MD00G1044200.v1.1

gag-polypeptide of LTR copia-type

Design Primers CRISPR Design

Basic Information

Type: gene
Biological Identity
malus_domestica
Chr00
OG0002402
Physical Location & Seq
Forward (+)
8082615 .. 8086071
3457 bp
Loading structure...
UTR
Exon/CDS
Intron
MD00G1044200.v1.1.491

Sequence Viewer

Length: 864 bp
ATGTATATAGATATGGTTGGAAGCACACTCGCGAAAATACTCGACAAACATTGCCTAGAGGGGCACAATTTCCCATCATGGTATCGTAATGTCAAGATTCTCCTAACCTTGGAGAAAATTGTTTACGTACTAGACAAGGCTCCACCTCACATACCTCTTGGCCCTGACGCCACTGAGGATGAACGTGCTAAGTATGACAAGCACGTTGAGGATGATACACAAGCCAAGTGCTATCTGTTGGCTTCCATGAATGAGGAGCTACAGAGACAGCACGAGGGCATGGACAGTGCATCTTCCATAATACTCCATCTTACGGAGTTATATGGTGAAGGGACGCGCAACCGTCGCTTTAGCACTGTCTGTGAACTTGTGAAGACCAAGATGGTCAAGGGGGCTCCAGTGCATCAACATGTACTGAAGATGATAGGATTCATTGAACAATTGGAGAACCTTGGTACTCCACTTGACGGGGAATTAGCCCAGGACTTCATATTGGCTTCTCTTTCTGATTCATTCTCGCAGTTCGTAATGAACTACAACATGAATAAGATGGATAGCACTCTCTCCGAGTTACTAAACATGTTAGTAACCGCCGAGAAGACTATGAAGAAAGAGAACGTTGTAGGGACTGCTGCAGTAGCCTACAATAAGCCATCCTCTTCCAAGGCCAAGCCGCAAGGCAAAGGCAAAGGGAAGGAGAAGAAGTCTCCCACTCCTAAGCCGAAAGGAGGAGTGAGGAAAAAGAAGGCAATGGAGCCCAAAGGGACTTGCCACCACTGTGGAAAAGAGGGGCATTGGAAGAGGAATTGCAGGTTATACCTTGCAACTCTTAAGGACAAGCCACAAGGTGGAGGAGCCAAGTAG
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 zf-CCHC

Protein Analysis

288

Amino Acids

32.04

Weight (kDa)

9.15

Isoelectric Point (pI)

37.64

Instability Index
Protein Domains (Pfam)
Domain Name Pfam ID Position E-value Description
Retrotran_gag_2 PF14223 47 - 206 1.2e-17 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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Restriction Enzyme Sites

1 / 10
Enzyme Recognition Site Cut Count Positions (bp)
Acc36I ACCTGC 1 cut(s) 801
AccB7I CCANNNNNTGG 1 cut(s) 848
AccII CGCG 2 cut(s) 32, 337
AciI CCGC 2 cut(s) 591, 674
AclI AACGTT 1 cut(s) 618
AcuI CTGAAG 1 cut(s) 437
AcyI GRCGYC 1 cut(s) 168
AdeI CACNNNGTG 1 cut(s) 848
AfaI GTAC 3 cut(s) 129, 414, 457
AfiI CCNNNNNNNGG 5 cut(s) 109, 313, 467, 728, 848
AflII CTTAAG 1 cut(s) 830
AflIII ACRYGT 2 cut(s) 409, 579
AgsI TTSAA 1 cut(s) 437
AjnI CCWGG 1 cut(s) 480
AleI CACNNNNGTG 1 cut(s) 777
AluBI AGCT 1 cut(s) 259
AluI AGCT 1 cut(s) 259
Alw26I GTCTC 2 cut(s) 259, 711
AoxI GGCC 2 cut(s) 160, 666
ApeKI GCWGC 1 cut(s) 632
AspLEI GCGC 1 cut(s) 339
AspS9I GGNCC 1 cut(s) 161
AsuHPI GGTGA 1 cut(s) 338
BaeGI GKGCMC 1 cut(s) 66
BanII GRGCYC 2 cut(s) 397, 759
BauI CACGAG 1 cut(s) 272
BbsI GAAGAC 2 cut(s) 380, 605
BbvI GCAGC 1 cut(s) 619
BccI CCATC 5 cut(s) 82, 315, 376, 544, 661
BciT130I CCWGG 1 cut(s) 482
BcoDI GTCTC 2 cut(s) 259, 711
BfaI CTAG 2 cut(s) 56, 131
BfmI CTRYAG 2 cut(s) 260, 633
BfrI CTTAAG 1 cut(s) 830
BfuAI ACCTGC 1 cut(s) 801
BisI GCNGC 2 cut(s) 633, 674
BlsI GCNGC 2 cut(s) 634, 675
Bme1390I CCNGG 1 cut(s) 482
BmgT120I GGNCC 1 cut(s) 161
BmiI GGNNCC 4 cut(s) 141, 396, 756, 856
BmrFI CCNGG 1 cut(s) 482
BmsI GCATC 2 cut(s) 299, 412
BpiI GAAGAC 2 cut(s) 380, 605
BpmI CTGGAG 1 cut(s) 381
Bpu10I CCTNAGC 1 cut(s) 717
BsaAI YACGTR 1 cut(s) 127
BsaHI GRCGYC 1 cut(s) 168
BsaJI CCNNGG 4 cut(s) 108, 451, 480, 663
BsaXI ACNNNNNCTCC 2 cut(s) 689, 719
Bsc4I CCNNNNNNNGG 5 cut(s) 109, 313, 467, 728, 848
Bse1I ACTGG 1 cut(s) 398
Bse3DI GCAATG 2 cut(s) 49, 756
BseBI CCWGG 1 cut(s) 482
BseDI CCNNGG 4 cut(s) 108, 451, 480, 663
BseGI GGATG 3 cut(s) 184, 217, 653
BseLI CCNNNNNNNGG 5 cut(s) 109, 313, 467, 728, 848
BseMI GCAATG 2 cut(s) 49, 756
BseMII CTCAG 1 cut(s) 165
BseNI ACTGG 1 cut(s) 398
BseRI GAGGAG 2 cut(s) 269, 744
BseSI GKGCMC 1 cut(s) 66
BseXI GCAGC 1 cut(s) 619
Bsh1236I CGCG 2 cut(s) 32, 337
BshFI GGCC 2 cut(s) 162, 668
BslFI GGGAC 3 cut(s) 346, 640, 778
BslI CCNNNNNNNGG 5 cut(s) 109, 313, 467, 728, 848
BsmAI GTCTC 2 cut(s) 259, 711
BsmFI GGGAC 3 cut(s) 346, 640, 778
BsnI GGCC 2 cut(s) 162, 668
Bsp1286I GDGCHC 3 cut(s) 66, 397, 759
Bsp68I TCGCGA 1 cut(s) 32
BspACI CCGC 2 cut(s) 591, 674
BspANI GGCC 2 cut(s) 162, 668
BspCNI CTCAG 1 cut(s) 166
BspFNI CGCG 2 cut(s) 32, 337
BspLI GGNNCC 4 cut(s) 141, 396, 756, 856
BspMAI CTGCAG 1 cut(s) 637
BspMI ACCTGC 1 cut(s) 801
BspTI CTTAAG 1 cut(s) 830
BsrDI GCAATG 2 cut(s) 49, 756
BsrI ACTGG 1 cut(s) 398
BssECI CCNNGG 4 cut(s) 108, 451, 480, 663
BssNI GRCGYC 1 cut(s) 168
BssSI CACGAG 1 cut(s) 272
BssT1I CCWWGG 3 cut(s) 108, 451, 663
Bst2BI CACGAG 1 cut(s) 272
Bst2UI CCWGG 1 cut(s) 482
Bst4CI ACNGT 4 cut(s) 287, 344, 358, 779
Bst6I CTCTTC 2 cut(s) 664, 794
BstACI GRCGYC 1 cut(s) 168
BstAFI CTTAAG 1 cut(s) 830
BstBAI YACGTR 1 cut(s) 127
BstDEI CTNAG 3 cut(s) 174, 189, 717
BstF5I GGATG 3 cut(s) 184, 217, 653
BstFNI CGCG 2 cut(s) 32, 337
BstHHI GCGC 1 cut(s) 339
BstMAI GTCTC 2 cut(s) 259, 711
BstMWI GCNNNNNNNGC 2 cut(s) 345, 638
BstNI CCWGG 1 cut(s) 482
BstNSI RCATGY 2 cut(s) 413, 583
BstSCI CCNGG 1 cut(s) 480
BstSFI CTRYAG 2 cut(s) 260, 633
BstSLI GKGCMC 1 cut(s) 66
BstSNI TACGTA 1 cut(s) 127
BstUI CGCG 2 cut(s) 32, 337
BstV1I GCAGC 1 cut(s) 619
BstV2I GAAGAC 2 cut(s) 380, 605
BstXI CCANNNNNNTGG 1 cut(s) 779
BsuRI GGCC 2 cut(s) 162, 668
BtsCI GGATG 3 cut(s) 184, 217, 653
BtsIMutI CAGTG 5 cut(s) 171, 292, 354, 405, 775
BtuMI TCGCGA 1 cut(s) 32
BveI ACCTGC 1 cut(s) 801
CfoI GCGC 1 cut(s) 339
Cfr13I GGNCC 1 cut(s) 161
CseI GACGC 2 cut(s) 176, 343
Csp6I GTAC 3 cut(s) 128, 413, 456
CviAII CATG 6 cut(s) 78, 247, 280, 410, 541, 580
CviQI GTAC 3 cut(s) 128, 413, 456
DdeI CTNAG 3 cut(s) 174, 189, 717
DraIII CACNNNGTG 1 cut(s) 848
Eam1104I CTCTTC 2 cut(s) 664, 794
EarI CTCTTC 2 cut(s) 664, 794
Eco105I TACGTA 1 cut(s) 127
Eco130I CCWWGG 3 cut(s) 108, 451, 663
Eco24I GRGCYC 2 cut(s) 397, 759
Eco57I CTGAAG 1 cut(s) 437
EcoRII CCWGG 1 cut(s) 480
EcoT14I CCWWGG 3 cut(s) 108, 451, 663
EcoT38I GRGCYC 2 cut(s) 397, 759
ErhI CCWWGG 3 cut(s) 108, 451, 663
FaeI CATG 6 cut(s) 81, 250, 283, 413, 544, 583
FaqI GGGAC 3 cut(s) 346, 640, 778
FatI CATG 6 cut(s) 77, 246, 279, 409, 540, 579
Fnu4HI GCNGC 2 cut(s) 633, 674
FokI GGATG 3 cut(s) 191, 224, 640
FriOI GRGCYC 2 cut(s) 397, 759
Fsp4HI GCNGC 2 cut(s) 633, 674
FspBI CTAG 2 cut(s) 56, 131
GlaI GCGC 1 cut(s) 338
GluI GCNGC 2 cut(s) 633, 674
GsuI CTGGAG 1 cut(s) 381
HaeIII GGCC 2 cut(s) 162, 668
HgaI GACGC 2 cut(s) 176, 343
HhaI GCGC 1 cut(s) 339
Hin1I GRCGYC 1 cut(s) 168
Hin1II CATG 6 cut(s) 81, 250, 283, 413, 544, 583
Hin6I GCGC 1 cut(s) 337
HinP1I GCGC 1 cut(s) 337
HinfI GANTC 3 cut(s) 97, 429, 509
HphI GGTGA 1 cut(s) 338
Hpy166II GTNNAC 2 cut(s) 124, 365
Hpy188I TCNGA 2 cut(s) 508, 568
Hpy188III TCNNGA 2 cut(s) 31, 94
Hpy8I GTNNAC 2 cut(s) 124, 365
Hpy99I CGWCG 1 cut(s) 348
HpyAV CCTTC 3 cut(s) 323, 688, 739
HpyCH4III ACNGT 4 cut(s) 287, 344, 358, 779
HpyCH4IV ACGT 4 cut(s) 126, 184, 204, 618
HpyCH4V TGCA 5 cut(s) 290, 403, 635, 810, 824
HpyF10VI GCNNNNNNNGC 2 cut(s) 345, 638
HpyF3I CTNAG 3 cut(s) 174, 189, 717
HpySE526I ACGT 4 cut(s) 126, 184, 204, 618
Hsp92I GRCGYC 1 cut(s) 168
Hsp92II CATG 6 cut(s) 81, 250, 283, 413, 544, 583
HspAI GCGC 1 cut(s) 337
LmnI GCTCC 5 cut(s) 145, 256, 400, 754, 854
LpnPI CCDG 5 cut(s) 177, 411, 467, 494, 796
Lsp1109I GCAGC 1 cut(s) 619
LweI GCATC 2 cut(s) 299, 412
MaeI CTAG 2 cut(s) 56, 131
MaeII ACGT 4 cut(s) 126, 184, 204, 618
MaeIII GTNAC 2 cut(s) 570, 586
MboII GAAGA 8 cut(s) 285, 385, 430, 610, 619, 651, 712, 811
MfeI CAATTG 1 cut(s) 440
MhlI GDGCHC 3 cut(s) 66, 397, 759
MluCI AATT 5 cut(s) 67, 117, 440, 473, 805
MseI TTAA 1 cut(s) 831
MslI CAYNNNNRTG 2 cut(s) 408, 777
MspCI CTTAAG 1 cut(s) 830
MspR9I CCNGG 1 cut(s) 482
MunI CAATTG 1 cut(s) 440
MvaI CCWGG 1 cut(s) 482
MvnI CGCG 2 cut(s) 32, 337
MwoI GCNNNNNNNGC 2 cut(s) 345, 638
NlaIII CATG 6 cut(s) 81, 250, 283, 413, 544, 583
NlaIV GGNNCC 4 cut(s) 141, 396, 756, 856
NmeAIII GCCGAG 1 cut(s) 619
NruI TCGCGA 1 cut(s) 32
NspI RCATGY 2 cut(s) 413, 583
OliI CACNNNNGTG 1 cut(s) 777
PciI ACATGT 2 cut(s) 409, 579
PfeI GAWTC 3 cut(s) 97, 429, 509
PflMI CCANNNNNTGG 1 cut(s) 848
PkrI GCNGC 2 cut(s) 634, 675
Ppu21I YACGTR 1 cut(s) 127
PscI ACATGT 2 cut(s) 409, 579
Psp1406I AACGTT 1 cut(s) 618
Psp6I CCWGG 1 cut(s) 480
PspGI CCWGG 1 cut(s) 480
PspN4I GGNNCC 4 cut(s) 141, 396, 756, 856
PspPI GGNCC 1 cut(s) 161
PstI CTGCAG 1 cut(s) 637
RruI TCGCGA 1 cut(s) 32
RsaI GTAC 3 cut(s) 129, 414, 457
RsaNI GTAC 3 cut(s) 128, 413, 456
RseI CAYNNNNRTG 2 cut(s) 408, 777
SaqAI TTAA 1 cut(s) 831
SatI GCNGC 2 cut(s) 633, 674
Sau96I GGNCC 1 cut(s) 161
ScrFI CCNGG 1 cut(s) 482
SduI GDGCHC 3 cut(s) 66, 397, 759
SfaNI GCATC 2 cut(s) 299, 412
SfcI CTRYAG 2 cut(s) 260, 633
SmiMI CAYNNNNRTG 2 cut(s) 408, 777
SmlI CTYRAG 1 cut(s) 830
SmoI CTYRAG 1 cut(s) 830
SnaBI TACGTA 1 cut(s) 127
Sse9I AATT 5 cut(s) 67, 117, 440, 473, 805
SsiI CCGC 2 cut(s) 591, 674
SspMI CTAG 2 cut(s) 56, 131
StyD4I CCNGG 1 cut(s) 480
StyI CCWWGG 3 cut(s) 108, 451, 663
TaaI ACNGT 4 cut(s) 287, 344, 358, 779
TaiI ACGT 4 cut(s) 129, 187, 207, 621
TaqI TCGA 1 cut(s) 42
TasI AATT 5 cut(s) 67, 117, 440, 473, 805
TatI WGTACW 1 cut(s) 412
TauI GCSGC 1 cut(s) 676
TfiI GAWTC 3 cut(s) 97, 429, 509
Tru1I TTAA 1 cut(s) 831
Tru9I TTAA 1 cut(s) 831
TscAI CASTG 5 cut(s) 178, 292, 361, 405, 782
TseI GCWGC 1 cut(s) 632
TspDTI ATGAA 8 cut(s) 195, 263, 421, 478, 501, 545, 557, 620
TspGWI ACGGA 1 cut(s) 329
TspRI CASTG 5 cut(s) 178, 292, 361, 405, 782
Van91I CCANNNNNTGG 1 cut(s) 848
Vha464I CTTAAG 1 cut(s) 830
XceI RCATGY 2 cut(s) 413, 583
XspI CTAG 2 cut(s) 56, 131
Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.