pycom12397g00170

Bacterial RNA polymerase, alpha chain C terminal domain

Design Primers CRISPR Design

Basic Information

Type: gene
Biological Identity
pyrus_communis
tig00012397
OG0016509
Physical Location & Seq
Forward (+)
101930 .. 102346
417 bp
Loading structure...
UTR
Exon/CDS
Intron
N/A

Sequence Viewer

Length: 417 bp
ATGGCAAAACCTATACCAAAAATTGGTTCGCGTAGAAATAGACGTATTGGTTCACGTAAGAATACACGTAGAATCCCCAAGGGAGTTATTCATGTTCAAGCAAGTTTCAACAATACCATTGTGACTGTTACAGATGTACGGGGTCGAGTAATTTCTTGGTCCTCTGCCGGGGCTTGTGGATTCAAGGGTACAAGAAGGGGTACACCATTTGCCGCTCAAACCGCAGCAGGAAATGCTATTCGGACAGTAGTGGATCAAGGTATGCAACGAGCAGAAGTTATGATAAAAGGCCCGGGTCTCGGAAGAGATGCGGCATTAAGAGCTATTCGTAGAAGTGGTATACTATTAAGTTTCATACGGGATGTAACTCCTATGCCACATAATGGCTGTAGGCCTCCTAAAAAAAGACGTGTGTAA

Protein Analysis

139

Amino Acids

15.05

Weight (kDa)

12.0

Isoelectric Point (pI)

45.91

Instability Index
Protein Domains (Pfam)
Domain Name Pfam ID Position E-value Description
Ribosomal_S11 PF00411 28 - 137 1.5e-51 Ribosomal protein S11
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: OG0016509)

Species Orthologous Gene IDs
arabidopsis_thaliana ATCG00750
fragaria_vesca FvH4_c3g00200
pyrus_communis pycom12397g00170
rosa_chinensis RchiOBHm_CPg0501901
rosa_laevigata RLG00000000055 RLG00000000071 RLG00000000177 RLG00000000219 RLG00000037103
rosa_roxburghii Rroxscaffold_2G00119010
rosa_rugosa RorugMtG0002700.1
rosa_samantha Rh1CG032700
rosa_wichuraiana Rw7G013550 Rw7G013560

Restriction Enzyme Sites

1 / 10
Enzyme Recognition Site Cut Count Positions (bp)
AccB7I CCANNNNNTGG 2 cut(s) 23, 383
AccBSI CCGCTC 1 cut(s) 215
AccI GTMKAC 1 cut(s) 340
AccII CGCG 1 cut(s) 31
AciI CCGC 3 cut(s) 213, 222, 311
AclWI GGATC 1 cut(s) 261
AfaI GTAC 3 cut(s) 138, 190, 202
AfiI CCNNNNNNNGG 4 cut(s) 23, 168, 299, 383
AflIII ACRYGT 2 cut(s) 65, 409
AgsI TTSAA 3 cut(s) 98, 109, 184
AjiI CACGTC 1 cut(s) 410
AjuI GAANNNNNNNTTGG 2 cut(s) 10, 42
AluBI AGCT 1 cut(s) 323
AluI AGCT 1 cut(s) 323
Alw26I GTCTC 1 cut(s) 302
AlwI GGATC 1 cut(s) 261
Ama87I CYCGRG 1 cut(s) 292
AoxI GGCC 2 cut(s) 289, 392
ApeKI GCWGC 1 cut(s) 224
AspS9I GGNCC 2 cut(s) 159, 290
AsuC2I CCSGG 3 cut(s) 169, 293, 294
AvaI CYCGRG 1 cut(s) 292
AvaII GGWCC 1 cut(s) 159
BbvI GCAGC 1 cut(s) 236
BcnI CCSGG 3 cut(s) 169, 293, 294
BcoDI GTCTC 1 cut(s) 302
BfmI CTRYAG 1 cut(s) 388
BisI GCNGC 3 cut(s) 213, 225, 312
BlsI GCNGC 3 cut(s) 214, 226, 313
Bme1390I CCNGG 3 cut(s) 169, 293, 294
Bme18I GGWCC 1 cut(s) 159
BmeT110I CYCGRG 1 cut(s) 292
BmgBI CACGTC 1 cut(s) 410
BmgT120I GGNCC 2 cut(s) 159, 290
BmrFI CCNGG 3 cut(s) 169, 293, 294
BmsI GCATC 1 cut(s) 298
BpuMI CCSGG 3 cut(s) 169, 293, 294
BsaAI YACGTR 2 cut(s) 56, 68
BsaI GGTCTC 1 cut(s) 302
BsaJI CCNNGG 3 cut(s) 78, 168, 292
Bsc4I CCNNNNNNNGG 4 cut(s) 23, 168, 299, 383
BseDI CCNNGG 3 cut(s) 78, 168, 292
BseGI GGATG 1 cut(s) 367
BseLI CCNNNNNNNGG 4 cut(s) 23, 168, 299, 383
BseXI GCAGC 1 cut(s) 236
Bsh1236I CGCG 1 cut(s) 31
BshFI GGCC 2 cut(s) 291, 394
BsiHKCI CYCGRG 1 cut(s) 292
BsiSI CCGG 2 cut(s) 168, 293
BslI CCNNNNNNNGG 4 cut(s) 23, 168, 299, 383
BsmAI GTCTC 1 cut(s) 302
BsnI GGCC 2 cut(s) 291, 394
Bso31I GGTCTC 1 cut(s) 302
BsoBI CYCGRG 1 cut(s) 292
Bsp143I GATC 1 cut(s) 253
BspACI CCGC 3 cut(s) 213, 222, 311
BspANI GGCC 2 cut(s) 291, 394
BspFNI CGCG 1 cut(s) 31
BspPI GGATC 1 cut(s) 261
BspTNI GGTCTC 1 cut(s) 302
BsrBI CCGCTC 1 cut(s) 215
BssECI CCNNGG 3 cut(s) 78, 168, 292
BssMI GATC 1 cut(s) 253
BssNAI GTATAC 1 cut(s) 341
BssT1I CCWWGG 1 cut(s) 78
Bst1107I GTATAC 1 cut(s) 341
Bst4CI ACNGT 2 cut(s) 127, 247
Bst6I CTCTTC 1 cut(s) 298
BstAPI GCANNNNNTGC 1 cut(s) 233
BstBAI YACGTR 2 cut(s) 56, 68
BstF5I GGATG 1 cut(s) 367
BstFNI CGCG 1 cut(s) 31
BstKTI GATC 1 cut(s) 256
BstMAI GTCTC 1 cut(s) 302
BstMBI GATC 1 cut(s) 253
BstMWI GCNNNNNNNGC 3 cut(s) 221, 233, 320
BstSCI CCNGG 3 cut(s) 167, 291, 292
BstSFI CTRYAG 1 cut(s) 388
BstUI CGCG 1 cut(s) 31
BstV1I GCAGC 1 cut(s) 236
BstZ17I GTATAC 1 cut(s) 341
BsuRI GGCC 2 cut(s) 291, 394
BtrI CACGTC 1 cut(s) 410
BtsCI GGATG 1 cut(s) 367
Cfr13I GGNCC 2 cut(s) 159, 290
Cfr9I CCCGGG 1 cut(s) 292
Csp6I GTAC 3 cut(s) 137, 189, 201
CviAII CATG 1 cut(s) 92
CviJI RGCY 5 cut(s) 173, 291, 323, 387, 394
CviKI_1 RGCY 5 cut(s) 173, 291, 323, 387, 394
CviQI GTAC 3 cut(s) 137, 189, 201
DpnI GATC 1 cut(s) 255
DpnII GATC 1 cut(s) 253
Eam1104I CTCTTC 1 cut(s) 298
EarI CTCTTC 1 cut(s) 298
Eco130I CCWWGG 1 cut(s) 78
Eco147I AGGCCT 1 cut(s) 394
Eco31I GGTCTC 1 cut(s) 302
Eco47I GGWCC 1 cut(s) 159
Eco88I CYCGRG 1 cut(s) 292
EcoT14I CCWWGG 1 cut(s) 78
ErhI CCWWGG 1 cut(s) 78
FaeI CATG 1 cut(s) 95
FaiI YATR 8 cut(s) 14, 93, 263, 281, 341, 356, 374, 381
FatI CATG 1 cut(s) 91
FblI GTMKAC 1 cut(s) 340
Fnu4HI GCNGC 3 cut(s) 213, 225, 312
FokI GGATG 1 cut(s) 374
Fsp4HI GCNGC 3 cut(s) 213, 225, 312
GluI GCNGC 3 cut(s) 213, 225, 312
HaeIII GGCC 2 cut(s) 291, 394
HapII CCGG 2 cut(s) 168, 293
Hin1II CATG 1 cut(s) 95
HinfI GANTC 2 cut(s) 72, 180
HpaII CCGG 2 cut(s) 168, 293
Hpy166II GTNNAC 3 cut(s) 53, 203, 341
Hpy188I TCNGA 2 cut(s) 243, 302
Hpy8I GTNNAC 3 cut(s) 53, 203, 341
HpyAV CCTTC 1 cut(s) 189
HpyCH4III ACNGT 2 cut(s) 127, 247
HpyCH4IV ACGT 4 cut(s) 43, 55, 67, 409
HpyCH4V TGCA 1 cut(s) 265
HpyF10VI GCNNNNNNNGC 3 cut(s) 221, 233, 320
HpySE526I ACGT 4 cut(s) 43, 55, 67, 409
Hsp92II CATG 1 cut(s) 95
Kzo9I GATC 1 cut(s) 253
LpnPI CCDG 3 cut(s) 181, 213, 306
Lsp1109I GCAGC 1 cut(s) 236
LweI GCATC 1 cut(s) 298
MaeII ACGT 4 cut(s) 43, 55, 67, 409
MaeIII GTNAC 3 cut(s) 121, 127, 364
MalI GATC 1 cut(s) 255
MbiI CCGCTC 1 cut(s) 215
MboI GATC 1 cut(s) 253
MboII GAAGA 1 cut(s) 315
MluCI AATT 2 cut(s) 21, 150
MnlI CCTC 2 cut(s) 172, 405
MseI TTAA 2 cut(s) 317, 347
MspI CCGG 2 cut(s) 168, 293
MspR9I CCNGG 3 cut(s) 169, 293, 294
MvnI CGCG 1 cut(s) 31
MwoI GCNNNNNNNGC 3 cut(s) 221, 233, 320
NciI CCSGG 3 cut(s) 169, 293, 294
NdeII GATC 1 cut(s) 253
NlaIII CATG 1 cut(s) 95
NmuCI GTSAC 1 cut(s) 121
PceI AGGCCT 1 cut(s) 394
PfeI GAWTC 2 cut(s) 72, 180
PflMI CCANNNNNTGG 2 cut(s) 23, 383
PkrI GCNGC 3 cut(s) 214, 226, 313
Ppu21I YACGTR 2 cut(s) 56, 68
PspPI GGNCC 2 cut(s) 159, 290
RsaI GTAC 3 cut(s) 138, 190, 202
RsaNI GTAC 3 cut(s) 137, 189, 201
SaqAI TTAA 2 cut(s) 317, 347
SatI GCNGC 3 cut(s) 213, 225, 312
Sau3AI GATC 1 cut(s) 253
Sau96I GGNCC 2 cut(s) 159, 290
ScrFI CCNGG 3 cut(s) 169, 293, 294
SetI ASST 7 cut(s) 13, 46, 58, 70, 262, 325, 412
SfaNI GCATC 1 cut(s) 298
SfcI CTRYAG 1 cut(s) 388
SinI GGWCC 1 cut(s) 159
SmaI CCCGGG 1 cut(s) 294
Sse9I AATT 2 cut(s) 21, 150
SseBI AGGCCT 1 cut(s) 394
SsiI CCGC 3 cut(s) 213, 222, 311
StuI AGGCCT 1 cut(s) 394
StyD4I CCNGG 3 cut(s) 167, 291, 292
StyI CCWWGG 1 cut(s) 78
TaaI ACNGT 2 cut(s) 127, 247
TaiI ACGT 4 cut(s) 46, 58, 70, 412
TaqI TCGA 1 cut(s) 145
TasI AATT 2 cut(s) 21, 150
TauI GCSGC 2 cut(s) 215, 314
TfiI GAWTC 2 cut(s) 72, 180
Tru1I TTAA 2 cut(s) 317, 347
Tru9I TTAA 2 cut(s) 317, 347
TseFI GTSAC 1 cut(s) 121
TseI GCWGC 1 cut(s) 224
Tsp45I GTSAC 1 cut(s) 121
TspDTI ATGAA 2 cut(s) 80, 343
TspMI CCCGGG 1 cut(s) 292
Van91I CCANNNNNTGG 2 cut(s) 23, 383
VpaK11BI GGWCC 1 cut(s) 159
XmaI CCCGGG 1 cut(s) 292
XmiI GTMKAC 1 cut(s) 340
Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.