MD15G1331500.v1.1

DNA-directed RNA polymerase II subunit

Design Primers CRISPR Design

Basic Information

Type: gene
Biological Identity
malus_domestica
Chr15
OG0002628
Physical Location & Seq
Forward (+)
36770820 .. 36772986
2167 bp
Loading structure...
UTR
Exon/CDS
Intron
MD15G1331500.v1.1.491

Sequence Viewer

Length: 417 bp
ATGTCTGGGGAAGAGGAAGAAAACGCCGCCGAGCTTAAAATCGGAGACGAGTTTTTGAAGGCAAAGTGCTTAATGAACTGCGAAGTTTCTTTGATTCTCGAACACAAGTTCGAGCAGCTTCAACAGATGTCTGATGATCCCAGGAACCAAATTTCTCAAGTATTTGAGAAGTCACTGCAGTATGTGAAGCGCTTCAGCCGTTACAAAAATCCCGACGCTGTTAAACAAGTTCGAGAAATCCTTAGTAGATATCAGCTGACTGAGTTCGAGCTCTGTGTTCTTGGCAATCTCTGCCCTGAAACTGTTGAGGAAGCTATTGCTATGGTGCCATCTATAAAGGCAAAAGGACGGGTTCACGACGATGATGCAATTGATAAAATGTTGAATGACCTGGCGCTAATCAAGAAATTTGAGTAG
Functional Annotation
Gene Ontology
Molecular Function
Biological Process
Cellular Component
GO:0000288 GO:0000428 GO:0000932 GO:0000956 GO:0003674 GO:0003824 GO:0003899 GO:0005488 GO:0005515 GO:0005575 GO:0005622 GO:0005623 GO:0005634 GO:0005654 GO:0005665 GO:0005737 GO:0005829 GO:0006139 GO:0006351 GO:0006352 GO:0006366 GO:0006367 GO:0006396 GO:0006397 GO:0006401 GO:0006402 GO:0006403 GO:0006405 GO:0006406 GO:0006417 GO:0006446 GO:0006611 GO:0006725 GO:0006807 GO:0006810 GO:0006886 GO:0006913 GO:0006950 GO:0008104 GO:0008150 GO:0008152 GO:0009056 GO:0009057 GO:0009058 GO:0009059 GO:0009266 GO:0009408 GO:0009628 GO:0009889 GO:0009891 GO:0009892 GO:0009893 GO:0009987 GO:0010467 GO:0010468 GO:0010556 GO:0010557 GO:0010604 GO:0010605 GO:0010608 GO:0010628 GO:0010629 GO:0015031 GO:0015833 GO:0015931 GO:0016043 GO:0016070 GO:0016071 GO:0016591 GO:0016604 GO:0016607 GO:0016740 GO:0016772 GO:0016779 GO:0018130 GO:0019222 GO:0019438 GO:0019439 GO:0022607 GO:0022613 GO:0022618 GO:0030880 GO:0031123 GO:0031124 GO:0031323 GO:0031325 GO:0031326 GO:0031328 GO:0031369 GO:0031503 GO:0031974 GO:0031981 GO:0031990 GO:0032268 GO:0032270 GO:0032774 GO:0032991 GO:0033036 GO:0033554 GO:0034062 GO:0034248 GO:0034250 GO:0034402 GO:0034605 GO:0034613 GO:0034622 GO:0034641 GO:0034645 GO:0034654 GO:0034655 GO:0035770 GO:0036464 GO:0042886 GO:0043170 GO:0043226 GO:0043227 GO:0043228 GO:0043229 GO:0043231 GO:0043232 GO:0043233 GO:0043933 GO:0044085 GO:0044237 GO:0044238 GO:0044248 GO:0044249 GO:0044260 GO:0044265 GO:0044270 GO:0044271 GO:0044422 GO:0044424 GO:0044428 GO:0044444 GO:0044446 GO:0044451 GO:0044464 GO:0045184 GO:0045727 GO:0045948 GO:0046483 GO:0046700 GO:0046907 GO:0048518 GO:0048519 GO:0048522 GO:0050657 GO:0050658 GO:0050789 GO:0050794 GO:0050896 GO:0051028 GO:0051168 GO:0051169 GO:0051171 GO:0051173 GO:0051179 GO:0051234 GO:0051236 GO:0051246 GO:0051247 GO:0051641 GO:0051649 GO:0051716 GO:0055029 GO:0060255 GO:0061695 GO:0065003 GO:0065007 GO:0070013 GO:0070727 GO:0071166 GO:0071426 GO:0071427 GO:0071702 GO:0071704 GO:0071705 GO:0071826 GO:0071840 GO:0080090 GO:0090304 GO:0097659 GO:0097747 GO:0140098 GO:1901360 GO:1901361 GO:1901362 GO:1901575 GO:1901576 GO:1902494 GO:1990234 GO:1990904 GO:2000112
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

15.93

Weight (kDa)

4.98

Isoelectric Point (pI)

47.15

Instability Index
Protein Domains (Pfam)
Domain Name Pfam ID Position E-value Description
RNA_pol_Rpb4 PF03874 23 - 132 8.1e-28 RNA polymerase Rpb4
Hydrophobicity Profile (Kyte-Doolittle)
AI Structure Prediction Report
Calculating structure properties...

Genomic Context

Gene Family Tree

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Restriction Enzyme Sites

1 / 10
Enzyme Recognition Site Cut Count Positions (bp)
AccB1I GGYRCC 1 cut(s) 325
AciI CCGC 1 cut(s) 27
AclWI GGATC 1 cut(s) 131
AcsI RAATTY 2 cut(s) 150, 407
AcuI CTGAAG 1 cut(s) 178
AfeI AGCGCT 1 cut(s) 191
AgsI TTSAA 3 cut(s) 58, 122, 385
AjnI CCWGG 2 cut(s) 140, 390
AluBI AGCT 5 cut(s) 34, 118, 256, 271, 314
AluI AGCT 5 cut(s) 34, 118, 256, 271, 314
Alw21I GWGCWC 1 cut(s) 273
Alw26I GTCTC 1 cut(s) 39
AlwI GGATC 1 cut(s) 131
Aor51HI AGCGCT 1 cut(s) 191
ApeKI GCWGC 1 cut(s) 115
ApoI RAATTY 2 cut(s) 150, 407
Asp700I GAANNNNTTC 1 cut(s) 191
AspLEI GCGC 2 cut(s) 192, 397
BanI GGYRCC 1 cut(s) 325
BanII GRGCYC 1 cut(s) 273
Bbv12I GWGCWC 1 cut(s) 273
BbvI GCAGC 1 cut(s) 127
BccI CCATC 1 cut(s) 337
BceAI ACGGC 1 cut(s) 183
BcgI CGANNNNNNTGC 2 cut(s) 347, 381
BciT130I CCWGG 2 cut(s) 142, 392
BcoDI GTCTC 1 cut(s) 39
BfmI CTRYAG 1 cut(s) 176
BfoI RGCGCY 2 cut(s) 193, 398
BisI GCNGC 2 cut(s) 27, 116
BlsI GCNGC 2 cut(s) 28, 117
Bme1390I CCNGG 2 cut(s) 142, 392
BmiI GGNNCC 2 cut(s) 146, 327
BmrFI CCNGG 2 cut(s) 142, 392
BmsI GCATC 1 cut(s) 355
BpuEI CTTGAG 1 cut(s) 141
BsaJI CCNNGG 1 cut(s) 140
BseBI CCWGG 2 cut(s) 142, 392
BseDI CCNNGG 1 cut(s) 140
BseMII CTCAG 1 cut(s) 252
BseXI GCAGC 1 cut(s) 127
BshNI GGYRCC 1 cut(s) 325
BsiHKAI GWGCWC 1 cut(s) 273
BsmAI GTCTC 1 cut(s) 39
BsmBI CGTCTC 1 cut(s) 39
Bsp1286I GDGCHC 1 cut(s) 273
Bsp143I GATC 1 cut(s) 136
BspACI CCGC 1 cut(s) 27
BspCNI CTCAG 1 cut(s) 253
BspLI GGNNCC 2 cut(s) 146, 327
BspMAI CTGCAG 1 cut(s) 180
BspPI GGATC 1 cut(s) 131
BspT107I GGYRCC 1 cut(s) 325
BssECI CCNNGG 1 cut(s) 140
BssMI GATC 1 cut(s) 136
Bst2UI CCWGG 2 cut(s) 142, 392
Bst4CI ACNGT 1 cut(s) 304
Bst6I CTCTTC 1 cut(s) 6
BstAPI GCANNNNNTGC 1 cut(s) 291
BstDEI CTNAG 2 cut(s) 242, 261
BstH2I RGCGCY 2 cut(s) 193, 398
BstHHI GCGC 2 cut(s) 192, 397
BstKTI GATC 1 cut(s) 139
BstMAI GTCTC 1 cut(s) 39
BstMBI GATC 1 cut(s) 136
BstMWI GCNNNNNNNGC 1 cut(s) 291
BstNI CCWGG 2 cut(s) 142, 392
BstSCI CCNGG 2 cut(s) 140, 390
BstSFI CTRYAG 1 cut(s) 176
BstV1I GCAGC 1 cut(s) 127
BtsI GCAGTG 1 cut(s) 173
BtsIMutI CAGTG 1 cut(s) 173
CfoI GCGC 2 cut(s) 192, 397
CseI GACGC 1 cut(s) 224
CviJI RGCY 6 cut(s) 34, 118, 198, 256, 271, 314
CviKI_1 RGCY 6 cut(s) 34, 118, 198, 256, 271, 314
DdeI CTNAG 2 cut(s) 242, 261
DpnI GATC 1 cut(s) 138
DpnII GATC 1 cut(s) 136
Eam1104I CTCTTC 1 cut(s) 6
EarI CTCTTC 1 cut(s) 6
Ecl136II GAGCTC 1 cut(s) 271
Eco24I GRGCYC 1 cut(s) 273
Eco32I GATATC 1 cut(s) 251
Eco47III AGCGCT 1 cut(s) 191
Eco53kI GAGCTC 1 cut(s) 271
Eco57I CTGAAG 1 cut(s) 178
EcoICRI GAGCTC 1 cut(s) 271
EcoRII CCWGG 2 cut(s) 140, 390
EcoRV GATATC 1 cut(s) 251
EcoT38I GRGCYC 1 cut(s) 273
Esp3I CGTCTC 1 cut(s) 39
FaiI YATR 3 cut(s) 183, 323, 335
Fnu4HI GCNGC 2 cut(s) 27, 116
FriOI GRGCYC 1 cut(s) 273
Fsp4HI GCNGC 2 cut(s) 27, 116
GlaI GCGC 2 cut(s) 191, 396
GluI GCNGC 2 cut(s) 27, 116
HaeII RGCGCY 2 cut(s) 193, 398
HgaI GACGC 1 cut(s) 224
HhaI GCGC 2 cut(s) 192, 397
Hin6I GCGC 2 cut(s) 190, 395
HinP1I GCGC 2 cut(s) 190, 395
HinfI GANTC 1 cut(s) 94
Hpy166II GTNNAC 1 cut(s) 355
Hpy188I TCNGA 2 cut(s) 44, 133
Hpy188III TCNNGA 5 cut(s) 98, 212, 233, 356, 403
Hpy8I GTNNAC 1 cut(s) 355
Hpy99I CGWCG 2 cut(s) 218, 362
HpyAV CCTTC 1 cut(s) 52
HpyCH4III ACNGT 1 cut(s) 304
HpyCH4V TGCA 2 cut(s) 178, 368
HpyF10VI GCNNNNNNNGC 1 cut(s) 291
HpyF3I CTNAG 2 cut(s) 242, 261
HspAI GCGC 2 cut(s) 190, 395
Kzo9I GATC 1 cut(s) 136
LpnPI CCDG 5 cut(s) 127, 154, 309, 377, 404
Lsp1109I GCAGC 1 cut(s) 127
LweI GCATC 1 cut(s) 355
MaeIII GTNAC 2 cut(s) 171, 200
MalI GATC 1 cut(s) 138
MboI GATC 1 cut(s) 136
MboII GAAGA 2 cut(s) 23, 29
MfeI CAATTG 1 cut(s) 369
MhlI GDGCHC 1 cut(s) 273
MluCI AATT 3 cut(s) 150, 369, 407
MnlI CCTC 2 cut(s) 7, 301
MroXI GAANNNNTTC 1 cut(s) 191
MseI TTAA 3 cut(s) 36, 71, 222
MslI CAYNNNNRTG 1 cut(s) 360
MspA1I CMGCKG 1 cut(s) 256
MspR9I CCNGG 2 cut(s) 142, 392
MunI CAATTG 1 cut(s) 369
MvaI CCWGG 2 cut(s) 142, 392
MwoI GCNNNNNNNGC 1 cut(s) 291
NdeII GATC 1 cut(s) 136
NlaIV GGNNCC 2 cut(s) 146, 327
NmeAIII GCCGAG 1 cut(s) 55
NmuCI GTSAC 1 cut(s) 171
PdmI GAANNNNTTC 1 cut(s) 191
PfeI GAWTC 1 cut(s) 94
PkrI GCNGC 2 cut(s) 28, 117
Psp124BI GAGCTC 1 cut(s) 273
Psp6I CCWGG 2 cut(s) 140, 390
PspGI CCWGG 2 cut(s) 140, 390
PspN4I GGNNCC 2 cut(s) 146, 327
PstI CTGCAG 1 cut(s) 180
PvuII CAGCTG 1 cut(s) 256
RseI CAYNNNNRTG 1 cut(s) 360
SacI GAGCTC 1 cut(s) 273
SaqAI TTAA 3 cut(s) 36, 71, 222
SatI GCNGC 2 cut(s) 27, 116
Sau3AI GATC 1 cut(s) 136
ScrFI CCNGG 2 cut(s) 142, 392
SduI GDGCHC 1 cut(s) 273
SetI ASST 6 cut(s) 36, 120, 258, 273, 316, 393
SfaNI GCATC 1 cut(s) 355
SfcI CTRYAG 1 cut(s) 176
SmiMI CAYNNNNRTG 1 cut(s) 360
SmlI CTYRAG 1 cut(s) 156
SmoI CTYRAG 1 cut(s) 156
Sse9I AATT 3 cut(s) 150, 369, 407
SsiI CCGC 1 cut(s) 27
SstI GAGCTC 1 cut(s) 273
StyD4I CCNGG 2 cut(s) 140, 390
TaaI ACNGT 1 cut(s) 304
TaqI TCGA 4 cut(s) 99, 111, 232, 267
TasI AATT 3 cut(s) 150, 369, 407
TauI GCSGC 1 cut(s) 29
TfiI GAWTC 1 cut(s) 94
Tru1I TTAA 3 cut(s) 36, 71, 222
Tru9I TTAA 3 cut(s) 36, 71, 222
TscAI CASTG 1 cut(s) 180
TseFI GTSAC 1 cut(s) 171
TseI GCWGC 1 cut(s) 115
Tsp45I GTSAC 1 cut(s) 171
TspDTI ATGAA 1 cut(s) 89
TspRI CASTG 1 cut(s) 180
XapI RAATTY 2 cut(s) 150, 407
XmnI GAANNNNTTC 1 cut(s) 191
Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.