MD09G1098100.v1.1

gag-polypeptide of LTR copia-type

Design Primers CRISPR Design

Basic Information

Type: gene
Biological Identity
malus_domestica
Chr09
OG0000278
Physical Location & Seq
Forward (+)
7127247 .. 7130223
2977 bp
Loading structure...
UTR
Exon/CDS
Intron
MD09G1098100.v1.1.491

Sequence Viewer

Length: 1071 bp
ATGTGGCCTTTTGTTTATATTAAGGCATTTGGTTATGCCTTTATAAAAGAGAGAGTTGAGAACGGCAGATTAGAGAGAAGAAAGAGAAGGGTTGCTGTTATCTATCCTTCCCATTTGTTTGGTGTGGAGGCCTTGCCACAAGATTGGTCTGCTGAAGAAAAAGAAGACACTTTGAATCGAGCACATAGTGCAATTATGTTATCACTATCTGATGAAGTTCTTCGTGAGATGGAAAATGAAATTACTGCAGCTGGTTTGTGGCTTAAGTTGGAGAGTATATACATGACCAAATCCCTCACCAATCTTTTGTATTTGAAGCAACGTTTGTACACTCTCCGTATGACTGAAGGTACACCTATTCAAAACCATCTTGATGAGTTTAATAAGGTTATTATGGATTTGAAAAGTATGGATAATAAAATTGATGATGAGGATCAATCTTTGATTTTGTTGTGTTCTTTACCTCCTTCGTATGCGAATTTTGTTGAAACTTTGTTATATGGGAGAGATTCTATTTGTATGGAGAATGTGAAAGCCGCTTTGAATTCAAGAGAGTTAAAGAACAAAGTATTTGGAAATTTGAATGATTCTCATTCTGAGGCTTTTATAGCAAGAGGCAGAGATAGGGAATATGGTTCAGGTAGTAATAAAGGAAATTTGAGATCGAAGTCTAAGACCAGAAACAACACATGCAACTATTGTCGCAAGGAAGGGCATTGGAAAGTTGATTGCCCAAAATTGAAAGATAATGCTGTTGCTCTTCATCGGTGTTTTTATTGTTTTGGATATTGGTGGAGTTCGTTGTGTGTCCAACTTTGGTATGGTGTGCTTGATCTTTTGTTGGCGATATTGAAGAATTTCAGTTCTTCGTTTGAATCACCTTTTGTTTTGATCAAGGCACTTATGGTTTGCAAATTTGGAGAAGACGGTAAAGAAATGGTCTACTTTTGTTGGCTTTGGTACAATTTGAGTCGAGGTGGAAATTGTTATGAGCACTGGACGATAGCTCTGAAAAGACAGATTTCCTATCTTTTCTTTAATTTTGGGCGAAATATGATCAGGAATGGTTAA
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

357

Amino Acids

41.53

Weight (kDa)

8.73

Isoelectric Point (pI)

35.53

Instability Index
Protein Domains (Pfam)
Domain Name Pfam ID Position E-value Description
Retrotran_gag_2 PF14223 59 - 185 2.2e-31 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: OG0000278)

Species Orthologous Gene IDs
arabidopsis_thaliana AT3G29785
fragaria_vesca FvH4_1g10046 FvH4_1g17351 FvH4_1g18441 FvH4_1g24222 FvH4_2g00141 FvH4_2g05931 FvH4_2g06671 FvH4_2g14030 FvH4_2g15291 FvH4_2g22611 FvH4_2g22612 FvH4_2g26380 FvH4_2g39202 FvH4_2g39202 FvH4_3g06691 FvH4_3g08580 FvH4_3g20502 FvH4_3g20503 FvH4_3g22421 FvH4_3g42580 FvH4_4g02061 FvH4_4g06794 FvH4_4g08661 FvH4_4g11771 FvH4_4g14601 FvH4_4g14721 FvH4_4g20921 FvH4_4g33601 FvH4_4g33602 FvH4_5g07492 FvH4_5g20321 FvH4_5g21591 FvH4_5g30343 FvH4_5g37875 FvH4_6g04372 FvH4_6g04373 FvH4_6g04373 FvH4_6g21377 FvH4_6g23760 FvH4_6g29471 FvH4_6g43142 FvH4_7g14351 FvH4_7g14352 FvH4_7g22582 FvH4_7g22583 FvH4_7g22584
malus_domestica MD00G1179400.v1.1 MD01G1170500.v1.1 MD03G1286700.v1.1 MD04G1054600.v1.1 MD04G1071700.v1.1 MD04G1193900.v1.1 MD08G1054300.v1.1 MD08G1217500.v1.1 MD09G1034600.v1.1 MD09G1098100.v1.1 MD10G1018300.v1.1 MD10G1220000.v1.1 MD10G1250300.v1.1 MD12G1014400.v1.1 MD15G1021000.v1.1 MD16G1112200.v1.1
prunus_persica Prupe.1G188900_v2.0.a1 Prupe.1G258000_v2.0.a1 Prupe.4G233400_v2.0.a1
pyrus_communis pycom01g10100 pycom02g01340 pycom03g19700 pycom05g01320 pycom07g16000 pycom07g16520 pycom11g26500 pycom13g09380 pycom13g13960 pycom14g08180 pycom14g16810 pycom16g09590
rosa_chinensis RchiOBHm_Chr1g0319891 RchiOBHm_Chr1g0333711 RchiOBHm_Chr2g0115331 RchiOBHm_Chr2g0143411 RchiOBHm_Chr2g0167631 RchiOBHm_Chr3g0448581 RchiOBHm_Chr3g0494991 RchiOBHm_Chr4g0442471 RchiOBHm_Chr6g0262311 RchiOBHm_Chr6g0301831 RchiOBHm_Chr6g0301841 RchiOBHm_Chr7g0183451
rosa_roxburghii Rroxscaffold_1G00039280 Rroxscaffold_1G00047670 Rroxscaffold_1G00066330 Rroxscaffold_2G00107510 Rroxscaffold_3G00255410 Rroxscaffold_4G00301460 Rroxscaffold_5G00352730 Rroxscaffold_7G00166350 Rroxscaffold_7G00166360 Rroxscaffold_7G00203820
rosa_rugosa Rorug03G0240500 Rorug05G0191700 Rorug06G0310200
rosa_samantha Rh2BG287000 Rh4CG073500 Rh4CG176200 Rh4CG191400 Rh5BG356100 Rh5BG434100 Rh6AG110600 Rh6AG421900 Rh6AG422000 Rh6AG422100 Rh6BG428600 Rh6BG428700 Rh6BG428800 Rh6CG435200 Rh6CG435300 Rh6CG435400 Rh6DG422000 Rh6DG422100 Rh6DG422200 Rh7BG190500 Rh7CG172800 Rh7CG225200
rosa_wichuraiana Rw2G044060 Rw6G036540

Restriction Enzyme Sites

1 / 10
Enzyme Recognition Site Cut Count Positions (bp)
AanI TTATAA 1 cut(s) 44
AccI GTMKAC 1 cut(s) 942
AciI CCGC 1 cut(s) 537
AclI AACGTT 1 cut(s) 322
AclWI GGATC 1 cut(s) 441
AcsI RAATTY 6 cut(s) 478, 544, 577, 655, 856, 914
AcuI CTGAAG 2 cut(s) 174, 366
AdeI CACNNNGTG 1 cut(s) 188
AfaI GTAC 3 cut(s) 329, 352, 962
AflII CTTAAG 1 cut(s) 263
AluBI AGCT 2 cut(s) 251, 1007
AluI AGCT 2 cut(s) 251, 1007
Alw21I GWGCWC 2 cut(s) 184, 996
AlwI GGATC 1 cut(s) 441
AoxI GGCC 2 cut(s) 5, 129
ApeKI GCWGC 1 cut(s) 248
ApoI RAATTY 6 cut(s) 478, 544, 577, 655, 856, 914
Asp700I GAANNNNTTC 2 cut(s) 219, 857
AsuHPI GGTGA 2 cut(s) 289, 870
BbsI GAAGAC 2 cut(s) 171, 930
Bbv12I GWGCWC 2 cut(s) 184, 996
BbvI GCAGC 1 cut(s) 260
BccI CCATC 2 cut(s) 223, 375
BceAI ACGGC 1 cut(s) 79
BclI TGATCA 2 cut(s) 891, 1056
BfmI CTRYAG 1 cut(s) 246
BfrI CTTAAG 1 cut(s) 263
BisI GCNGC 2 cut(s) 249, 537
BlsI GCNGC 2 cut(s) 250, 538
BpiI GAAGAC 2 cut(s) 171, 930
BsaBI GATNNNNATC 1 cut(s) 432
Bse1I ACTGG 1 cut(s) 1001
Bse8I GATNNNNATC 1 cut(s) 432
BseJI GATNNNNATC 1 cut(s) 432
BseMII CTCAG 1 cut(s) 588
BseNI ACTGG 1 cut(s) 1001
BseXI GCAGC 1 cut(s) 260
BshFI GGCC 2 cut(s) 7, 131
BsiHKAI GWGCWC 2 cut(s) 184, 996
BsnI GGCC 2 cut(s) 7, 131
Bsp1286I GDGCHC 2 cut(s) 184, 996
Bsp1407I TGTACA 1 cut(s) 327
Bsp143I GATC 5 cut(s) 433, 662, 832, 891, 1056
BspACI CCGC 1 cut(s) 537
BspANI GGCC 2 cut(s) 7, 131
BspCNI CTCAG 1 cut(s) 589
BspMAI CTGCAG 1 cut(s) 250
BspPI GGATC 1 cut(s) 441
BspQI GCTCTTC 1 cut(s) 765
BspTI CTTAAG 1 cut(s) 263
BsrGI TGTACA 1 cut(s) 327
BsrI ACTGG 1 cut(s) 1001
BssMI GATC 5 cut(s) 433, 662, 832, 891, 1056
Bst4CI ACNGT 1 cut(s) 929
Bst6I CTCTTC 1 cut(s) 765
BstAFI CTTAAG 1 cut(s) 263
BstAPI GCANNNNNTGC 1 cut(s) 188
BstAUI TGTACA 1 cut(s) 327
BstDEI CTNAG 2 cut(s) 597, 672
BstKTI GATC 5 cut(s) 436, 665, 835, 894, 1059
BstMBI GATC 5 cut(s) 433, 662, 832, 891, 1056
BstMWI GCNNNNNNNGC 2 cut(s) 188, 608
BstNSI RCATGY 1 cut(s) 693
BstSFI CTRYAG 1 cut(s) 246
BstV1I GCAGC 1 cut(s) 260
BstV2I GAAGAC 2 cut(s) 171, 930
BstXI CCANNNNNNTGG 2 cut(s) 119, 144
BsuRI GGCC 2 cut(s) 7, 131
BtsIMutI CAGTG 1 cut(s) 994
Csp6I GTAC 3 cut(s) 328, 351, 961
CviAII CATG 2 cut(s) 283, 690
CviJI RGCY 8 cut(s) 7, 131, 251, 262, 536, 602, 955, 1007
CviKI_1 RGCY 8 cut(s) 7, 131, 251, 262, 536, 602, 955, 1007
CviQI GTAC 3 cut(s) 328, 351, 961
DdeI CTNAG 2 cut(s) 597, 672
DpnI GATC 5 cut(s) 435, 664, 834, 893, 1058
DpnII GATC 5 cut(s) 433, 662, 832, 891, 1056
DraIII CACNNNGTG 1 cut(s) 188
Eam1104I CTCTTC 1 cut(s) 765
EarI CTCTTC 1 cut(s) 765
Eco147I AGGCCT 1 cut(s) 131
Eco57I CTGAAG 2 cut(s) 174, 366
EcoRI GAATTC 1 cut(s) 544
FaeI CATG 2 cut(s) 286, 693
FatI CATG 2 cut(s) 282, 689
FbaI TGATCA 2 cut(s) 891, 1056
FblI GTMKAC 1 cut(s) 942
Fnu4HI GCNGC 2 cut(s) 249, 537
Fsp4HI GCNGC 2 cut(s) 249, 537
GluI GCNGC 2 cut(s) 249, 537
HaeIII GGCC 2 cut(s) 7, 131
Hin1II CATG 2 cut(s) 286, 693
HinfI GANTC 5 cut(s) 175, 509, 587, 875, 970
HphI GGTGA 2 cut(s) 289, 870
Hpy166II GTNNAC 3 cut(s) 330, 353, 943
Hpy188I TCNGA 3 cut(s) 211, 598, 1011
Hpy188III TCNNGA 4 cut(s) 224, 371, 549, 1060
Hpy8I GTNNAC 3 cut(s) 330, 353, 943
HpyAV CCTTC 5 cut(s) 81, 117, 341, 477, 704
HpyCH4III ACNGT 1 cut(s) 929
HpyCH4IV ACGT 1 cut(s) 322
HpyCH4V TGCA 4 cut(s) 191, 248, 693, 912
HpyF10VI GCNNNNNNNGC 2 cut(s) 188, 608
HpyF3I CTNAG 2 cut(s) 597, 672
HpySE526I ACGT 1 cut(s) 322
Hsp92II CATG 2 cut(s) 286, 693
Ksp22I TGATCA 2 cut(s) 891, 1056
Kzo9I GATC 5 cut(s) 433, 662, 832, 891, 1056
LguI GCTCTTC 1 cut(s) 765
LpnPI CCDG 5 cut(s) 237, 624, 691, 982, 1045
Lsp1109I GCAGC 1 cut(s) 260
MaeII ACGT 1 cut(s) 322
MalI GATC 5 cut(s) 435, 664, 834, 893, 1058
MboI GATC 5 cut(s) 433, 662, 832, 891, 1056
MboII GAAGA 8 cut(s) 90, 167, 176, 212, 752, 858, 865, 935
MhlI GDGCHC 2 cut(s) 184, 996
MlyI GAGTC 1 cut(s) 979
MmeI TCCRAC 2 cut(s) 249, 835
MnlI CCTC 7 cut(s) 121, 305, 424, 474, 592, 608, 968
MroXI GAANNNNTTC 2 cut(s) 219, 857
MseI TTAA 6 cut(s) 21, 264, 381, 557, 1038, 1069
MslI CAYNNNNRTG 1 cut(s) 372
MspA1I CMGCKG 1 cut(s) 251
MspCI CTTAAG 1 cut(s) 263
MwoI GCNNNNNNNGC 2 cut(s) 188, 608
NdeII GATC 5 cut(s) 433, 662, 832, 891, 1056
NlaIII CATG 2 cut(s) 286, 693
NspI RCATGY 1 cut(s) 693
PceI AGGCCT 1 cut(s) 131
PciSI GCTCTTC 1 cut(s) 765
PdmI GAANNNNTTC 2 cut(s) 219, 857
PfeI GAWTC 4 cut(s) 175, 509, 587, 875
PkrI GCNGC 2 cut(s) 250, 538
PleI GAGTC 1 cut(s) 978
PpsI GAGTC 1 cut(s) 978
PsiI TTATAA 1 cut(s) 44
Psp1406I AACGTT 1 cut(s) 322
PstI CTGCAG 1 cut(s) 250
PvuII CAGCTG 1 cut(s) 251
RsaI GTAC 3 cut(s) 329, 352, 962
RsaNI GTAC 3 cut(s) 328, 351, 961
RseI CAYNNNNRTG 1 cut(s) 372
SapI GCTCTTC 1 cut(s) 765
SaqAI TTAA 6 cut(s) 21, 264, 381, 557, 1038, 1069
SatI GCNGC 2 cut(s) 249, 537
Sau3AI GATC 5 cut(s) 433, 662, 832, 891, 1056
SchI GAGTC 1 cut(s) 979
SduI GDGCHC 2 cut(s) 184, 996
SfcI CTRYAG 1 cut(s) 246
SmiMI CAYNNNNRTG 1 cut(s) 372
SmlI CTYRAG 1 cut(s) 263
SmoI CTYRAG 1 cut(s) 263
SseBI AGGCCT 1 cut(s) 131
SsiI CCGC 1 cut(s) 537
StuI AGGCCT 1 cut(s) 131
TaaI ACNGT 1 cut(s) 929
TaiI ACGT 1 cut(s) 325
TaqI TCGA 3 cut(s) 178, 665, 973
TatI WGTACW 1 cut(s) 327
TauI GCSGC 1 cut(s) 539
TfiI GAWTC 4 cut(s) 175, 509, 587, 875
Tru1I TTAA 6 cut(s) 21, 264, 381, 557, 1038, 1069
Tru9I TTAA 6 cut(s) 21, 264, 381, 557, 1038, 1069
TscAI CASTG 1 cut(s) 1001
TseI GCWGC 1 cut(s) 248
TspDTI ATGAA 3 cut(s) 228, 252, 752
TspGWI ACGGA 1 cut(s) 326
TspRI CASTG 1 cut(s) 1001
Vha464I CTTAAG 1 cut(s) 263
XapI RAATTY 6 cut(s) 478, 544, 577, 655, 856, 914
XceI RCATGY 1 cut(s) 693
XcmI CCANNNNNNNNNTGG 1 cut(s) 818
XmiI GTMKAC 1 cut(s) 942
XmnI GAANNNNTTC 2 cut(s) 219, 857
Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.