MD10G1237700.v1.1

gag-polypeptide of LTR copia-type

Design Primers CRISPR Design

Basic Information

Type: gene
Biological Identity
malus_domestica
Chr10
OG0000562
Physical Location & Seq
Forward (+)
33396499 .. 33398354
1856 bp
Loading structure...
UTR
Exon/CDS
Intron
MD10G1237700.v1.1.491

Sequence Viewer

Length: 1116 bp
ATGGAAGAAGAAAATATACTTGCTGCTTCATCCGAGAACATCCTTGGTTCTTCATCAGTTTCTTCAAGTGAAGCTGATGGAAATCCCAATCAACGTCTTTGTTCCATACTCCTAACTGAGTTTAATTATCTTCCTTGGTCAAGAGCTATTACTTTAGCTCTTGGAGGAAGATCTAAGCTTGGTTTCATCAATGGAACTATCGTACCTCCCAAGGTTGGTGATTCTAAGTATGAAGAATGGTTCTGCAAGGATCAGCTCGTCATGTCCTGGTTGCTCAACTCAATGGGCTCAAAGGTATCAGAAATTTTCAGCTTTTCAGAATCAGCTTTTGATCTGTGGAAGGCTGTCAAGGAGATGTATGGAAATCAAAATAATGCAGCCAGGATATTTGAGCTGCAGAAGAGTCTTTCTGTTTTGAATCAAGATGGAAAGACTTTTATCGAGCACTTGGGAAGACTGAAGTCTATGTGGAATGAGCTGAATCTCTATCGACCTCACACTACAGACCCAGCAATCCTTCTTAAGCAGGCTGAAGAAGACAAGGTCTTTCAGCTTTTATCCAGTCTTGACTCTACCTATGAGGACCTGCGAAGCCACATATTGATGAGTGTTGAACTACCATCTCTCAATACTGTGTGCACTATCGTTCAACGAGAAGAAGCAAGAAGGAAAGTTATGAGTACTAAGGTTGGTGATCCTGAGTCTAGAGCTTTCGTTGCAAGTGATAGAAGGTTTGAAGGAAAAAATTTCAAAGGAAAGAAAGGAGAAATGCAATGCAGTCATTGTGGACAGAAGAATCATCTCAGAGACACTTGTTGGGTGTTGTATCCACACCTTAAGCCTAACTTTTCCAAACAAACCAAACCTGGTCGCAGTGCAAATCAAGTCCCTCGCTTGCAGACTGCCTCAACTGTTGGGAACTTCACATCTAATCCCTCAGCTCTCTTGAGTGAGTTCACTTCCTTCACTCAGAAGAAAGATGAAAGCAATCTTCATAAAGGAAACAGTGAAGCTAGCACCACTGAATTATTTGAGCAGTTCGCAAAATTTCTTCAGACAAAGGTGTCATCTTCCGTTGATATGTCAGGATCGTATCACGAAGAAGAAGATTGGTGA
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

372

Amino Acids

41.82

Weight (kDa)

6.29

Isoelectric Point (pI)

50.98

Instability Index
Protein Domains (Pfam)
Domain Name Pfam ID Position E-value Description
Retrotran_gag_3 PF14244 29 - 71 2.3e-14 gag-polypeptide of LTR copia-type
Retrotran_gag_2 PF14223 62 - 225 6.2e-14 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: OG0000562)

Species Orthologous Gene IDs
fragaria_vesca FvH4_2g17331 FvH4_3g36541
malus_domestica MD07G1078600.v1.1 MD10G1237700.v1.1 MD10G1333400.v1.1 MD11G1102200.v1.1 MD13G1138400.v1.1 MD14G1033400.v1.1 MD15G1053300.v1.1
prunus_persica Prupe.1G465400_v2.0.a1 Prupe.3G136000_v2.0.a1 Prupe.7G119900_v2.0.a1
pyrus_communis pycom01g04630 pycom03g13050 pycom04g21190 pycom05g04910 pycom05g05510 pycom08g15850 pycom09g15040 pycom1094g00010 pycom11g02000 pycom12g06150 pycom13g24110 pycom13g24910 pycom14g00050 pycom15g21970 pycom15g35170 pycom15g35180 pycom16g14620 pycom16g14630 pycom808g00110
rosa_chinensis RchiOBHm_Chr1g0322851 RchiOBHm_Chr1g0365941 RchiOBHm_Chr3g0453341 RchiOBHm_Chr4g0388371 RchiOBHm_Chr4g0394021 RchiOBHm_Chr5g0013181 RchiOBHm_Chr6g0261721 RchiOBHm_Chr6g0261731 RchiOBHm_Chr7g0188861 RchiOBHm_Chr7g0192331 RchiOBHm_Chr7g0231721
rosa_multiflora Rmu_sc0002521.1_g000006 Rmu_sc0003255.1_g000026 Rmu_sc0004191.1_g000036 Rmu_sc0004414.1_g000014 Rmu_sc0005670.1_g000006 Rmu_sc0006081.1_g000001 Rmu_sc0007215.1_g000004 Rmu_sc0010088.1_g000010 Rmu_sc0020285.1_g000003 Rmu_sc0026896.1_g000002 Rmu_ssc0000019.1_g000029
rosa_roxburghii Rroxscaffold_3G00224890 Rroxscaffold_6G00400640 Rroxscaffold_7G00176590 Rroxscaffold_7G00189230
rosa_samantha Rh4BG046700
rosa_wichuraiana Rw1G012690 Rw1G031370 Rw2G042180 Rw2G043670 Rw2G046240 Rw2G049890 Rw2G050760 Rw2G051280 Rw2G053590 Rw3G007590 Rw3G026850 Rw4G001540 Rw4G009760 Rw4G019270 Rw5G000720 Rw5G005620 Rw5G041560 Rw6G007370 Rw6G009830 Rw6G015360 Rw6G031160 Rw7G004930 Rw7G011010 Rw7G024230 Rw7G028240

Restriction Enzyme Sites

1 / 10
Enzyme Recognition Site Cut Count Positions (bp)
AasI GACNNNNNNGTC 1 cut(s) 1063
Acc36I ACCTGC 1 cut(s) 594
AclWI GGATC 3 cut(s) 258, 689, 1096
AcsI RAATTY 3 cut(s) 303, 745, 1046
AcuI CTGAAG 3 cut(s) 479, 552, 1037
AfaI GTAC 2 cut(s) 204, 682
AfiI CCNNNNNNNGG 1 cut(s) 215
AflII CTTAAG 2 cut(s) 521, 836
AgsI TTSAA 6 cut(s) 66, 418, 614, 650, 737, 751
AjnI CCWGG 3 cut(s) 266, 380, 865
Alw21I GWGCWC 2 cut(s) 447, 641
Alw26I GTCTC 1 cut(s) 801
Alw44I GTGCAC 1 cut(s) 637
AlwI GGATC 3 cut(s) 258, 689, 1096
ApaLI GTGCAC 1 cut(s) 637
ApeKI GCWGC 3 cut(s) 23, 377, 394
ApoI RAATTY 3 cut(s) 303, 745, 1046
AspS9I GGNCC 1 cut(s) 583
AsuHPI GGTGA 2 cut(s) 230, 704
AsuNHI GCTAGC 1 cut(s) 1013
AvaII GGWCC 1 cut(s) 583
BaeGI GKGCMC 1 cut(s) 641
BaeI ACNNNNGTAYC 2 cut(s) 186, 219
BanII GRGCYC 1 cut(s) 290
BarI GAAGNNNNNNTAC 1 cut(s) 32
BbsI GAAGAC 2 cut(s) 460, 543
Bbv12I GWGCWC 2 cut(s) 447, 641
BbvCI CCTCAGC 1 cut(s) 937
BbvI GCAGC 3 cut(s) 10, 381, 389
BccI CCATC 3 cut(s) 71, 419, 628
BciT130I CCWGG 3 cut(s) 268, 382, 867
BciVI GTATCC 1 cut(s) 837
BcoDI GTCTC 1 cut(s) 801
BfaI CTAG 2 cut(s) 705, 1014
BfmI CTRYAG 2 cut(s) 395, 501
BfrI CTTAAG 2 cut(s) 521, 836
BfuAI ACCTGC 1 cut(s) 594
BfuI GTATCC 1 cut(s) 837
BglII AGATCT 1 cut(s) 170
BisI GCNGC 3 cut(s) 24, 378, 395
BlsI GCNGC 3 cut(s) 25, 379, 396
BmcAI AGTACT 1 cut(s) 682
Bme1390I CCNGG 3 cut(s) 268, 382, 867
Bme18I GGWCC 1 cut(s) 583
BmgT120I GGNCC 1 cut(s) 583
BmrFI CCNGG 3 cut(s) 268, 382, 867
BmtI GCTAGC 1 cut(s) 1017
BoxI GACNNNNGTC 1 cut(s) 460
BpiI GAAGAC 2 cut(s) 460, 543
Bpu10I CCTNAGC 1 cut(s) 937
BpuEI CTTGAG 1 cut(s) 967
BsaBI GATNNNNATC 1 cut(s) 81
BsaJI CCNNGG 3 cut(s) 43, 134, 210
Bsc4I CCNNNNNNNGG 1 cut(s) 215
Bse1I ACTGG 1 cut(s) 561
Bse3DI GCAATG 1 cut(s) 779
Bse8I GATNNNNATC 1 cut(s) 81
BseBI CCWGG 3 cut(s) 268, 382, 867
BseDI CCNNGG 3 cut(s) 43, 134, 210
BseGI GGATG 2 cut(s) 29, 39
BseJI GATNNNNATC 1 cut(s) 81
BseLI CCNNNNNNNGG 1 cut(s) 215
BseMI GCAATG 1 cut(s) 779
BseMII CTCAG 5 cut(s) 108, 690, 817, 951, 983
BseNI ACTGG 1 cut(s) 561
BseSI GKGCMC 1 cut(s) 641
BseXI GCAGC 3 cut(s) 10, 381, 389
BseYI CCCAGC 1 cut(s) 508
BsiHKAI GWGCWC 2 cut(s) 447, 641
BslFI GGGAC 1 cut(s) 872
BslI CCNNNNNNNGG 1 cut(s) 215
BsmAI GTCTC 1 cut(s) 801
BsmFI GGGAC 1 cut(s) 872
Bsp1286I GDGCHC 3 cut(s) 290, 447, 641
Bsp143I GATC 5 cut(s) 170, 250, 331, 694, 1088
BspCNI CTCAG 5 cut(s) 109, 691, 816, 950, 982
BspMAI CTGCAG 1 cut(s) 399
BspMI ACCTGC 1 cut(s) 594
BspOI GCTAGC 1 cut(s) 1017
BspPI GGATC 3 cut(s) 258, 689, 1096
BspTI CTTAAG 2 cut(s) 521, 836
BsrDI GCAATG 1 cut(s) 779
BsrI ACTGG 1 cut(s) 561
BssECI CCNNGG 3 cut(s) 43, 134, 210
BssMI GATC 5 cut(s) 170, 250, 331, 694, 1088
BssT1I CCWWGG 3 cut(s) 43, 134, 210
Bst2UI CCWGG 3 cut(s) 268, 382, 867
Bst4CI ACNGT 3 cut(s) 634, 913, 1007
Bst6I CTCTTC 1 cut(s) 395
BstAFI CTTAAG 2 cut(s) 521, 836
BstC8I GCNNGC 3 cut(s) 528, 896, 1015
BstDEI CTNAG 8 cut(s) 117, 174, 225, 684, 699, 803, 937, 969
BstF5I GGATG 2 cut(s) 29, 39
BstKTI GATC 5 cut(s) 173, 253, 334, 697, 1091
BstMAI GTCTC 1 cut(s) 801
BstMBI GATC 5 cut(s) 170, 250, 331, 694, 1088
BstMWI GCNNNNNNNGC 1 cut(s) 716
BstNI CCWGG 3 cut(s) 268, 382, 867
BstPAI GACNNNNGTC 1 cut(s) 460
BstSCI CCNGG 3 cut(s) 266, 380, 865
BstSFI CTRYAG 2 cut(s) 395, 501
BstSLI GKGCMC 1 cut(s) 641
BstV1I GCAGC 3 cut(s) 10, 381, 389
BstV2I GAAGAC 2 cut(s) 460, 543
BstX2I RGATCY 1 cut(s) 170
BstYI RGATCY 1 cut(s) 170
BsuI GTATCC 1 cut(s) 837
BtsCI GGATG 2 cut(s) 29, 39
BtsI GCAGTG 1 cut(s) 880
BtsIMutI CAGTG 3 cut(s) 880, 1012, 1020
BveI ACCTGC 1 cut(s) 594
Cac8I GCNNGC 3 cut(s) 528, 896, 1015
Cfr13I GGNCC 1 cut(s) 583
CsiI ACCWGGT 1 cut(s) 865
Csp6I GTAC 2 cut(s) 203, 681
CviAII CATG 1 cut(s) 262
CviQI GTAC 2 cut(s) 203, 681
DdeI CTNAG 8 cut(s) 117, 174, 225, 684, 699, 803, 937, 969
DpnI GATC 5 cut(s) 172, 252, 333, 696, 1090
DpnII GATC 5 cut(s) 170, 250, 331, 694, 1088
DrdI GACNNNNNNGTC 1 cut(s) 1063
DseDI GACNNNNNNGTC 1 cut(s) 1063
Eam1104I CTCTTC 1 cut(s) 395
EarI CTCTTC 1 cut(s) 395
Eco130I CCWWGG 3 cut(s) 43, 134, 210
Eco24I GRGCYC 1 cut(s) 290
Eco47I GGWCC 1 cut(s) 583
Eco57I CTGAAG 3 cut(s) 479, 552, 1037
EcoO109I RGGNCCY 1 cut(s) 583
EcoRII CCWGG 3 cut(s) 266, 380, 865
EcoT14I CCWWGG 3 cut(s) 43, 134, 210
EcoT38I GRGCYC 1 cut(s) 290
ErhI CCWWGG 3 cut(s) 43, 134, 210
FaeI CATG 1 cut(s) 265
FalI AAGNNNNNCTT 2 cut(s) 830, 862
FaqI GGGAC 1 cut(s) 872
FatI CATG 1 cut(s) 261
Fnu4HI GCNGC 3 cut(s) 24, 378, 395
FokI GGATG 2 cut(s) 16, 26
FriOI GRGCYC 1 cut(s) 290
Fsp4HI GCNGC 3 cut(s) 24, 378, 395
FspBI CTAG 2 cut(s) 705, 1014
GluI GCNGC 3 cut(s) 24, 378, 395
GsaI CCCAGC 1 cut(s) 512
Hin1II CATG 1 cut(s) 265
HindIII AAGCTT 1 cut(s) 176
HinfI GANTC 8 cut(s) 221, 320, 403, 418, 481, 569, 701, 796
HphI GGTGA 2 cut(s) 230, 704
Hpy166II GTNNAC 3 cut(s) 639, 788, 957
Hpy188I TCNGA 6 cut(s) 34, 301, 319, 806, 972, 1056
Hpy188III TCNNGA 8 cut(s) 141, 422, 566, 698, 705, 946, 1086, 1097
Hpy8I GTNNAC 3 cut(s) 639, 788, 957
HpyAV CCTTC 6 cut(s) 334, 527, 660, 723, 731, 973
HpyCH4III ACNGT 3 cut(s) 634, 913, 1007
HpyCH4IV ACGT 1 cut(s) 94
HpyCH4V TGCA 9 cut(s) 246, 377, 397, 639, 719, 772, 777, 878, 898
HpyF10VI GCNNNNNNNGC 1 cut(s) 716
HpyF3I CTNAG 8 cut(s) 117, 174, 225, 684, 699, 803, 937, 969
HpySE526I ACGT 1 cut(s) 94
Hsp92II CATG 1 cut(s) 265
Kzo9I GATC 5 cut(s) 170, 250, 331, 694, 1088
Lsp1109I GCAGC 3 cut(s) 10, 381, 389
MabI ACCWGGT 1 cut(s) 865
MaeI CTAG 2 cut(s) 705, 1014
MaeII ACGT 1 cut(s) 94
MalI GATC 5 cut(s) 172, 252, 333, 696, 1090
MboI GATC 5 cut(s) 170, 250, 331, 694, 1088
MflI RGATCY 1 cut(s) 170
MhlI GDGCHC 3 cut(s) 290, 447, 641
MluCI AATT 5 cut(s) 124, 303, 745, 1025, 1046
MlyI GAGTC 3 cut(s) 412, 563, 710
MnlI CCTC 7 cut(s) 158, 216, 504, 574, 900, 916, 946
MseI TTAA 3 cut(s) 123, 522, 837
MslI CAYNNNNRTG 1 cut(s) 602
MspCI CTTAAG 2 cut(s) 521, 836
MspR9I CCNGG 3 cut(s) 268, 382, 867
MvaI CCWGG 3 cut(s) 268, 382, 867
MwoI GCNNNNNNNGC 1 cut(s) 716
NdeII GATC 5 cut(s) 170, 250, 331, 694, 1088
NheI GCTAGC 1 cut(s) 1013
NlaIII CATG 1 cut(s) 265
PfeI GAWTC 5 cut(s) 221, 320, 418, 481, 796
PflFI GACNNNGTC 1 cut(s) 542
PkrI GCNGC 3 cut(s) 25, 379, 396
PleI GAGTC 3 cut(s) 411, 563, 709
PpsI GAGTC 3 cut(s) 411, 563, 709
PpuMI RGGWCCY 1 cut(s) 583
PshAI GACNNNNGTC 1 cut(s) 460
Psp5II RGGWCCY 1 cut(s) 583
Psp6I CCWGG 3 cut(s) 266, 380, 865
PspFI CCCAGC 1 cut(s) 508
PspGI CCWGG 3 cut(s) 266, 380, 865
PspPI GGNCC 1 cut(s) 583
PspPPI RGGWCCY 1 cut(s) 583
PstI CTGCAG 1 cut(s) 399
PsuI RGATCY 1 cut(s) 170
PsyI GACNNNGTC 1 cut(s) 542
RsaI GTAC 2 cut(s) 204, 682
RsaNI GTAC 2 cut(s) 203, 681
RseI CAYNNNNRTG 1 cut(s) 602
SaqAI TTAA 3 cut(s) 123, 522, 837
SatI GCNGC 3 cut(s) 24, 378, 395
Sau3AI GATC 5 cut(s) 170, 250, 331, 694, 1088
Sau96I GGNCC 1 cut(s) 583
ScaI AGTACT 1 cut(s) 682
SchI GAGTC 3 cut(s) 412, 563, 710
ScrFI CCNGG 3 cut(s) 268, 382, 867
SduI GDGCHC 3 cut(s) 290, 447, 641
SexAI ACCWGGT 1 cut(s) 865
SfcI CTRYAG 2 cut(s) 395, 501
SinI GGWCC 1 cut(s) 583
SmiMI CAYNNNNRTG 1 cut(s) 602
SmlI CTYRAG 3 cut(s) 521, 836, 946
SmoI CTYRAG 3 cut(s) 521, 836, 946
Sse9I AATT 5 cut(s) 124, 303, 745, 1025, 1046
SspMI CTAG 2 cut(s) 705, 1014
StyD4I CCNGG 3 cut(s) 266, 380, 865
StyI CCWWGG 3 cut(s) 43, 134, 210
TaaI ACNGT 3 cut(s) 634, 913, 1007
TaiI ACGT 1 cut(s) 97
TaqI TCGA 2 cut(s) 441, 490
TasI AATT 5 cut(s) 124, 303, 745, 1025, 1046
TatI WGTACW 1 cut(s) 680
TfiI GAWTC 5 cut(s) 221, 320, 418, 481, 796
Tru1I TTAA 3 cut(s) 123, 522, 837
Tru9I TTAA 3 cut(s) 123, 522, 837
TscAI CASTG 3 cut(s) 880, 1012, 1027
TseI GCWGC 3 cut(s) 23, 377, 394
TspDTI ATGAA 6 cut(s) 18, 42, 175, 246, 983, 996
TspGWI ACGGA 1 cut(s) 1063
TspRI CASTG 3 cut(s) 880, 1012, 1027
Tth111I GACNNNGTC 1 cut(s) 542
Vha464I CTTAAG 2 cut(s) 521, 836
VneI GTGCAC 1 cut(s) 637
VpaK11BI GGWCC 1 cut(s) 583
XapI RAATTY 3 cut(s) 303, 745, 1046
XbaI TCTAGA 1 cut(s) 704
XspI CTAG 2 cut(s) 705, 1014
ZrmI AGTACT 1 cut(s) 682
Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.