RchiOBHm_Chr5g0042231

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_chinensis
5
OG0022785
Physical Location & Seq
Reverse (-)
37005837 .. 37007478
1642 bp
Loading structure...
UTR
Exon/CDS
Intron
N/A

Sequence Viewer

Length: 435 bp
ATGTTCAGAAGGTTGTACTTTCCTCTAATGACGAGGGAAAGAATTTTGGTGTTGTTTGTTCTCCTTGTCTTGGAGACAAGTTCTCAAGCATGCACGGGTGTCCTAGGCTTTTTGGAGTCTGAAGAGAACTTCCCCTTTACAATACAGGGGATTGTTCCAGATATTGTAATTAATCCACATGCTTTTCCTTCACGACAAGCTCCTGGTCAACTCCTAGAGGCTGCTTTGGGGAAGGGGATTGCCTGTGGTGGCTCAATGAGATATGCAACTCCTTTCTCTACTCCCTCTGTTGATGACATCACAGATCAGCTTCATGGAGCTGGATTTCAAAGATGGGGAAATGAGAGTATACAGTGGTCAAACTGGTCAAATGGTTCGCCAACTGATATTTATGGGCCCAACATTTTATCAACGTCTCATTCACATTCTCATTAA
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

144

Amino Acids

15.87

Weight (kDa)

5.63

Isoelectric Point (pI)

48.04

Instability Index
Protein Domains (Pfam)
Domain Name Pfam ID Position E-value Description
RNA_pol_Rpb2_6 PF00562 32 - 117 1e-24 RNA polymerase Rpb2, domain 6
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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Orthologous Genes (Group: OG0022785)

Species Orthologous Gene IDs
rosa_chinensis RchiOBHm_Chr5g0042231
rosa_samantha Rh5AG283500 Rh5BG289500 Rh5DG298800

Restriction Enzyme Sites

1 / 10
Enzyme Recognition Site Cut Count Positions (bp)
AccI GTMKAC 1 cut(s) 349
AcsI RAATTY 1 cut(s) 42
AcuI CTGAAG 1 cut(s) 141
AfaI GTAC 1 cut(s) 17
AfiI CCNNNNNNNGG 1 cut(s) 70
AgsI TTSAA 1 cut(s) 329
AjnI CCWGG 1 cut(s) 202
AluBI AGCT 3 cut(s) 200, 310, 320
AluI AGCT 3 cut(s) 200, 310, 320
Alw26I GTCTC 2 cut(s) 68, 420
AoxI GGCC 1 cut(s) 395
ApaI GGGCCC 1 cut(s) 399
ApeKI GCWGC 1 cut(s) 221
ApoI RAATTY 1 cut(s) 42
AseI ATTAAT 1 cut(s) 171
AspA2I CCTAGG 1 cut(s) 103
AspS9I GGNCC 2 cut(s) 395, 396
AvrII CCTAGG 1 cut(s) 103
BaeGI GKGCMC 1 cut(s) 399
BanII GRGCYC 1 cut(s) 399
BbvI GCAGC 1 cut(s) 208
BccI CCATC 1 cut(s) 327
BciT130I CCWGG 1 cut(s) 204
BcoDI GTCTC 2 cut(s) 68, 420
BfaI CTAG 2 cut(s) 104, 215
BisI GCNGC 1 cut(s) 222
BlnI CCTAGG 1 cut(s) 103
BlsI GCNGC 1 cut(s) 223
Bme1390I CCNGG 1 cut(s) 204
BmgT120I GGNCC 2 cut(s) 395, 396
BmiI GGNNCC 1 cut(s) 397
BmrFI CCNGG 1 cut(s) 204
BpuEI CTTGAG 1 cut(s) 69
BsaJI CCNNGG 1 cut(s) 103
Bsc4I CCNNNNNNNGG 1 cut(s) 70
Bse1I ACTGG 1 cut(s) 368
BseBI CCWGG 1 cut(s) 204
BseDI CCNNGG 1 cut(s) 103
BseLI CCNNNNNNNGG 1 cut(s) 70
BseNI ACTGG 1 cut(s) 368
BseSI GKGCMC 1 cut(s) 399
BseXI GCAGC 1 cut(s) 208
BshFI GGCC 1 cut(s) 397
BslI CCNNNNNNNGG 1 cut(s) 70
BsmAI GTCTC 2 cut(s) 68, 420
BsmBI CGTCTC 1 cut(s) 420
BsnI GGCC 1 cut(s) 397
Bsp120I GGGCCC 1 cut(s) 395
Bsp1286I GDGCHC 1 cut(s) 399
Bsp143I GATC 1 cut(s) 304
BspANI GGCC 1 cut(s) 397
BspLI GGNNCC 1 cut(s) 397
BsrI ACTGG 1 cut(s) 368
BssECI CCNNGG 1 cut(s) 103
BssMI GATC 1 cut(s) 304
BssNAI GTATAC 1 cut(s) 350
BssT1I CCWWGG 1 cut(s) 103
Bst1107I GTATAC 1 cut(s) 350
Bst2UI CCWGG 1 cut(s) 204
Bst4CI ACNGT 1 cut(s) 354
Bst6I CTCTTC 1 cut(s) 117
BstC8I GCNNGC 1 cut(s) 91
BstKTI GATC 1 cut(s) 307
BstMAI GTCTC 2 cut(s) 68, 420
BstMBI GATC 1 cut(s) 304
BstNI CCWGG 1 cut(s) 204
BstNSI RCATGY 2 cut(s) 93, 182
BstSCI CCNGG 1 cut(s) 202
BstSLI GKGCMC 1 cut(s) 399
BstV1I GCAGC 1 cut(s) 208
BstZ17I GTATAC 1 cut(s) 350
BsuRI GGCC 1 cut(s) 397
BtsIMutI CAGTG 1 cut(s) 359
Cac8I GCNNGC 1 cut(s) 91
Cfr13I GGNCC 2 cut(s) 395, 396
Csp6I GTAC 1 cut(s) 16
CviAII CATG 3 cut(s) 90, 179, 314
CviJI RGCY 7 cut(s) 108, 200, 221, 252, 310, 320, 397
CviKI_1 RGCY 7 cut(s) 108, 200, 221, 252, 310, 320, 397
CviQI GTAC 1 cut(s) 16
DpnI GATC 1 cut(s) 306
DpnII GATC 1 cut(s) 304
Eam1104I CTCTTC 1 cut(s) 117
EarI CTCTTC 1 cut(s) 117
Eco130I CCWWGG 1 cut(s) 103
Eco24I GRGCYC 1 cut(s) 399
Eco57I CTGAAG 1 cut(s) 141
EcoRII CCWGG 1 cut(s) 202
EcoT14I CCWWGG 1 cut(s) 103
EcoT38I GRGCYC 1 cut(s) 399
ErhI CCWWGG 1 cut(s) 103
Esp3I CGTCTC 1 cut(s) 420
FaeI CATG 3 cut(s) 93, 182, 317
FaiI YATR 6 cut(s) 91, 180, 264, 315, 350, 393
FatI CATG 3 cut(s) 89, 178, 313
FblI GTMKAC 1 cut(s) 349
Fnu4HI GCNGC 1 cut(s) 222
FriOI GRGCYC 1 cut(s) 399
Fsp4HI GCNGC 1 cut(s) 222
FspBI CTAG 2 cut(s) 104, 215
GluI GCNGC 1 cut(s) 222
HaeIII GGCC 1 cut(s) 397
Hin1II CATG 3 cut(s) 93, 182, 317
HincII GTYRAC 1 cut(s) 209
HindII GTYRAC 1 cut(s) 209
HinfI GANTC 1 cut(s) 116
Hpy166II GTNNAC 2 cut(s) 209, 350
Hpy188I TCNGA 2 cut(s) 8, 121
Hpy188III TCNNGA 2 cut(s) 158, 192
Hpy8I GTNNAC 2 cut(s) 209, 350
HpyAV CCTTC 3 cut(s) 3, 198, 226
HpyCH4III ACNGT 1 cut(s) 354
HpyCH4IV ACGT 1 cut(s) 413
HpyCH4V TGCA 2 cut(s) 93, 266
HpySE526I ACGT 1 cut(s) 413
Hsp92II CATG 3 cut(s) 93, 182, 317
Kzo9I GATC 1 cut(s) 304
LmnI GCTCC 2 cut(s) 205, 317
LpnPI CCDG 7 cut(s) 131, 171, 189, 216, 256, 306, 349
Lsp1109I GCAGC 1 cut(s) 208
MaeI CTAG 2 cut(s) 104, 215
MaeII ACGT 1 cut(s) 413
MalI GATC 1 cut(s) 306
MboI GATC 1 cut(s) 304
MboII GAAGA 1 cut(s) 134
MhlI GDGCHC 1 cut(s) 399
MluCI AATT 2 cut(s) 42, 168
MlyI GAGTC 1 cut(s) 125
MnlI CCTC 4 cut(s) 27, 33, 211, 295
MseI TTAA 2 cut(s) 171, 433
MspR9I CCNGG 1 cut(s) 204
MvaI CCWGG 1 cut(s) 204
NdeII GATC 1 cut(s) 304
NlaIII CATG 3 cut(s) 93, 182, 317
NlaIV GGNNCC 1 cut(s) 397
NspI RCATGY 2 cut(s) 93, 182
PaeI GCATGC 1 cut(s) 93
PkrI GCNGC 1 cut(s) 223
PleI GAGTC 1 cut(s) 124
PpsI GAGTC 1 cut(s) 124
PshBI ATTAAT 1 cut(s) 171
Psp6I CCWGG 1 cut(s) 202
PspGI CCWGG 1 cut(s) 202
PspN4I GGNNCC 1 cut(s) 397
PspOMI GGGCCC 1 cut(s) 395
PspPI GGNCC 2 cut(s) 395, 396
RsaI GTAC 1 cut(s) 17
RsaNI GTAC 1 cut(s) 16
SaqAI TTAA 2 cut(s) 171, 433
SatI GCNGC 1 cut(s) 222
Sau3AI GATC 1 cut(s) 304
Sau96I GGNCC 2 cut(s) 395, 396
SchI GAGTC 1 cut(s) 125
ScrFI CCNGG 1 cut(s) 204
SduI GDGCHC 1 cut(s) 399
SetI ASST 5 cut(s) 14, 202, 312, 322, 416
SmlI CTYRAG 1 cut(s) 84
SmoI CTYRAG 1 cut(s) 84
SphI GCATGC 1 cut(s) 93
Sse9I AATT 2 cut(s) 42, 168
SspMI CTAG 2 cut(s) 104, 215
StyD4I CCNGG 1 cut(s) 202
StyI CCWWGG 1 cut(s) 103
TaaI ACNGT 1 cut(s) 354
TaiI ACGT 1 cut(s) 416
TasI AATT 2 cut(s) 42, 168
TatI WGTACW 1 cut(s) 15
Tru1I TTAA 2 cut(s) 171, 433
Tru9I TTAA 2 cut(s) 171, 433
TscAI CASTG 1 cut(s) 359
TseI GCWGC 1 cut(s) 221
TspDTI ATGAA 1 cut(s) 302
TspRI CASTG 1 cut(s) 359
VspI ATTAAT 1 cut(s) 171
XapI RAATTY 1 cut(s) 42
XceI RCATGY 2 cut(s) 93, 182
XmaJI CCTAGG 1 cut(s) 103
XmiI GTMKAC 1 cut(s) 349
XspI CTAG 2 cut(s) 104, 215
Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.