MD12G1011200.v1.1

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

Design Primers CRISPR Design

Basic Information

Type: gene
Biological Identity
malus_domestica
Chr12
OG0012428
Physical Location & Seq
Forward (+)
1143849 .. 1146687
2839 bp
Loading structure...
UTR
Exon/CDS
Intron
MD12G1011200.v1.1.491

Sequence Viewer

Length: 438 bp
ATGGCGGACGACGACTACAACGACGTTGACATGGGATACCAGGATGAGCCTCCGGAGCCCGAAATTGAAGAAGGTGCAGAGGAGGAGGATGTTGACAATTTAAACAATGATGATGACGTTGCAGGAGATCCCATCGAAGCGGAGGAGAAGGAAGAACAAGAGGGGGTGGAACGGCCTCGGAAAACCTCGAAATATATGACCAAGTATGAGCGTGCTAGAATCTTGGGTACCCGTGCTCTGCAGATTAGCATGAATGCCCCTGTTATGGTTGAATTGGAGGGCGAGACTGACCCGCTTGAGATTGCTATGAAGGAGCTTCGTGAGCGGAAGATACCATTCACCATACGCCGTTACCTGCCTGATGGAAGCTATGAAGACTGGGGCGTAGATGAATTGATCGTCGAAGACTCCTGGAAGAGGCAGGTGGGAGGTGATTGA
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

146

Amino Acids

16.72

Weight (kDa)

4.12

Isoelectric Point (pI)

57.41

Instability Index
Protein Domains (Pfam)
Domain Name Pfam ID Position E-value Description
RNA_pol_Rpb6 PF01192 62 - 113 6.1e-13 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) 412
Acc36I ACCTGC 2 cut(s) 363, 412
Acc65I GGTACC 1 cut(s) 227
AccB1I GGYRCC 1 cut(s) 227
AccBSI CCGCTC 1 cut(s) 325
AccIII TCCGGA 1 cut(s) 52
AciI CCGC 4 cut(s) 5, 140, 293, 325
AclWI GGATC 1 cut(s) 122
AfaI GTAC 1 cut(s) 229
AfiI CCNNNNNNNGG 2 cut(s) 265, 417
AgsI TTSAA 2 cut(s) 68, 272
AjnI CCWGG 2 cut(s) 39, 410
AluBI AGCT 2 cut(s) 316, 369
AluI AGCT 2 cut(s) 316, 369
Alw21I GWGCWC 1 cut(s) 238
Alw26I GTCTC 1 cut(s) 278
AlwI GGATC 1 cut(s) 122
Aor13HI TCCGGA 1 cut(s) 52
AoxI GGCC 1 cut(s) 173
Asp718I GGTACC 1 cut(s) 227
AsuHPI GGTGA 1 cut(s) 331
BanI GGYRCC 1 cut(s) 227
BanII GRGCYC 1 cut(s) 60
BbsI GAAGAC 2 cut(s) 381, 411
Bbv12I GWGCWC 1 cut(s) 238
BccI CCATC 2 cut(s) 140, 356
BceAI ACGGC 2 cut(s) 188, 333
BciT130I CCWGG 2 cut(s) 41, 412
BciVI GTATCC 1 cut(s) 29
BcoDI GTCTC 1 cut(s) 278
BfaI CTAG 1 cut(s) 216
BfmI CTRYAG 1 cut(s) 239
BfuAI ACCTGC 2 cut(s) 363, 412
BfuI GTATCC 1 cut(s) 29
Bme1390I CCNGG 2 cut(s) 41, 412
BmiI GGNNCC 2 cut(s) 57, 229
BmrFI CCNGG 2 cut(s) 41, 412
BmrI ACTGGG 1 cut(s) 388
BmuI ACTGGG 1 cut(s) 388
BpiI GAAGAC 2 cut(s) 381, 411
BpuEI CTTGAG 1 cut(s) 317
BsaJI CCNNGG 1 cut(s) 176
BsaWI WCCGGW 1 cut(s) 52
Bsc4I CCNNNNNNNGG 2 cut(s) 265, 417
Bse1I ACTGG 1 cut(s) 383
BseAI TCCGGA 1 cut(s) 52
BseBI CCWGG 2 cut(s) 41, 412
BseDI CCNNGG 1 cut(s) 176
BseGI GGATG 2 cut(s) 49, 94
BseLI CCNNNNNNNGG 2 cut(s) 265, 417
BseNI ACTGG 1 cut(s) 383
BseRI GAGGAG 3 cut(s) 95, 98, 158
BsgI GTGCAG 1 cut(s) 96
BshFI GGCC 1 cut(s) 175
BshNI GGYRCC 1 cut(s) 227
BsiHKAI GWGCWC 1 cut(s) 238
BsiSI CCGG 1 cut(s) 53
BslI CCNNNNNNNGG 2 cut(s) 265, 417
BsmAI GTCTC 1 cut(s) 278
BsmI GAATGC 1 cut(s) 259
BsnI GGCC 1 cut(s) 175
Bsp1286I GDGCHC 2 cut(s) 60, 238
Bsp13I TCCGGA 1 cut(s) 52
Bsp143I GATC 2 cut(s) 127, 396
BspACI CCGC 4 cut(s) 5, 140, 293, 325
BspANI GGCC 1 cut(s) 175
BspEI TCCGGA 1 cut(s) 52
BspLI GGNNCC 2 cut(s) 57, 229
BspMAI CTGCAG 1 cut(s) 243
BspMI ACCTGC 2 cut(s) 363, 412
BspPI GGATC 1 cut(s) 122
BspT107I GGYRCC 1 cut(s) 227
BsrBI CCGCTC 1 cut(s) 325
BsrI ACTGG 1 cut(s) 383
BssECI CCNNGG 1 cut(s) 176
BssMI GATC 2 cut(s) 127, 396
Bst2UI CCWGG 2 cut(s) 41, 412
Bst6I CTCTTC 1 cut(s) 410
BstC8I GCNNGC 1 cut(s) 213
BstENI CCTNNNNNAGG 1 cut(s) 415
BstF5I GGATG 2 cut(s) 49, 94
BstKTI GATC 2 cut(s) 130, 399
BstMAI GTCTC 1 cut(s) 278
BstMBI GATC 2 cut(s) 127, 396
BstMWI GCNNNNNNNGC 2 cut(s) 55, 322
BstNI CCWGG 2 cut(s) 41, 412
BstSCI CCNGG 2 cut(s) 39, 410
BstSFI CTRYAG 1 cut(s) 239
BstV2I GAAGAC 2 cut(s) 381, 411
BstX2I RGATCY 1 cut(s) 127
BstYI RGATCY 1 cut(s) 127
BsuI GTATCC 1 cut(s) 29
BsuRI GGCC 1 cut(s) 175
BtsCI GGATG 2 cut(s) 49, 94
BveI ACCTGC 2 cut(s) 363, 412
Cac8I GCNNGC 1 cut(s) 213
Csp6I GTAC 1 cut(s) 228
CviAII CATG 2 cut(s) 31, 250
CviJI RGCY 5 cut(s) 49, 58, 175, 316, 369
CviKI_1 RGCY 5 cut(s) 49, 58, 175, 316, 369
CviQI GTAC 1 cut(s) 228
DpnI GATC 2 cut(s) 129, 398
DpnII GATC 2 cut(s) 127, 396
DraI TTTAAA 1 cut(s) 102
Eam1104I CTCTTC 1 cut(s) 410
EarI CTCTTC 1 cut(s) 410
EciI GGCGGA 1 cut(s) 20
Eco24I GRGCYC 1 cut(s) 60
EcoNI CCTNNNNNAGG 1 cut(s) 415
EcoRII CCWGG 2 cut(s) 39, 410
EcoT38I GRGCYC 1 cut(s) 60
FaeI CATG 2 cut(s) 34, 253
FaiI YATR 9 cut(s) 32, 195, 197, 207, 251, 266, 308, 344, 372
FatI CATG 2 cut(s) 30, 249
FauI CCCGC 1 cut(s) 300
FokI GGATG 2 cut(s) 56, 101
FriOI GRGCYC 1 cut(s) 60
FspBI CTAG 1 cut(s) 216
HaeIII GGCC 1 cut(s) 175
HapII CCGG 1 cut(s) 53
Hin1II CATG 2 cut(s) 34, 253
HincII GTYRAC 2 cut(s) 28, 94
HindII GTYRAC 2 cut(s) 28, 94
HinfI GANTC 2 cut(s) 219, 407
HpaII CCGG 1 cut(s) 53
HphI GGTGA 1 cut(s) 331
Hpy166II GTNNAC 2 cut(s) 28, 94
Hpy188I TCNGA 1 cut(s) 180
Hpy188III TCNNGA 2 cut(s) 53, 320
Hpy8I GTNNAC 2 cut(s) 28, 94
Hpy99I CGWCG 3 cut(s) 14, 26, 404
HpyAV CCTTC 3 cut(s) 65, 142, 304
HpyCH4IV ACGT 2 cut(s) 24, 117
HpyCH4V TGCA 3 cut(s) 77, 122, 241
HpyF10VI GCNNNNNNNGC 2 cut(s) 55, 322
HpySE526I ACGT 2 cut(s) 24, 117
Hsp92II CATG 2 cut(s) 34, 253
Kpn2I TCCGGA 1 cut(s) 52
KpnI GGTACC 1 cut(s) 231
Kzo9I GATC 2 cut(s) 127, 396
LmnI GCTCC 2 cut(s) 55, 313
MaeI CTAG 1 cut(s) 216
MaeII ACGT 2 cut(s) 24, 117
MaeIII GTNAC 1 cut(s) 350
MalI GATC 2 cut(s) 129, 398
MbiI CCGCTC 1 cut(s) 325
MboI GATC 2 cut(s) 127, 396
MboII GAAGA 6 cut(s) 80, 164, 340, 386, 416, 427
MflI RGATCY 1 cut(s) 127
MhlI GDGCHC 2 cut(s) 60, 238
MluCI AATT 4 cut(s) 63, 97, 272, 392
MlyI GAGTC 1 cut(s) 401
MroI TCCGGA 1 cut(s) 52
MseI TTAA 1 cut(s) 101
MspI CCGG 1 cut(s) 53
MspR9I CCNGG 2 cut(s) 41, 412
Mva1269I GAATGC 1 cut(s) 259
MvaI CCWGG 2 cut(s) 41, 412
MwoI GCNNNNNNNGC 2 cut(s) 55, 322
NdeII GATC 2 cut(s) 127, 396
NlaIII CATG 2 cut(s) 34, 253
NlaIV GGNNCC 2 cut(s) 57, 229
PaqCI CACCTGC 1 cut(s) 412
PcsI WCGNNNNNNNCGW 1 cut(s) 18
PctI GAATGC 1 cut(s) 259
PfeI GAWTC 1 cut(s) 219
PfoI TCCNGGA 1 cut(s) 410
PleI GAGTC 1 cut(s) 401
PpsI GAGTC 1 cut(s) 401
Psp6I CCWGG 2 cut(s) 39, 410
PspGI CCWGG 2 cut(s) 39, 410
PspN4I GGNNCC 2 cut(s) 57, 229
PstI CTGCAG 1 cut(s) 243
PsuI RGATCY 1 cut(s) 127
RsaI GTAC 1 cut(s) 229
RsaNI GTAC 1 cut(s) 228
SaqAI TTAA 1 cut(s) 101
Sau3AI GATC 2 cut(s) 127, 396
SchI GAGTC 1 cut(s) 401
ScrFI CCNGG 2 cut(s) 41, 412
SduI GDGCHC 2 cut(s) 60, 238
SetI ASST 9 cut(s) 27, 76, 120, 188, 318, 357, 371, 426, 433
SfcI CTRYAG 1 cut(s) 239
SmlI CTYRAG 1 cut(s) 296
SmoI CTYRAG 1 cut(s) 296
Sse9I AATT 4 cut(s) 63, 97, 272, 392
SsiI CCGC 4 cut(s) 5, 140, 293, 325
SspMI CTAG 1 cut(s) 216
StyD4I CCNGG 2 cut(s) 39, 410
TaiI ACGT 2 cut(s) 27, 120
TaqI TCGA 3 cut(s) 135, 188, 402
TasI AATT 4 cut(s) 63, 97, 272, 392
TfiI GAWTC 1 cut(s) 219
Tru1I TTAA 1 cut(s) 101
Tru9I TTAA 1 cut(s) 101
TspDTI ATGAA 4 cut(s) 266, 323, 387, 405
XagI CCTNNNNNAGG 1 cut(s) 415
XspI CTAG 1 cut(s) 216
Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.