MD03G1006400.v1.1

gag-polypeptide of LTR copia-type

Design Primers CRISPR Design

Basic Information

Type: gene
Biological Identity
malus_domestica
Chr03
OG0004021
Physical Location & Seq
Reverse (-)
526896 .. 534523
7628 bp
Loading structure...
UTR
Exon/CDS
Intron
MD03G1006400.v1.1.491

Sequence Viewer

Length: 528 bp
ATGGCCAAAACCATCTCCGACCTCTCAGATATCACTGACTTTGTTATAAACAAAGGCAATGGAGTAAAGGGTCTCTCAGAATTGGGCCTCAAAAGCATCCCCAACCAATACATCCAACCCCTTGAAGAAAGAATCAGTACTATGATAATGTCCCAAGACTCCATTCCTATCATTGACATGTCGAATTGGAACGACCCGAAAGTGGTAGAATCTATTTGCAGTGCAGCAGAGAAGTTGGGGTTCTTTCTACTAGTGAATCACGGGGTGCCGGTTGAAGTGCTTGAGAATGTGAAGGAAGCAACTCATCGCTTCTTTGTATTGCCAGCTGAGGAGAAGAGTAAGTACTCGAAAGAGCATTCGCCTTCGAAAAATGTCCAATATGGCACGAGCTTTAATCCTCAAGCAGAGAAGGCTCTGGAGTGGAAGGATTTCCTTGGTCTCTATGCTTATGAGGACAAGATGAGGCCTCTGCGTTTTGGCCTCCTGTGTGCAGTGTCAAGAACATGCTGGTGTTGTGGCCTATTTTAG
Functional Annotation
Gene Ontology
Molecular Function
Biological Process
Cellular Component
No ontology terms assigned.
KEGG Pathways
Metabolic & Signaling
ko00940 ko01110 map00940 map01110
Pfam Domains
Protein Families
Retrotran_gag_2

Protein Analysis

176

Amino Acids

19.71

Weight (kDa)

5.66

Isoelectric Point (pI)

34.6

Instability Index
Protein Domains (Pfam)
Domain Name Pfam ID Position E-value Description
DIOX_N PF14226 55 - 152 3.1e-25 non-haem dioxygenase in morphine synthesis N-terminal
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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Restriction Enzyme Sites

1 / 10
Enzyme Recognition Site Cut Count Positions (bp)
AanI TTATAA 1 cut(s) 47
AccB1I GGYRCC 1 cut(s) 265
AcoI YGGCCR 1 cut(s) 3
AdeI CACNNNGTG 1 cut(s) 265
AfaI GTAC 2 cut(s) 139, 344
AfiI CCNNNNNNNGG 1 cut(s) 202
AflIII ACRYGT 1 cut(s) 177
AgsI TTSAA 2 cut(s) 125, 275
AhlI ACTAGT 1 cut(s) 250
AjuI GAANNNNNNNTTGG 2 cut(s) 147, 179
AluBI AGCT 2 cut(s) 326, 390
AluI AGCT 2 cut(s) 326, 390
Alw26I GTCTC 2 cut(s) 77, 443
AoxI GGCC 5 cut(s) 3, 85, 464, 478, 517
ApeKI GCWGC 1 cut(s) 224
Asp700I GAANNNNTTC 1 cut(s) 428
AspS9I GGNCC 1 cut(s) 85
AsuII TTCGAA 1 cut(s) 365
BalI TGGCCA 1 cut(s) 5
BanI GGYRCC 1 cut(s) 265
BarI GAAGNNNNNNTAC 2 cut(s) 326, 358
BauI CACGAG 1 cut(s) 385
BbvCI CCTCAGC 1 cut(s) 327
BbvI GCAGC 1 cut(s) 236
BccI CCATC 1 cut(s) 20
BcoDI GTCTC 2 cut(s) 77, 443
BcuI ACTAGT 1 cut(s) 250
BfaI CTAG 1 cut(s) 251
BisI GCNGC 1 cut(s) 225
BlsI GCNGC 1 cut(s) 226
BmcAI AGTACT 2 cut(s) 139, 344
BmgT120I GGNCC 1 cut(s) 85
BmiI GGNNCC 1 cut(s) 267
BmsI GCATC 1 cut(s) 105
BpmI CTGGAG 1 cut(s) 437
Bpu10I CCTNAGC 1 cut(s) 327
Bpu14I TTCGAA 1 cut(s) 365
BpuEI CTTGAG 2 cut(s) 302, 384
BsaI GGTCTC 2 cut(s) 77, 443
BsaJI CCNNGG 1 cut(s) 433
Bsc4I CCNNNNNNNGG 1 cut(s) 202
Bse118I RCCGGY 1 cut(s) 268
Bse3DI GCAATG 1 cut(s) 64
BseDI CCNNGG 1 cut(s) 433
BseGI GGATG 2 cut(s) 96, 111
BseLI CCNNNNNNNGG 1 cut(s) 202
BseMI GCAATG 1 cut(s) 64
BseMII CTCAG 3 cut(s) 39, 90, 318
BseRI GAGGAG 1 cut(s) 344
BseXI GCAGC 1 cut(s) 236
BsgI GTGCAG 2 cut(s) 243, 510
BshFI GGCC 5 cut(s) 5, 87, 466, 480, 519
BshNI GGYRCC 1 cut(s) 265
BsiSI CCGG 1 cut(s) 269
BslFI GGGAC 1 cut(s) 136
BslI CCNNNNNNNGG 1 cut(s) 202
BsmAI GTCTC 2 cut(s) 77, 443
BsmFI GGGAC 1 cut(s) 136
BsmI GAATGC 1 cut(s) 355
BsnI GGCC 5 cut(s) 5, 87, 466, 480, 519
Bso31I GGTCTC 2 cut(s) 77, 443
Bsp119I TTCGAA 1 cut(s) 365
BspANI GGCC 5 cut(s) 5, 87, 466, 480, 519
BspCNI CTCAG 3 cut(s) 38, 89, 319
BspLI GGNNCC 1 cut(s) 267
BspT104I TTCGAA 1 cut(s) 365
BspT107I GGYRCC 1 cut(s) 265
BspTNI GGTCTC 2 cut(s) 77, 443
BsrDI GCAATG 1 cut(s) 64
BsrFI RCCGGY 1 cut(s) 268
BssAI RCCGGY 1 cut(s) 268
BssECI CCNNGG 1 cut(s) 433
BssSI CACGAG 1 cut(s) 385
BssT1I CCWWGG 1 cut(s) 433
Bst2BI CACGAG 1 cut(s) 385
Bst6I CTCTTC 1 cut(s) 329
BstBI TTCGAA 1 cut(s) 365
BstC8I GCNNGC 1 cut(s) 324
BstDEI CTNAG 3 cut(s) 25, 76, 327
BstF5I GGATG 2 cut(s) 96, 111
BstMAI GTCTC 2 cut(s) 77, 443
BstMWI GCNNNNNNNGC 2 cut(s) 93, 410
BstNSI RCATGY 2 cut(s) 181, 507
BstV1I GCAGC 1 cut(s) 236
BsuRI GGCC 5 cut(s) 5, 87, 466, 480, 519
BtgZI GCGATG 1 cut(s) 290
BtsCI GGATG 2 cut(s) 96, 111
BtsI GCAGTG 2 cut(s) 226, 498
BtsIMutI CAGTG 3 cut(s) 33, 226, 498
Cac8I GCNNGC 1 cut(s) 324
Cfr10I RCCGGY 1 cut(s) 268
Cfr13I GGNCC 1 cut(s) 85
Csp6I GTAC 2 cut(s) 138, 343
CviAII CATG 2 cut(s) 178, 504
CviJI RGCY 8 cut(s) 5, 87, 326, 390, 413, 466, 480, 519
CviKI_1 RGCY 8 cut(s) 5, 87, 326, 390, 413, 466, 480, 519
CviQI GTAC 2 cut(s) 138, 343
DdeI CTNAG 3 cut(s) 25, 76, 327
DraIII CACNNNGTG 1 cut(s) 265
EaeI YGGCCR 1 cut(s) 3
Eam1104I CTCTTC 1 cut(s) 329
EarI CTCTTC 1 cut(s) 329
Eco130I CCWWGG 1 cut(s) 433
Eco147I AGGCCT 1 cut(s) 466
Eco31I GGTCTC 2 cut(s) 77, 443
Eco32I GATATC 1 cut(s) 31
EcoRV GATATC 1 cut(s) 31
EcoT14I CCWWGG 1 cut(s) 433
ErhI CCWWGG 1 cut(s) 433
FaeI CATG 2 cut(s) 181, 507
FaiI YATR 7 cut(s) 47, 143, 179, 381, 444, 450, 505
FaqI GGGAC 1 cut(s) 136
FatI CATG 2 cut(s) 177, 503
Fnu4HI GCNGC 1 cut(s) 225
FokI GGATG 2 cut(s) 83, 98
Fsp4HI GCNGC 1 cut(s) 225
FspBI CTAG 1 cut(s) 251
GluI GCNGC 1 cut(s) 225
GsuI CTGGAG 1 cut(s) 437
HaeIII GGCC 5 cut(s) 5, 87, 466, 480, 519
HapII CCGG 1 cut(s) 269
Hin1II CATG 2 cut(s) 181, 507
HinfI GANTC 4 cut(s) 132, 158, 209, 256
HpaII CCGG 1 cut(s) 269
Hpy188I TCNGA 3 cut(s) 19, 28, 79
Hpy188III TCNNGA 2 cut(s) 416, 498
HpyAV CCTTC 4 cut(s) 286, 372, 403, 418
HpyCH4V TGCA 3 cut(s) 219, 224, 491
HpyF10VI GCNNNNNNNGC 2 cut(s) 93, 410
HpyF3I CTNAG 3 cut(s) 25, 76, 327
Hsp92II CATG 2 cut(s) 181, 507
LpnPI CCDG 5 cut(s) 282, 336, 401, 493, 497
Lsp1109I GCAGC 1 cut(s) 236
LweI GCATC 1 cut(s) 105
MaeI CTAG 1 cut(s) 251
MboII GAAGA 2 cut(s) 137, 346
MlsI TGGCCA 1 cut(s) 5
MluCI AATT 2 cut(s) 80, 184
MluNI TGGCCA 1 cut(s) 5
MlyI GAGTC 1 cut(s) 152
MmeI TCCRAC 2 cut(s) 42, 139
MnlI CCTC 8 cut(s) 32, 98, 322, 408, 445, 456, 477, 491
Mox20I TGGCCA 1 cut(s) 5
MroXI GAANNNNTTC 1 cut(s) 428
MscI TGGCCA 1 cut(s) 5
MseI TTAA 1 cut(s) 393
MslI CAYNNNNRTG 2 cut(s) 176, 508
Msp20I TGGCCA 1 cut(s) 5
MspA1I CMGCKG 1 cut(s) 326
MspI CCGG 1 cut(s) 269
Mva1269I GAATGC 1 cut(s) 355
MwoI GCNNNNNNNGC 2 cut(s) 93, 410
NlaIII CATG 2 cut(s) 181, 507
NlaIV GGNNCC 1 cut(s) 267
NspI RCATGY 2 cut(s) 181, 507
NspV TTCGAA 1 cut(s) 365
PceI AGGCCT 1 cut(s) 466
PciI ACATGT 1 cut(s) 177
PctI GAATGC 1 cut(s) 355
PdmI GAANNNNTTC 1 cut(s) 428
PfeI GAWTC 3 cut(s) 132, 209, 256
PkrI GCNGC 1 cut(s) 226
PleI GAGTC 1 cut(s) 152
PpsI GAGTC 1 cut(s) 152
PscI ACATGT 1 cut(s) 177
PsiI TTATAA 1 cut(s) 47
PspN4I GGNNCC 1 cut(s) 267
PspPI GGNCC 1 cut(s) 85
PvuII CAGCTG 1 cut(s) 326
RsaI GTAC 2 cut(s) 139, 344
RsaNI GTAC 2 cut(s) 138, 343
RseI CAYNNNNRTG 2 cut(s) 176, 508
SaqAI TTAA 1 cut(s) 393
SatI GCNGC 1 cut(s) 225
Sau96I GGNCC 1 cut(s) 85
ScaI AGTACT 2 cut(s) 139, 344
SchI GAGTC 1 cut(s) 152
SetI ASST 3 cut(s) 24, 328, 392
SfaNI GCATC 1 cut(s) 105
SfuI TTCGAA 1 cut(s) 365
SmiMI CAYNNNNRTG 2 cut(s) 176, 508
SmlI CTYRAG 2 cut(s) 281, 399
SmoI CTYRAG 2 cut(s) 281, 399
SpeI ACTAGT 1 cut(s) 250
Sse9I AATT 2 cut(s) 80, 184
SseBI AGGCCT 1 cut(s) 466
SspMI CTAG 1 cut(s) 251
StuI AGGCCT 1 cut(s) 466
StyI CCWWGG 1 cut(s) 433
TaqI TCGA 3 cut(s) 182, 347, 365
TasI AATT 2 cut(s) 80, 184
TatI WGTACW 2 cut(s) 137, 342
TfiI GAWTC 3 cut(s) 132, 209, 256
Tru1I TTAA 1 cut(s) 393
Tru9I TTAA 1 cut(s) 393
TscAI CASTG 3 cut(s) 40, 226, 498
TseI GCWGC 1 cut(s) 224
TspRI CASTG 3 cut(s) 40, 226, 498
XceI RCATGY 2 cut(s) 181, 507
XmnI GAANNNNTTC 1 cut(s) 428
XspI CTAG 1 cut(s) 251
ZrmI AGTACT 2 cut(s) 139, 344
Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.