MD10G1340900.v1.1

DNA-directed RNA polymerases IV and V subunit

Design Primers CRISPR Design

Basic Information

Type: gene
Biological Identity
malus_domestica
Chr10
OG0005178
Physical Location & Seq
Forward (+)
41611005 .. 41614405
3401 bp
Loading structure...
UTR
Exon/CDS
Intron
MD10G1340900.v1.1.491

Sequence Viewer

Length: 657 bp
ATGTCGGAGAAAGGAGGAAAGGGGTTTTCTTTGCCTAAATCTTCGCTGAAATCTACCCCTCCTAGCACAAAGGATGGTAAGGATGATAGCTCAACCAAGTCCAAGAAGGGAAGACGAGTTCAGTTCGATTCTGAAGGTTCCCGGGAACCCAAATCACACTTTTCGTCAAAATTTGATAGCCGATCTGCTGCTTCAGGGAAAGCTGATTGGGGCAAAGGGGGGAAAGGAGACACCATCGGAAATGGTAGAAAGAAAGAACCACAGCCACTGGAGCTCAAAATTGAGCAGGAACTTCCAAAGAGTGCCAAATGTATGATGGATTGTGAGGCTGCCGATATATTACAAGGCATCCAGGAGCAGATGGTCATGTTGTCAAAAGATCCTACTATTAAAATCCCTGTATCATTCGACAAGGGACTGCAGTACGCAAACAGCTCCAGCCGTTATACTCATCCCCAGTCTGCGAGACACATTCTTGAGGCACTAAAAAAATATGGTGTCAAGGATGGCGAGATATGTGTGATTGCCAATGTTTGTCCAGAAACCACAGATGAAGTTTTTGCTTTAGTGCCATCCTTGAAGGCTAAAAGAAGCACGCTCAGCCAACCACTCAAAGATGTTTTAAGTGAGCTGACGAGGTTTAAAAAGGCAACATAA
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

219

Amino Acids

23.8

Weight (kDa)

9.43

Isoelectric Point (pI)

52.66

Instability Index
Protein Domains (Pfam)
Domain Name Pfam ID Position E-value Description
RNA_pol_Rpb4 PF03874 104 - 211 1.8e-12 RNA polymerase Rpb4
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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Restriction Enzyme Sites

1 / 10
Enzyme Recognition Site Cut Count Positions (bp)
AclWI GGATC 1 cut(s) 374
AcsI RAATTY 1 cut(s) 170
AcuI CTGAAG 2 cut(s) 153, 177
AfaI GTAC 1 cut(s) 425
AgsI TTSAA 1 cut(s) 580
AjnI CCWGG 1 cut(s) 351
AloI GAACNNNNNNTCC 2 cut(s) 102, 134
AluBI AGCT 5 cut(s) 90, 203, 274, 435, 631
AluI AGCT 5 cut(s) 90, 203, 274, 435, 631
Alw21I GWGCWC 1 cut(s) 276
Alw26I GTCTC 2 cut(s) 222, 460
AlwI GGATC 1 cut(s) 374
AlwNI CAGNNNCTG 1 cut(s) 268
Ama87I CYCGRG 1 cut(s) 141
ApeKI GCWGC 2 cut(s) 188, 329
ApoI RAATTY 1 cut(s) 170
AsuC2I CCSGG 2 cut(s) 142, 143
AvaI CYCGRG 1 cut(s) 141
BanII GRGCYC 1 cut(s) 276
BbsI GAAGAC 1 cut(s) 118
Bbv12I GWGCWC 1 cut(s) 276
BbvI GCAGC 2 cut(s) 175, 316
BccI CCATC 6 cut(s) 68, 242, 310, 355, 500, 580
BceAI ACGGC 1 cut(s) 426
BciT130I CCWGG 1 cut(s) 353
BcnI CCSGG 2 cut(s) 142, 143
BcoDI GTCTC 2 cut(s) 222, 460
BfaI CTAG 1 cut(s) 63
BfmI CTRYAG 1 cut(s) 419
BisI GCNGC 2 cut(s) 189, 330
BlpI GCTNAGC 1 cut(s) 599
BlsI GCNGC 2 cut(s) 190, 331
Bme1390I CCNGG 3 cut(s) 142, 143, 353
BmeT110I CYCGRG 1 cut(s) 141
BmiI GGNNCC 2 cut(s) 139, 147
BmrFI CCNGG 3 cut(s) 142, 143, 353
BmrI ACTGGG 1 cut(s) 451
BmsI GCATC 1 cut(s) 357
BmuI ACTGGG 1 cut(s) 451
BpiI GAAGAC 1 cut(s) 118
BpmI CTGGAG 2 cut(s) 290, 421
Bpu1102I GCTNAGC 1 cut(s) 599
BpuEI CTTGAG 1 cut(s) 497
BpuMI CCSGG 2 cut(s) 142, 143
BsaJI CCNNGG 1 cut(s) 141
Bse1I ACTGG 2 cut(s) 273, 457
BseBI CCWGG 1 cut(s) 353
BseDI CCNNGG 1 cut(s) 141
BseGI GGATG 6 cut(s) 79, 88, 348, 451, 511, 572
BseMII CTCAG 1 cut(s) 613
BseNI ACTGG 2 cut(s) 273, 457
BseXI GCAGC 2 cut(s) 175, 316
BsiHKAI GWGCWC 1 cut(s) 276
BsiHKCI CYCGRG 1 cut(s) 141
BsiSI CCGG 1 cut(s) 142
BslFI GGGAC 1 cut(s) 429
BsmAI GTCTC 2 cut(s) 222, 460
BsmFI GGGAC 1 cut(s) 429
BsoBI CYCGRG 1 cut(s) 141
Bsp1286I GDGCHC 1 cut(s) 276
Bsp143I GATC 2 cut(s) 182, 379
Bsp1720I GCTNAGC 1 cut(s) 599
BspCNI CTCAG 1 cut(s) 612
BspLI GGNNCC 2 cut(s) 139, 147
BspMAI CTGCAG 1 cut(s) 423
BspPI GGATC 1 cut(s) 374
BsrI ACTGG 2 cut(s) 273, 457
BssECI CCNNGG 1 cut(s) 141
BssMI GATC 2 cut(s) 182, 379
Bst2UI CCWGG 1 cut(s) 353
BstC8I GCNNGC 1 cut(s) 596
BstDEI CTNAG 1 cut(s) 599
BstF5I GGATG 6 cut(s) 79, 88, 348, 451, 511, 572
BstKTI GATC 2 cut(s) 185, 382
BstMAI GTCTC 2 cut(s) 222, 460
BstMBI GATC 2 cut(s) 182, 379
BstMWI GCNNNNNNNGC 2 cut(s) 271, 600
BstNI CCWGG 1 cut(s) 353
BstSCI CCNGG 3 cut(s) 140, 141, 351
BstSFI CTRYAG 1 cut(s) 419
BstV1I GCAGC 2 cut(s) 175, 316
BstV2I GAAGAC 1 cut(s) 118
BstX2I RGATCY 1 cut(s) 379
BstYI RGATCY 1 cut(s) 379
BtsCI GGATG 6 cut(s) 79, 88, 348, 451, 511, 572
BtsIMutI CAGTG 1 cut(s) 266
Cac8I GCNNGC 1 cut(s) 596
CaiI CAGNNNCTG 1 cut(s) 268
Cfr9I CCCGGG 1 cut(s) 141
Csp6I GTAC 1 cut(s) 424
CviAII CATG 1 cut(s) 367
CviQI GTAC 1 cut(s) 424
DdeI CTNAG 1 cut(s) 599
DpnI GATC 2 cut(s) 184, 381
DpnII GATC 2 cut(s) 182, 379
DraI TTTAAA 1 cut(s) 643
Ecl136II GAGCTC 1 cut(s) 274
Eco24I GRGCYC 1 cut(s) 276
Eco53kI GAGCTC 1 cut(s) 274
Eco57I CTGAAG 2 cut(s) 153, 177
Eco88I CYCGRG 1 cut(s) 141
EcoICRI GAGCTC 1 cut(s) 274
EcoRII CCWGG 1 cut(s) 351
EcoT38I GRGCYC 1 cut(s) 276
FaeI CATG 1 cut(s) 370
FaiI YATR 7 cut(s) 314, 338, 368, 447, 495, 517, 655
FaqI GGGAC 1 cut(s) 429
FatI CATG 1 cut(s) 366
Fnu4HI GCNGC 2 cut(s) 189, 330
FokI GGATG 6 cut(s) 86, 95, 335, 438, 518, 559
FriOI GRGCYC 1 cut(s) 276
Fsp4HI GCNGC 2 cut(s) 189, 330
FspBI CTAG 1 cut(s) 63
GluI GCNGC 2 cut(s) 189, 330
GsuI CTGGAG 2 cut(s) 290, 421
HapII CCGG 1 cut(s) 142
Hin1II CATG 1 cut(s) 370
HinfI GANTC 1 cut(s) 128
HpaII CCGG 1 cut(s) 142
Hpy188I TCNGA 3 cut(s) 7, 133, 239
Hpy188III TCNNGA 2 cut(s) 476, 539
HpyAV CCTTC 3 cut(s) 100, 128, 574
HpyCH4V TGCA 1 cut(s) 421
HpyF10VI GCNNNNNNNGC 2 cut(s) 271, 600
HpyF3I CTNAG 1 cut(s) 599
Hsp92II CATG 1 cut(s) 370
Kzo9I GATC 2 cut(s) 182, 379
LmnI GCTCC 3 cut(s) 271, 355, 440
Lsp1109I GCAGC 2 cut(s) 175, 316
LweI GCATC 1 cut(s) 357
MaeI CTAG 1 cut(s) 63
MalI GATC 2 cut(s) 184, 381
MboI GATC 2 cut(s) 182, 379
MboII GAAGA 2 cut(s) 33, 123
MflI RGATCY 1 cut(s) 379
MhlI GDGCHC 1 cut(s) 276
MluCI AATT 2 cut(s) 170, 279
MnlI CCTC 5 cut(s) 8, 69, 319, 472, 630
MseI TTAA 3 cut(s) 390, 623, 642
MspI CCGG 1 cut(s) 142
MspR9I CCNGG 3 cut(s) 142, 143, 353
MvaI CCWGG 1 cut(s) 353
MwoI GCNNNNNNNGC 2 cut(s) 271, 600
NciI CCSGG 2 cut(s) 142, 143
NdeII GATC 2 cut(s) 182, 379
NlaIII CATG 1 cut(s) 370
NlaIV GGNNCC 2 cut(s) 139, 147
PfeI GAWTC 1 cut(s) 128
PfoI TCCNGGA 1 cut(s) 351
PkrI GCNGC 2 cut(s) 190, 331
Psp124BI GAGCTC 1 cut(s) 276
Psp6I CCWGG 1 cut(s) 351
PspGI CCWGG 1 cut(s) 351
PspN4I GGNNCC 2 cut(s) 139, 147
PstI CTGCAG 1 cut(s) 423
PstNI CAGNNNCTG 1 cut(s) 268
PsuI RGATCY 1 cut(s) 379
RsaI GTAC 1 cut(s) 425
RsaNI GTAC 1 cut(s) 424
SacI GAGCTC 1 cut(s) 276
SaqAI TTAA 3 cut(s) 390, 623, 642
SatI GCNGC 2 cut(s) 189, 330
Sau3AI GATC 2 cut(s) 182, 379
ScrFI CCNGG 3 cut(s) 142, 143, 353
SduI GDGCHC 1 cut(s) 276
SetI ASST 7 cut(s) 92, 139, 205, 276, 437, 633, 641
SfaNI GCATC 1 cut(s) 357
SfcI CTRYAG 1 cut(s) 419
SmaI CCCGGG 1 cut(s) 143
SmlI CTYRAG 1 cut(s) 476
SmoI CTYRAG 1 cut(s) 476
Sse9I AATT 2 cut(s) 170, 279
SspMI CTAG 1 cut(s) 63
SstI GAGCTC 1 cut(s) 276
StyD4I CCNGG 3 cut(s) 140, 141, 351
TaqI TCGA 2 cut(s) 126, 408
TasI AATT 2 cut(s) 170, 279
TfiI GAWTC 1 cut(s) 128
Tru1I TTAA 3 cut(s) 390, 623, 642
Tru9I TTAA 3 cut(s) 390, 623, 642
TscAI CASTG 1 cut(s) 273
TseI GCWGC 2 cut(s) 188, 329
TspDTI ATGAA 1 cut(s) 567
TspMI CCCGGG 1 cut(s) 141
TspRI CASTG 1 cut(s) 273
XapI RAATTY 1 cut(s) 170
XcmI CCANNNNNNNNNTGG 1 cut(s) 313
XmaI CCCGGG 1 cut(s) 141
XspI CTAG 1 cut(s) 63
Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.