MD09G1260000.v1.1

RNA polymerase II transcription elongation factor

Design Primers CRISPR Design

Basic Information

Type: gene
Biological Identity
malus_domestica
Chr09
OG0021905
Physical Location & Seq
Forward (+)
33274649 .. 33277920
3272 bp
Loading structure...
UTR
Exon/CDS
Intron
MD09G1260000.v1.1.491

Sequence Viewer

Length: 1266 bp
ATGGCGACGAATCGGAAGAGCAACGAAGACGACGAGCCAAACGGTGCTCCGGAGACCGACCGGTGGTACAGCCTAACCCTAGGTTCTTCCTTCGTGGACCACCGTCCCTCCCCCAAGTTCTGCACCTTACGCTATGAATTTAAACCGGCTTCAATTGACAAGAACCAACCAGGGTTGTTACACAAGAGCAAGGATAATAGAGTTGCATTAGAATTTCACAACAACCAACACGGAAAACCCAAAGTGACTTTTGAAGGTGTGAGTGAGGATCACAAGAAAGACGAGGCCGTTTTGTTCTTTGACGGTGAGGGTTTTCGGTTGGAGAGGTTGCACCGAGCAGTGAAGCGGTTGAGGCATGTCAGGCTGCCTGGTGAATCTACAGCTCCAGTGGCCGCAGTCACGAGTACATCAGTTTCAGCGGTGGAATCTTATTCTCCACCAACCGGTGGCAAAGGACCAAAGCTTCAGTCTTTGAACAAGGACATTCTTCCTAATATGCCTCCGGTGGAGATGAAAGAAATTGATAACAACAGCTCAGCGTGCTTAGACCCAGGGCCAAAACCTGAAACCGGCGAGAATTTTGACTGTCCGCCTTCCTTACCAAATCCACCAACTGCATCTCCTGATGCACAAAGAAGCGATGAAATGGAGGAAGAAGTGGATGTTGTCATTGATGATGATGACAATGAAGATGACGGTGATAATGATGATGATATATCTGAGAAGGGAAGATCTCCTGGAAAGGAATTTCACACCGGCATTGACATTAACTTACCTCATCCAGGAGTTATGGATGATGAGATTGCTGATGCGGATGTAAGTGATGATGTGATGTATAATGGCCCAAATGCTGCCAAAGCGCTCAGAGGTCAGGTTAATGCTGAGGTGGGAGAGAAGCACACTGATATGGATGATGAGGTTGTGGATGTAAGTGATGATATGATGGATAACGGCCCAAATGCTGCAGAAGCCCTCAAAGCTCAGGTGAATGCCGAGGTGGGAGAGAAGCAGACTTATCTGGATGATGAGATTGTGGATGTAAGTGATGATGTGATGGATAATGGCCCAAATGCTGCTGAAGCCCTCAGAGCTCAGGTGAATGCCGAGGTGGGAGAGAAAGAGACGTCAAGCTCAAACGATACTAGTGAGAGTGAGAGTAGCAGTGGAAGCGGAAGCGGAAGTGGAAGCGAAAGTGAAAGCGAGAGTGAGAGTAGCAGCAGTGATAATGAAAGCAGTGAAGGTGGCGACTCAGTAAATTCTATCTAG
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
EAF

Protein Analysis

422

Amino Acids

45.31

Weight (kDa)

4.28

Isoelectric Point (pI)

45.44

Instability Index
Protein Domains (Pfam)
Domain Name Pfam ID Position E-value Description
EAF PF09816 23 - 121 1.2e-21 RNA polymerase II transcription elongation factor
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: OG0021905)

Species Orthologous Gene IDs
arabidopsis_thaliana AT5G38050
malus_domestica MD09G1260000.v1.1
prunus_persica Prupe.3G151600_v2.0.a1
pyrus_communis pycom09g17460

Restriction Enzyme Sites

1 / 10
Enzyme Recognition Site Cut Count Positions (bp)
AatII GACGTC 1 cut(s) 1127
AccB7I CCANNNNNTGG 1 cut(s) 446
AccIII TCCGGA 1 cut(s) 49
AciI CCGC 7 cut(s) 346, 393, 419, 590, 812, 1170, 1176
AclWI GGATC 1 cut(s) 276
AcoI YGGCCR 1 cut(s) 390
AcsI RAATTY 5 cut(s) 137, 212, 577, 746, 1255
AcuI CTGAAG 2 cut(s) 449, 1098
AcyI GRCGYC 1 cut(s) 1124
AfaI GTAC 2 cut(s) 68, 406
AfeI AGCGCT 1 cut(s) 861
AfiI CCNNNNNNNGG 5 cut(s) 63, 443, 446, 569, 782
AgeI ACCGGT 2 cut(s) 60, 443
AgsI TTSAA 3 cut(s) 153, 254, 475
AhlI ACTAGT 1 cut(s) 1142
AjnI CCWGG 5 cut(s) 169, 367, 550, 736, 781
AluBI AGCT 6 cut(s) 383, 463, 534, 980, 1091, 1131
AluI AGCT 6 cut(s) 383, 463, 534, 980, 1091, 1131
Alw21I GWGCWC 2 cut(s) 49, 1093
Alw26I GTCTC 2 cut(s) 47, 1115
AlwI GGATC 1 cut(s) 276
Aor13HI TCCGGA 1 cut(s) 49
Aor51HI AGCGCT 1 cut(s) 861
AoxI GGCC 6 cut(s) 285, 390, 554, 841, 952, 1063
ApeKI GCWGC 5 cut(s) 364, 851, 962, 1073, 1215
ApoI RAATTY 5 cut(s) 137, 212, 577, 746, 1255
ArsI GACNNNNNNTTYG 2 cut(s) 452, 484
AsiGI ACCGGT 2 cut(s) 60, 443
AspA2I CCTAGG 1 cut(s) 79
AspLEI GCGC 1 cut(s) 862
AspS9I GGNCC 6 cut(s) 97, 455, 554, 842, 953, 1064
AsuHPI GGTGA 5 cut(s) 317, 383, 710, 997, 1108
AvaII GGWCC 2 cut(s) 97, 455
AvrII CCTAGG 1 cut(s) 79
BanII GRGCYC 1 cut(s) 1093
BauI CACGAG 1 cut(s) 400
BbsI GAAGAC 1 cut(s) 33
Bbv12I GWGCWC 2 cut(s) 49, 1093
BbvCI CCTCAGC 1 cut(s) 882
BbvI GCAGC 5 cut(s) 351, 838, 949, 1060, 1227
BccI CCATC 2 cut(s) 937, 1048
BceAI ACGGC 2 cut(s) 272, 967
BciT130I CCWGG 5 cut(s) 171, 369, 552, 738, 783
BcoDI GTCTC 2 cut(s) 47, 1115
BcuI ACTAGT 1 cut(s) 1142
BfaI CTAG 3 cut(s) 80, 1143, 1264
BfmI CTRYAG 2 cut(s) 378, 963
BfoI RGCGCY 1 cut(s) 863
BglII AGATCT 1 cut(s) 731
BisI GCNGC 6 cut(s) 365, 393, 852, 963, 1074, 1216
BlnI CCTAGG 1 cut(s) 79
BlpI GCTNAGC 1 cut(s) 535
BlsI GCNGC 6 cut(s) 366, 394, 853, 964, 1075, 1217
Bme1390I CCNGG 5 cut(s) 171, 369, 552, 738, 783
Bme18I GGWCC 2 cut(s) 97, 455
BmgT120I GGNCC 6 cut(s) 97, 455, 554, 842, 953, 1064
BmrFI CCNGG 5 cut(s) 171, 369, 552, 738, 783
BmsI GCATC 3 cut(s) 616, 626, 799
BoxI GACNNNNGTC 1 cut(s) 102
BpiI GAAGAC 1 cut(s) 33
BpmI CTGGAG 1 cut(s) 369
Bpu10I CCTNAGC 3 cut(s) 882, 981, 1092
Bpu1102I GCTNAGC 1 cut(s) 535
BsaHI GRCGYC 1 cut(s) 1124
BsaI GGTCTC 1 cut(s) 47
BsaJI CCNNGG 6 cut(s) 79, 170, 550, 551, 993, 1104
BsaWI WCCGGW 4 cut(s) 49, 60, 443, 502
BsaXI ACNNNNNCTCC 4 cut(s) 92, 122, 604, 634
Bsc4I CCNNNNNNNGG 5 cut(s) 63, 443, 446, 569, 782
Bse118I RCCGGY 5 cut(s) 60, 145, 443, 569, 755
Bse1I ACTGG 1 cut(s) 386
BseAI TCCGGA 1 cut(s) 49
BseBI CCWGG 5 cut(s) 171, 369, 552, 738, 783
BseDI CCNNGG 6 cut(s) 79, 170, 550, 551, 993, 1104
BseGI GGATG 8 cut(s) 667, 778, 799, 820, 916, 931, 1027, 1042
BseLI CCNNNNNNNGG 5 cut(s) 63, 443, 446, 569, 782
BseMII CTCAG 8 cut(s) 549, 711, 873, 877, 995, 1099, 1106, 1263
BseNI ACTGG 1 cut(s) 386
BseXI GCAGC 5 cut(s) 351, 838, 949, 1060, 1227
BsgI GTGCAG 1 cut(s) 106
Bsh1285I CGRYCG 1 cut(s) 61
BshFI GGCC 6 cut(s) 287, 392, 556, 843, 954, 1065
BshTI ACCGGT 2 cut(s) 60, 443
BsiEI CGRYCG 1 cut(s) 61
BsiHKAI GWGCWC 2 cut(s) 49, 1093
BsiSI CCGG 7 cut(s) 50, 61, 146, 444, 503, 570, 756
BslFI GGGAC 1 cut(s) 90
BslI CCNNNNNNNGG 5 cut(s) 63, 443, 446, 569, 782
BsmAI GTCTC 2 cut(s) 47, 1115
BsmBI CGTCTC 1 cut(s) 1115
BsmFI GGGAC 1 cut(s) 90
BsmI GAATGC 2 cut(s) 994, 1105
BsnI GGCC 6 cut(s) 287, 392, 556, 843, 954, 1065
Bso31I GGTCTC 1 cut(s) 47
Bsp1286I GDGCHC 2 cut(s) 49, 1093
Bsp13I TCCGGA 1 cut(s) 49
Bsp143I GATC 2 cut(s) 268, 731
Bsp1720I GCTNAGC 1 cut(s) 535
BspACI CCGC 7 cut(s) 346, 393, 419, 590, 812, 1170, 1176
BspANI GGCC 6 cut(s) 287, 392, 556, 843, 954, 1065
BspCNI CTCAG 8 cut(s) 548, 712, 874, 876, 994, 1098, 1105, 1262
BspEI TCCGGA 1 cut(s) 49
BspMAI CTGCAG 1 cut(s) 967
BspPI GGATC 1 cut(s) 276
BspQI GCTCTTC 1 cut(s) 11
BspTNI GGTCTC 1 cut(s) 47
BsrFI RCCGGY 5 cut(s) 60, 145, 443, 569, 755
BsrI ACTGG 1 cut(s) 386
BssAI RCCGGY 5 cut(s) 60, 145, 443, 569, 755
BssECI CCNNGG 6 cut(s) 79, 170, 550, 551, 993, 1104
BssMI GATC 2 cut(s) 268, 731
BssNI GRCGYC 1 cut(s) 1124
BssSI CACGAG 1 cut(s) 400
BssT1I CCWWGG 1 cut(s) 79
Bst2BI CACGAG 1 cut(s) 400
Bst2UI CCWGG 5 cut(s) 171, 369, 552, 738, 783
Bst4CI ACNGT 5 cut(s) 44, 104, 305, 587, 698
Bst6I CTCTTC 1 cut(s) 11
BstACI GRCGYC 1 cut(s) 1124
BstC8I GCNNGC 1 cut(s) 541
BstDEI CTNAG 9 cut(s) 535, 544, 720, 863, 882, 981, 1085, 1092, 1249
BstENI CCTNNNNNAGG 1 cut(s) 780
BstF5I GGATG 8 cut(s) 667, 778, 799, 820, 916, 931, 1027, 1042
BstH2I RGCGCY 1 cut(s) 863
BstHHI GCGC 1 cut(s) 862
BstKTI GATC 2 cut(s) 271, 734
BstMAI GTCTC 2 cut(s) 47, 1115
BstMBI GATC 2 cut(s) 268, 731
BstMCI CGRYCG 1 cut(s) 61
BstNI CCWGG 5 cut(s) 171, 369, 552, 738, 783
BstNSI RCATGY 1 cut(s) 359
BstPAI GACNNNNGTC 1 cut(s) 102
BstSCI CCNGG 5 cut(s) 169, 367, 550, 736, 781
BstSFI CTRYAG 2 cut(s) 378, 963
BstV1I GCAGC 5 cut(s) 351, 838, 949, 1060, 1227
BstV2I GAAGAC 1 cut(s) 33
BstX2I RGATCY 1 cut(s) 731
BstYI RGATCY 1 cut(s) 731
BsuRI GGCC 6 cut(s) 287, 392, 556, 843, 954, 1065
BtgZI GCGATG 1 cut(s) 654
BtsCI GGATG 8 cut(s) 667, 778, 799, 820, 916, 931, 1027, 1042
BtsI GCAGTG 4 cut(s) 345, 1168, 1225, 1240
BtsIMutI CAGTG 6 cut(s) 345, 393, 900, 1168, 1225, 1240
Cac8I GCNNGC 1 cut(s) 541
CfoI GCGC 1 cut(s) 862
Cfr10I RCCGGY 5 cut(s) 60, 145, 443, 569, 755
Cfr13I GGNCC 6 cut(s) 97, 455, 554, 842, 953, 1064
Csp6I GTAC 2 cut(s) 67, 405
CspAI ACCGGT 2 cut(s) 60, 443
CviAII CATG 1 cut(s) 356
CviQI GTAC 2 cut(s) 67, 405
DdeI CTNAG 9 cut(s) 535, 544, 720, 863, 882, 981, 1085, 1092, 1249
DpnI GATC 2 cut(s) 270, 733
DpnII GATC 2 cut(s) 268, 731
DraI TTTAAA 1 cut(s) 142
EaeI YGGCCR 1 cut(s) 390
Eam1104I CTCTTC 1 cut(s) 11
EarI CTCTTC 1 cut(s) 11
EciI GGCGGA 1 cut(s) 579
Ecl136II GAGCTC 1 cut(s) 1091
Eco130I CCWWGG 1 cut(s) 79
Eco24I GRGCYC 1 cut(s) 1093
Eco31I GGTCTC 1 cut(s) 47
Eco47I GGWCC 2 cut(s) 97, 455
Eco47III AGCGCT 1 cut(s) 861
Eco53kI GAGCTC 1 cut(s) 1091
Eco57I CTGAAG 2 cut(s) 449, 1098
EcoICRI GAGCTC 1 cut(s) 1091
EcoNI CCTNNNNNAGG 1 cut(s) 780
EcoRII CCWGG 5 cut(s) 169, 367, 550, 736, 781
EcoT14I CCWWGG 1 cut(s) 79
EcoT38I GRGCYC 1 cut(s) 1093
ErhI CCWWGG 1 cut(s) 79
Esp3I CGTCTC 1 cut(s) 1115
FaeI CATG 1 cut(s) 359
FaiI YATR 8 cut(s) 135, 357, 497, 716, 791, 837, 908, 941
FaqI GGGAC 1 cut(s) 90
FatI CATG 1 cut(s) 355
Fnu4HI GCNGC 6 cut(s) 365, 393, 852, 963, 1074, 1216
FokI GGATG 8 cut(s) 674, 765, 806, 827, 923, 938, 1034, 1049
FriOI GRGCYC 1 cut(s) 1093
Fsp4HI GCNGC 6 cut(s) 365, 393, 852, 963, 1074, 1216
FspBI CTAG 3 cut(s) 80, 1143, 1264
GlaI GCGC 1 cut(s) 861
GluI GCNGC 6 cut(s) 365, 393, 852, 963, 1074, 1216
GsuI CTGGAG 1 cut(s) 369
HaeII RGCGCY 1 cut(s) 863
HaeIII GGCC 6 cut(s) 287, 392, 556, 843, 954, 1065
HapII CCGG 7 cut(s) 50, 61, 146, 444, 503, 570, 756
HhaI GCGC 1 cut(s) 862
Hin1I GRCGYC 1 cut(s) 1124
Hin1II CATG 1 cut(s) 359
Hin6I GCGC 1 cut(s) 860
HinP1I GCGC 1 cut(s) 860
HindIII AAGCTT 1 cut(s) 461
HinfI GANTC 4 cut(s) 10, 374, 425, 1247
HpaII CCGG 7 cut(s) 50, 61, 146, 444, 503, 570, 756
HphI GGTGA 5 cut(s) 317, 383, 710, 997, 1108
Hpy166II GTNNAC 1 cut(s) 97
Hpy188I TCNGA 4 cut(s) 15, 721, 866, 1088
Hpy188III TCNNGA 4 cut(s) 50, 400, 623, 1019
Hpy8I GTNNAC 1 cut(s) 97
Hpy99I CGWCG 2 cut(s) 10, 35
HpyAV CCTTC 5 cut(s) 100, 248, 603, 718, 1232
HpyCH4III ACNGT 5 cut(s) 44, 104, 305, 587, 698
HpyCH4IV ACGT 1 cut(s) 1124
HpyCH4V TGCA 6 cut(s) 123, 206, 331, 617, 629, 965
HpyF3I CTNAG 9 cut(s) 535, 544, 720, 863, 882, 981, 1085, 1092, 1249
HpySE526I ACGT 1 cut(s) 1124
Hsp92I GRCGYC 1 cut(s) 1124
Hsp92II CATG 1 cut(s) 359
HspAI GCGC 1 cut(s) 860
Kpn2I TCCGGA 1 cut(s) 49
Kzo9I GATC 2 cut(s) 268, 731
LguI GCTCTTC 1 cut(s) 11
LmnI GCTCC 2 cut(s) 52, 388
Lsp1109I GCAGC 5 cut(s) 351, 838, 949, 1060, 1227
LweI GCATC 3 cut(s) 616, 626, 799
MaeI CTAG 3 cut(s) 80, 1143, 1264
MaeII ACGT 1 cut(s) 1124
MaeIII GTNAC 3 cut(s) 177, 244, 397
MalI GATC 2 cut(s) 270, 733
MboI GATC 2 cut(s) 268, 731
MboII GAAGA 7 cut(s) 28, 38, 78, 479, 665, 701, 741
MfeI CAATTG 1 cut(s) 153
MflI RGATCY 1 cut(s) 731
MhlI GDGCHC 2 cut(s) 49, 1093
MluCI AATT 7 cut(s) 137, 153, 212, 519, 577, 746, 1255
MlyI GAGTC 1 cut(s) 1241
MmeI TCCRAC 1 cut(s) 300
MroI TCCGGA 1 cut(s) 49
MseI TTAA 3 cut(s) 141, 768, 876
MslI CAYNNNNRTG 1 cut(s) 905
MspA1I CMGCKG 1 cut(s) 419
MspI CCGG 7 cut(s) 50, 61, 146, 444, 503, 570, 756
MspR9I CCNGG 5 cut(s) 171, 369, 552, 738, 783
MunI CAATTG 1 cut(s) 153
Mva1269I GAATGC 2 cut(s) 994, 1105
MvaI CCWGG 5 cut(s) 171, 369, 552, 738, 783
NdeII GATC 2 cut(s) 268, 731
NlaIII CATG 1 cut(s) 359
NmeAIII GCCGAG 2 cut(s) 1018, 1129
NmuCI GTSAC 2 cut(s) 244, 397
NspI RCATGY 1 cut(s) 359
PasI CCCWGGG 1 cut(s) 551
PciSI GCTCTTC 1 cut(s) 11
PcsI WCGNNNNNNNCGW 1 cut(s) 30
PctI GAATGC 2 cut(s) 994, 1105
PfeI GAWTC 3 cut(s) 10, 374, 425
PflMI CCANNNNNTGG 1 cut(s) 446
PfoI TCCNGGA 2 cut(s) 736, 781
PinAI ACCGGT 2 cut(s) 60, 443
PkrI GCNGC 6 cut(s) 366, 394, 853, 964, 1075, 1217
PleI GAGTC 1 cut(s) 1241
PpsI GAGTC 1 cut(s) 1241
PshAI GACNNNNGTC 1 cut(s) 102
Psp124BI GAGCTC 1 cut(s) 1093
Psp6I CCWGG 5 cut(s) 169, 367, 550, 736, 781
PspGI CCWGG 5 cut(s) 169, 367, 550, 736, 781
PspPI GGNCC 6 cut(s) 97, 455, 554, 842, 953, 1064
PstI CTGCAG 1 cut(s) 967
PsuI RGATCY 1 cut(s) 731
RsaI GTAC 2 cut(s) 68, 406
RsaNI GTAC 2 cut(s) 67, 405
RseI CAYNNNNRTG 1 cut(s) 905
SacI GAGCTC 1 cut(s) 1093
SapI GCTCTTC 1 cut(s) 11
SaqAI TTAA 3 cut(s) 141, 768, 876
SatI GCNGC 6 cut(s) 365, 393, 852, 963, 1074, 1216
Sau3AI GATC 2 cut(s) 268, 731
Sau96I GGNCC 6 cut(s) 97, 455, 554, 842, 953, 1064
SchI GAGTC 1 cut(s) 1241
ScrFI CCNGG 5 cut(s) 171, 369, 552, 738, 783
SduI GDGCHC 2 cut(s) 49, 1093
SfaNI GCATC 3 cut(s) 616, 626, 799
SfcI CTRYAG 2 cut(s) 378, 963
SinI GGWCC 2 cut(s) 97, 455
SmiMI CAYNNNNRTG 1 cut(s) 905
SpeI ACTAGT 1 cut(s) 1142
Sse9I AATT 7 cut(s) 137, 153, 212, 519, 577, 746, 1255
SsiI CCGC 7 cut(s) 346, 393, 419, 590, 812, 1170, 1176
SspMI CTAG 3 cut(s) 80, 1143, 1264
SstI GAGCTC 1 cut(s) 1093
StyD4I CCNGG 5 cut(s) 169, 367, 550, 736, 781
StyI CCWWGG 1 cut(s) 79
TaaI ACNGT 5 cut(s) 44, 104, 305, 587, 698
TaiI ACGT 1 cut(s) 1127
TaqII GACCGA 1 cut(s) 71
TasI AATT 7 cut(s) 137, 153, 212, 519, 577, 746, 1255
TatI WGTACW 1 cut(s) 404
TauI GCSGC 1 cut(s) 395
TfiI GAWTC 3 cut(s) 10, 374, 425
Tru1I TTAA 3 cut(s) 141, 768, 876
Tru9I TTAA 3 cut(s) 141, 768, 876
TscAI CASTG 6 cut(s) 345, 393, 907, 1168, 1225, 1240
TseFI GTSAC 2 cut(s) 244, 397
TseI GCWGC 5 cut(s) 364, 851, 962, 1073, 1215
Tsp45I GTSAC 2 cut(s) 244, 397
TspDTI ATGAA 5 cut(s) 150, 527, 657, 702, 1242
TspGWI ACGGA 1 cut(s) 246
TspRI CASTG 6 cut(s) 345, 393, 907, 1168, 1225, 1240
Van91I CCANNNNNTGG 1 cut(s) 446
VpaK11BI GGWCC 2 cut(s) 97, 455
XagI CCTNNNNNAGG 1 cut(s) 780
XapI RAATTY 5 cut(s) 137, 212, 577, 746, 1255
XceI RCATGY 1 cut(s) 359
XmaJI CCTAGG 1 cut(s) 79
XspI CTAG 3 cut(s) 80, 1143, 1264
ZraI GACGTC 1 cut(s) 1125
Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.