Rh5AG284000

DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates

Design Primers CRISPR Design

Basic Information

Type: gene
Biological Identity
rosa_samantha
Chr5A
OG0017267
Physical Location & Seq
Reverse (-)
38459731 .. 38462323
2593 bp
Loading structure...
UTR
Exon/CDS
Intron
Rh5AG284000.1

Sequence Viewer

Length: 543 bp
ATGGTTCGCCAACTGATATTTATGGGCCCAACATTCTATCAACGTCTCATTCACATGTCTGAAGACAAAGTGAAGTTTTGGAACACTGGGCCAGTTCACCCTCTCACCCGACAGCCAGTGGGAAACAGGAAGAGATTTCGTGGGGTAAAGTTCAGTGAGATGGAGCGCGACTGCCTTATAGCCCATGGAGCATCAGCAAACTTACATGAACGCCTTTTCACTCTTAGTGACTCCTCCCAAATGCATGCTTGCCAGAAATGCAAAAATGCGGCTAATGTGATAGATGGAACAGTTGATGGCAGTAGAATCAGGGGTCTATATTACCGGGTCTGTAAGTCTGTTGATGACATTATCAGGTTGAATGTTCCATATGGGGCCAAGTTATTGTGCCAGGAACTTTTCAGCATTGGCATAAGTTTTGAGACCAGGCTCTGCAGAAATCTAACCACGGACTCTCCAGAAGTCGAATCGGAAAGGTCTAAATACGCTCCACCTGAATTACTTCTTCCTAGATTGTTCTACACAACAAAAGTTGGCCGTTAA
Functional Annotation
Gene Ontology
Molecular Function
Biological Process
Cellular Component
GO:0000228 GO:0000418 GO:0000419 GO:0000428 GO:0000785 GO:0000790 GO:0000792 GO:0002682 GO:0003674 GO:0003824 GO:0003899 GO:0005575 GO:0005622 GO:0005623 GO:0005634 GO:0005654 GO:0005694 GO:0005720 GO:0005730 GO:0005736 GO:0006139 GO:0006259 GO:0006304 GO:0006305 GO:0006306 GO:0006396 GO:0006725 GO:0006807 GO:0006950 GO:0006952 GO:0008150 GO:0008152 GO:0009058 GO:0009059 GO:0009605 GO:0009607 GO:0009620 GO:0009892 GO:0009987 GO:0010033 GO:0010467 GO:0010468 GO:0010605 GO:0010608 GO:0010629 GO:0014070 GO:0016020 GO:0016070 GO:0016246 GO:0016441 GO:0016458 GO:0016740 GO:0016772 GO:0016779 GO:0018130 GO:0019222 GO:0019438 GO:0030422 GO:0030880 GO:0031047 GO:0031050 GO:0031974 GO:0031981 GO:0032259 GO:0032774 GO:0032991 GO:0034062 GO:0034641 GO:0034654 GO:0035194 GO:0040029 GO:0042221 GO:0043170 GO:0043207 GO:0043226 GO:0043227 GO:0043228 GO:0043229 GO:0043231 GO:0043232 GO:0043233 GO:0043331 GO:0043412 GO:0043414 GO:0044237 GO:0044238 GO:0044249 GO:0044260 GO:0044271 GO:0044422 GO:0044424 GO:0044427 GO:0044428 GO:0044446 GO:0044451 GO:0044452 GO:0044454 GO:0044464 GO:0044728 GO:0046483 GO:0048519 GO:0048583 GO:0050776 GO:0050789 GO:0050832 GO:0050896 GO:0051704 GO:0051707 GO:0051716 GO:0055029 GO:0060255 GO:0061695 GO:0065007 GO:0070013 GO:0070887 GO:0070918 GO:0071310 GO:0071359 GO:0071407 GO:0071704 GO:0090304 GO:0097747 GO:0098542 GO:0140098 GO:1901360 GO:1901362 GO:1901576 GO:1901698 GO:1901699 GO:1902494 GO:1990234
KEGG Pathways
Metabolic & Signaling
ko00230 ko00240 ko01100 ko03020 ko05016 ko05169 map00230 map00240 map01100 map03020 map05016 map05169
Pfam Domains
Protein Families
RNA_pol_Rpb2_1 RNA_pol_Rpb2_2 RNA_pol_Rpb2_3 RNA_pol_Rpb2_4 RNA_pol_Rpb2_5 RNA_pol_Rpb2_6 RNA_pol_Rpb2_7

Protein Analysis

180

Amino Acids

20.64

Weight (kDa)

9.45

Isoelectric Point (pI)

44.06

Instability Index
Protein Domains (Pfam)
Domain Name Pfam ID Position E-value Description
RNA_pol_Rpb2_6 PF00562 2 - 45 2.5e-12 RNA polymerase Rpb2, domain 6
RNA_pol_Rpb2_7 PF04560 48 - 142 1.5e-21 RNA polymerase Rpb2, domain 7
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)
AccII CGCG 1 cut(s) 168
AciI CCGC 1 cut(s) 269
AcoI YGGCCR 1 cut(s) 535
AcuI CTGAAG 1 cut(s) 81
AflIII ACRYGT 1 cut(s) 54
AgsI TTSAA 1 cut(s) 361
AjnI CCWGG 2 cut(s) 390, 425
Alw26I GTCTC 2 cut(s) 50, 416
AlwNI CAGNNNCTG 1 cut(s) 432
AoxI GGCC 4 cut(s) 25, 89, 375, 535
ApaI GGGCCC 1 cut(s) 29
Asp700I GAANNNNTTC 1 cut(s) 501
AspLEI GCGC 1 cut(s) 168
AspS9I GGNCC 4 cut(s) 25, 26, 89, 375
AsuC2I CCSGG 1 cut(s) 326
AsuHPI GGTGA 2 cut(s) 89, 97
BaeGI GKGCMC 1 cut(s) 29
BanII GRGCYC 1 cut(s) 29
BbsI GAAGAC 1 cut(s) 69
BccI CCATC 3 cut(s) 154, 278, 290
BceAI ACGGC 1 cut(s) 522
BciT130I CCWGG 2 cut(s) 392, 427
BcnI CCSGG 1 cut(s) 326
BcoDI GTCTC 2 cut(s) 50, 416
BfaI CTAG 1 cut(s) 510
BfmI CTRYAG 1 cut(s) 433
BisI GCNGC 1 cut(s) 270
BlsI GCNGC 1 cut(s) 271
Bme1390I CCNGG 3 cut(s) 326, 392, 427
BmgT120I GGNCC 4 cut(s) 25, 26, 89, 375
BmiI GGNNCC 2 cut(s) 27, 376
BmrFI CCNGG 3 cut(s) 326, 392, 427
BmrI ACTGGG 1 cut(s) 96
BmsI GCATC 1 cut(s) 200
BmuI ACTGGG 1 cut(s) 96
BpiI GAAGAC 1 cut(s) 69
BpmI CTGGAG 1 cut(s) 441
BpuMI CCSGG 1 cut(s) 326
BsaI GGTCTC 1 cut(s) 416
BsaJI CCNNGG 2 cut(s) 184, 447
BsaXI ACNNNNNCTCC 2 cut(s) 439, 469
Bse1I ACTGG 3 cut(s) 91, 92, 116
BseBI CCWGG 2 cut(s) 392, 427
BseDI CCNNGG 2 cut(s) 184, 447
BseNI ACTGG 3 cut(s) 91, 92, 116
BseRI GAGGAG 1 cut(s) 223
BseSI GKGCMC 1 cut(s) 29
Bsh1236I CGCG 1 cut(s) 168
BshFI GGCC 4 cut(s) 27, 91, 377, 537
BsiSI CCGG 1 cut(s) 325
BsmAI GTCTC 2 cut(s) 50, 416
BsmBI CGTCTC 1 cut(s) 50
BsnI GGCC 4 cut(s) 27, 91, 377, 537
Bso31I GGTCTC 1 cut(s) 416
Bsp120I GGGCCC 1 cut(s) 25
Bsp1286I GDGCHC 1 cut(s) 29
Bsp19I CCATGG 1 cut(s) 184
BspACI CCGC 1 cut(s) 269
BspANI GGCC 4 cut(s) 27, 91, 377, 537
BspFNI CGCG 1 cut(s) 168
BspLI GGNNCC 2 cut(s) 27, 376
BspMAI CTGCAG 1 cut(s) 437
BspTNI GGTCTC 1 cut(s) 416
BsrI ACTGG 3 cut(s) 91, 92, 116
BssECI CCNNGG 2 cut(s) 184, 447
BssT1I CCWWGG 1 cut(s) 184
Bst2UI CCWGG 2 cut(s) 392, 427
Bst4CI ACNGT 1 cut(s) 292
Bst6I CTCTTC 1 cut(s) 125
BstC8I GCNNGC 2 cut(s) 246, 250
BstDEI CTNAG 1 cut(s) 224
BstDSI CCRYGG 2 cut(s) 184, 447
BstFNI CGCG 1 cut(s) 168
BstHHI GCGC 1 cut(s) 168
BstMAI GTCTC 2 cut(s) 50, 416
BstMWI GCNNNNNNNGC 2 cut(s) 188, 258
BstNI CCWGG 2 cut(s) 392, 427
BstNSI RCATGY 2 cut(s) 58, 248
BstSCI CCNGG 3 cut(s) 324, 390, 425
BstSFI CTRYAG 1 cut(s) 433
BstSLI GKGCMC 1 cut(s) 29
BstUI CGCG 1 cut(s) 168
BstV2I GAAGAC 1 cut(s) 69
BsuRI GGCC 4 cut(s) 27, 91, 377, 537
BtgI CCRYGG 2 cut(s) 184, 447
BtsIMutI CAGTG 3 cut(s) 84, 123, 160
Cac8I GCNNGC 2 cut(s) 246, 250
CaiI CAGNNNCTG 1 cut(s) 432
CfoI GCGC 1 cut(s) 168
Cfr13I GGNCC 4 cut(s) 25, 26, 89, 375
CviAII CATG 4 cut(s) 55, 185, 206, 245
CviJI RGCY 8 cut(s) 27, 91, 115, 182, 272, 377, 430, 537
CviKI_1 RGCY 8 cut(s) 27, 91, 115, 182, 272, 377, 430, 537
DdeI CTNAG 1 cut(s) 224
EaeI YGGCCR 1 cut(s) 535
Eam1104I CTCTTC 1 cut(s) 125
EarI CTCTTC 1 cut(s) 125
Eco130I CCWWGG 1 cut(s) 184
Eco24I GRGCYC 1 cut(s) 29
Eco31I GGTCTC 1 cut(s) 416
Eco57I CTGAAG 1 cut(s) 81
EcoRII CCWGG 2 cut(s) 390, 425
EcoT14I CCWWGG 1 cut(s) 184
EcoT22I ATGCAT 1 cut(s) 246
EcoT38I GRGCYC 1 cut(s) 29
ErhI CCWWGG 1 cut(s) 184
Esp3I CGTCTC 1 cut(s) 50
FaeI CATG 4 cut(s) 58, 188, 209, 248
FatI CATG 4 cut(s) 54, 184, 205, 244
FauNDI CATATG 1 cut(s) 370
Fnu4HI GCNGC 1 cut(s) 270
FriOI GRGCYC 1 cut(s) 29
Fsp4HI GCNGC 1 cut(s) 270
FspBI CTAG 1 cut(s) 510
GlaI GCGC 1 cut(s) 167
GluI GCNGC 1 cut(s) 270
GsuI CTGGAG 1 cut(s) 441
HaeIII GGCC 4 cut(s) 27, 91, 377, 537
HapII CCGG 1 cut(s) 325
HhaI GCGC 1 cut(s) 168
Hin1II CATG 4 cut(s) 58, 188, 209, 248
Hin6I GCGC 1 cut(s) 166
HinP1I GCGC 1 cut(s) 166
HinfI GANTC 4 cut(s) 230, 306, 452, 467
HpaII CCGG 1 cut(s) 325
HphI GGTGA 2 cut(s) 89, 97
Hpy166II GTNNAC 1 cut(s) 97
Hpy188I TCNGA 2 cut(s) 61, 472
Hpy188III TCNNGA 1 cut(s) 458
Hpy8I GTNNAC 1 cut(s) 97
HpyCH4III ACNGT 1 cut(s) 292
HpyCH4IV ACGT 1 cut(s) 43
HpyCH4V TGCA 3 cut(s) 244, 261, 435
HpyF10VI GCNNNNNNNGC 2 cut(s) 188, 258
HpyF3I CTNAG 1 cut(s) 224
HpySE526I ACGT 1 cut(s) 43
Hsp92II CATG 4 cut(s) 58, 188, 209, 248
HspAI GCGC 1 cut(s) 166
LmnI GCTCC 3 cut(s) 163, 188, 493
LweI GCATC 1 cut(s) 200
MaeI CTAG 1 cut(s) 510
MaeII ACGT 1 cut(s) 43
MaeIII GTNAC 1 cut(s) 227
MboII GAAGA 3 cut(s) 74, 142, 497
MhlI GDGCHC 1 cut(s) 29
MluCI AATT 1 cut(s) 497
MlyI GAGTC 2 cut(s) 224, 446
MnlI CCTC 2 cut(s) 111, 244
Mph1103I ATGCAT 1 cut(s) 246
MroXI GAANNNNTTC 1 cut(s) 501
MseI TTAA 1 cut(s) 541
MslI CAYNNNNRTG 1 cut(s) 53
MspI CCGG 1 cut(s) 325
MspR9I CCNGG 3 cut(s) 326, 392, 427
MvaI CCWGG 2 cut(s) 392, 427
MvnI CGCG 1 cut(s) 168
MwoI GCNNNNNNNGC 2 cut(s) 188, 258
NciI CCSGG 1 cut(s) 326
NcoI CCATGG 1 cut(s) 184
NdeI CATATG 1 cut(s) 370
NlaIII CATG 4 cut(s) 58, 188, 209, 248
NlaIV GGNNCC 2 cut(s) 27, 376
NmuCI GTSAC 1 cut(s) 227
NsiI ATGCAT 1 cut(s) 246
NspI RCATGY 2 cut(s) 58, 248
PaeI GCATGC 1 cut(s) 248
PciI ACATGT 1 cut(s) 54
PdmI GAANNNNTTC 1 cut(s) 501
PfeI GAWTC 2 cut(s) 306, 467
PkrI GCNGC 1 cut(s) 271
PleI GAGTC 2 cut(s) 224, 446
PpsI GAGTC 2 cut(s) 224, 446
PscI ACATGT 1 cut(s) 54
Psp6I CCWGG 2 cut(s) 390, 425
PspGI CCWGG 2 cut(s) 390, 425
PspN4I GGNNCC 2 cut(s) 27, 376
PspOMI GGGCCC 1 cut(s) 25
PspPI GGNCC 4 cut(s) 25, 26, 89, 375
PstI CTGCAG 1 cut(s) 437
PstNI CAGNNNCTG 1 cut(s) 432
RseI CAYNNNNRTG 1 cut(s) 53
SaqAI TTAA 1 cut(s) 541
SatI GCNGC 1 cut(s) 270
Sau96I GGNCC 4 cut(s) 25, 26, 89, 375
SchI GAGTC 2 cut(s) 224, 446
ScrFI CCNGG 3 cut(s) 326, 392, 427
SduI GDGCHC 1 cut(s) 29
SetI ASST 4 cut(s) 46, 359, 479, 496
SfaNI GCATC 1 cut(s) 200
SfcI CTRYAG 1 cut(s) 433
SmiMI CAYNNNNRTG 1 cut(s) 53
SphI GCATGC 1 cut(s) 248
Sse9I AATT 1 cut(s) 497
SsiI CCGC 1 cut(s) 269
SspMI CTAG 1 cut(s) 510
StyD4I CCNGG 3 cut(s) 324, 390, 425
StyI CCWWGG 1 cut(s) 184
TaaI ACNGT 1 cut(s) 292
TaiI ACGT 1 cut(s) 46
TaqI TCGA 1 cut(s) 465
TasI AATT 1 cut(s) 497
TauI GCSGC 1 cut(s) 272
TfiI GAWTC 2 cut(s) 306, 467
Tru1I TTAA 1 cut(s) 541
Tru9I TTAA 1 cut(s) 541
TscAI CASTG 3 cut(s) 91, 123, 160
TseFI GTSAC 1 cut(s) 227
Tsp45I GTSAC 1 cut(s) 227
TspDTI ATGAA 1 cut(s) 222
TspGWI ACGGA 1 cut(s) 464
TspRI CASTG 3 cut(s) 91, 123, 160
XceI RCATGY 2 cut(s) 58, 248
XmnI GAANNNNTTC 1 cut(s) 501
XspI CTAG 1 cut(s) 510
Zsp2I ATGCAT 1 cut(s) 246
Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.