom11g02000 pycom12g06150 pycom13g24110 pycom13g24910 pycom14g00050 pycom15g21970 pycom15g35170 pycom15g35180 pycom16g14620 pycom16g14630 pycom808g00110
rosa_chinensis RchiOBHm_Chr1g0322851 RchiOBHm_Chr1g0365941 RchiOBHm_Chr3g0453341 RchiOBHm_Chr4g0388371 RchiOBHm_Chr4g0394021 RchiOBHm_Chr5g0013181 RchiOBHm_Chr6g0261721 RchiOBHm_Chr6g0261731 RchiOBHm_Chr7g0188861 RchiOBHm_Chr7g0192331 RchiOBHm_Chr7g0231721
rosa_multiflora Rmu_sc0002521.1_g000006 Rmu_sc0003255.1_g000026 Rmu_sc0004191.1_g000036 Rmu_sc0004414.1_g000014 Rmu_sc0005670.1_g000006 Rmu_sc0006081.1_g000001 Rmu_sc0007215.1_g000004 Rmu_sc0010088.1_g000010 Rmu_sc0020285.1_g000003 Rmu_sc0026896.1_g000002 Rmu_ssc0000019.1_g000029
rosa_roxburghii Rroxscaffold_3G00224890 Rroxscaffold_6G00400640 Rroxscaffold_7G00176590 Rroxscaffold_7G00189230
rosa_samantha Rh4BG046700
rosa_wichuraiana Rw1G012690 Rw1G031370 Rw2G042180 Rw2G043670 Rw2G046240 Rw2G049890 Rw2G050760 Rw2G051280 Rw2G053590 Rw3G007590 Rw3G026850 Rw4G001540 Rw4G009760 Rw4G019270 Rw5G000720 Rw5G005620 Rw5G041560 Rw6G007370 Rw6G009830 Rw6G015360 Rw6G031160 Rw7G004930 Rw7G011010 Rw7G024230 Rw7G028240

Restriction Enzyme Sites

1 / 10
Enzyme Recognition Site Cut Count Positions (bp)
AclI AACGTT 1 cut(s) 579
AclWI GGATC 1 cut(s) 188
AcoI YGGCCR 1 cut(s) 70
AcsI RAATTY 1 cut(s) 100
AfaI GTAC 3 cut(s) 269, 466, 528
AgsI TTSAA 4 cut(s) 85, 241, 310, 504
AluBI AGCT 7 cut(s) 204, 236, 351, 479, 489, 546, 646
AluI AGCT 7 cut(s) 204, 236, 351, 479, 489, 546, 646
Alw26I GTCTC 1 cut(s) 21
AlwI GGATC 1 cut(s) 188
AoxI GGCC 2 cut(s) 70, 451
ApeKI GCWGC 1 cut(s) 554
ApoI RAATTY 1 cut(s) 100
AseI ATTAAT 2 cut(s) 119, 123
AsuHPI GGTGA 1 cut(s) 558
BbvI GCAGC 1 cut(s) 541
BccI CCATC 1 cut(s) 568
BcoDI GTCTC 1 cut(s) 21
BfaI CTAG 3 cut(s) 108, 324, 692
BisI GCNGC 1 cut(s) 555
BlsI GCNGC 1 cut(s) 556
BplI GAGNNNNNCTC 4 cut(s) 51, 83, 671, 703
BpuEI CTTGAG 2 cut(s) 187, 493
BsaBI GATNNNNATC 1 cut(s) 319
BsaJI CCNNGG 2 cut(s) 67, 602
Bse118I RCCGGY 2 cut(s) 72, 449
Bse3DI GCAATG 1 cut(s) 444
Bse8I GATNNNNATC 1 cut(s) 319
BseDI CCNNGG 2 cut(s) 67, 602
BseGI GGATG 2 cut(s) 320, 517
BseJI GATNNNNATC 1 cut(s) 319
BseMI GCAATG 1 cut(s) 444
BseMII CTCAG 1 cut(s) 669
BseX3I CGGCCG 1 cut(s) 70
BseXI GCAGC 1 cut(s) 541
Bsh1285I CGRYCG 1 cut(s) 73
BshFI GGCC 2 cut(s) 72, 453
BsiEI CGRYCG 1 cut(s) 73
BsiSI CCGG 2 cut(s) 73, 450
BsmAI GTCTC 1 cut(s) 21
BsnI GGCC 2 cut(s) 72, 453
Bsp143I GATC 3 cut(s) 180, 198, 638
BspANI GGCC 2 cut(s) 72, 453
BspCNI CTCAG 1 cut(s) 670
BspPI GGATC 1 cut(s) 188
BsrDI GCAATG 1 cut(s) 444
BsrFI RCCGGY 2 cut(s) 72, 449
BssAI RCCGGY 2 cut(s) 72, 449
BssECI CCNNGG 2 cut(s) 67, 602
BssMI GATC 3 cut(s) 180, 198, 638
BssT1I CCWWGG 1 cut(s) 602
Bst6I CTCTTC 2 cut(s) 255, 401
BstC8I GCNNGC 1 cut(s) 74
BstDEI CTNAG 2 cut(s) 678, 705
BstF5I GGATG 2 cut(s) 320, 517
BstKTI GATC 3 cut(s) 183, 201, 641
BstMAI GTCTC 1 cut(s) 21
BstMBI GATC 3 cut(s) 180, 198, 638
BstMCI CGRYCG 1 cut(s) 73
BstMWI GCNNNNNNNGC 1 cut(s) 357
BstNSI RCATGY 1 cut(s) 80
BstV1I GCAGC 1 cut(s) 541
BstZI CGGCCG 1 cut(s) 70
BsuRI GGCC 2 cut(s) 72, 453
BtsCI GGATG 2 cut(s) 320, 517
Cac8I GCNNGC 1 cut(s) 74
Cfr10I RCCGGY 2 cut(s) 72, 449
Csp6I GTAC 3 cut(s) 268, 465, 527
CviAII CATG 6 cut(s) 77, 209, 272, 508, 530, 551
CviQI GTAC 3 cut(s) 268, 465, 527
DdeI CTNAG 2 cut(s) 678, 705
DpnI GATC 3 cut(s) 182, 200, 640
DpnII GATC 3 cut(s) 180, 198, 638
EaeI YGGCCR 1 cut(s) 70
EagI CGGCCG 1 cut(s) 70
Eam1104I CTCTTC 2 cut(s) 255, 401
EarI CTCTTC 2 cut(s) 255, 401
EclXI CGGCCG 1 cut(s) 70
Eco130I CCWWGG 1 cut(s) 602
Eco52I CGGCCG 1 cut(s) 70
EcoT14I CCWWGG 1 cut(s) 602
ErhI CCWWGG 1 cut(s) 602
FaeI CATG 6 cut(s) 80, 212, 275, 511, 533, 554
FatI CATG 6 cut(s) 76, 208, 271, 507, 529, 550
Fnu4HI GCNGC 1 cut(s) 555
FokI GGATG 2 cut(s) 327, 524
Fsp4HI GCNGC 1 cut(s) 555
FspBI CTAG 3 cut(s) 108, 324, 692
GluI GCNGC 1 cut(s) 555
HaeIII GGCC 2 cut(s) 72, 453
HapII CCGG 2 cut(s) 73, 450
Hin1II CATG 6 cut(s) 80, 212, 275, 511, 533, 554
HindIII AAGCTT 1 cut(s) 644
HpaII CCGG 2 cut(s) 73, 450
HphI GGTGA 1 cut(s) 558
Hpy166II GTNNAC 3 cut(s) 268, 335, 465
Hpy188I TCNGA 1 cut(s) 434
Hpy188III TCNNGA 1 cut(s) 472
Hpy8I GTNNAC 3 cut(s) 268, 335, 465
HpyAV CCTTC 3 cut(s) 305, 401, 530
HpyCH4IV ACGT 1 cut(s) 579
HpyF10VI GCNNNNNNNGC 1 cut(s) 357
HpyF3I CTNAG 2 cut(s) 678, 705
HpySE526I ACGT 1 cut(s) 579
Hsp92II CATG 6 cut(s) 80, 212, 275, 511, 533, 554
KroI GCCGGC 1 cut(s) 72
KroNI GCCGGC 1 cut(s) 74
Kzo9I GATC 3 cut(s) 180, 198, 638
LmnI GCTCC 1 cut(s) 562
LpnPI CCDG 6 cut(s) 86, 125, 241, 463, 467, 690
Lsp1109I GCAGC 1 cut(s) 541
MaeI CTAG 3 cut(s) 108, 324, 692
MaeII ACGT 1 cut(s) 579
MaeIII GTNAC 3 cut(s) 161, 211, 616
MalI GATC 3 cut(s) 182, 200, 640
MboI GATC 3 cut(s) 180, 198, 638
MboII GAAGA 8 cut(s) 103, 131, 242, 290, 388, 492, 527, 590
MluCI AATT 4 cut(s) 100, 120, 152, 242
MnlI CCTC 5 cut(s) 77, 365, 579, 626, 697
MroNI GCCGGC 1 cut(s) 72
MseI TTAA 6 cut(s) 119, 123, 224, 245, 362, 591
MspI CCGG 2 cut(s) 73, 450
MwoI GCNNNNNNNGC 1 cut(s) 357
NaeI GCCGGC 1 cut(s) 74
NdeII GATC 3 cut(s) 180, 198, 638
NgoMIV GCCGGC 1 cut(s) 72
NlaIII CATG 6 cut(s) 80, 212, 275, 511, 533, 554
NmeAIII GCCGAG 1 cut(s) 48
NmuCI GTSAC 1 cut(s) 616
NspI RCATGY 1 cut(s) 80
PacI TTAATTAA 1 cut(s) 123
PdiI GCCGGC 1 cut(s) 74
PkrI GCNGC 1 cut(s) 556
PshBI ATTAAT 2 cut(s) 119, 123
Psp1406I AACGTT 1 cut(s) 579
RsaI GTAC 3 cut(s) 269, 466, 528
RsaNI GTAC 3 cut(s) 268, 465, 527
SaqAI TTAA 6 cut(s) 119, 123, 224, 245, 362, 591
SatI GCNGC 1 cut(s) 555
Sau3AI GATC 3 cut(s) 180, 198, 638
SmlI CTYRAG 2 cut(s) 166, 472
SmoI CTYRAG 2 cut(s) 166, 472
Sse9I AATT 4 cut(s) 100, 120, 152, 242
SspMI CTAG 3 cut(s) 108, 324, 692
StyI CCWWGG 1 cut(s) 602
TaiI ACGT 1 cut(s) 582
TaqI TCGA 1 cut(s) 399
TasI AATT 4 cut(s) 100, 120, 152, 242
TatI WGTACW 2 cut(s) 464, 526
Tru1I TTAA 6 cut(s) 119, 123, 224, 245, 362, 591
Tru9I TTAA 6 cut(s) 119, 123, 224, 245, 362, 591
TseFI GTSAC 1 cut(s) 616
TseI GCWGC 1 cut(s) 554
Tsp45I GTSAC 1 cut(s) 616
TspDTI ATGAA 5 cut(s) 17, 104, 125, 528, 539
TspGWI ACGGA 1 cut(s) 176
VspI ATTAAT 2 cut(s) 119, 123
XapI RAATTY 1 cut(s) 100
XceI RCATGY 1 cut(s) 80
XspI CTAG 3 cut(s) 108, 324, 692
Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.