Rroxscaffold_7G00173000

DNA-directed RNA polymerase III subunit

Design Primers CRISPR Design

Basic Information

Type: gene
Biological Identity
rosa_roxburghii
GWHEROQ00000007
OG0000459
Physical Location & Seq
Reverse (-)
13101204 .. 13106199
4996 bp
Loading structure...
UTR
Exon/CDS
Intron
Rroxscaffold_7G00173000.1

Sequence Viewer

Length: 630 bp
ATGGCATATAGAGGTCGTGGAGGAGGATTTGGACATGGTAACTATGCTAAGGAAGAGCCCTTTGTGCCATTTCCTGATATTCATTTACCTGATGCCGGAGGTATTTTGTCTGAGCTAGATCAAAAGAAAAACAAAGGTTTGAAGGAGGAAGAAACATTAATCAGAGATACTCTGAATTGGCTAATGAAATCCGAATATAATCTTGACAAGACTGTTTCAGATAGACAAGACAAGGATGTTGAAATATCTGAGAGAACCAAGCGAAAGGCTAAGAGAGAAATTGATTCTTTCTCACAGTATTTGGTGCCCAGTATGTTTCCTAGAGAACTGACTAGAGGTTCAAATGTGCGGCAGGTGAGCAGAGAAAATGTTAAATGGGACAAACGGAACACAGAAAAGAACTCTGAGATATACTGGAATCAAATTGAAAAGCGAGAACAGAATTCGGCTGCAAAGAAACAGAAAGAAGGTGAAAATGATGAGGAAGAGGACGAAGATGCGGATGCGGAAGAGGAGGAAGATGAGGACCCTAGTGATGATGATTATGCTCAGAACATAGACTTTGATGACGATGAGGATGATTTTAATGCAGACGATGGTGATGATGAACCTCTTTTGGAGGAAGATTAG
Functional Annotation
Gene Ontology
Molecular Function
Biological Process
Cellular Component
No ontology terms assigned.
KEGG Pathways
Metabolic & Signaling
ko00230 ko00240 ko01100 ko03020 ko04623 ko05169 map00230 map00240 map01100 map03020 map04623 map05169
Pfam Domains
Protein Families
RNA_pol_3_Rpc31

Protein Analysis

209

Amino Acids

24.34

Weight (kDa)

4.35

Isoelectric Point (pI)

62.65

Instability Index
Protein Domains (Pfam)
No Pfam domains detected for this protein.
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: OG0000459)

Species Orthologous Gene IDs
arabidopsis_thaliana AT4G01590 AT4G01590 AT4G01590 AT4G35685
fragaria_vesca FvH4_2g26230 FvH4_3g43010 FvH4_3g43011 FvH4_4g18161 FvH4_4g18202 FvH4_5g23500 FvH4_6g36040 FvH4_6g36040 FvH4_6g36040
malus_domestica MD08G1165000.v1.1 MD08G1171800.v1.1 MD15G1357300.v1.1 MD15G1382800.v1.1
prunus_persica Prupe.1G504500_v2.0.a1 Prupe.1G504500_v2.0.a1 Prupe.1G504500_v2.0.a1 Prupe.1G504500_v2.0.a1 Prupe.1G504500_v2.0.a1 Prupe.1G504500_v2.0.a1 Prupe.1G582300_v2.0.a1 Prupe.6G034400_v2.0.a1 Prupe.6G034600_v2.0.a1
pyrus_communis pycom02g25390 pycom08g14650
rosa_chinensis RchiOBHm_Chr2g0143271 RchiOBHm_Chr4g0422341 RchiOBHm_Chr6g0253151 RchiOBHm_Chr6g0294801
rosa_laevigata RLG00000007621 RLG00000011839 RLG00000020015 RLG00000020019 RLG00000020023 RLG00000036652 RLG00000036658
rosa_multiflora Rmu_co8140216.1_g000001 Rmu_co8510555.1_g000002 Rmu_sc0003323.1_g000013 Rmu_sc0003323.1_g000024 Rmu_sc0003323.1_g000031 Rmu_sc0013245.1_g000016 Rmu_sc0030690.1_g000001
rosa_roxburghii Rroxscaffold_1G00005030 Rroxscaffold_2G00101900 Rroxscaffold_2G00102030 Rroxscaffold_4G00318680 Rroxscaffold_5G00364400 Rroxscaffold_5G00364410 Rroxscaffold_7G00173000 Rroxscaffold_7G00212110
rosa_rugosa Rorug04G0179200 Rorug05G0451000 Rorug05G0451400.1 Rorug05G0451500 Rorug06G0246900
rosa_samantha Rh1AG104900 Rh1CG244000 Rh1DG126500 Rh2AG432700 Rh2CG418500 Rh4AG238500 Rh4BG241700 Rh4BG242000 Rh4CG253500 Rh4CG253600 Rh4DG237400 Rh5AG505300 Rh5AG505500 Rh5BG527000 Rh5BG527200 Rh5BG527500 Rh5CG551000 Rh5CG551300 Rh5CG551800 Rh5DG539300 Rh5DG539900 Rh6AG057300 Rh6AG360500 Rh6BG051900 Rh6BG367200 Rh6CG049800 Rh6CG374200 Rh6DG046000
rosa_wichuraiana Rw1G009810 Rw5G047080 Rw5G047100 Rw6G031450

Restriction Enzyme Sites

1 / 10
Enzyme Recognition Site Cut Count Positions (bp)
AarI CACCTGC 1 cut(s) 343
Acc36I ACCTGC 1 cut(s) 343
AccB1I GGYRCC 1 cut(s) 304
AciI CCGC 3 cut(s) 349, 500, 506
AcsI RAATTY 1 cut(s) 442
AfiI CCNNNNNNNGG 1 cut(s) 95
AgsI TTSAA 4 cut(s) 142, 242, 342, 428
AluBI AGCT 1 cut(s) 115
AluI AGCT 1 cut(s) 115
ApeKI GCWGC 1 cut(s) 449
ApoI RAATTY 1 cut(s) 442
AseI ATTAAT 1 cut(s) 158
AspS9I GGNCC 1 cut(s) 526
AsuHPI GGTGA 3 cut(s) 367, 482, 611
AvaII GGWCC 1 cut(s) 526
BaeGI GKGCMC 1 cut(s) 309
BanI GGYRCC 1 cut(s) 304
BanII GRGCYC 1 cut(s) 60
BbvI GCAGC 1 cut(s) 436
BccI CCATC 1 cut(s) 590
BfaI CTAG 4 cut(s) 116, 321, 333, 531
BfuAI ACCTGC 1 cut(s) 343
BisI GCNGC 2 cut(s) 350, 450
BlsI GCNGC 2 cut(s) 351, 451
Bme18I GGWCC 1 cut(s) 526
BmgT120I GGNCC 1 cut(s) 526
BmiI GGNNCC 2 cut(s) 306, 528
BmrI ACTGGG 1 cut(s) 303
BmsI GCATC 3 cut(s) 82, 487, 493
BmuI ACTGGG 1 cut(s) 303
Bpu10I CCTNAGC 1 cut(s) 48
Bsc4I CCNNNNNNNGG 1 cut(s) 95
Bse1I ACTGG 2 cut(s) 309, 419
BseGI GGATG 3 cut(s) 241, 508, 583
BseLI CCNNNNNNNGG 1 cut(s) 95
BseMII CTCAG 4 cut(s) 102, 240, 396, 563
BseNI ACTGG 2 cut(s) 309, 419
BseRI GAGGAG 2 cut(s) 36, 527
BseSI GKGCMC 1 cut(s) 309
BseXI GCAGC 1 cut(s) 436
BshNI GGYRCC 1 cut(s) 304
BsiSI CCGG 1 cut(s) 96
BslFI GGGAC 1 cut(s) 392
BslI CCNNNNNNNGG 1 cut(s) 95
BsmFI GGGAC 1 cut(s) 392
Bsp1286I GDGCHC 2 cut(s) 60, 309
Bsp143I GATC 1 cut(s) 118
BspACI CCGC 3 cut(s) 349, 500, 506
BspCNI CTCAG 4 cut(s) 103, 241, 397, 562
BspLI GGNNCC 2 cut(s) 306, 528
BspMI ACCTGC 1 cut(s) 343
BspQI GCTCTTC 1 cut(s) 48
BspT107I GGYRCC 1 cut(s) 304
BsrI ACTGG 2 cut(s) 309, 419
BssMI GATC 1 cut(s) 118
Bst4CI ACNGT 2 cut(s) 214, 297
Bst6I CTCTTC 3 cut(s) 48, 480, 504
BstDEI CTNAG 6 cut(s) 48, 111, 249, 270, 405, 549
BstF5I GGATG 3 cut(s) 241, 508, 583
BstKTI GATC 1 cut(s) 121
BstMBI GATC 1 cut(s) 118
BstMWI GCNNNNNNNGC 1 cut(s) 64
BstSLI GKGCMC 1 cut(s) 309
BstV1I GCAGC 1 cut(s) 436
BtsCI GGATG 3 cut(s) 241, 508, 583
BveI ACCTGC 1 cut(s) 343
Cfr13I GGNCC 1 cut(s) 526
CviAII CATG 1 cut(s) 35
CviJI RGCY 5 cut(s) 58, 115, 181, 269, 449
CviKI_1 RGCY 5 cut(s) 58, 115, 181, 269, 449
DdeI CTNAG 6 cut(s) 48, 111, 249, 270, 405, 549
DpnI GATC 1 cut(s) 120
DpnII GATC 1 cut(s) 118
Eam1104I CTCTTC 3 cut(s) 48, 480, 504
EarI CTCTTC 3 cut(s) 48, 480, 504
Eco24I GRGCYC 1 cut(s) 60
Eco47I GGWCC 1 cut(s) 526
EcoO109I RGGNCCY 1 cut(s) 526
EcoRI GAATTC 1 cut(s) 442
EcoT38I GRGCYC 1 cut(s) 60
FaeI CATG 1 cut(s) 38
FaiI YATR 9 cut(s) 7, 9, 36, 45, 198, 314, 412, 546, 557
FaqI GGGAC 1 cut(s) 392
FatI CATG 1 cut(s) 34
Fnu4HI GCNGC 2 cut(s) 350, 450
FokI GGATG 3 cut(s) 248, 515, 590
FriOI GRGCYC 1 cut(s) 60
Fsp4HI GCNGC 2 cut(s) 350, 450
FspBI CTAG 4 cut(s) 116, 321, 333, 531
GluI GCNGC 2 cut(s) 350, 450
HapII CCGG 1 cut(s) 96
Hin1II CATG 1 cut(s) 38
HinfI GANTC 2 cut(s) 284, 418
HpaII CCGG 1 cut(s) 96
HphI GGTGA 3 cut(s) 367, 482, 611
Hpy188I TCNGA 8 cut(s) 112, 164, 174, 193, 220, 250, 406, 552
Hpy188III TCNNGA 2 cut(s) 74, 203
HpyAV CCTTC 2 cut(s) 136, 461
HpyCH4III ACNGT 2 cut(s) 214, 297
HpyCH4V TGCA 2 cut(s) 452, 590
HpyF10VI GCNNNNNNNGC 1 cut(s) 64
HpyF3I CTNAG 6 cut(s) 48, 111, 249, 270, 405, 549
Hsp92II CATG 1 cut(s) 38
Kzo9I GATC 1 cut(s) 118
LguI GCTCTTC 1 cut(s) 48
LpnPI CCDG 6 cut(s) 87, 102, 109, 322, 338, 400
Lsp1109I GCAGC 1 cut(s) 436
LweI GCATC 3 cut(s) 82, 487, 493
MaeI CTAG 4 cut(s) 116, 321, 333, 531
MaeIII GTNAC 1 cut(s) 38
MalI GATC 1 cut(s) 120
MboI GATC 1 cut(s) 118
MboII GAAGA 6 cut(s) 65, 161, 497, 506, 521, 530
MhlI GDGCHC 2 cut(s) 60, 309
MluCI AATT 4 cut(s) 175, 279, 423, 442
MseI TTAA 3 cut(s) 158, 372, 585
MspI CCGG 1 cut(s) 96
MwoI GCNNNNNNNGC 1 cut(s) 64
NdeII GATC 1 cut(s) 118
NlaIII CATG 1 cut(s) 38
NlaIV GGNNCC 2 cut(s) 306, 528
PaqCI CACCTGC 1 cut(s) 343
PciSI GCTCTTC 1 cut(s) 48
PfeI GAWTC 2 cut(s) 284, 418
PkrI GCNGC 2 cut(s) 351, 451
PpuMI RGGWCCY 1 cut(s) 526
PshBI ATTAAT 1 cut(s) 158
Psp5II RGGWCCY 1 cut(s) 526
PspN4I GGNNCC 2 cut(s) 306, 528
PspPI GGNCC 1 cut(s) 526
PspPPI RGGWCCY 1 cut(s) 526
SapI GCTCTTC 1 cut(s) 48
SaqAI TTAA 3 cut(s) 158, 372, 585
SatI GCNGC 2 cut(s) 350, 450
Sau3AI GATC 1 cut(s) 118
Sau96I GGNCC 1 cut(s) 526
SduI GDGCHC 2 cut(s) 60, 309
SetI ASST 9 cut(s) 16, 91, 103, 117, 139, 340, 357, 472, 613
SfaNI GCATC 3 cut(s) 82, 487, 493
SinI GGWCC 1 cut(s) 526
Sse9I AATT 4 cut(s) 175, 279, 423, 442
SsiI CCGC 3 cut(s) 349, 500, 506
SspMI CTAG 4 cut(s) 116, 321, 333, 531
TaaI ACNGT 2 cut(s) 214, 297
TasI AATT 4 cut(s) 175, 279, 423, 442
TauI GCSGC 1 cut(s) 352
TfiI GAWTC 2 cut(s) 284, 418
Tru1I TTAA 3 cut(s) 158, 372, 585
Tru9I TTAA 3 cut(s) 158, 372, 585
TseI GCWGC 1 cut(s) 449
TspDTI ATGAA 3 cut(s) 71, 200, 621
TspGWI ACGGA 1 cut(s) 400
VpaK11BI GGWCC 1 cut(s) 526
VspI ATTAAT 1 cut(s) 158
XapI RAATTY 1 cut(s) 442
XspI CTAG 4 cut(s) 116, 321, 333, 531
Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.