MD06G1233600.v1.1

DNA-directed RNA-polymerase II subunit

Design Primers CRISPR Design

Basic Information

Type: gene
Biological Identity
malus_domestica
Chr06
OG0002628
Physical Location & Seq
Forward (+)
36467315 .. 36469064
1750 bp
Loading structure...
UTR
Exon/CDS
Intron
MD06G1233600.v1.1.491

Sequence Viewer

Length: 417 bp
ATGCTAAGAGCAGAAGATGAAGACGCTTCAGAACTCAAACTTGGAGACGATTTTTTGAAGGCAAAGTGTCTAATGAATAGTGAGGTTGCCATTCTTCTTGAGCATAGATGTGATCAGATGAAGCATATGTCCGGCGAATCAATGCACCAACTTCCCCAAGTGTTGGAGAAATCACTGCAGTATGTTAAGCGCTTTAGTCGCTTCACGAATCAGGGCTCTGTGAAGCAAGTTCGAGAAGTTCTCAGTAGATACCAGTTGGCTGAATTCGAGCTTGCTGTGATTGGAAATCTTTGTCCTGAAACTGTGGAGGAAGCCAAGGCAGTTGTGCCTTCTCTCAAGACGAAAGGACGTGGGCACGACGATGAAGCCATTGACAGACTGTTGAATGACCTAATGATGATTAAAAAGTTTGAGTGA
Functional Annotation
Gene Ontology
Molecular Function
Biological Process
Cellular Component
No ontology terms assigned.
KEGG Pathways
Metabolic & Signaling
ko00230 ko00240 ko01100 ko03020 ko05016 ko05169 map00230 map00240 map01100 map03020 map05016 map05169
Pfam Domains
Protein Families
RNA_pol_Rpb4

Protein Analysis

139

Amino Acids

15.81

Weight (kDa)

5.63

Isoelectric Point (pI)

38.1

Instability Index
Protein Domains (Pfam)
Domain Name Pfam ID Position E-value Description
RNA_pol_Rpb4 PF03874 23 - 131 2.1e-26 RNA polymerase Rpb4
Hydrophobicity Profile (Kyte-Doolittle)
AI Structure Prediction Report
Calculating structure properties...

Genomic Context

Gene Family Tree

Species Filter
Loading...
Style Settings
Image
Tree File
Tip: Beautify your tree with professional tools

Download the Full Tree (.nwk) file, then upload it to any of the following tools to customize colors, fonts, annotations, clades, and branch support.

Publication-ready
iTOL Interactive Tree Of Life · Most popular EvolView Flexible annotations MEGA Desktop phylogenetics suite FigTree Desktop tree editor

Restriction Enzyme Sites

1 / 10
Enzyme Recognition Site Cut Count Positions (bp)
AccB7I CCANNNNNTGG 1 cut(s) 163
AcsI RAATTY 1 cut(s) 263
AcuI CTGAAG 1 cut(s) 12
AfeI AGCGCT 1 cut(s) 191
AfiI CCNNNNNNNGG 1 cut(s) 163
AgsI TTSAA 2 cut(s) 58, 385
AjiI CACGTC 1 cut(s) 350
AjuI GAANNNNNNNTTGG 2 cut(s) 24, 56
AluBI AGCT 1 cut(s) 271
AluI AGCT 1 cut(s) 271
Alw26I GTCTC 1 cut(s) 39
Aor51HI AGCGCT 1 cut(s) 191
ApoI RAATTY 1 cut(s) 263
AspLEI GCGC 1 cut(s) 192
BaeGI GKGCMC 1 cut(s) 357
BanII GRGCYC 1 cut(s) 218
BbsI GAAGAC 1 cut(s) 27
BclI TGATCA 1 cut(s) 112
BcoDI GTCTC 1 cut(s) 39
BfmI CTRYAG 1 cut(s) 176
BfoI RGCGCY 1 cut(s) 193
BmgBI CACGTC 1 cut(s) 350
BpiI GAAGAC 1 cut(s) 27
BplI GAGNNNNNCTC 2 cut(s) 225, 257
BpuEI CTTGAG 2 cut(s) 119, 320
BsaJI CCNNGG 1 cut(s) 315
Bsc4I CCNNNNNNNGG 1 cut(s) 163
Bse1I ACTGG 1 cut(s) 253
BseDI CCNNGG 1 cut(s) 315
BseLI CCNNNNNNNGG 1 cut(s) 163
BseMII CTCAG 1 cut(s) 256
BseNI ACTGG 1 cut(s) 253
BseSI GKGCMC 1 cut(s) 357
BsiSI CCGG 1 cut(s) 132
BslI CCNNNNNNNGG 1 cut(s) 163
BsmAI GTCTC 1 cut(s) 39
BsmBI CGTCTC 1 cut(s) 39
Bsp1286I GDGCHC 2 cut(s) 218, 357
Bsp143I GATC 1 cut(s) 112
BspCNI CTCAG 1 cut(s) 255
BspMAI CTGCAG 1 cut(s) 180
BsrI ACTGG 1 cut(s) 253
BssECI CCNNGG 1 cut(s) 315
BssMI GATC 1 cut(s) 112
BssT1I CCWWGG 1 cut(s) 315
Bst4CI ACNGT 2 cut(s) 304, 381
BstC8I GCNNGC 1 cut(s) 273
BstDEI CTNAG 2 cut(s) 5, 242
BstH2I RGCGCY 1 cut(s) 193
BstHHI GCGC 1 cut(s) 192
BstKTI GATC 1 cut(s) 115
BstMAI GTCTC 1 cut(s) 39
BstMBI GATC 1 cut(s) 112
BstMWI GCNNNNNNNGC 1 cut(s) 198
BstSFI CTRYAG 1 cut(s) 176
BstSLI GKGCMC 1 cut(s) 357
BstV2I GAAGAC 1 cut(s) 27
BtrI CACGTC 1 cut(s) 350
BtsI GCAGTG 1 cut(s) 173
BtsIMutI CAGTG 1 cut(s) 173
Cac8I GCNNGC 1 cut(s) 273
CfoI GCGC 1 cut(s) 192
CseI GACGC 1 cut(s) 32
CviJI RGCY 5 cut(s) 216, 260, 271, 314, 368
CviKI_1 RGCY 5 cut(s) 216, 260, 271, 314, 368
DdeI CTNAG 2 cut(s) 5, 242
DpnI GATC 1 cut(s) 114
DpnII GATC 1 cut(s) 112
Eco130I CCWWGG 1 cut(s) 315
Eco24I GRGCYC 1 cut(s) 218
Eco47III AGCGCT 1 cut(s) 191
Eco57I CTGAAG 1 cut(s) 12
EcoRI GAATTC 1 cut(s) 263
EcoT14I CCWWGG 1 cut(s) 315
EcoT38I GRGCYC 1 cut(s) 218
ErhI CCWWGG 1 cut(s) 315
Esp3I CGTCTC 1 cut(s) 39
FaiI YATR 4 cut(s) 105, 126, 128, 183
FauNDI CATATG 1 cut(s) 126
FbaI TGATCA 1 cut(s) 112
FriOI GRGCYC 1 cut(s) 218
GlaI GCGC 1 cut(s) 191
HaeII RGCGCY 1 cut(s) 193
HapII CCGG 1 cut(s) 132
HgaI GACGC 1 cut(s) 32
HhaI GCGC 1 cut(s) 192
Hin6I GCGC 1 cut(s) 190
HinP1I GCGC 1 cut(s) 190
HinfI GANTC 2 cut(s) 137, 208
HpaII CCGG 1 cut(s) 132
Hpy188I TCNGA 2 cut(s) 31, 117
Hpy188III TCNNGA 5 cut(s) 98, 205, 233, 296, 337
Hpy99I CGWCG 1 cut(s) 362
HpyAV CCTTC 2 cut(s) 52, 339
HpyCH4III ACNGT 2 cut(s) 304, 381
HpyCH4IV ACGT 1 cut(s) 349
HpyCH4V TGCA 2 cut(s) 145, 178
HpyF10VI GCNNNNNNNGC 1 cut(s) 198
HpyF3I CTNAG 2 cut(s) 5, 242
HpySE526I ACGT 1 cut(s) 349
HspAI GCGC 1 cut(s) 190
Ksp22I TGATCA 1 cut(s) 112
Kzo9I GATC 1 cut(s) 112
LpnPI CCDG 4 cut(s) 145, 197, 266, 309
MaeII ACGT 1 cut(s) 349
MalI GATC 1 cut(s) 114
MboI GATC 1 cut(s) 112
MboII GAAGA 3 cut(s) 26, 32, 86
MhlI GDGCHC 2 cut(s) 218, 357
MluCI AATT 1 cut(s) 263
MmeI TCCRAC 1 cut(s) 144
MnlI CCTC 2 cut(s) 76, 301
MseI TTAA 2 cut(s) 186, 402
MslI CAYNNNNRTG 2 cut(s) 108, 360
MspI CCGG 1 cut(s) 132
MwoI GCNNNNNNNGC 1 cut(s) 198
NdeI CATATG 1 cut(s) 126
NdeII GATC 1 cut(s) 112
PfeI GAWTC 2 cut(s) 137, 208
PflMI CCANNNNNTGG 1 cut(s) 163
PstI CTGCAG 1 cut(s) 180
RseI CAYNNNNRTG 2 cut(s) 108, 360
SaqAI TTAA 2 cut(s) 186, 402
Sau3AI GATC 1 cut(s) 112
SduI GDGCHC 2 cut(s) 218, 357
SetI ASST 4 cut(s) 87, 273, 352, 393
SfcI CTRYAG 1 cut(s) 176
SmiMI CAYNNNNRTG 2 cut(s) 108, 360
SmlI CTYRAG 2 cut(s) 98, 335
SmoI CTYRAG 2 cut(s) 98, 335
Sse9I AATT 1 cut(s) 263
StyI CCWWGG 1 cut(s) 315
TaaI ACNGT 2 cut(s) 304, 381
TaiI ACGT 1 cut(s) 352
TaqI TCGA 2 cut(s) 232, 267
TasI AATT 1 cut(s) 263
TfiI GAWTC 2 cut(s) 137, 208
Tru1I TTAA 2 cut(s) 186, 402
Tru9I TTAA 2 cut(s) 186, 402
TscAI CASTG 1 cut(s) 180
TspDTI ATGAA 4 cut(s) 33, 89, 134, 378
TspRI CASTG 1 cut(s) 180
Van91I CCANNNNNTGG 1 cut(s) 163
XapI RAATTY 1 cut(s) 263
Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.