RLG00000000249

RNA polymerase Rpb1, domain 5

Design Primers CRISPR Design

Basic Information

Type: gene
Biological Identity
rosa_laevigata
Chr1
OG0017882
Physical Location & Seq
Forward (+)
188361 .. 189071
711 bp
Loading structure...
UTR
Exon/CDS
Intron
RLM00000000249

Sequence Viewer

Length: 711 bp
ATGACAAGAAGATATTGGAACATCAATTTGGAAGAGATGATGGAAGCAGGAGTTCATTTTGGTCATGGTACTAGGAAATGGAATCCTAGGATGGCACCTTATATCTCTGCAAAGCGAAAGGGTATTCATATTATAAATCTTACTAGAACTGCTCGGTTTTTATCAGAAGCTTGTGATTTAGTTTTTGATGCAGCAAGTAGGGGAAAACAATTCTTAATTGTCGGTACAAAAAATAAAGCGGCTGATTCAGTAGCGCGGGCTGCAATAAGGGCTCGGTGTCATTATGTTAATAAAAAATGGCTCGGTGGTATGTTAACGAATTGGTATACTACAGAAACGAGACTTCATAAGTTCAGGGACTTGAGAACGGAACAAAAGACGGGGAGACTTAACCGTCTTCCGAAAAGAGATGCGGCTGTGTTGAAGAGACAATTATTTCACTTGCAAACATATCTGGGCGGAATAAAATATATGACGGGGTTACCCGATATTGTAATAATCGTTGATCAGCAAGAAGAATATACGGCTCTTCGAGAATGTATCACTTTGGGAATTCCAACGATTTGTTTAATCGATACAAATTGTGACCCGAATCTCGCAGATATTTCGATTCCAGCCAACGATGACGCTATAGCTTCAATCCGATTAATTCTTAACAAATTAGTATTTGCAATTTGTGAGGGTCGTTCTAGCTATATACGAAATTCTTGA
Functional Annotation
Gene Ontology
Molecular Function
Biological Process
Cellular Component
No ontology terms assigned.
KEGG Pathways
Metabolic & Signaling
ko00190 ko00195 ko00230 ko00240 ko01100 ko03020 map00190 map00195 map00230 map00240 map01100 map03020
Pfam Domains
Protein Families
RNA_pol_Rpb1_3 RNA_pol_Rpb1_4 RNA_pol_Rpb1_5 Ribosomal_S2

Protein Analysis

237

Amino Acids

26.94

Weight (kDa)

9.74

Isoelectric Point (pI)

47.14

Instability Index
Protein Domains (Pfam)
Domain Name Pfam ID Position E-value Description
Ribosomal_S2 PF00318 13 - 228 2e-81 Ribosomal protein S2
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)
AanI TTATAA 1 cut(s) 134
AasI GACNNNNNNGTC 1 cut(s) 393
AccB1I GGYRCC 1 cut(s) 94
AccI GTMKAC 1 cut(s) 326
AccII CGCG 1 cut(s) 256
AciI CCGC 4 cut(s) 239, 256, 413, 459
AcsI RAATTY 2 cut(s) 552, 703
AfaI GTAC 2 cut(s) 70, 226
AgsI TTSAA 2 cut(s) 424, 639
AjuI GAANNNNNNNTTGG 2 cut(s) 11, 43
AluBI AGCT 3 cut(s) 170, 635, 693
AluI AGCT 3 cut(s) 170, 635, 693
Alw26I GTCTC 3 cut(s) 334, 379, 421
ApeKI GCWGC 2 cut(s) 191, 260
ApoI RAATTY 2 cut(s) 552, 703
AseI ATTAAT 1 cut(s) 647
AspA2I CCTAGG 1 cut(s) 86
AspLEI GCGC 1 cut(s) 256
AvrII CCTAGG 1 cut(s) 86
BanI GGYRCC 1 cut(s) 94
BanII GRGCYC 1 cut(s) 274
BbsI GAAGAC 1 cut(s) 389
BbvI GCAGC 2 cut(s) 203, 247
BccI CCATC 2 cut(s) 34, 85
BceAI ACGGC 1 cut(s) 540
BcgI CGANNNNNNTGC 2 cut(s) 588, 622
BclI TGATCA 1 cut(s) 505
BcoDI GTCTC 3 cut(s) 334, 379, 421
BfaI CTAG 4 cut(s) 72, 87, 144, 690
BfmI CTRYAG 2 cut(s) 330, 630
BisI GCNGC 4 cut(s) 192, 240, 261, 414
BlnI CCTAGG 1 cut(s) 86
BlsI GCNGC 4 cut(s) 193, 241, 262, 415
BmiI GGNNCC 1 cut(s) 96
BmsI GCATC 2 cut(s) 178, 400
BpiI GAAGAC 1 cut(s) 389
BpuEI CTTGAG 1 cut(s) 382
Bsa29I ATCGAT 1 cut(s) 573
BsaJI CCNNGG 1 cut(s) 86
BseCI ATCGAT 1 cut(s) 573
BseDI CCNNGG 1 cut(s) 86
BseGI GGATG 1 cut(s) 96
BseXI GCAGC 2 cut(s) 203, 247
Bsh1236I CGCG 1 cut(s) 256
BshNI GGYRCC 1 cut(s) 94
BshVI ATCGAT 1 cut(s) 573
BslFI GGGAC 1 cut(s) 371
BsmAI GTCTC 3 cut(s) 334, 379, 421
BsmFI GGGAC 1 cut(s) 371
Bsp1286I GDGCHC 1 cut(s) 274
Bsp143I GATC 1 cut(s) 505
BspACI CCGC 4 cut(s) 239, 256, 413, 459
BspDI ATCGAT 1 cut(s) 573
BspFNI CGCG 1 cut(s) 256
BspLI GGNNCC 1 cut(s) 96
BspQI GCTCTTC 1 cut(s) 534
BspT107I GGYRCC 1 cut(s) 94
BssECI CCNNGG 1 cut(s) 86
BssMI GATC 1 cut(s) 505
BssNAI GTATAC 1 cut(s) 327
BssT1I CCWWGG 1 cut(s) 86
Bst1107I GTATAC 1 cut(s) 327
Bst4CI ACNGT 1 cut(s) 395
Bst6I CTCTTC 3 cut(s) 27, 419, 534
BstC8I GCNNGC 1 cut(s) 258
BstEII GGTNACC 1 cut(s) 480
BstF5I GGATG 1 cut(s) 96
BstFNI CGCG 1 cut(s) 256
BstHHI GCGC 1 cut(s) 256
BstKTI GATC 1 cut(s) 508
BstMAI GTCTC 3 cut(s) 334, 379, 421
BstMBI GATC 1 cut(s) 505
BstMWI GCNNNNNNNGC 2 cut(s) 260, 269
BstPI GGTNACC 1 cut(s) 480
BstSFI CTRYAG 2 cut(s) 330, 630
BstUI CGCG 1 cut(s) 256
BstV1I GCAGC 2 cut(s) 203, 247
BstV2I GAAGAC 1 cut(s) 389
BstZ17I GTATAC 1 cut(s) 327
Bsu15I ATCGAT 1 cut(s) 573
BsuTUI ATCGAT 1 cut(s) 573
BtsCI GGATG 1 cut(s) 96
Cac8I GCNNGC 1 cut(s) 258
CfoI GCGC 1 cut(s) 256
ClaI ATCGAT 1 cut(s) 573
CseI GACGC 1 cut(s) 635
Csp6I GTAC 2 cut(s) 69, 225
CviAII CATG 1 cut(s) 65
CviQI GTAC 2 cut(s) 69, 225
DpnI GATC 1 cut(s) 507
DpnII GATC 1 cut(s) 505
DrdI GACNNNNNNGTC 1 cut(s) 393
DseDI GACNNNNNNGTC 1 cut(s) 393
Eam1104I CTCTTC 3 cut(s) 27, 419, 534
EarI CTCTTC 3 cut(s) 27, 419, 534
EciI GGCGGA 1 cut(s) 474
Eco130I CCWWGG 1 cut(s) 86
Eco24I GRGCYC 1 cut(s) 274
Eco91I GGTNACC 1 cut(s) 480
EcoO65I GGTNACC 1 cut(s) 480
EcoRI GAATTC 1 cut(s) 552
EcoT14I CCWWGG 1 cut(s) 86
EcoT38I GRGCYC 1 cut(s) 274
ErhI CCWWGG 1 cut(s) 86
FaeI CATG 1 cut(s) 68
FaqI GGGAC 1 cut(s) 371
FatI CATG 1 cut(s) 64
FauI CCCGC 1 cut(s) 249
FbaI TGATCA 1 cut(s) 505
FblI GTMKAC 1 cut(s) 326
Fnu4HI GCNGC 4 cut(s) 192, 240, 261, 414
FokI GGATG 1 cut(s) 103
FriOI GRGCYC 1 cut(s) 274
Fsp4HI GCNGC 4 cut(s) 192, 240, 261, 414
FspBI CTAG 4 cut(s) 72, 87, 144, 690
GlaI GCGC 1 cut(s) 255
GluI GCNGC 4 cut(s) 192, 240, 261, 414
HgaI GACGC 1 cut(s) 635
HhaI GCGC 1 cut(s) 256
Hin1II CATG 1 cut(s) 68
Hin6I GCGC 1 cut(s) 254
HinP1I GCGC 1 cut(s) 254
HincII GTYRAC 1 cut(s) 315
HindII GTYRAC 1 cut(s) 315
HindIII AAGCTT 1 cut(s) 168
HinfI GANTC 4 cut(s) 82, 245, 592, 610
HpaI GTTAAC 1 cut(s) 315
Hpy166II GTNNAC 2 cut(s) 315, 327
Hpy188I TCNGA 3 cut(s) 166, 402, 644
Hpy188III TCNNGA 2 cut(s) 533, 708
Hpy8I GTNNAC 2 cut(s) 315, 327
HpyCH4III ACNGT 1 cut(s) 395
HpyCH4V TGCA 5 cut(s) 110, 191, 263, 445, 671
HpyF10VI GCNNNNNNNGC 2 cut(s) 260, 269
Hsp92II CATG 1 cut(s) 68
HspAI GCGC 1 cut(s) 254
Ksp22I TGATCA 1 cut(s) 505
KspAI GTTAAC 1 cut(s) 315
Kzo9I GATC 1 cut(s) 505
LguI GCTCTTC 1 cut(s) 534
LpnPI CCDG 4 cut(s) 33, 340, 440, 627
Lsp1109I GCAGC 2 cut(s) 203, 247
LweI GCATC 2 cut(s) 178, 400
MaeI CTAG 4 cut(s) 72, 87, 144, 690
MaeIII GTNAC 2 cut(s) 480, 584
MalI GATC 1 cut(s) 507
MboI GATC 1 cut(s) 505
MboII GAAGA 6 cut(s) 21, 44, 389, 436, 521, 527
MhlI GDGCHC 1 cut(s) 274
MmeI TCCRAC 1 cut(s) 581
MnlI CCTC 1 cut(s) 673
MseI TTAA 7 cut(s) 215, 288, 314, 390, 569, 647, 654
MvnI CGCG 1 cut(s) 256
MwoI GCNNNNNNNGC 2 cut(s) 260, 269
NdeII GATC 1 cut(s) 505
NlaIII CATG 1 cut(s) 68
NlaIV GGNNCC 1 cut(s) 96
NmuCI GTSAC 1 cut(s) 584
PciSI GCTCTTC 1 cut(s) 534
PfeI GAWTC 4 cut(s) 82, 245, 592, 610
PkrI GCNGC 4 cut(s) 193, 241, 262, 415
PshBI ATTAAT 1 cut(s) 647
PsiI TTATAA 1 cut(s) 134
PspEI GGTNACC 1 cut(s) 480
PspN4I GGNNCC 1 cut(s) 96
RsaI GTAC 2 cut(s) 70, 226
RsaNI GTAC 2 cut(s) 69, 225
SapI GCTCTTC 1 cut(s) 534
SaqAI TTAA 7 cut(s) 215, 288, 314, 390, 569, 647, 654
SatI GCNGC 4 cut(s) 192, 240, 261, 414
Sau3AI GATC 1 cut(s) 505
SduI GDGCHC 1 cut(s) 274
SetI ASST 4 cut(s) 100, 172, 637, 695
SfaNI GCATC 2 cut(s) 178, 400
SfcI CTRYAG 2 cut(s) 330, 630
SmlI CTYRAG 1 cut(s) 361
SmoI CTYRAG 1 cut(s) 361
SsiI CCGC 4 cut(s) 239, 256, 413, 459
SspMI CTAG 4 cut(s) 72, 87, 144, 690
StyI CCWWGG 1 cut(s) 86
TaaI ACNGT 1 cut(s) 395
TaqI TCGA 3 cut(s) 532, 573, 608
TauI GCSGC 2 cut(s) 242, 416
TfiI GAWTC 4 cut(s) 82, 245, 592, 610
Tru1I TTAA 7 cut(s) 215, 288, 314, 390, 569, 647, 654
Tru9I TTAA 7 cut(s) 215, 288, 314, 390, 569, 647, 654
TseFI GTSAC 1 cut(s) 584
TseI GCWGC 2 cut(s) 191, 260
Tsp45I GTSAC 1 cut(s) 584
TspDTI ATGAA 3 cut(s) 44, 116, 335
TspGWI ACGGA 1 cut(s) 383
VspI ATTAAT 1 cut(s) 647
XapI RAATTY 2 cut(s) 552, 703
XmaJI CCTAGG 1 cut(s) 86
XmiI GTMKAC 1 cut(s) 326
XspI CTAG 4 cut(s) 72, 87, 144, 690
Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.