RchiOBHm_Chr7g0184721

mediator of RNA polymerase II transcription subunit

Design Primers CRISPR Design

Basic Information

Type: gene
Biological Identity
rosa_chinensis
7
OG0017665
Physical Location & Seq
Forward (+)
5170790 .. 5171566
777 bp
Loading structure...
UTR
Exon/CDS
Intron
N/A

Sequence Viewer

Length: 486 bp
ATGCATGCAGGTTCCTTAACGCGACCAAGTCCTTGGACTAGAAATGTGGATGGGTTTCTTGAAGGGCTCTCGGCTTTACATTTTTCTGGTGGTGGTGGTCCTAATGAAGCCGCCATTGCTGGGGGACTGGCAGAAGCACTTGTGATGTTTCCGAAGCCTACTCCCACTGGAACTGGAACTGAAACTGAAACTGATCAAGTTCAAGACCATAATGCCAGAGAAAGGCATTGTATTCTTGTGGCTGCAAGCAACCCTGTGTTGTTTCGAACCGCCGTTCAGATACCGATAATAAGTAATGGCCAATTTTCTTCTGGTACACAAACTCGATGGACTCTTGCTGATGCTCAAGATGTTGCCAAATTATATGCTGAGTGCTCTGTATCTCTTTCTGTGATCTCACCAAAACAGTTTCCAAAACTCAGAGAGATATACAATGCGGTACAAATAACCAACACCTTATTTGTTCTTTTTCTTGAATTGAATTAA
Functional Annotation
Gene Ontology
Molecular Function
Biological Process
Cellular Component
No ontology terms assigned.
KEGG Pathways
Metabolic & Signaling
No pathways identified.
Pfam Domains
Protein Families
Med25_VWA

Protein Analysis

161

Amino Acids

17.31

Weight (kDa)

5.75

Isoelectric Point (pI)

37.3

Instability Index
Protein Domains (Pfam)
Domain Name Pfam ID Position E-value Description
Med25_VWA PF11265 5 - 146 5.3e-20 Mediator complex subunit 25 von Willebrand factor type A
Hydrophobicity Profile (Kyte-Doolittle)
AI Structure Prediction Report
Calculating structure properties...

Genomic Context

Gene Family Tree

Species Filter
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Orthologous Genes (Group: OG0017665)

Species Orthologous Gene IDs
fragaria_vesca FvH4_5g12601 FvH4_5g12610
rosa_chinensis RchiOBHm_Chr7g0184721
rosa_laevigata RLG00000004956
rosa_multiflora Rmu_ssc0000289.1_g000020
rosa_roxburghii Rroxscaffold_3G00269400
rosa_rugosa Rorug06G0464700
rosa_samantha Rh7AG078200 Rh7BG069100 Rh7CG069900 Rh7DG069300
rosa_wichuraiana Rw7G005720

Restriction Enzyme Sites

1 / 10
Enzyme Recognition Site Cut Count Positions (bp)
AccII CGCG 1 cut(s) 22
AciI CCGC 3 cut(s) 111, 270, 437
AcoI YGGCCR 1 cut(s) 298
AfaI GTAC 2 cut(s) 316, 441
AfiI CCNNNNNNNGG 2 cut(s) 120, 222
AgsI TTSAA 4 cut(s) 62, 203, 476, 481
Alw21I GWGCWC 1 cut(s) 377
AoxI GGCC 1 cut(s) 298
ApeKI GCWGC 1 cut(s) 242
AspS9I GGNCC 1 cut(s) 98
AsuHPI GGTGA 1 cut(s) 390
AsuII TTCGAA 1 cut(s) 265
AvaII GGWCC 1 cut(s) 98
BalI TGGCCA 1 cut(s) 300
BanII GRGCYC 1 cut(s) 69
Bbv12I GWGCWC 1 cut(s) 377
BbvI GCAGC 1 cut(s) 229
BccI CCATC 2 cut(s) 44, 321
BceAI ACGGC 1 cut(s) 257
BclI TGATCA 1 cut(s) 193
BfaI CTAG 1 cut(s) 39
BisI GCNGC 2 cut(s) 111, 243
BlsI GCNGC 2 cut(s) 112, 244
Bme18I GGWCC 1 cut(s) 98
BmgT120I GGNCC 1 cut(s) 98
BmiI GGNNCC 1 cut(s) 13
BmsI GCATC 1 cut(s) 331
Bpu14I TTCGAA 1 cut(s) 265
BpuEI CTTGAG 1 cut(s) 330
BsaJI CCNNGG 1 cut(s) 32
Bsc4I CCNNNNNNNGG 2 cut(s) 120, 222
Bse1I ACTGG 3 cut(s) 132, 172, 178
Bse3DI GCAATG 1 cut(s) 114
BseDI CCNNGG 1 cut(s) 32
BseGI GGATG 1 cut(s) 55
BseLI CCNNNNNNNGG 2 cut(s) 120, 222
BseMI GCAATG 1 cut(s) 114
BseMII CTCAG 2 cut(s) 360, 433
BseNI ACTGG 3 cut(s) 132, 172, 178
BseXI GCAGC 1 cut(s) 229
BseYI CCCAGC 1 cut(s) 119
Bsh1236I CGCG 1 cut(s) 22
BshFI GGCC 1 cut(s) 300
BsiHKAI GWGCWC 1 cut(s) 377
BslFI GGGAC 1 cut(s) 138
BslI CCNNNNNNNGG 2 cut(s) 120, 222
BsmFI GGGAC 1 cut(s) 138
BsnI GGCC 1 cut(s) 300
Bsp119I TTCGAA 1 cut(s) 265
Bsp1286I GDGCHC 2 cut(s) 69, 377
Bsp143I GATC 2 cut(s) 193, 393
BspACI CCGC 3 cut(s) 111, 270, 437
BspANI GGCC 1 cut(s) 300
BspCNI CTCAG 2 cut(s) 361, 432
BspFNI CGCG 1 cut(s) 22
BspLI GGNNCC 1 cut(s) 13
BspT104I TTCGAA 1 cut(s) 265
BsrDI GCAATG 1 cut(s) 114
BsrI ACTGG 3 cut(s) 132, 172, 178
BssECI CCNNGG 1 cut(s) 32
BssMI GATC 2 cut(s) 193, 393
BssT1I CCWWGG 1 cut(s) 32
Bst4CI ACNGT 1 cut(s) 408
BstBI TTCGAA 1 cut(s) 265
BstC8I GCNNGC 2 cut(s) 6, 247
BstDEI CTNAG 2 cut(s) 369, 419
BstF5I GGATG 1 cut(s) 55
BstFNI CGCG 1 cut(s) 22
BstKTI GATC 2 cut(s) 196, 396
BstMBI GATC 2 cut(s) 193, 393
BstMWI GCNNNNNNNGC 1 cut(s) 116
BstNSI RCATGY 1 cut(s) 8
BstUI CGCG 1 cut(s) 22
BstV1I GCAGC 1 cut(s) 229
BstXI CCANNNNNNTGG 1 cut(s) 33
BsuRI GGCC 1 cut(s) 300
BtsCI GGATG 1 cut(s) 55
BtsIMutI CAGTG 1 cut(s) 165
Cac8I GCNNGC 2 cut(s) 6, 247
Cfr13I GGNCC 1 cut(s) 98
Csp6I GTAC 2 cut(s) 315, 440
CviAII CATG 1 cut(s) 5
CviJI RGCY 6 cut(s) 67, 74, 110, 157, 242, 300
CviKI_1 RGCY 6 cut(s) 67, 74, 110, 157, 242, 300
CviQI GTAC 2 cut(s) 315, 440
DdeI CTNAG 2 cut(s) 369, 419
DpnI GATC 2 cut(s) 195, 395
DpnII GATC 2 cut(s) 193, 393
EaeI YGGCCR 1 cut(s) 298
Eco130I CCWWGG 1 cut(s) 32
Eco24I GRGCYC 1 cut(s) 69
Eco47I GGWCC 1 cut(s) 98
EcoT14I CCWWGG 1 cut(s) 32
EcoT22I ATGCAT 1 cut(s) 6
EcoT38I GRGCYC 1 cut(s) 69
ErhI CCWWGG 1 cut(s) 32
FaeI CATG 1 cut(s) 8
FaiI YATR 5 cut(s) 6, 210, 364, 366, 430
FaqI GGGAC 1 cut(s) 138
FatI CATG 1 cut(s) 4
FbaI TGATCA 1 cut(s) 193
Fnu4HI GCNGC 2 cut(s) 111, 243
FokI GGATG 1 cut(s) 62
FriOI GRGCYC 1 cut(s) 69
Fsp4HI GCNGC 2 cut(s) 111, 243
FspBI CTAG 1 cut(s) 39
GluI GCNGC 2 cut(s) 111, 243
GsaI CCCAGC 1 cut(s) 123
HaeIII GGCC 1 cut(s) 300
Hin1II CATG 1 cut(s) 8
HinfI GANTC 1 cut(s) 331
HphI GGTGA 1 cut(s) 390
Hpy166II GTNNAC 1 cut(s) 317
Hpy188I TCNGA 3 cut(s) 153, 279, 422
Hpy188III TCNNGA 4 cut(s) 59, 203, 347, 473
Hpy8I GTNNAC 1 cut(s) 317
HpyAV CCTTC 1 cut(s) 56
HpyCH4III ACNGT 1 cut(s) 408
HpyCH4V TGCA 3 cut(s) 4, 8, 245
HpyF10VI GCNNNNNNNGC 1 cut(s) 116
HpyF3I CTNAG 2 cut(s) 369, 419
Hsp92II CATG 1 cut(s) 8
Ksp22I TGATCA 1 cut(s) 193
Kzo9I GATC 2 cut(s) 193, 393
LpnPI CCDG 8 cut(s) 72, 105, 113, 153, 159, 229, 267, 297
Lsp1109I GCAGC 1 cut(s) 229
LweI GCATC 1 cut(s) 331
MaeI CTAG 1 cut(s) 39
MalI GATC 2 cut(s) 195, 395
MboI GATC 2 cut(s) 193, 393
MboII GAAGA 1 cut(s) 300
MhlI GDGCHC 2 cut(s) 69, 377
MlsI TGGCCA 1 cut(s) 300
MluCI AATT 4 cut(s) 302, 359, 476, 481
MluNI TGGCCA 1 cut(s) 300
MlyI GAGTC 1 cut(s) 325
Mox20I TGGCCA 1 cut(s) 300
Mph1103I ATGCAT 1 cut(s) 6
MscI TGGCCA 1 cut(s) 300
MseI TTAA 2 cut(s) 17, 484
Msp20I TGGCCA 1 cut(s) 300
MvnI CGCG 1 cut(s) 22
MwoI GCNNNNNNNGC 1 cut(s) 116
NdeII GATC 2 cut(s) 193, 393
NlaIII CATG 1 cut(s) 8
NlaIV GGNNCC 1 cut(s) 13
NmeAIII GCCGAG 1 cut(s) 50
NsiI ATGCAT 1 cut(s) 6
NspI RCATGY 1 cut(s) 8
NspV TTCGAA 1 cut(s) 265
PaeI GCATGC 1 cut(s) 8
PflFI GACNNNGTC 1 cut(s) 27
PkrI GCNGC 2 cut(s) 112, 244
PleI GAGTC 1 cut(s) 325
PpsI GAGTC 1 cut(s) 325
PspFI CCCAGC 1 cut(s) 119
PspN4I GGNNCC 1 cut(s) 13
PspPI GGNCC 1 cut(s) 98
PsyI GACNNNGTC 1 cut(s) 27
RsaI GTAC 2 cut(s) 316, 441
RsaNI GTAC 2 cut(s) 315, 440
SaqAI TTAA 2 cut(s) 17, 484
SatI GCNGC 2 cut(s) 111, 243
Sau3AI GATC 2 cut(s) 193, 393
Sau96I GGNCC 1 cut(s) 98
SchI GAGTC 1 cut(s) 325
SduI GDGCHC 2 cut(s) 69, 377
SetI ASST 2 cut(s) 13, 458
SfaNI GCATC 1 cut(s) 331
SfuI TTCGAA 1 cut(s) 265
SinI GGWCC 1 cut(s) 98
SmlI CTYRAG 1 cut(s) 345
SmoI CTYRAG 1 cut(s) 345
SphI GCATGC 1 cut(s) 8
Sse9I AATT 4 cut(s) 302, 359, 476, 481
SsiI CCGC 3 cut(s) 111, 270, 437
SspMI CTAG 1 cut(s) 39
StyI CCWWGG 1 cut(s) 32
TaaI ACNGT 1 cut(s) 408
TaqI TCGA 2 cut(s) 265, 325
TasI AATT 4 cut(s) 302, 359, 476, 481
TauI GCSGC 1 cut(s) 113
Tru1I TTAA 2 cut(s) 17, 484
Tru9I TTAA 2 cut(s) 17, 484
TscAI CASTG 1 cut(s) 172
TseI GCWGC 1 cut(s) 242
TspDTI ATGAA 1 cut(s) 120
TspRI CASTG 1 cut(s) 172
Tth111I GACNNNGTC 1 cut(s) 27
VpaK11BI GGWCC 1 cut(s) 98
XceI RCATGY 1 cut(s) 8
XcmI CCANNNNNNNNNTGG 1 cut(s) 308
XspI CTAG 1 cut(s) 39
Zsp2I ATGCAT 1 cut(s) 6
Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.