pycom12g00870

DNA-directed RNA polymerases II, IV and V subunit 6A-like

Design Primers CRISPR Design

Basic Information

Type: gene
Biological Identity
pyrus_communis
Chr12
OG0012428
Physical Location & Seq
Forward (+)
733967 .. 736633
2667 bp
Loading structure...
UTR
Exon/CDS
Intron
N/A

Sequence Viewer

Length: 579 bp
ATGGATTTGGACTTTAGAAACTTTACGGTGGTCGTTGCCACACCTGATCGTTCAAAAACCTTATTTCAAACCCTAATCCCTTCCCACATTATTCCAGACGCTCTCTCTCGAAAGTTCTTAAACCCTAAACCAGAACTTCTTCACCCATCAACAATGGCGGACGACGACTACAACGACGTTGACATGGGATACCAGGATGAGCCTCCAGAGCCCGAAATTGAAGAAGGGGCAGAGGAGGAGGATGTTGACAATTTGAACAATGATGATGATGTTGCAGGAGATCCCATCGAAGCCGAGGAGAAGGAAGAACAAGAGGGGGTGGAACGGCCTCGGAAAACCTCGAAATATATGACCAAGTATGAGCGTGCTAGAATCTTGGGTACCCGTGCTCTGCAGATTAGCATGAATGCCCCTGTTATGGTTGAATTGGAGGGCGAGACTGACCCGCTTGAGGAGCTCCGTGAGCGGAAGATACCATTCACCATACGCCGCTACCTGCCTGATGGAAGCTACGAAGACTGGGGCGTAGATGAATTGATCGTCGAAGACTCCTGGAAGAGGCAGGTGGGAGGTGATTGA
Functional Annotation
Gene Ontology
Molecular Function
Biological Process
Cellular Component
No ontology terms assigned.
KEGG Pathways
Metabolic & Signaling
ko00230 ko00240 ko01100 ko03020 ko04623 ko05016 ko05169 map00230 map00240 map01100 map03020 map04623 map05016 map05169
Pfam Domains
Protein Families
RNA_pol_Rpb6

Protein Analysis

193

Amino Acids

22.07

Weight (kDa)

4.29

Isoelectric Point (pI)

52.29

Instability Index
Protein Domains (Pfam)
Domain Name Pfam ID Position E-value Description
RNA_pol_Rpb6 PF01192 113 - 160 1.2e-07 RNA polymerase Rpb6
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: OG0012428)

Species Orthologous Gene IDs
arabidopsis_thaliana AT2G04630 AT5G51940
fragaria_vesca FvH4_2g14180
malus_domestica MD09G1242800.v1.1 MD12G1011200.v1.1 MD17G1234800.v1.1
prunus_persica Prupe.3G134400_v2.0.a1 Prupe.7G013200_v2.0.a1
pyrus_communis pycom09g16110 pycom12g00870 pycom17g23820
rosa_chinensis RchiOBHm_Chr6g0276321
rosa_laevigata RLG00000013404
rosa_multiflora Rmu_sc0003665.1_g000006
rosa_roxburghii Rroxscaffold_7G00192390
rosa_rugosa Rorug06G0099900 Rorug06G0100000
rosa_samantha Rh6DG207900
rosa_wichuraiana Rw6G018430

Restriction Enzyme Sites

1 / 10
Enzyme Recognition Site Cut Count Positions (bp)
AarI CACCTGC 1 cut(s) 553
Acc36I ACCTGC 2 cut(s) 504, 553
Acc65I GGTACC 1 cut(s) 380
AccB1I GGYRCC 1 cut(s) 380
AccBSI CCGCTC 1 cut(s) 466
AciI CCGC 4 cut(s) 158, 446, 466, 490
AclWI GGATC 1 cut(s) 275
AfaI GTAC 1 cut(s) 382
AfiI CCNNNNNNNGG 3 cut(s) 418, 451, 558
AgsI TTSAA 5 cut(s) 54, 68, 221, 256, 425
AjnI CCWGG 2 cut(s) 192, 551
AluBI AGCT 2 cut(s) 457, 510
AluI AGCT 2 cut(s) 457, 510
Alw21I GWGCWC 2 cut(s) 391, 459
Alw26I GTCTC 1 cut(s) 431
AlwI GGATC 1 cut(s) 275
AoxI GGCC 1 cut(s) 326
Asp700I GAANNNNTTC 1 cut(s) 138
Asp718I GGTACC 1 cut(s) 380
AsuHPI GGTGA 2 cut(s) 134, 472
BanI GGYRCC 1 cut(s) 380
BanII GRGCYC 2 cut(s) 213, 459
BbsI GAAGAC 2 cut(s) 522, 552
Bbv12I GWGCWC 2 cut(s) 391, 459
BccI CCATC 3 cut(s) 154, 293, 497
BceAI ACGGC 1 cut(s) 341
BciT130I CCWGG 2 cut(s) 194, 553
BciVI GTATCC 1 cut(s) 182
BcoDI GTCTC 1 cut(s) 431
BfaI CTAG 1 cut(s) 369
BfmI CTRYAG 1 cut(s) 392
BfuAI ACCTGC 2 cut(s) 504, 553
BfuI GTATCC 1 cut(s) 182
BisI GCNGC 1 cut(s) 490
BlsI GCNGC 1 cut(s) 491
Bme1390I CCNGG 2 cut(s) 194, 553
BmiI GGNNCC 1 cut(s) 382
BmrFI CCNGG 2 cut(s) 194, 553
BmrI ACTGGG 1 cut(s) 529
BmuI ACTGGG 1 cut(s) 529
BpiI GAAGAC 2 cut(s) 522, 552
BpmI CTGGAG 1 cut(s) 189
BpuEI CTTGAG 1 cut(s) 470
BsaJI CCNNGG 2 cut(s) 294, 329
Bsc4I CCNNNNNNNGG 3 cut(s) 418, 451, 558
Bse1I ACTGG 1 cut(s) 524
BseBI CCWGG 2 cut(s) 194, 553
BseDI CCNNGG 2 cut(s) 294, 329
BseGI GGATG 2 cut(s) 202, 247
BseLI CCNNNNNNNGG 3 cut(s) 418, 451, 558
BseNI ACTGG 1 cut(s) 524
BseRI GAGGAG 4 cut(s) 248, 251, 311, 467
BshFI GGCC 1 cut(s) 328
BshNI GGYRCC 1 cut(s) 380
BsiHKAI GWGCWC 2 cut(s) 391, 459
BslI CCNNNNNNNGG 3 cut(s) 418, 451, 558
BsmAI GTCTC 1 cut(s) 431
BsmI GAATGC 1 cut(s) 412
BsnI GGCC 1 cut(s) 328
Bsp1286I GDGCHC 3 cut(s) 213, 391, 459
Bsp143I GATC 3 cut(s) 46, 280, 537
BspACI CCGC 4 cut(s) 158, 446, 466, 490
BspANI GGCC 1 cut(s) 328
BspLI GGNNCC 1 cut(s) 382
BspMAI CTGCAG 1 cut(s) 396
BspMI ACCTGC 2 cut(s) 504, 553
BspPI GGATC 1 cut(s) 275
BspT107I GGYRCC 1 cut(s) 380
BsrBI CCGCTC 1 cut(s) 466
BsrI ACTGG 1 cut(s) 524
BssECI CCNNGG 2 cut(s) 294, 329
BssMI GATC 3 cut(s) 46, 280, 537
Bst2UI CCWGG 2 cut(s) 194, 553
Bst4CI ACNGT 1 cut(s) 28
Bst6I CTCTTC 1 cut(s) 551
BstC8I GCNNGC 1 cut(s) 366
BstENI CCTNNNNNAGG 1 cut(s) 556
BstF5I GGATG 2 cut(s) 202, 247
BstKTI GATC 3 cut(s) 49, 283, 540
BstMAI GTCTC 1 cut(s) 431
BstMBI GATC 3 cut(s) 46, 280, 537
BstMWI GCNNNNNNNGC 3 cut(s) 208, 454, 463
BstNI CCWGG 2 cut(s) 194, 553
BstSCI CCNGG 2 cut(s) 192, 551
BstSFI CTRYAG 1 cut(s) 392
BstV2I GAAGAC 2 cut(s) 522, 552
BstX2I RGATCY 1 cut(s) 280
BstYI RGATCY 1 cut(s) 280
BsuI GTATCC 1 cut(s) 182
BsuRI GGCC 1 cut(s) 328
BtsCI GGATG 2 cut(s) 202, 247
BveI ACCTGC 2 cut(s) 504, 553
Cac8I GCNNGC 1 cut(s) 366
CseI GACGC 1 cut(s) 107
Csp6I GTAC 1 cut(s) 381
CviAII CATG 2 cut(s) 184, 403
CviJI RGCY 6 cut(s) 202, 211, 293, 328, 457, 510
CviKI_1 RGCY 6 cut(s) 202, 211, 293, 328, 457, 510
CviQI GTAC 1 cut(s) 381
DpnI GATC 3 cut(s) 48, 282, 539
DpnII GATC 3 cut(s) 46, 280, 537
Eam1104I CTCTTC 1 cut(s) 551
EarI CTCTTC 1 cut(s) 551
EciI GGCGGA 1 cut(s) 173
Ecl136II GAGCTC 1 cut(s) 457
Eco24I GRGCYC 2 cut(s) 213, 459
Eco53kI GAGCTC 1 cut(s) 457
EcoICRI GAGCTC 1 cut(s) 457
EcoNI CCTNNNNNAGG 1 cut(s) 556
EcoRII CCWGG 2 cut(s) 192, 551
EcoT38I GRGCYC 2 cut(s) 213, 459
FaeI CATG 2 cut(s) 187, 406
FaiI YATR 7 cut(s) 185, 348, 350, 360, 404, 419, 485
FatI CATG 2 cut(s) 183, 402
FauI CCCGC 1 cut(s) 453
Fnu4HI GCNGC 1 cut(s) 490
FokI GGATG 2 cut(s) 209, 254
FriOI GRGCYC 2 cut(s) 213, 459
Fsp4HI GCNGC 1 cut(s) 490
FspBI CTAG 1 cut(s) 369
GluI GCNGC 1 cut(s) 490
GsuI CTGGAG 1 cut(s) 189
HaeIII GGCC 1 cut(s) 328
HgaI GACGC 1 cut(s) 107
Hin1II CATG 2 cut(s) 187, 406
HincII GTYRAC 2 cut(s) 181, 247
HindII GTYRAC 2 cut(s) 181, 247
HinfI GANTC 2 cut(s) 372, 548
HphI GGTGA 2 cut(s) 134, 472
Hpy166II GTNNAC 2 cut(s) 181, 247
Hpy188I TCNGA 1 cut(s) 333
Hpy188III TCNNGA 3 cut(s) 95, 108, 206
Hpy8I GTNNAC 2 cut(s) 181, 247
Hpy99I CGWCG 3 cut(s) 167, 179, 545
HpyAV CCTTC 3 cut(s) 90, 218, 295
HpyCH4III ACNGT 1 cut(s) 28
HpyCH4IV ACGT 1 cut(s) 177
HpyCH4V TGCA 2 cut(s) 275, 394
HpyF10VI GCNNNNNNNGC 3 cut(s) 208, 454, 463
HpySE526I ACGT 1 cut(s) 177
Hsp92II CATG 2 cut(s) 187, 406
KpnI GGTACC 1 cut(s) 384
Kzo9I GATC 3 cut(s) 46, 280, 537
LmnI GCTCC 2 cut(s) 454, 462
MaeI CTAG 1 cut(s) 369
MaeII ACGT 1 cut(s) 177
MalI GATC 3 cut(s) 48, 282, 539
MbiI CCGCTC 1 cut(s) 466
MboI GATC 3 cut(s) 46, 280, 537
MboII GAAGA 7 cut(s) 131, 233, 317, 481, 527, 557, 568
MflI RGATCY 1 cut(s) 280
MhlI GDGCHC 3 cut(s) 213, 391, 459
MluCI AATT 4 cut(s) 216, 250, 425, 533
MlyI GAGTC 1 cut(s) 542
MroXI GAANNNNTTC 1 cut(s) 138
MseI TTAA 1 cut(s) 119
MspR9I CCNGG 2 cut(s) 194, 553
Mva1269I GAATGC 1 cut(s) 412
MvaI CCWGG 2 cut(s) 194, 553
MwoI GCNNNNNNNGC 3 cut(s) 208, 454, 463
NdeII GATC 3 cut(s) 46, 280, 537
NlaIII CATG 2 cut(s) 187, 406
NlaIV GGNNCC 1 cut(s) 382
NmeAIII GCCGAG 1 cut(s) 319
PaqCI CACCTGC 1 cut(s) 553
PcsI WCGNNNNNNNCGW 1 cut(s) 171
PctI GAATGC 1 cut(s) 412
PdmI GAANNNNTTC 1 cut(s) 138
PfeI GAWTC 1 cut(s) 372
PfoI TCCNGGA 1 cut(s) 551
PkrI GCNGC 1 cut(s) 491
PleI GAGTC 1 cut(s) 542
PpsI GAGTC 1 cut(s) 542
Psp124BI GAGCTC 1 cut(s) 459
Psp6I CCWGG 2 cut(s) 192, 551
PspGI CCWGG 2 cut(s) 192, 551
PspN4I GGNNCC 1 cut(s) 382
PstI CTGCAG 1 cut(s) 396
PsuI RGATCY 1 cut(s) 280
RsaI GTAC 1 cut(s) 382
RsaNI GTAC 1 cut(s) 381
SacI GAGCTC 1 cut(s) 459
SaqAI TTAA 1 cut(s) 119
SatI GCNGC 1 cut(s) 490
Sau3AI GATC 3 cut(s) 46, 280, 537
SchI GAGTC 1 cut(s) 542
ScrFI CCNGG 2 cut(s) 194, 553
SduI GDGCHC 3 cut(s) 213, 391, 459
SetI ASST 9 cut(s) 46, 62, 180, 341, 459, 498, 512, 567, 574
SfcI CTRYAG 1 cut(s) 392
SmlI CTYRAG 1 cut(s) 449
SmoI CTYRAG 1 cut(s) 449
Sse9I AATT 4 cut(s) 216, 250, 425, 533
SsiI CCGC 4 cut(s) 158, 446, 466, 490
SspMI CTAG 1 cut(s) 369
SstI GAGCTC 1 cut(s) 459
StyD4I CCNGG 2 cut(s) 192, 551
TaaI ACNGT 1 cut(s) 28
TaiI ACGT 1 cut(s) 180
TaqI TCGA 4 cut(s) 109, 288, 341, 543
TasI AATT 4 cut(s) 216, 250, 425, 533
TauI GCSGC 1 cut(s) 492
TfiI GAWTC 1 cut(s) 372
Tru1I TTAA 1 cut(s) 119
Tru9I TTAA 1 cut(s) 119
TspDTI ATGAA 2 cut(s) 419, 546
TspGWI ACGGA 1 cut(s) 449
XagI CCTNNNNNAGG 1 cut(s) 556
XmnI GAANNNNTTC 1 cut(s) 138
XspI CTAG 1 cut(s) 369
Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.