AT1G56440

RNA polymerase II-associated protein 3-like isoform X1

Design Primers CRISPR Design

Basic Information

Type: gene
Biological Identity
arabidopsis_thaliana
1
OG0005138
Physical Location & Seq
Reverse (-)
21138515 .. 21141644
3130 bp
Loading structure...
UTR
Exon/CDS
Intron
AT1G56440.1

Sequence Viewer

Length: 1431 bp
ATGGCTAGGTCACCGAGCAAACACGGCCGCGATCAAACTCAGGATTTCCAGGGATTTTTCAATGACTTGCAGGATTGGGAACTCTCATTGAAGGATAAAGACAAGAAGATTAAGCAACAACCTGCTAATTCGTCGAATCCGAGTAGTGAGACGTTCAGACCAAGTGGGTCAGGGAAATATGACTTTGCTAAAAAGTATCGTTCCATTAGGGATTTGTCGAGTAGTTTGATTGGAGAAAGTCTATTGGATTCTAGTTCAGAGAAGGAGCAGGGTAATGAATTCTTCAAGCAGAAGAAGTTCAATGAGGCGATTGATTGTTACTCTCGGAGCATTGCTTTATCGCCAAATGCTGTGACTTATGCAAATCGAGCAATGGCTTACCTTAAAATCAAAAGATATCGAGAGGCTGAGGTTGACTGCACAGAAGCTTTAAATCTGGATGATCGATATATAAAAGCTTACTCACGCCGAGCAACAGCAAGAAAAGAACTCGGCATGATTAAAGAAGCCAAAGAAGATGCTGAGTTTGCCTTAAGATTGGAGCCTGAGAGCCAGGAACTTAAGAAGCAATATGCCGATATCAAATCTTTGCTCGAGAAAGAAATCATTGAGAAAGCCACTGGAGCAATGCAAAGCACTGCACAAGAATTACTCAAAACATCAGGTTTAGATAAGAAAATACAAAAGCCAAAGACAGAAATGACTTCAAAGCCAGTGACCCTAGTGGCCAAAACGAACAGGGATATTGTTCAGCCTGTTCTAGGTAGCAATGAAAGTTCGGGAAAGAAGCTCATTGAAAATATACAACCTGAGGAGAAAAGCAAAGAAGGTTCCATGAAAATTCCAGCTATCACGGAAATTCTAGACAGCAAGAAAGTGACGCCTGGAAGCCAAAGTTATGAAAAGGAGGCGAAGCCTTCTGACAGAAATGGTACTCAGCCTTCTGGACCGGAAAACCAGGTTTCTAAACAGCTGGAACTAAAGCCATCAGTACAAGAGCTTGCTGCTCATGCAGCGTCACTTGCGATGACTGAAGCTTCTAAAAACATTAAAACCCCAAAATCTGCTTACGAATTTGAGAACTCTTGGCGGAGTTTTTCCGGCGACAGTGCCCTACGAAGCCAATTGTTGAAGGTCACGACTCCGAGCTCTTTACCTCAGATTTTCAAGAACGCCCTGACCTCTCCGGTGCTGGTTGACATAATCAAATGTGTAGCCTCATTCTTCACTGAAGACATGGATTTGGCAGTTAAATACATTGAGAACCTAACAAAGGTTCCTAGATTCAACATGCTCGTCATGTGCCTTACCTCAACCGAGAAAAACGAGCTACTGAAGATATGGGAAGATGTTTTCTGCAATAAAGCAACCCCAATGGAGTATGCAGAGGTCTTAGACAAACTAAGGTCAAGATACTGCCTTAAACAGTAA
Functional Annotation
Gene Ontology
Molecular Function
Biological Process
Cellular Component
GO:0005575 GO:0005622 GO:0005623 GO:0005737 GO:0005829 GO:0032991 GO:0044424 GO:0044444 GO:0044464 GO:0097255
KEGG Pathways
Metabolic & Signaling
No pathways identified.
Pfam Domains
Protein Families
RPAP3_C TPR_1 TPR_8

Protein Analysis

476

Amino Acids

53.64

Weight (kDa)

8.85

Isoelectric Point (pI)

48.64

Instability Index
Protein Domains (Pfam)
Domain Name Pfam ID Position E-value Description
TPR_BSK1_C PF25575 70 - 152 4.5e-08 Serine/threonine-protein kinase BSK1-like, TPR repeats
TPR_1 PF00515 90 - 116 2.2e-06 Tetratricopeptide repeat
TPR_11 PF13414 91 - 129 5.8e-06 TPR repeat
TPR_1 PF00515 117 - 147 6.9e-06 Tetratricopeptide repeat
RPAP3_C PF13877 353 - 441 1.7e-26 Potential Monad-binding region of RPAP3
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) 130
AccII CGCG 1 cut(s) 30
AciI CCGC 2 cut(s) 28, 1090
AcoI YGGCCR 2 cut(s) 25, 726
AcsI RAATTY 4 cut(s) 278, 840, 858, 1073
AcuI CTGAAG 3 cut(s) 1053, 1251, 1355
AcyI GRCGYC 1 cut(s) 881
AfaI GTAC 2 cut(s) 934, 993
AfiI CCNNNNNNNGG 2 cut(s) 761, 1273
AflII CTTAAG 2 cut(s) 532, 560
AgsI TTSAA 9 cut(s) 61, 91, 286, 301, 708, 797, 1132, 1168, 1288
AjnI CCWGG 4 cut(s) 48, 552, 883, 957
AluBI AGCT 9 cut(s) 428, 458, 790, 848, 973, 1000, 1037, 1149, 1330
AluI AGCT 9 cut(s) 428, 458, 790, 848, 973, 1000, 1037, 1149, 1330
Alw21I GWGCWC 1 cut(s) 1151
Alw26I GTCTC 1 cut(s) 143
Ama87I CYCGRG 1 cut(s) 593
AoxI GGCC 2 cut(s) 25, 726
ApeKI GCWGC 2 cut(s) 1004, 1013
ApoI RAATTY 4 cut(s) 278, 840, 858, 1073
Asp700I GAANNNNTTC 1 cut(s) 296
AspS9I GGNCC 1 cut(s) 947
AsuHPI GGTGA 1 cut(s) 3
AvaI CYCGRG 1 cut(s) 593
AvaII GGWCC 1 cut(s) 947
AxyI CCTNAGG 1 cut(s) 810
BaeGI GKGCMC 1 cut(s) 1114
BalI TGGCCA 1 cut(s) 728
BanII GRGCYC 1 cut(s) 1151
BarI GAAGNNNNNNTAC 2 cut(s) 925, 957
BbsI GAAGAC 1 cut(s) 1239
Bbv12I GWGCWC 1 cut(s) 1151
BbvCI CCTCAGC 1 cut(s) 408
BbvI GCAGC 2 cut(s) 991, 1025
BccI CCATC 1 cut(s) 994
BceAI ACGGC 1 cut(s) 40
BciT130I CCWGG 4 cut(s) 50, 554, 885, 959
BcoDI GTCTC 1 cut(s) 143
BfaI CTAG 6 cut(s) 6, 252, 722, 761, 863, 1281
BfrI CTTAAG 2 cut(s) 532, 560
BfuAI ACCTGC 1 cut(s) 130
BisI GCNGC 3 cut(s) 28, 1005, 1014
BlsI GCNGC 3 cut(s) 29, 1006, 1015
Bme1390I CCNGG 4 cut(s) 50, 554, 885, 959
Bme18I GGWCC 1 cut(s) 947
BmeT110I CYCGRG 1 cut(s) 593
BmgT120I GGNCC 1 cut(s) 947
BmiI GGNNCC 3 cut(s) 543, 832, 1278
BmrFI CCNGG 4 cut(s) 50, 554, 885, 959
BmsI GCATC 1 cut(s) 508
BpiI GAAGAC 1 cut(s) 1239
BpmI CTGGAG 1 cut(s) 642
Bpu10I CCTNAGC 1 cut(s) 408
Bsa29I ATCGAT 1 cut(s) 445
BsaHI GRCGYC 1 cut(s) 881
BsaJI CCNNGG 1 cut(s) 49
BsaWI WCCGGW 2 cut(s) 949, 1186
Bsc4I CCNNNNNNNGG 2 cut(s) 761, 1273
Bse1I ACTGG 2 cut(s) 625, 713
Bse21I CCTNAGG 1 cut(s) 810
Bse3DI GCAATG 4 cut(s) 330, 378, 633, 775
BseBI CCWGG 4 cut(s) 50, 554, 885, 959
BseCI ATCGAT 1 cut(s) 445
BseDI CCNNGG 1 cut(s) 49
BseGI GGATG 1 cut(s) 445
BseLI CCNNNNNNNGG 2 cut(s) 761, 1273
BseMI GCAATG 4 cut(s) 330, 378, 633, 775
BseMII CTCAG 7 cut(s) 53, 399, 513, 537, 801, 950, 1172
BseNI ACTGG 2 cut(s) 625, 713
BseRI GAGGAG 1 cut(s) 827
BseSI GKGCMC 1 cut(s) 1114
BseX3I CGGCCG 1 cut(s) 25
BseXI GCAGC 2 cut(s) 991, 1025
BsgI GTGCAG 2 cut(s) 403, 624
Bsh1236I CGCG 1 cut(s) 30
Bsh1285I CGRYCG 1 cut(s) 28
BshFI GGCC 2 cut(s) 27, 728
BshVI ATCGAT 1 cut(s) 445
BsiEI CGRYCG 1 cut(s) 28
BsiHKAI GWGCWC 1 cut(s) 1151
BsiHKCI CYCGRG 1 cut(s) 593
BsiSI CCGG 3 cut(s) 950, 1101, 1187
BslI CCNNNNNNNGG 2 cut(s) 761, 1273
BsmAI GTCTC 1 cut(s) 143
BsmBI CGTCTC 1 cut(s) 143
BsnI GGCC 2 cut(s) 27, 728
BsoBI CYCGRG 1 cut(s) 593
Bsp1286I GDGCHC 2 cut(s) 1114, 1151
Bsp143I GATC 2 cut(s) 31, 442
BspACI CCGC 2 cut(s) 28, 1090
BspANI GGCC 2 cut(s) 27, 728
BspCNI CTCAG 7 cut(s) 52, 400, 514, 538, 802, 949, 1171
BspDI ATCGAT 1 cut(s) 445
BspFNI CGCG 1 cut(s) 30
BspLI GGNNCC 3 cut(s) 543, 832, 1278
BspMI ACCTGC 1 cut(s) 130
BspTI CTTAAG 2 cut(s) 532, 560
BsrDI GCAATG 4 cut(s) 330, 378, 633, 775
BsrI ACTGG 2 cut(s) 625, 713
BssECI CCNNGG 1 cut(s) 49
BssMI GATC 2 cut(s) 31, 442
BssNI GRCGYC 1 cut(s) 881
Bst2UI CCWGG 4 cut(s) 50, 554, 885, 959
Bst4CI ACNGT 2 cut(s) 1109, 1428
BstACI GRCGYC 1 cut(s) 881
BstAFI CTTAAG 2 cut(s) 532, 560
BstC8I GCNNGC 1 cut(s) 1002
BstDEI CTNAG 9 cut(s) 39, 408, 522, 546, 810, 936, 1158, 1393, 1403
BstEII GGTNACC 1 cut(s) 9
BstENI CCTNNNNNAGG 2 cut(s) 759, 1271
BstF5I GGATG 1 cut(s) 445
BstFNI CGCG 1 cut(s) 30
BstKTI GATC 2 cut(s) 34, 445
BstMAI GTCTC 1 cut(s) 143
BstMBI GATC 2 cut(s) 31, 442
BstMCI CGRYCG 1 cut(s) 28
BstMWI GCNNNNNNNGC 7 cut(s) 24, 368, 527, 623, 1010, 1013, 1022
BstNI CCWGG 4 cut(s) 50, 554, 885, 959
BstNSI RCATGY 1 cut(s) 1294
BstPI GGTNACC 1 cut(s) 9
BstSCI CCNGG 4 cut(s) 48, 552, 883, 957
BstSLI GKGCMC 1 cut(s) 1114
BstUI CGCG 1 cut(s) 30
BstV1I GCAGC 2 cut(s) 991, 1025
BstV2I GAAGAC 1 cut(s) 1239
BstZI CGGCCG 1 cut(s) 25
Bsu15I ATCGAT 1 cut(s) 445
Bsu36I CCTNAGG 1 cut(s) 810
BsuRI GGCC 2 cut(s) 27, 728
BsuTUI ATCGAT 1 cut(s) 445
BtgZI GCGATG 1 cut(s) 1040
BtsCI GGATG 1 cut(s) 445
BtsI GCAGTG 1 cut(s) 636
BtsIMutI CAGTG 5 cut(s) 618, 636, 720, 1114, 1227
BveI ACCTGC 1 cut(s) 130
Cac8I GCNNGC 1 cut(s) 1002
Cfr13I GGNCC 1 cut(s) 947
ClaI ATCGAT 1 cut(s) 445
CseI GACGC 2 cut(s) 889, 1005
CsiI ACCWGGT 1 cut(s) 957
Csp6I GTAC 2 cut(s) 933, 992
CviAII CATG 6 cut(s) 496, 835, 1010, 1237, 1291, 1300
CviQI GTAC 2 cut(s) 933, 992
DdeI CTNAG 9 cut(s) 39, 408, 522, 546, 810, 936, 1158, 1393, 1403
DpnI GATC 2 cut(s) 33, 444
DpnII GATC 2 cut(s) 31, 442
DraI TTTAAA 1 cut(s) 432
EaeI YGGCCR 2 cut(s) 25, 726
EagI CGGCCG 1 cut(s) 25
EciI GGCGGA 1 cut(s) 1105
Ecl136II GAGCTC 1 cut(s) 1149
EclXI CGGCCG 1 cut(s) 25
Eco24I GRGCYC 1 cut(s) 1151
Eco32I GATATC 2 cut(s) 398, 580
Eco47I GGWCC 1 cut(s) 947
Eco52I CGGCCG 1 cut(s) 25
Eco53kI GAGCTC 1 cut(s) 1149
Eco57I CTGAAG 3 cut(s) 1053, 1251, 1355
Eco81I CCTNAGG 1 cut(s) 810
Eco88I CYCGRG 1 cut(s) 593
Eco91I GGTNACC 1 cut(s) 9
EcoICRI GAGCTC 1 cut(s) 1149
EcoNI CCTNNNNNAGG 2 cut(s) 759, 1271
EcoO65I GGTNACC 1 cut(s) 9
EcoRI GAATTC 1 cut(s) 278
EcoRII CCWGG 4 cut(s) 48, 552, 883, 957
EcoRV GATATC 2 cut(s) 398, 580
EcoT38I GRGCYC 1 cut(s) 1151
Esp3I CGTCTC 1 cut(s) 143
FaeI CATG 6 cut(s) 499, 838, 1013, 1240, 1294, 1303
FatI CATG 6 cut(s) 495, 834, 1009, 1236, 1290, 1299
Fnu4HI GCNGC 3 cut(s) 28, 1005, 1014
FokI GGATG 1 cut(s) 452
FriOI GRGCYC 1 cut(s) 1151
Fsp4HI GCNGC 3 cut(s) 28, 1005, 1014
FspBI CTAG 6 cut(s) 6, 252, 722, 761, 863, 1281
GluI GCNGC 3 cut(s) 28, 1005, 1014
GsuI CTGGAG 1 cut(s) 642
HaeIII GGCC 2 cut(s) 27, 728
HapII CCGG 3 cut(s) 950, 1101, 1187
HgaI GACGC 2 cut(s) 889, 1005
Hin1I GRCGYC 1 cut(s) 881
Hin1II CATG 6 cut(s) 499, 838, 1013, 1240, 1294, 1303
HincII GTYRAC 2 cut(s) 415, 1198
HindII GTYRAC 2 cut(s) 415, 1198
HindIII AAGCTT 3 cut(s) 426, 456, 1035
HinfI GANTC 4 cut(s) 136, 248, 1141, 1284
HpaII CCGG 3 cut(s) 950, 1101, 1187
HphI GGTGA 1 cut(s) 3
Hpy166II GTNNAC 2 cut(s) 415, 1198
Hpy188I TCNGA 7 cut(s) 141, 158, 259, 327, 922, 1146, 1161
Hpy8I GTNNAC 2 cut(s) 415, 1198
Hpy99I CGWCG 1 cut(s) 136
HpyAV CCTTC 6 cut(s) 85, 256, 821, 927, 951, 1126
HpyCH4III ACNGT 2 cut(s) 1109, 1428
HpyCH4IV ACGT 1 cut(s) 152
HpyCH4V TGCA 8 cut(s) 70, 362, 420, 631, 641, 1013, 1359, 1385
HpyF10VI GCNNNNNNNGC 7 cut(s) 24, 368, 527, 623, 1010, 1013, 1022
HpyF3I CTNAG 9 cut(s) 39, 408, 522, 546, 810, 936, 1158, 1393, 1403
HpySE526I ACGT 1 cut(s) 152
Hsp92I GRCGYC 1 cut(s) 881
Hsp92II CATG 6 cut(s) 499, 838, 1013, 1240, 1294, 1303
Kzo9I GATC 2 cut(s) 31, 442
LmnI GCTCC 4 cut(s) 265, 327, 541, 623
Lsp1109I GCAGC 2 cut(s) 991, 1025
LweI GCATC 1 cut(s) 508
MabI ACCWGGT 1 cut(s) 957
MaeI CTAG 6 cut(s) 6, 252, 722, 761, 863, 1281
MaeII ACGT 1 cut(s) 152
MaeIII GTNAC 7 cut(s) 9, 317, 352, 715, 877, 1017, 1135
MalI GATC 2 cut(s) 33, 444
MboI GATC 2 cut(s) 31, 442
MboII GAAGA 8 cut(s) 118, 274, 304, 527, 1216, 1244, 1348, 1358
MfeI CAATTG 1 cut(s) 1124
MhlI GDGCHC 2 cut(s) 1114, 1151
MlsI TGGCCA 1 cut(s) 728
MluCI AATT 7 cut(s) 127, 278, 647, 840, 858, 1073, 1124
MluNI TGGCCA 1 cut(s) 728
MlyI GAGTC 1 cut(s) 1135
Mox20I TGGCCA 1 cut(s) 728
MroXI GAANNNNTTC 1 cut(s) 296
MscI TGGCCA 1 cut(s) 728
MseI TTAA 9 cut(s) 111, 384, 431, 501, 533, 561, 1050, 1251, 1422
Msp20I TGGCCA 1 cut(s) 728
MspA1I CMGCKG 1 cut(s) 973
MspCI CTTAAG 2 cut(s) 532, 560
MspI CCGG 3 cut(s) 950, 1101, 1187
MspR9I CCNGG 4 cut(s) 50, 554, 885, 959
MunI CAATTG 1 cut(s) 1124
MvaI CCWGG 4 cut(s) 50, 554, 885, 959
MvnI CGCG 1 cut(s) 30
MwoI GCNNNNNNNGC 7 cut(s) 24, 368, 527, 623, 1010, 1013, 1022
NdeII GATC 2 cut(s) 31, 442
NlaIII CATG 6 cut(s) 499, 838, 1013, 1240, 1294, 1303
NlaIV GGNNCC 3 cut(s) 543, 832, 1278
NmeAIII GCCGAG 2 cut(s) 471, 494
NmuCI GTSAC 6 cut(s) 9, 352, 715, 877, 1017, 1135
NspI RCATGY 1 cut(s) 1294
PaeR7I CTCGAG 1 cut(s) 593
PcsI WCGNNNNNNNCGW 1 cut(s) 137
PdmI GAANNNNTTC 1 cut(s) 296
PfeI GAWTC 3 cut(s) 136, 248, 1284
PkrI GCNGC 3 cut(s) 29, 1006, 1015
PleI GAGTC 1 cut(s) 1135
PpsI GAGTC 1 cut(s) 1135
Psp124BI GAGCTC 1 cut(s) 1151
Psp6I CCWGG 4 cut(s) 48, 552, 883, 957
PspEI GGTNACC 1 cut(s) 9
PspGI CCWGG 4 cut(s) 48, 552, 883, 957
PspN4I GGNNCC 3 cut(s) 543, 832, 1278
PspPI GGNCC 1 cut(s) 947
PvuII CAGCTG 1 cut(s) 973
RsaI GTAC 2 cut(s) 934, 993
RsaNI GTAC 2 cut(s) 933, 992
SacI GAGCTC 1 cut(s) 1151
SaqAI TTAA 9 cut(s) 111, 384, 431, 501, 533, 561, 1050, 1251, 1422
SatI GCNGC 3 cut(s) 28, 1005, 1014
Sau3AI GATC 2 cut(s) 31, 442
Sau96I GGNCC 1 cut(s) 947
SchI GAGTC 1 cut(s) 1135
ScrFI CCNGG 4 cut(s) 50, 554, 885, 959
SduI GDGCHC 2 cut(s) 1114, 1151
SexAI ACCWGGT 1 cut(s) 957
SfaNI GCATC 1 cut(s) 508
Sfr274I CTCGAG 1 cut(s) 593
SinI GGWCC 1 cut(s) 947
SlaI CTCGAG 1 cut(s) 593
SmlI CTYRAG 3 cut(s) 532, 560, 593
SmoI CTYRAG 3 cut(s) 532, 560, 593
Sse9I AATT 7 cut(s) 127, 278, 647, 840, 858, 1073, 1124
SsiI CCGC 2 cut(s) 28, 1090
SspMI CTAG 6 cut(s) 6, 252, 722, 761, 863, 1281
SstI GAGCTC 1 cut(s) 1151
StyD4I CCNGG 4 cut(s) 48, 552, 883, 957
TaaI ACNGT 2 cut(s) 1109, 1428
TaiI ACGT 1 cut(s) 155
TaqI TCGA 6 cut(s) 134, 218, 367, 400, 445, 594
TasI AATT 7 cut(s) 127, 278, 647, 840, 858, 1073, 1124
TatI WGTACW 1 cut(s) 991
TauI GCSGC 1 cut(s) 30
TfiI GAWTC 3 cut(s) 136, 248, 1284
Tru1I TTAA 9 cut(s) 111, 384, 431, 501, 533, 561, 1050, 1251, 1422
Tru9I TTAA 9 cut(s) 111, 384, 431, 501, 533, 561, 1050, 1251, 1422
TscAI CASTG 5 cut(s) 625, 643, 720, 1114, 1234
TseFI GTSAC 6 cut(s) 9, 352, 715, 877, 1017, 1135
TseI GCWGC 2 cut(s) 1004, 1013
Tsp45I GTSAC 6 cut(s) 9, 352, 715, 877, 1017, 1135
TspDTI ATGAA 4 cut(s) 291, 786, 851, 915
TspGWI ACGGA 1 cut(s) 869
TspRI CASTG 5 cut(s) 625, 643, 720, 1114, 1234
Vha464I CTTAAG 2 cut(s) 532, 560
VpaK11BI GGWCC 1 cut(s) 947
XagI CCTNNNNNAGG 2 cut(s) 759, 1271
XapI RAATTY 4 cut(s) 278, 840, 858, 1073
XbaI TCTAGA 1 cut(s) 862
XceI RCATGY 1 cut(s) 1294
XhoI CTCGAG 1 cut(s) 593
XmnI GAANNNNTTC 1 cut(s) 296
XspI CTAG 6 cut(s) 6, 252, 722, 761, 863, 1281
Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.