MD05G1032500.v1.1

gag-polypeptide of LTR copia-type

Design Primers CRISPR Design

Basic Information

Type: gene
Biological Identity
malus_domestica
Chr05
OG0001471
Physical Location & Seq
Forward (+)
5305689 .. 5308549
2861 bp
Loading structure...
UTR
Exon/CDS
Intron
MD05G1032500.v1.1.491

Sequence Viewer

Length: 1977 bp
ATGATCACTACCTCGATGCCCTTTATGTCTGCAATGATGGCCAAGAACAATAGTCAAGGATCACAAAGTTATGCTGCTGGGAATTCTTCTACAAATGGTCTTTATAGTCATTCTCCGACAATCAACAATGGTGGTAATTTTGGATTTACTGGTCAACCTGGACAATCCAAATTTTTCAATGGTGGAAATCGATCAAAGTATAAAGGGAAAGGGAAATTTAACAACAATCAAGGACAGAGATATTATAAGCCTGTGGTCCATGATTTTGCACCTGGAATTCTTGGGACTCCATCTTCCTATCATAATGGTGCTTCTTCTTCAATTGTTATCTGTCAGATTTGCTCTAAACATGGTCATTCTGCTGCCACTTGTAACTATAGAGATGCTGAACCTGTTGAGCCTTGTCAAATCTGTGACAAGAAAAATCATACTGCCAGAACCTGTTTCTTCAGGAATAAATCTCCCAATCAAGTCCCACACATGGCTTCCATGAATACTACATACTCAAATTCAGTGCCATCTACTCACATAATGTCCTCTCAAATGTCCAACTCTGTCCCTTTGGCCACCACAACACAATATTCACCTAAAGTTTGGCTCACGGATTCTGGGGCCACAAACCATATGACTACTGATATGAGGAATCTAAGCTTGGCATCACCATATCCAGTCTTCAGACTGCAAATGGGGAAGGTTTGCAATGATGGAGGAGGAGAGTTTATAAGCAAAAAGTTTCAAGCTTTTCTTACTGCACAAGGTGTGTTTCATCAGCTTTCATGCCCCTATACACCTGAACAAAATGGGTTGGCTGAACGAAAACATAGACATATTGTCGAGACTGCCCTTACTTTGTTGCAAACTGCTCATTTATCCCCATCATTTTGGACCTATGCCTGTCATACTGCAACCTATTTGATCAATAGAATGCCAACCACTGTCCTTCAAAACAAATCACCATTTGAACTTCTATATAAAGTTGTCCCTGACCTTTCTCACTTAAGGGTGTTCGGTTGTTCGTGCTATCCTCTCCTTAAATCATATAACATCTCCAAACTGCAACCTAAAACCTCTCGATGGTTATTTTTAGGATATGCTTCTCATTATAAAGGTTATATCTGTTATCATTTACAAACCAAAACAACCTACATTTCGAGACATGTCCTGTTTAATGAACTTGAATTTCCATTCTCATCACTACCAGTTTACCCAACCTCTAAGGTCATTGCTCTCACTCCATCACTTGACACTGCACCATTACCAACTCCAAACCTTCAAAATGTCCTTGTCTCACCAATTTCAACCTCTAGAGCGCAAACTTCATCTTCGTTTAGGGATACTTCATATTCATCACCTCAAGGGCATGCACAGTCACCTTCATCCAATTGTCAATCACCTCGCTGCCAATTGTATTCTCCAATGGCTTCTCATTATTTAGCTGTGAAGAGAATCTTGAGGTATCTCAAAGGGACTATGACACATGGAATTCGATATACAAAAGGCAGTTTAACACTTAGATCGTTTAGTGATGCAGATTGGGCTGGAGACCCTAATGATAGGCGGTCTACAACATGTTTGGTGGTGTTTCTTGGTAACAATCCTATCTCTTGGGCTTCAAAGAAACAACAAACCGTATCAAGGTCATCAACTGAAGCTGAATATCGCGCCCTTTCATCCACTGCTGCTGAATTGGATTGGCTGCAACAACTGTTTCAAGTTCTACAAGTTCATATTCCTCACCTCTCAGTTCTTTTTTGTGACAATCTTTCGGCAATCGCCCTATCCTTTAATCCAGTTCAACATCAGCGCACTAAACATATTGAAGTTGATGTTCACTTTGTGAGAGAACGGGTTGCAAGTAAGAAGCTCTTGGTTCAGTTTGTCTCTTCTTCCGAGCAATTTGCTGATATTCTTACCAAAGGTCTGAGTTCGCCAGTGTTCAAGACTCACTGCAACAATCTCATGCTTGGACCACCATGA
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
RVT_2 Retrotran_gag_2

Protein Analysis

659

Amino Acids

73.11

Weight (kDa)

9.5

Isoelectric Point (pI)

54.02

Instability Index
Protein Domains (Pfam)
Domain Name Pfam ID Position E-value Description
SH3_retrovirus PF25597 338 - 398 4e-18 Retroviral polymerase SH3-like domain
Hydrophobicity Profile (Kyte-Doolittle)
AI Structure Prediction Report
Calculating structure properties...

Genomic Context

Gene Family Tree

Species Filter
Loading...
Style Settings
Image
Tree File
Tip: Beautify your tree with professional tools

Download the Full Tree (.nwk) file, then upload it to any of the following tools to customize colors, fonts, annotations, clades, and branch support.

Publication-ready
iTOL Interactive Tree Of Life · Most popular EvolView Flexible annotations MEGA Desktop phylogenetics suite FigTree Desktop tree editor

Restriction Enzyme Sites

1 / 10
Enzyme Recognition Site Cut Count Positions (bp)
AanI TTATAA 3 cut(s) 246, 722, 1104
AccI GTMKAC 1 cut(s) 1562
AccII CGCG 1 cut(s) 1662
AciI CCGC 1 cut(s) 1558
AclWI GGATC 1 cut(s) 67
AcoI YGGCCR 2 cut(s) 39, 564
AcsI RAATTY 7 cut(s) 82, 170, 215, 276, 508, 1178, 1482
AcuI CTGAAG 3 cut(s) 433, 658, 1668
AdeI CACNNNGTG 2 cut(s) 758, 1837
AfiI CCNNNNNNNGG 3 cut(s) 481, 1074, 1635
AflII CTTAAG 1 cut(s) 997
AflIII ACRYGT 2 cut(s) 1156, 1568
AhdI GACNNNNNGTC 1 cut(s) 830
AjnI CCWGG 2 cut(s) 157, 271
AjuI GAANNNNNNNTTGG 2 cut(s) 635, 667
AluBI AGCT 6 cut(s) 651, 740, 772, 1436, 1652, 1864
AluI AGCT 6 cut(s) 651, 740, 772, 1436, 1652, 1864
Alw26I GTCTC 5 cut(s) 830, 1147, 1291, 1536, 1885
AlwI GGATC 1 cut(s) 67
AlwNI CAGNNNCTG 1 cut(s) 441
AoxI GGCC 3 cut(s) 39, 564, 612
ApeKI GCWGC 5 cut(s) 74, 362, 1398, 1679, 1696
ApoI RAATTY 7 cut(s) 82, 170, 215, 276, 508, 1178, 1482
AspLEI GCGC 3 cut(s) 1312, 1664, 1806
AspS9I GGNCC 4 cut(s) 256, 612, 885, 1967
AsuHPI GGTGA 8 cut(s) 576, 651, 945, 1281, 1341, 1362, 1383, 1727
AvaII GGWCC 3 cut(s) 256, 885, 1967
BalI TGGCCA 2 cut(s) 41, 566
BbsI GAAGAC 1 cut(s) 664
BbvI GCAGC 5 cut(s) 61, 349, 1385, 1666, 1683
BccI CCATC 7 cut(s) 31, 298, 526, 698, 883, 1068, 1243
BcgI CGANNNNNNTGC 2 cut(s) 1880, 1914
BciT130I CCWGG 2 cut(s) 159, 273
BciVI GTATCC 1 cut(s) 1327
BclI TGATCA 2 cut(s) 3, 915
BcoDI GTCTC 5 cut(s) 830, 1147, 1291, 1536, 1885
BfaI CTAG 1 cut(s) 1305
BfmI CTRYAG 1 cut(s) 376
BfrI CTTAAG 1 cut(s) 997
BfuI GTATCC 1 cut(s) 1327
BisI GCNGC 5 cut(s) 75, 363, 1399, 1680, 1697
BlsI GCNGC 5 cut(s) 76, 364, 1400, 1681, 1698
Bme1390I CCNGG 2 cut(s) 159, 273
Bme18I GGWCC 3 cut(s) 256, 885, 1967
BmeRI GACNNNNNGTC 1 cut(s) 830
BmgT120I GGNCC 4 cut(s) 256, 612, 885, 1967
BmiI GGNNCC 1 cut(s) 613
BmrFI CCNGG 2 cut(s) 159, 273
BmsI GCATC 4 cut(s) 6, 373, 665, 1516
BpiI GAAGAC 1 cut(s) 664
BpmI CTGGAG 1 cut(s) 1560
BpuEI CTTGAG 2 cut(s) 1338, 1471
Bsa29I ATCGAT 1 cut(s) 190
BsaI GGTCTC 1 cut(s) 1536
Bsc4I CCNNNNNNNGG 3 cut(s) 481, 1074, 1635
Bse1I ACTGG 5 cut(s) 154, 668, 1199, 1790, 1931
Bse3DI GCAATG 3 cut(s) 39, 706, 1221
BseBI CCWGG 2 cut(s) 159, 273
BseCI ATCGAT 1 cut(s) 190
BseGI GGATG 2 cut(s) 1376, 1670
BseLI CCNNNNNNNGG 3 cut(s) 481, 1074, 1635
BseMI GCAATG 3 cut(s) 39, 706, 1221
BseMII CTCAG 2 cut(s) 1755, 1913
BseNI ACTGG 5 cut(s) 154, 668, 1199, 1790, 1931
BseRI GAGGAG 2 cut(s) 723, 726
BseXI GCAGC 5 cut(s) 61, 349, 1385, 1666, 1683
BseYI CCCAGC 1 cut(s) 77
BsgI GTGCAG 2 cut(s) 735, 1233
Bsh1236I CGCG 1 cut(s) 1662
BshFI GGCC 3 cut(s) 41, 566, 614
BshVI ATCGAT 1 cut(s) 190
BslFI GGGAC 5 cut(s) 298, 458, 542, 965, 1480
BslI CCNNNNNNNGG 3 cut(s) 481, 1074, 1635
BsmAI GTCTC 5 cut(s) 830, 1147, 1291, 1536, 1885
BsmFI GGGAC 5 cut(s) 298, 458, 542, 965, 1480
BsmI GAATGC 1 cut(s) 930
BsnI GGCC 3 cut(s) 41, 566, 614
Bso31I GGTCTC 1 cut(s) 1536
Bsp143I GATC 5 cut(s) 3, 59, 191, 915, 1514
BspACI CCGC 1 cut(s) 1558
BspANI GGCC 3 cut(s) 41, 566, 614
BspCNI CTCAG 2 cut(s) 1754, 1914
BspDI ATCGAT 1 cut(s) 190
BspFNI CGCG 1 cut(s) 1662
BspLI GGNNCC 1 cut(s) 613
BspPI GGATC 1 cut(s) 67
BspTI CTTAAG 1 cut(s) 997
BspTNI GGTCTC 1 cut(s) 1536
BsrDI GCAATG 3 cut(s) 39, 706, 1221
BsrI ACTGG 5 cut(s) 154, 668, 1199, 1790, 1931
BssMI GATC 5 cut(s) 3, 59, 191, 915, 1514
Bst2UI CCWGG 2 cut(s) 159, 273
Bst4CI ACNGT 4 cut(s) 937, 1368, 1630, 1707
Bst6I CTCTTC 2 cut(s) 1436, 1888
BstAFI CTTAAG 1 cut(s) 997
BstC8I GCNNGC 1 cut(s) 1362
BstDEI CTNAG 5 cut(s) 647, 1215, 1511, 1741, 1922
BstF5I GGATG 2 cut(s) 1376, 1670
BstFNI CGCG 1 cut(s) 1662
BstHHI GCGC 3 cut(s) 1312, 1664, 1806
BstKTI GATC 5 cut(s) 6, 62, 194, 918, 1517
BstMAI GTCTC 5 cut(s) 830, 1147, 1291, 1536, 1885
BstMBI GATC 5 cut(s) 3, 59, 191, 915, 1514
BstMWI GCNNNNNNNGC 2 cut(s) 38, 1535
BstNI CCWGG 2 cut(s) 159, 273
BstNSI RCATGY 3 cut(s) 1160, 1364, 1572
BstSCI CCNGG 2 cut(s) 157, 271
BstSFI CTRYAG 1 cut(s) 376
BstUI CGCG 1 cut(s) 1662
BstV1I GCAGC 5 cut(s) 61, 349, 1385, 1666, 1683
BstV2I GAAGAC 1 cut(s) 664
BstXI CCANNNNNNTGG 1 cut(s) 882
Bsu15I ATCGAT 1 cut(s) 190
BsuI GTATCC 1 cut(s) 1327
BsuRI GGCC 3 cut(s) 41, 566, 614
BsuTUI ATCGAT 1 cut(s) 190
BtsCI GGATG 2 cut(s) 1376, 1670
BtsI GCAGTG 3 cut(s) 1245, 1674, 1945
BtsIMutI CAGTG 6 cut(s) 519, 933, 1245, 1674, 1938, 1945
Cac8I GCNNGC 1 cut(s) 1362
CaiI CAGNNNCTG 1 cut(s) 441
CfoI GCGC 3 cut(s) 1312, 1664, 1806
Cfr13I GGNCC 4 cut(s) 256, 612, 885, 1967
ClaI ATCGAT 1 cut(s) 190
CspCI CAANNNNNGTGG 2 cut(s) 112, 147
DdeI CTNAG 5 cut(s) 647, 1215, 1511, 1741, 1922
DpnI GATC 5 cut(s) 5, 61, 193, 917, 1516
DpnII GATC 5 cut(s) 3, 59, 191, 915, 1514
DraIII CACNNNGTG 2 cut(s) 758, 1837
DriI GACNNNNNGTC 1 cut(s) 830
EaeI YGGCCR 2 cut(s) 39, 564
Eam1104I CTCTTC 2 cut(s) 1436, 1888
Eam1105I GACNNNNNGTC 1 cut(s) 830
EarI CTCTTC 2 cut(s) 1436, 1888
Eco31I GGTCTC 1 cut(s) 1536
Eco47I GGWCC 3 cut(s) 256, 885, 1967
Eco57I CTGAAG 3 cut(s) 433, 658, 1668
EcoRI GAATTC 3 cut(s) 82, 276, 1482
EcoRII CCWGG 2 cut(s) 157, 271
FalI AAGNNNNNCTT 6 cut(s) 729, 761, 1433, 1465, 1850, 1882
FaqI GGGAC 5 cut(s) 298, 458, 542, 965, 1480
FauNDI CATATG 1 cut(s) 624
FbaI TGATCA 2 cut(s) 3, 915
FblI GTMKAC 1 cut(s) 1562
Fnu4HI GCNGC 5 cut(s) 75, 363, 1399, 1680, 1697
FokI GGATG 2 cut(s) 1363, 1657
Fsp4HI GCNGC 5 cut(s) 75, 363, 1399, 1680, 1697
FspBI CTAG 1 cut(s) 1305
GlaI GCGC 3 cut(s) 1311, 1663, 1805
GluI GCNGC 5 cut(s) 75, 363, 1399, 1680, 1697
GsaI CCCAGC 1 cut(s) 81
GsuI CTGGAG 1 cut(s) 1560
HaeIII GGCC 3 cut(s) 41, 566, 614
HhaI GCGC 3 cut(s) 1312, 1664, 1806
Hin6I GCGC 3 cut(s) 1310, 1662, 1804
HinP1I GCGC 3 cut(s) 1310, 1662, 1804
HincII GTYRAC 1 cut(s) 155
HindII GTYRAC 1 cut(s) 155
HindIII AAGCTT 2 cut(s) 649, 738
HinfI GANTC 5 cut(s) 286, 605, 643, 1446, 1942
HphI GGTGA 8 cut(s) 576, 651, 945, 1281, 1341, 1362, 1383, 1727
Hpy166II GTNNAC 4 cut(s) 155, 1204, 1563, 1831
Hpy188I TCNGA 5 cut(s) 117, 336, 677, 1891, 1923
Hpy188III TCNNGA 7 cut(s) 451, 835, 1071, 1152, 1305, 1450, 1939
Hpy8I GTNNAC 4 cut(s) 155, 1204, 1563, 1831
HpyAV CCTTC 4 cut(s) 685, 950, 1280, 1383
HpyCH4III ACNGT 4 cut(s) 937, 1368, 1630, 1707
HpyF10VI GCNNNNNNNGC 2 cut(s) 38, 1535
HpyF3I CTNAG 5 cut(s) 647, 1215, 1511, 1741, 1922
HspAI GCGC 3 cut(s) 1310, 1662, 1804
Ksp22I TGATCA 2 cut(s) 3, 915
Kzo9I GATC 5 cut(s) 3, 59, 191, 915, 1514
Lsp1109I GCAGC 5 cut(s) 61, 349, 1385, 1666, 1683
LweI GCATC 4 cut(s) 6, 373, 665, 1516
MaeI CTAG 1 cut(s) 1305
MaeIII GTNAC 5 cut(s) 371, 413, 1368, 1589, 1754
MalI GATC 5 cut(s) 5, 61, 193, 917, 1516
MboI GATC 5 cut(s) 3, 59, 191, 915, 1514
MfeI CAATTG 3 cut(s) 321, 1381, 1403
MlsI TGGCCA 2 cut(s) 41, 566
MluNI TGGCCA 2 cut(s) 41, 566
MlyI GAGTC 2 cut(s) 280, 1936
MmeI TCCRAC 2 cut(s) 140, 573
Mox20I TGGCCA 2 cut(s) 41, 566
MscI TGGCCA 2 cut(s) 41, 566
MseI TTAA 6 cut(s) 219, 998, 1032, 1167, 1505, 1785
MslI CAYNNNNRTG 1 cut(s) 306
Msp20I TGGCCA 2 cut(s) 41, 566
MspCI CTTAAG 1 cut(s) 997
MspR9I CCNGG 2 cut(s) 159, 273
MunI CAATTG 3 cut(s) 321, 1381, 1403
Mva1269I GAATGC 1 cut(s) 930
MvaI CCWGG 2 cut(s) 159, 273
MvnI CGCG 1 cut(s) 1662
MwoI GCNNNNNNNGC 2 cut(s) 38, 1535
NdeI CATATG 1 cut(s) 624
NdeII GATC 5 cut(s) 3, 59, 191, 915, 1514
NlaIV GGNNCC 1 cut(s) 613
NmuCI GTSAC 3 cut(s) 413, 1368, 1754
NspI RCATGY 3 cut(s) 1160, 1364, 1572
PaeI GCATGC 1 cut(s) 1364
PciI ACATGT 2 cut(s) 1156, 1568
PctI GAATGC 1 cut(s) 930
PfeI GAWTC 3 cut(s) 605, 643, 1446
PkrI GCNGC 5 cut(s) 76, 364, 1400, 1681, 1698
PleI GAGTC 2 cut(s) 280, 1936
PpsI GAGTC 2 cut(s) 280, 1936
PscI ACATGT 2 cut(s) 1156, 1568
PsiI TTATAA 3 cut(s) 246, 722, 1104
Psp6I CCWGG 2 cut(s) 157, 271
PspFI CCCAGC 1 cut(s) 77
PspGI CCWGG 2 cut(s) 157, 271
PspN4I GGNNCC 1 cut(s) 613
PspPI GGNCC 4 cut(s) 256, 612, 885, 1967
PstNI CAGNNNCTG 1 cut(s) 441
RseI CAYNNNNRTG 1 cut(s) 306
SaqAI TTAA 6 cut(s) 219, 998, 1032, 1167, 1505, 1785
SatI GCNGC 5 cut(s) 75, 363, 1399, 1680, 1697
Sau3AI GATC 5 cut(s) 3, 59, 191, 915, 1514
Sau96I GGNCC 4 cut(s) 256, 612, 885, 1967
SchI GAGTC 2 cut(s) 280, 1936
ScrFI CCNGG 2 cut(s) 159, 273
SfaNI GCATC 4 cut(s) 6, 373, 665, 1516
SfcI CTRYAG 1 cut(s) 376
SinI GGWCC 3 cut(s) 256, 885, 1967
SmiMI CAYNNNNRTG 1 cut(s) 306
SmlI CTYRAG 3 cut(s) 997, 1353, 1450
SmoI CTYRAG 3 cut(s) 997, 1353, 1450
SphI GCATGC 1 cut(s) 1364
SsiI CCGC 1 cut(s) 1558
SspI AATATT 1 cut(s) 581
SspMI CTAG 1 cut(s) 1305
StyD4I CCNGG 2 cut(s) 157, 271
TaaI ACNGT 4 cut(s) 937, 1368, 1630, 1707
TaqI TCGA 6 cut(s) 14, 190, 834, 1072, 1151, 1486
TfiI GAWTC 3 cut(s) 605, 643, 1446
Tru1I TTAA 6 cut(s) 219, 998, 1032, 1167, 1505, 1785
Tru9I TTAA 6 cut(s) 219, 998, 1032, 1167, 1505, 1785
TscAI CASTG 6 cut(s) 519, 940, 1252, 1681, 1938, 1952
TseFI GTSAC 3 cut(s) 413, 1368, 1754
TseI GCWGC 5 cut(s) 74, 362, 1398, 1679, 1696
Tsp45I GTSAC 3 cut(s) 413, 1368, 1754
TspGWI ACGGA 1 cut(s) 617
TspRI CASTG 6 cut(s) 519, 940, 1252, 1681, 1938, 1952
Vha464I CTTAAG 1 cut(s) 997
VpaK11BI GGWCC 3 cut(s) 256, 885, 1967
XapI RAATTY 7 cut(s) 82, 170, 215, 276, 508, 1178, 1482
XbaI TCTAGA 1 cut(s) 1304
XceI RCATGY 3 cut(s) 1160, 1364, 1572
XmiI GTMKAC 1 cut(s) 1562
XspI CTAG 1 cut(s) 1305
Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.