pycom05g09230

gag-polypeptide of LTR copia-type

Design Primers CRISPR Design

Basic Information

Type: gene
Biological Identity
pyrus_communis
Chr5
OG0000258
Physical Location & Seq
Reverse (-)
12336554 .. 12337104
551 bp
Loading structure...
UTR
Exon/CDS
Intron
pycom05g09230.1

Sequence Viewer

Length: 420 bp
ATGGATCAATCAAATGTTGGTGTTATCAAGCAACACGTTGAGAAACCTGAGAAGTTCAAGGGAGTTGATTTCAAACGTTGGCAACAGAAGATGTTGAACTACATTCTGAATGCTTTAGATGACTGTTTGTATGATGTTTATTCATCATATAAGACAGCGAAAGAACTGTGGGAGTCTCTGGACAAGAAGTATAAGTCTGAAGTGGCTAGTTCCAAGAAGTTTCTGATTGAAAAATTCCTGAATTACAAGATGAGTGACAACAAATTTGTTGTCAAGCAAGTTGAAGAACTCCAAGTGATCATTCATGAGTTAGGTGAAGAGAATCTTGGTCTGAAAGAATGTTTTGTGGTTGGCTCTATTATAGAGAAACTGCCTTCGAATTGGAAGGACTTTAATATTTATTTGAAGTATCTAACTTAA
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

140

Amino Acids

16.47

Weight (kDa)

7.67

Isoelectric Point (pI)

57.33

Instability Index
Protein Domains (Pfam)
Domain Name Pfam ID Position E-value Description
Retrotran_gag_2 PF14223 20 - 131 7.8e-19 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)
AclI AACGTT 1 cut(s) 76
AclWI GGATC 1 cut(s) 12
AcsI RAATTY 2 cut(s) 233, 263
AcuI CTGAAG 1 cut(s) 219
AflIII ACRYGT 1 cut(s) 34
AgsI TTSAA 6 cut(s) 58, 73, 97, 230, 284, 406
AjuI GAANNNNNNNTTGG 4 cut(s) 285, 309, 317, 341
Alw26I GTCTC 1 cut(s) 180
AlwI GGATC 1 cut(s) 12
ApoI RAATTY 2 cut(s) 233, 263
ArsI GACNNNNNNTTYG 4 cut(s) 248, 255, 280, 287
AsuHPI GGTGA 1 cut(s) 326
AsuII TTCGAA 1 cut(s) 377
BclI TGATCA 1 cut(s) 297
BcoDI GTCTC 1 cut(s) 180
BfaI CTAG 1 cut(s) 207
Bpu14I TTCGAA 1 cut(s) 377
BseMII CTCAG 1 cut(s) 39
BsmAI GTCTC 1 cut(s) 180
BsmI GAATGC 1 cut(s) 115
Bsp119I TTCGAA 1 cut(s) 377
Bsp143I GATC 2 cut(s) 4, 297
BspCNI CTCAG 1 cut(s) 40
BspHI TCATGA 1 cut(s) 304
BspPI GGATC 1 cut(s) 12
BspT104I TTCGAA 1 cut(s) 377
BssMI GATC 2 cut(s) 4, 297
Bst4CI ACNGT 2 cut(s) 125, 168
Bst6I CTCTTC 1 cut(s) 312
BstBI TTCGAA 1 cut(s) 377
BstDEI CTNAG 1 cut(s) 48
BstKTI GATC 2 cut(s) 7, 300
BstMAI GTCTC 1 cut(s) 180
BstMBI GATC 2 cut(s) 4, 297
CciI TCATGA 1 cut(s) 304
CviAII CATG 1 cut(s) 305
CviJI RGCY 2 cut(s) 206, 354
CviKI_1 RGCY 2 cut(s) 206, 354
DdeI CTNAG 1 cut(s) 48
DpnI GATC 2 cut(s) 6, 299
DpnII GATC 2 cut(s) 4, 297
Eam1104I CTCTTC 1 cut(s) 312
EarI CTCTTC 1 cut(s) 312
Eco57I CTGAAG 1 cut(s) 219
FaeI CATG 1 cut(s) 308
FaiI YATR 6 cut(s) 132, 148, 150, 192, 306, 362
FalI AAGNNNNNCTT 2 cut(s) 309, 341
FatI CATG 1 cut(s) 304
FbaI TGATCA 1 cut(s) 297
FspBI CTAG 1 cut(s) 207
Hin1II CATG 1 cut(s) 308
HinfI GANTC 2 cut(s) 173, 322
HphI GGTGA 1 cut(s) 326
Hpy188I TCNGA 4 cut(s) 108, 199, 225, 333
Hpy188III TCNNGA 3 cut(s) 179, 238, 305
HpyAV CCTTC 2 cut(s) 379, 384
HpyCH4III ACNGT 2 cut(s) 125, 168
HpyCH4IV ACGT 2 cut(s) 36, 76
HpyF3I CTNAG 1 cut(s) 48
HpySE526I ACGT 2 cut(s) 36, 76
Hsp92II CATG 1 cut(s) 308
Ksp22I TGATCA 1 cut(s) 297
Kzo9I GATC 2 cut(s) 4, 297
LpnPI CCDG 3 cut(s) 60, 164, 251
MaeI CTAG 1 cut(s) 207
MaeII ACGT 2 cut(s) 36, 76
MaeIII GTNAC 1 cut(s) 254
MalI GATC 2 cut(s) 6, 299
MboI GATC 2 cut(s) 4, 297
MboII GAAGA 3 cut(s) 100, 296, 329
MluCI AATT 4 cut(s) 233, 241, 263, 379
MlyI GAGTC 1 cut(s) 182
MseI TTAA 2 cut(s) 393, 418
Mva1269I GAATGC 1 cut(s) 115
NdeII GATC 2 cut(s) 4, 297
NlaIII CATG 1 cut(s) 308
NmuCI GTSAC 1 cut(s) 254
NspV TTCGAA 1 cut(s) 377
PagI TCATGA 1 cut(s) 304
PctI GAATGC 1 cut(s) 115
PfeI GAWTC 1 cut(s) 322
PleI GAGTC 1 cut(s) 181
PpsI GAGTC 1 cut(s) 181
Psp1406I AACGTT 1 cut(s) 76
SaqAI TTAA 2 cut(s) 393, 418
Sau3AI GATC 2 cut(s) 4, 297
SchI GAGTC 1 cut(s) 182
SetI ASST 4 cut(s) 39, 49, 79, 316
SfuI TTCGAA 1 cut(s) 377
Sse9I AATT 4 cut(s) 233, 241, 263, 379
SspI AATATT 1 cut(s) 397
SspMI CTAG 1 cut(s) 207
TaaI ACNGT 2 cut(s) 125, 168
TaiI ACGT 2 cut(s) 39, 79
TaqI TCGA 1 cut(s) 377
TasI AATT 4 cut(s) 233, 241, 263, 379
TfiI GAWTC 1 cut(s) 322
Tru1I TTAA 2 cut(s) 393, 418
Tru9I TTAA 2 cut(s) 393, 418
TseFI GTSAC 1 cut(s) 254
Tsp45I GTSAC 1 cut(s) 254
TspDTI ATGAA 2 cut(s) 132, 293
XapI RAATTY 2 cut(s) 233, 263
XspI CTAG 1 cut(s) 207
Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.