MD16G1029500.v1.1

gag-polypeptide of LTR copia-type

Design Primers CRISPR Design

Basic Information

Type: gene
Biological Identity
malus_domestica
Chr16
OG0002557
Physical Location & Seq
Forward (+)
2108234 .. 2109822
1589 bp
Loading structure...
UTR
Exon/CDS
Intron
MD16G1029500.v1.1.491

Sequence Viewer

Length: 342 bp
ATGGGCGACAAGCCAGACTTGAGGTCAACCATTCAAGGCACGATTGTTCATTCAAAATGGAAAAACCCCAACCATCCGCTTTATCTCCACCACTCAGACCAACCTGGTGCAATCATCGTGCCACAACCATTAGTGGAAGACAACAACAACATATGGGTTCAATCCATGAATATGGCCTTAACGGTCAAGAACAAACTCGGACTTGGTCAAGACATGGCTGTTAGGTTCCATGTTGAAAGAGATTTCAGGGAGCGTCATCAACTACAAGGATGCTCGACAGATGTGCACCGATTTGCTGGAAAGGTTCTCACATATGAATATGGTTCAATTATTCCATGTTGA
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
No domains found.

Protein Analysis

114

Amino Acids

12.89

Weight (kDa)

7.88

Isoelectric Point (pI)

30.51

Instability Index
Protein Domains (Pfam)
Domain Name Pfam ID Position E-value Description
Retrotran_gag_3 PF14244 30 - 67 2.7e-09 gag-polypeptide of LTR copia-type
Hydrophobicity Profile (Kyte-Doolittle)
AI Structure Prediction Report
Calculating structure properties...

Genomic Context

Gene Family Tree

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Publication-ready
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Restriction Enzyme Sites

1 / 10
Enzyme Recognition Site Cut Count Positions (bp)
AciI CCGC 1 cut(s) 77
AgsI TTSAA 5 cut(s) 35, 54, 161, 236, 327
AhdI GACNNNNNGTC 1 cut(s) 22
AjnI CCWGG 1 cut(s) 103
Alw21I GWGCWC 1 cut(s) 288
Alw44I GTGCAC 1 cut(s) 284
AoxI GGCC 1 cut(s) 174
ApaLI GTGCAC 1 cut(s) 284
BaeGI GKGCMC 1 cut(s) 288
BbsI GAAGAC 1 cut(s) 144
Bbv12I GWGCWC 1 cut(s) 288
BccI CCATC 1 cut(s) 81
BcgI CGANNNNNNTGC 2 cut(s) 265, 299
BciT130I CCWGG 1 cut(s) 105
Bme1390I CCNGG 1 cut(s) 105
BmeRI GACNNNNNGTC 1 cut(s) 22
BmiI GGNNCC 1 cut(s) 227
BmrFI CCNGG 1 cut(s) 105
BmsI GCATC 1 cut(s) 260
BpiI GAAGAC 1 cut(s) 144
BpuEI CTTGAG 1 cut(s) 40
BseBI CCWGG 1 cut(s) 105
BseGI GGATG 2 cut(s) 73, 275
BseMII CTCAG 1 cut(s) 108
BseSI GKGCMC 1 cut(s) 288
BshFI GGCC 1 cut(s) 176
BsiHKAI GWGCWC 1 cut(s) 288
BsnI GGCC 1 cut(s) 176
Bsp1286I GDGCHC 1 cut(s) 288
BspACI CCGC 1 cut(s) 77
BspANI GGCC 1 cut(s) 176
BspCNI CTCAG 1 cut(s) 107
BspLI GGNNCC 1 cut(s) 227
Bst2UI CCWGG 1 cut(s) 105
Bst4CI ACNGT 1 cut(s) 184
BstDEI CTNAG 1 cut(s) 94
BstF5I GGATG 2 cut(s) 73, 275
BstNI CCWGG 1 cut(s) 105
BstSCI CCNGG 1 cut(s) 103
BstSLI GKGCMC 1 cut(s) 288
BstV2I GAAGAC 1 cut(s) 144
BstXI CCANNNNNNTGG 1 cut(s) 172
BsuRI GGCC 1 cut(s) 176
BtsCI GGATG 2 cut(s) 73, 275
CseI GACGC 1 cut(s) 242
CsiI ACCWGGT 1 cut(s) 103
CviAII CATG 4 cut(s) 166, 214, 230, 336
CviJI RGCY 3 cut(s) 13, 176, 218
CviKI_1 RGCY 3 cut(s) 13, 176, 218
DdeI CTNAG 1 cut(s) 94
DriI GACNNNNNGTC 1 cut(s) 22
Eam1105I GACNNNNNGTC 1 cut(s) 22
EcoRII CCWGG 1 cut(s) 103
FaeI CATG 4 cut(s) 169, 217, 233, 339
FalI AAGNNNNNCTT 1 cut(s) 34
FatI CATG 4 cut(s) 165, 213, 229, 335
FauNDI CATATG 2 cut(s) 152, 313
FokI GGATG 2 cut(s) 60, 282
HaeIII GGCC 1 cut(s) 176
HgaI GACGC 1 cut(s) 242
Hin1II CATG 4 cut(s) 169, 217, 233, 339
HincII GTYRAC 1 cut(s) 27
HindII GTYRAC 1 cut(s) 27
Hpy166II GTNNAC 2 cut(s) 27, 286
Hpy188I TCNGA 2 cut(s) 97, 200
Hpy188III TCNNGA 2 cut(s) 187, 209
Hpy8I GTNNAC 2 cut(s) 27, 286
HpyCH4III ACNGT 1 cut(s) 184
HpyCH4V TGCA 2 cut(s) 110, 286
HpyF3I CTNAG 1 cut(s) 94
Hsp92II CATG 4 cut(s) 169, 217, 233, 339
LmnI GCTCC 1 cut(s) 250
LpnPI CCDG 5 cut(s) 27, 90, 117, 232, 282
LweI GCATC 1 cut(s) 260
MabI ACCWGGT 1 cut(s) 103
MboII GAAGA 1 cut(s) 149
MhlI GDGCHC 1 cut(s) 288
MluCI AATT 1 cut(s) 327
MnlI CCTC 1 cut(s) 15
MseI TTAA 1 cut(s) 179
MslI CAYNNNNRTG 1 cut(s) 170
MspR9I CCNGG 1 cut(s) 105
MvaI CCWGG 1 cut(s) 105
NdeI CATATG 2 cut(s) 152, 313
NlaIII CATG 4 cut(s) 169, 217, 233, 339
NlaIV GGNNCC 1 cut(s) 227
PflFI GACNNNGTC 1 cut(s) 204
Psp6I CCWGG 1 cut(s) 103
PspGI CCWGG 1 cut(s) 103
PspN4I GGNNCC 1 cut(s) 227
PsyI GACNNNGTC 1 cut(s) 204
RseI CAYNNNNRTG 1 cut(s) 170
SaqAI TTAA 1 cut(s) 179
ScrFI CCNGG 1 cut(s) 105
SduI GDGCHC 1 cut(s) 288
SetI ASST 4 cut(s) 26, 106, 227, 306
SexAI ACCWGGT 1 cut(s) 103
SfaNI GCATC 1 cut(s) 260
SmiMI CAYNNNNRTG 1 cut(s) 170
SmlI CTYRAG 1 cut(s) 19
SmoI CTYRAG 1 cut(s) 19
Sse9I AATT 1 cut(s) 327
SsiI CCGC 1 cut(s) 77
StyD4I CCNGG 1 cut(s) 103
TaaI ACNGT 1 cut(s) 184
TaqI TCGA 1 cut(s) 275
TasI AATT 1 cut(s) 327
Tru1I TTAA 1 cut(s) 179
Tru9I TTAA 1 cut(s) 179
TspDTI ATGAA 3 cut(s) 38, 182, 330
Tth111I GACNNNGTC 1 cut(s) 204
VneI GTGCAC 1 cut(s) 284
Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.