ATCG00740

RNA polymerase subunit alpha

Design Primers CRISPR Design

Basic Information

Type: gene
Biological Identity
arabidopsis_thaliana
Pt
OG0026710
Physical Location & Seq
Reverse (-)
77901 .. 78890
990 bp
Loading structure...
UTR
Exon/CDS
Intron
ATCG00740.1

Sequence Viewer

Length: 990 bp
ATGGTTCGAGAGAAAGTCAAAGTATCTACTCGGACACTACAGTGGAAGTGTGTTGAATCAAAAAGAGACAGTAAGCGTCTTTATTATGGACGCTTTATTCTGTCTCCACTTATGAAAGGCCAAGCCGACACAATAGGCATTGCGATGCGAAGAGCTTTACTTGGCGAAATAGAAGGAACATGTATTACACGTGCAAAATCTGAGAACATACCACATGACTATTCTAACATAGCAGGTATTCAAGAATCAGTACATGAAATTTTAATGAATTTGAACGAGATTGTATTAAGAAGTAATCTATATGGAACGCGCAACGCGCTTATTTGTGTCCAAGGTCCTGGATATATAACTGCTCGAGACATTATTTTACCGCCCGCTGTGGAAATCATTGATAATACACAGCATATAGCTACCTTAACAGAACCAATAGATTTGTGTATTGAATTAAAAATTGAGAGGAATCGCGGATATAGTCTAAAAATGTCAAATAACTTTGAAGACAGAAGTTATCCTATCGATGCTGTATTCATGCCTGTTGAAAATGCCAATCATAGTATTCATTCTTATGGGAATGGGAATGAAAAACAAGAGATTCTTTTTCTAGAAATATGGACAAATGGAAGTTTAACTCCTAAAGAAGCACTTCATCAAGCCTCCCGGAATTTGATTAATTTATTTATTCCTTTTCTACATGTAGAAGAAGAAACGTTCTATTTAGAGAACAATCAACATCAAGTTACTTTACCCTTTTTTCCTTTTCATAATCGATTAGTTAACCTAAGAAAAAAAAAAAAAACAAAAGAACTAGCCTTTCAATATATTTTTATTGACCAATTAGAATTGCCTCCCAGAATCTACAATTGTCTCAAAAAATCCAATATACATACATTATTGGACCTTTTGAATAACAGTCAAGAAGACCTTATCAAAATTGAACATTTTCACGTAGAAGATGTAAAAAAGATATTAGACATTCTAGAAAAAAAATAG

Protein Analysis

329

Amino Acids

38.14

Weight (kDa)

7.2

Isoelectric Point (pI)

50.91

Instability Index
Protein Domains (Pfam)
Domain Name Pfam ID Position E-value Description
RNA_pol_L PF01193 36 - 225 1.1e-14 RNA polymerase Rpb3/Rpb11 dimerisation domain
RNA_pol_A_bac PF01000 69 - 177 4.2e-19 RNA polymerase Rpb3/RpoA insert domain
RNA_pol_A_CTD PF03118 263 - 328 1.4e-18 Bacterial RNA polymerase, alpha chain C terminal domain
HHH_XRCC3_RpoA PF26169 276 - 323 1.4e-06 XRCC3/RpoA-like, helix-hairpin-helix domain
Hydrophobicity Profile (Kyte-Doolittle)
AI Structure Prediction Report
Calculating structure properties...

Genomic Context

Gene Family Tree

Species Filter
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Orthologous Genes (Group: OG0026710)

Species Orthologous Gene IDs
arabidopsis_thaliana ATCG00740
rosa_chinensis RchiOBHm_Chr5g0083591

Restriction Enzyme Sites

1 / 10
Enzyme Recognition Site Cut Count Positions (bp)
Acc36I ACCTGC 1 cut(s) 224
AccII CGCG 3 cut(s) 310, 317, 465
AciI CCGC 3 cut(s) 371, 375, 465
AclI AACGTT 1 cut(s) 707
AcsI RAATTY 3 cut(s) 258, 268, 661
AcvI CACGTG 1 cut(s) 191
AfaI GTAC 1 cut(s) 252
AflIII ACRYGT 3 cut(s) 179, 188, 691
AgsI TTSAA 9 cut(s) 56, 242, 274, 443, 497, 539, 815, 904, 935
AjnI CCWGG 1 cut(s) 337
AleI CACNNNNGTG 1 cut(s) 40
AluBI AGCT 2 cut(s) 155, 410
AluI AGCT 2 cut(s) 155, 410
Alw26I GTCTC 4 cut(s) 60, 108, 351, 869
Ama87I CYCGRG 1 cut(s) 354
AoxI GGCC 1 cut(s) 118
ApoI RAATTY 3 cut(s) 258, 268, 661
AseI ATTAAT 1 cut(s) 669
Asp700I GAANNNNTTC 2 cut(s) 642, 939
AspLEI GCGC 2 cut(s) 312, 319
AspS9I GGNCC 2 cut(s) 335, 895
AsuC2I CCSGG 1 cut(s) 658
AvaI CYCGRG 1 cut(s) 354
AvaII GGWCC 2 cut(s) 335, 895
BbrPI CACGTG 1 cut(s) 191
BbsI GAAGAC 2 cut(s) 504, 924
BciT130I CCWGG 1 cut(s) 339
BcnI CCSGG 1 cut(s) 658
BcoDI GTCTC 4 cut(s) 60, 108, 351, 869
BfaI CTAG 3 cut(s) 602, 806, 977
BfmI CTRYAG 1 cut(s) 38
BfuAI ACCTGC 1 cut(s) 224
Bme1390I CCNGG 2 cut(s) 339, 658
Bme18I GGWCC 2 cut(s) 335, 895
BmeT110I CYCGRG 1 cut(s) 354
BmgT120I GGNCC 2 cut(s) 335, 895
BmrFI CCNGG 2 cut(s) 339, 658
BmsI GCATC 2 cut(s) 135, 508
BpiI GAAGAC 2 cut(s) 504, 924
BpuMI CCSGG 1 cut(s) 658
Bsa29I ATCGAT 2 cut(s) 516, 766
BsaAI YACGTR 2 cut(s) 191, 946
BsaJI CCNNGG 1 cut(s) 331
Bse3DI GCAATG 1 cut(s) 138
BseBI CCWGG 1 cut(s) 339
BseCI ATCGAT 2 cut(s) 516, 766
BseDI CCNNGG 1 cut(s) 331
BseMI GCAATG 1 cut(s) 138
BseMII CTCAG 1 cut(s) 192
Bsh1236I CGCG 3 cut(s) 310, 317, 465
BshFI GGCC 1 cut(s) 120
BshVI ATCGAT 2 cut(s) 516, 766
BsiHKCI CYCGRG 1 cut(s) 354
BsiSI CCGG 1 cut(s) 658
BsmAI GTCTC 4 cut(s) 60, 108, 351, 869
BsnI GGCC 1 cut(s) 120
BsoBI CYCGRG 1 cut(s) 354
BspACI CCGC 3 cut(s) 371, 375, 465
BspANI GGCC 1 cut(s) 120
BspCNI CTCAG 1 cut(s) 193
BspDI ATCGAT 2 cut(s) 516, 766
BspFNI CGCG 3 cut(s) 310, 317, 465
BspMI ACCTGC 1 cut(s) 224
BspQI GCTCTTC 1 cut(s) 145
BsrDI GCAATG 1 cut(s) 138
BssECI CCNNGG 1 cut(s) 331
BssT1I CCWWGG 1 cut(s) 331
Bst2UI CCWGG 1 cut(s) 339
Bst4CI ACNGT 3 cut(s) 42, 71, 911
Bst6I CTCTTC 1 cut(s) 145
BstBAI YACGTR 2 cut(s) 191, 946
BstC8I GCNNGC 1 cut(s) 375
BstDEI CTNAG 2 cut(s) 201, 779
BstFNI CGCG 3 cut(s) 310, 317, 465
BstHHI GCGC 2 cut(s) 312, 319
BstMAI GTCTC 4 cut(s) 60, 108, 351, 869
BstMWI GCNNNNNNNGC 1 cut(s) 316
BstNI CCWGG 1 cut(s) 339
BstNSI RCATGY 2 cut(s) 183, 695
BstSCI CCNGG 2 cut(s) 337, 656
BstSFI CTRYAG 1 cut(s) 38
BstUI CGCG 3 cut(s) 310, 317, 465
BstV2I GAAGAC 2 cut(s) 504, 924
BstXI CCANNNNNNTGG 1 cut(s) 338
Bsu15I ATCGAT 2 cut(s) 516, 766
BsuRI GGCC 1 cut(s) 120
BsuTUI ATCGAT 2 cut(s) 516, 766
BtgZI GCGATG 1 cut(s) 158
BtsIMutI CAGTG 1 cut(s) 47
BveI ACCTGC 1 cut(s) 224
Cac8I GCNNGC 1 cut(s) 375
CfoI GCGC 2 cut(s) 312, 319
Cfr13I GGNCC 2 cut(s) 335, 895
ClaI ATCGAT 2 cut(s) 516, 766
CseI GACGC 2 cut(s) 65, 99
Csp6I GTAC 1 cut(s) 251
CviAII CATG 5 cut(s) 180, 215, 254, 529, 692
CviJI RGCY 6 cut(s) 120, 125, 155, 410, 653, 809
CviKI_1 RGCY 6 cut(s) 120, 125, 155, 410, 653, 809
CviQI GTAC 1 cut(s) 251
DdeI CTNAG 2 cut(s) 201, 779
Eam1104I CTCTTC 1 cut(s) 145
EarI CTCTTC 1 cut(s) 145
Eco130I CCWWGG 1 cut(s) 331
Eco47I GGWCC 2 cut(s) 335, 895
Eco72I CACGTG 1 cut(s) 191
Eco88I CYCGRG 1 cut(s) 354
EcoO109I RGGNCCY 1 cut(s) 335
EcoRII CCWGG 1 cut(s) 337
EcoT14I CCWWGG 1 cut(s) 331
ErhI CCWWGG 1 cut(s) 331
FaeI CATG 5 cut(s) 183, 218, 257, 532, 695
FalI AAGNNNNNCTT 6 cut(s) 579, 611, 627, 659, 906, 938
FatI CATG 5 cut(s) 179, 214, 253, 528, 691
FauI CCCGC 1 cut(s) 382
FspBI CTAG 3 cut(s) 602, 806, 977
GlaI GCGC 2 cut(s) 311, 318
HaeIII GGCC 1 cut(s) 120
HapII CCGG 1 cut(s) 658
HgaI GACGC 2 cut(s) 65, 99
HhaI GCGC 2 cut(s) 312, 319
Hin1II CATG 5 cut(s) 183, 218, 257, 532, 695
Hin6I GCGC 2 cut(s) 310, 317
HinP1I GCGC 2 cut(s) 310, 317
HincII GTYRAC 1 cut(s) 775
HindII GTYRAC 1 cut(s) 775
HinfI GANTC 5 cut(s) 56, 245, 460, 592, 852
HpaI GTTAAC 1 cut(s) 775
HpaII CCGG 1 cut(s) 658
Hpy166II GTNNAC 1 cut(s) 775
Hpy188I TCNGA 2 cut(s) 33, 202
Hpy188III TCNNGA 6 cut(s) 8, 242, 356, 602, 914, 977
Hpy8I GTNNAC 1 cut(s) 775
HpyAV CCTTC 1 cut(s) 167
HpyCH4III ACNGT 3 cut(s) 42, 71, 911
HpyCH4IV ACGT 3 cut(s) 190, 707, 945
HpyCH4V TGCA 1 cut(s) 194
HpyF10VI GCNNNNNNNGC 1 cut(s) 316
HpyF3I CTNAG 2 cut(s) 201, 779
HpySE526I ACGT 3 cut(s) 190, 707, 945
Hsp92II CATG 5 cut(s) 183, 218, 257, 532, 695
HspAI GCGC 2 cut(s) 310, 317
KspAI GTTAAC 1 cut(s) 775
LguI GCTCTTC 1 cut(s) 145
LpnPI CCDG 6 cut(s) 219, 324, 351, 546, 671, 862
LweI GCATC 2 cut(s) 135, 508
MaeI CTAG 3 cut(s) 602, 806, 977
MaeII ACGT 3 cut(s) 190, 707, 945
MaeIII GTNAC 1 cut(s) 736
MboII GAAGA 6 cut(s) 162, 509, 710, 713, 929, 962
MfeI CAATTG 1 cut(s) 859
MnlI CCTC 3 cut(s) 450, 664, 855
MroXI GAANNNNTTC 2 cut(s) 642, 939
MseI TTAA 7 cut(s) 263, 287, 416, 446, 626, 669, 774
MslI CAYNNNNRTG 3 cut(s) 40, 143, 564
MspA1I CMGCKG 1 cut(s) 377
MspI CCGG 1 cut(s) 658
MspR9I CCNGG 2 cut(s) 339, 658
MunI CAATTG 1 cut(s) 859
MvaI CCWGG 1 cut(s) 339
MvnI CGCG 3 cut(s) 310, 317, 465
MwoI GCNNNNNNNGC 1 cut(s) 316
NciI CCSGG 1 cut(s) 658
NlaIII CATG 5 cut(s) 183, 218, 257, 532, 695
NspI RCATGY 2 cut(s) 183, 695
OliI CACNNNNGTG 1 cut(s) 40
PaeR7I CTCGAG 1 cut(s) 354
PciI ACATGT 2 cut(s) 179, 691
PciSI GCTCTTC 1 cut(s) 145
PdmI GAANNNNTTC 2 cut(s) 642, 939
PfeI GAWTC 5 cut(s) 56, 245, 460, 592, 852
PfoI TCCNGGA 2 cut(s) 337, 656
PmaCI CACGTG 1 cut(s) 191
PmlI CACGTG 1 cut(s) 191
Ppu21I YACGTR 2 cut(s) 191, 946
PpuMI RGGWCCY 1 cut(s) 335
PscI ACATGT 2 cut(s) 179, 691
PshBI ATTAAT 1 cut(s) 669
Psp1406I AACGTT 1 cut(s) 707
Psp5II RGGWCCY 1 cut(s) 335
Psp6I CCWGG 1 cut(s) 337
PspCI CACGTG 1 cut(s) 191
PspGI CCWGG 1 cut(s) 337
PspPI GGNCC 2 cut(s) 335, 895
PspPPI RGGWCCY 1 cut(s) 335
PsrI GAACNNNNNNTAC 2 cut(s) 169, 201
RsaI GTAC 1 cut(s) 252
RsaNI GTAC 1 cut(s) 251
RseI CAYNNNNRTG 3 cut(s) 40, 143, 564
SapI GCTCTTC 1 cut(s) 145
SaqAI TTAA 7 cut(s) 263, 287, 416, 446, 626, 669, 774
Sau96I GGNCC 2 cut(s) 335, 895
ScrFI CCNGG 2 cut(s) 339, 658
SfaNI GCATC 2 cut(s) 135, 508
SfcI CTRYAG 1 cut(s) 38
Sfr274I CTCGAG 1 cut(s) 354
SinI GGWCC 2 cut(s) 335, 895
SlaI CTCGAG 1 cut(s) 354
SmiMI CAYNNNNRTG 3 cut(s) 40, 143, 564
SmlI CTYRAG 1 cut(s) 354
SmoI CTYRAG 1 cut(s) 354
SsiI CCGC 3 cut(s) 371, 375, 465
SspMI CTAG 3 cut(s) 602, 806, 977
StyD4I CCNGG 2 cut(s) 337, 656
StyI CCWWGG 1 cut(s) 331
TaaI ACNGT 3 cut(s) 42, 71, 911
TaiI ACGT 3 cut(s) 193, 710, 948
TaqI TCGA 4 cut(s) 7, 355, 516, 766
TatI WGTACW 1 cut(s) 250
TfiI GAWTC 5 cut(s) 56, 245, 460, 592, 852
Tru1I TTAA 7 cut(s) 263, 287, 416, 446, 626, 669, 774
Tru9I TTAA 7 cut(s) 263, 287, 416, 446, 626, 669, 774
TscAI CASTG 1 cut(s) 47
TspDTI ATGAA 8 cut(s) 128, 270, 281, 517, 548, 594, 635, 749
TspRI CASTG 1 cut(s) 47
VpaK11BI GGWCC 2 cut(s) 335, 895
VspI ATTAAT 1 cut(s) 669
XapI RAATTY 3 cut(s) 258, 268, 661
XbaI TCTAGA 2 cut(s) 601, 976
XceI RCATGY 2 cut(s) 183, 695
XhoI CTCGAG 1 cut(s) 354
XmnI GAANNNNTTC 2 cut(s) 642, 939
XspI CTAG 3 cut(s) 602, 806, 977
Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.