Rh3CG287300

Transcription initiation factor

Design Primers CRISPR Design

Basic Information

Type: gene
Biological Identity
rosa_samantha
Chr3C
OG0014000
Physical Location & Seq
Forward (+)
29076504 .. 29082128
5625 bp
Loading structure...
UTR
Exon/CDS
Intron
Rh3CG287300.1

Sequence Viewer

Length: 939 bp
ATGTCCGATGCGTATTGCTCCGACTGCAAGCGCCAGACGGAGGTGGTATTCGATCACTCCGCTGGCGACACCGTCTGCTCCGAGTGCGGCCTCGTCCTCGAGTCCCATTCCATCGACGAGACGTCCGAGTGGCGAACCTTCGCCAACGAGTCCGGCGATAACGACCCCGTCCGTGTCGGTGGGCCCACCAACCCGCTCTTGGCCGATGGCGGATTGTCCACCGTCATCGCCAAGCCCAATGGAGCTTCCGGCGAGTTCCTCTCTTCGTCTTTGGGCAGGTGGCAGAACCGCGGCTCCAATCCGGATCGGGGCTTGATACTCGCCTTCAAAACCATCGCTACCATGTCCGATAGGTTGGGCCTTGTTGCAACCATCAAGGATCGAGCTAATGAGATATATAAGAGGGTGGAAGATCAAAAGTCTAGTAGAGGAAGAAATCAGGATGCATTATTGGCTGCTTGCCTATACATTGCTTGTCGACAAGAAGACAAGCCCCGCACTGTAAAGGAAATTTGCTCCGTTGCCAATGGAGCCACAAAGAAAGAAATTGGCCGAGCAAAAGAATACATAGTGAAACAGCTGGGATTGGAGAAGGGTCAGTCAGTGGAGATGGGAACGATACATGCCGGGGACTTTATGAGGCGTTTCTGTTCCAACCTTGGTATGAATAATCAAGCGGTCAAAGCTGCTCAAGAAGCTGTGCAGAAGTCGGAAGAATTTGATATAAGGAGGAGCCCTATATCAATAGCAGCAGCTGTTATATATATTATAACTCAACTTTCAGATGATAAGAAGCCTTTAAAAGATATCTCACTCGCTACTGGAGTAGCAGAAGGAACTATCAGAAACTCATACAAAGACCTTTATCCTCATGTAGCTAAGATAATACCCAACTGGTATGCCAAGGAGGAGGATCTGAAGAACCTTTGCAGCCCTTGA
Functional Annotation
Gene Ontology
Molecular Function
Biological Process
Cellular Component
GO:0005575 GO:0005622 GO:0005623 GO:0005634 GO:0043226 GO:0043227 GO:0043229 GO:0043231 GO:0044424 GO:0044464
KEGG Pathways
Metabolic & Signaling
ko03022 ko05169 ko05203 map03022 map05169 map05203
Pfam Domains
Protein Families
TFIIB TF_Zn_Ribbon

Protein Analysis

312

Amino Acids

34.15

Weight (kDa)

6.47

Isoelectric Point (pI)

40.16

Instability Index
Protein Domains (Pfam)
Domain Name Pfam ID Position E-value Description
Zn_Ribbon_TF PF08271 5 - 47 1.9e-15 TFIIB zinc-binding
TFIIB PF00382 103 - 185 9.3e-21 Transcription factor TFIIB repeat
TFIIB PF00382 204 - 290 6.5e-14 Transcription factor TFIIB repeat
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: OG0014000)

Species Orthologous Gene IDs
arabidopsis_thaliana AT3G10330
fragaria_vesca FvH4_6g24330
malus_domestica MD12G1075300.v1.1 MD14G1073800.v1.1
prunus_persica Prupe.7G055400_v2.0.a1
pyrus_communis pycom12g06480 pycom14g06300
rosa_chinensis RchiOBHm_Chr3g0483261
rosa_laevigata RLG00000023294
rosa_multiflora Rmu_sc0007550.1_g000009
rosa_roxburghii Rroxscaffold_6G00398520
rosa_rugosa Rorug03G0205000
rosa_samantha Rh3AG253400 Rh3BG290500 Rh3CG287300 Rh3DG283100
rosa_wichuraiana Rw3G022920

Restriction Enzyme Sites

1 / 10
Enzyme Recognition Site Cut Count Positions (bp)
AanI TTATAA 1 cut(s) 770
AarI CACCTGC 1 cut(s) 267
AatII GACGTC 1 cut(s) 125
Acc36I ACCTGC 1 cut(s) 267
AccBSI CCGCTC 1 cut(s) 196
AccI GTMKAC 1 cut(s) 478
AccII CGCG 1 cut(s) 291
AccIII TCCGGA 1 cut(s) 301
AciI CCGC 8 cut(s) 60, 87, 194, 210, 289, 291, 496, 677
AclWI GGATC 3 cut(s) 312, 387, 921
AcoI YGGCCR 2 cut(s) 201, 550
AcsI RAATTY 2 cut(s) 510, 716
AcuI CTGAAG 1 cut(s) 938
AcyI GRCGYC 1 cut(s) 122
AfiI CCNNNNNNNGG 3 cut(s) 40, 199, 308
AgsI TTSAA 1 cut(s) 328
AhdI GACNNNNNGTC 1 cut(s) 121
AloI GAACNNNNNNTCC 2 cut(s) 278, 310
AluBI AGCT 7 cut(s) 245, 386, 580, 686, 698, 755, 878
AluI AGCT 7 cut(s) 245, 386, 580, 686, 698, 755, 878
Alw26I GTCTC 1 cut(s) 113
AlwI GGATC 3 cut(s) 312, 387, 921
AlwNI CAGNNNCTG 1 cut(s) 755
Ama87I CYCGRG 1 cut(s) 98
Aor13HI TCCGGA 1 cut(s) 301
AoxI GGCC 5 cut(s) 88, 182, 201, 358, 550
ApaI GGGCCC 1 cut(s) 186
ApeKI GCWGC 5 cut(s) 455, 686, 749, 752, 930
ApoI RAATTY 2 cut(s) 510, 716
AspLEI GCGC 1 cut(s) 33
AspS9I GGNCC 3 cut(s) 182, 183, 358
AsuC2I CCSGG 1 cut(s) 628
AvaI CYCGRG 1 cut(s) 98
BaeGI GKGCMC 1 cut(s) 186
BanII GRGCYC 2 cut(s) 186, 737
BbsI GAAGAC 1 cut(s) 492
BbvI GCAGC 4 cut(s) 442, 673, 761, 764
BccI CCATC 5 cut(s) 119, 200, 341, 380, 604
BcnI CCSGG 1 cut(s) 628
BcoDI GTCTC 1 cut(s) 113
BfaI CTAG 1 cut(s) 423
BfoI RGCGCY 1 cut(s) 34
BfuAI ACCTGC 1 cut(s) 267
BisI GCNGC 7 cut(s) 88, 292, 456, 687, 750, 753, 931
BlsI GCNGC 7 cut(s) 89, 293, 457, 688, 751, 754, 932
Bme1390I CCNGG 1 cut(s) 628
BmeRI GACNNNNNGTC 1 cut(s) 121
BmeT110I CYCGRG 1 cut(s) 98
BmgT120I GGNCC 3 cut(s) 182, 183, 358
BmiI GGNNCC 4 cut(s) 184, 295, 532, 734
BmrFI CCNGG 1 cut(s) 628
BmsI GCATC 1 cut(s) 433
BpiI GAAGAC 1 cut(s) 492
BplI GAGNNNNNCTC 2 cut(s) 245, 277
BpmI CTGGAG 1 cut(s) 843
BpuEI CTTGAG 1 cut(s) 675
BpuMI CCSGG 1 cut(s) 628
BsaHI GRCGYC 1 cut(s) 122
BsaJI CCNNGG 4 cut(s) 289, 627, 658, 903
BsaWI WCCGGW 1 cut(s) 301
BsaXI ACNNNNNCTCC 2 cut(s) 278, 308
Bsc4I CCNNNNNNNGG 3 cut(s) 40, 199, 308
Bse1I ACTGG 2 cut(s) 826, 899
Bse3DI GCAATG 1 cut(s) 468
BseAI TCCGGA 1 cut(s) 301
BseDI CCNNGG 4 cut(s) 289, 627, 658, 903
BseGI GGATG 1 cut(s) 448
BseLI CCNNNNNNNGG 3 cut(s) 40, 199, 308
BseMI GCAATG 1 cut(s) 468
BseNI ACTGG 2 cut(s) 826, 899
BseRI GAGGAG 2 cut(s) 745, 923
BseSI GKGCMC 1 cut(s) 186
BseXI GCAGC 4 cut(s) 442, 673, 761, 764
BseYI CCCAGC 1 cut(s) 580
BsgI GTGCAG 1 cut(s) 722
Bsh1236I CGCG 1 cut(s) 291
BshFI GGCC 5 cut(s) 90, 184, 203, 360, 552
BsiHKCI CYCGRG 1 cut(s) 98
BsiSI CCGG 4 cut(s) 153, 249, 302, 627
BslFI GGGAC 2 cut(s) 88, 644
BslI CCNNNNNNNGG 3 cut(s) 40, 199, 308
BsmAI GTCTC 1 cut(s) 113
BsmBI CGTCTC 1 cut(s) 113
BsmFI GGGAC 2 cut(s) 88, 644
BsnI GGCC 5 cut(s) 90, 184, 203, 360, 552
BsoBI CYCGRG 1 cut(s) 98
Bsp120I GGGCCC 1 cut(s) 182
Bsp1286I GDGCHC 2 cut(s) 186, 737
Bsp13I TCCGGA 1 cut(s) 301
Bsp143I GATC 5 cut(s) 52, 304, 379, 412, 913
BspACI CCGC 8 cut(s) 60, 87, 194, 210, 289, 291, 496, 677
BspANI GGCC 5 cut(s) 90, 184, 203, 360, 552
BspEI TCCGGA 1 cut(s) 301
BspFNI CGCG 1 cut(s) 291
BspLI GGNNCC 4 cut(s) 184, 295, 532, 734
BspMI ACCTGC 1 cut(s) 267
BspPI GGATC 3 cut(s) 312, 387, 921
BsrBI CCGCTC 1 cut(s) 196
BsrDI GCAATG 1 cut(s) 468
BsrI ACTGG 2 cut(s) 826, 899
BssECI CCNNGG 4 cut(s) 289, 627, 658, 903
BssMI GATC 5 cut(s) 52, 304, 379, 412, 913
BssNI GRCGYC 1 cut(s) 122
BssT1I CCWWGG 2 cut(s) 658, 903
Bst4CI ACNGT 3 cut(s) 73, 223, 502
Bst6I CTCTTC 1 cut(s) 268
BstACI GRCGYC 1 cut(s) 122
BstC8I GCNNGC 3 cut(s) 29, 64, 460
BstDEI CTNAG 1 cut(s) 879
BstDSI CCRYGG 1 cut(s) 289
BstF5I GGATG 1 cut(s) 448
BstFNI CGCG 1 cut(s) 291
BstH2I RGCGCY 1 cut(s) 34
BstHHI GCGC 1 cut(s) 33
BstKTI GATC 5 cut(s) 55, 307, 382, 415, 916
BstMAI GTCTC 1 cut(s) 113
BstMBI GATC 5 cut(s) 52, 304, 379, 412, 913
BstMWI GCNNNNNNNGC 6 cut(s) 24, 84, 452, 530, 683, 695
BstNSI RCATGY 1 cut(s) 626
BstSCI CCNGG 1 cut(s) 626
BstSLI GKGCMC 1 cut(s) 186
BstUI CGCG 1 cut(s) 291
BstV1I GCAGC 4 cut(s) 442, 673, 761, 764
BstV2I GAAGAC 1 cut(s) 492
BstX2I RGATCY 1 cut(s) 913
BstYI RGATCY 1 cut(s) 913
BsuRI GGCC 5 cut(s) 90, 184, 203, 360, 552
BtgI CCRYGG 1 cut(s) 289
BtgZI GCGATG 2 cut(s) 211, 319
BtsCI GGATG 1 cut(s) 448
BtsIMutI CAGTG 2 cut(s) 498, 609
BveI ACCTGC 1 cut(s) 267
Cac8I GCNNGC 3 cut(s) 29, 64, 460
CaiI CAGNNNCTG 1 cut(s) 755
CfoI GCGC 1 cut(s) 33
Cfr13I GGNCC 3 cut(s) 182, 183, 358
Cfr42I CCGCGG 1 cut(s) 292
CviAII CATG 3 cut(s) 343, 623, 872
DdeI CTNAG 1 cut(s) 879
DpnI GATC 5 cut(s) 54, 306, 381, 414, 915
DpnII GATC 5 cut(s) 52, 304, 379, 412, 913
DraI TTTAAA 1 cut(s) 801
DriI GACNNNNNGTC 1 cut(s) 121
EaeI YGGCCR 2 cut(s) 201, 550
Eam1104I CTCTTC 1 cut(s) 268
Eam1105I GACNNNNNGTC 1 cut(s) 121
EarI CTCTTC 1 cut(s) 268
EciI GGCGGA 1 cut(s) 225
Eco130I CCWWGG 2 cut(s) 658, 903
Eco24I GRGCYC 2 cut(s) 186, 737
Eco32I GATATC 1 cut(s) 808
Eco57I CTGAAG 1 cut(s) 938
Eco88I CYCGRG 1 cut(s) 98
EcoRV GATATC 1 cut(s) 808
EcoT14I CCWWGG 2 cut(s) 658, 903
EcoT22I ATGCAT 1 cut(s) 448
EcoT38I GRGCYC 2 cut(s) 186, 737
ErhI CCWWGG 2 cut(s) 658, 903
Esp3I CGTCTC 1 cut(s) 113
FaeI CATG 3 cut(s) 346, 626, 875
FaqI GGGAC 2 cut(s) 88, 644
FatI CATG 3 cut(s) 342, 622, 871
FauI CCCGC 2 cut(s) 201, 503
FblI GTMKAC 1 cut(s) 478
Fnu4HI GCNGC 7 cut(s) 88, 292, 456, 687, 750, 753, 931
FokI GGATG 1 cut(s) 455
FriOI GRGCYC 2 cut(s) 186, 737
Fsp4HI GCNGC 7 cut(s) 88, 292, 456, 687, 750, 753, 931
FspBI CTAG 1 cut(s) 423
GlaI GCGC 1 cut(s) 32
GluI GCNGC 7 cut(s) 88, 292, 456, 687, 750, 753, 931
GsaI CCCAGC 1 cut(s) 584
GsuI CTGGAG 1 cut(s) 843
HaeII RGCGCY 1 cut(s) 34
HaeIII GGCC 5 cut(s) 90, 184, 203, 360, 552
HapII CCGG 4 cut(s) 153, 249, 302, 627
HhaI GCGC 1 cut(s) 33
Hin1I GRCGYC 1 cut(s) 122
Hin1II CATG 3 cut(s) 346, 626, 875
Hin6I GCGC 1 cut(s) 31
HinP1I GCGC 1 cut(s) 31
HincII GTYRAC 1 cut(s) 479
HindII GTYRAC 1 cut(s) 479
HinfI GANTC 2 cut(s) 101, 149
HpaII CCGG 4 cut(s) 153, 249, 302, 627
Hpy166II GTNNAC 2 cut(s) 219, 479
Hpy188I TCNGA 9 cut(s) 7, 22, 82, 127, 349, 712, 784, 845, 918
Hpy188III TCNNGA 3 cut(s) 302, 440, 692
Hpy8I GTNNAC 2 cut(s) 219, 479
Hpy99I CGWCG 1 cut(s) 119
HpyAV CCTTC 4 cut(s) 148, 334, 586, 827
HpyCH4III ACNGT 3 cut(s) 73, 223, 502
HpyCH4IV ACGT 1 cut(s) 122
HpyCH4V TGCA 5 cut(s) 27, 368, 446, 703, 930
HpyF10VI GCNNNNNNNGC 6 cut(s) 24, 84, 452, 530, 683, 695
HpyF3I CTNAG 1 cut(s) 879
HpySE526I ACGT 1 cut(s) 122
Hsp92I GRCGYC 1 cut(s) 122
Hsp92II CATG 3 cut(s) 346, 626, 875
HspAI GCGC 1 cut(s) 31
Kpn2I TCCGGA 1 cut(s) 301
KspI CCGCGG 1 cut(s) 292
Kzo9I GATC 5 cut(s) 52, 304, 379, 412, 913
LmnI GCTCC 7 cut(s) 23, 83, 242, 299, 521, 530, 732
Lsp1109I GCAGC 4 cut(s) 442, 673, 761, 764
LweI GCATC 1 cut(s) 433
MaeI CTAG 1 cut(s) 423
MaeII ACGT 1 cut(s) 122
MalI GATC 5 cut(s) 54, 306, 381, 414, 915
MbiI CCGCTC 1 cut(s) 196
MboI GATC 5 cut(s) 52, 304, 379, 412, 913
MboII GAAGA 6 cut(s) 255, 422, 444, 497, 725, 931
MflI RGATCY 1 cut(s) 913
MhlI GDGCHC 2 cut(s) 186, 737
MluCI AATT 3 cut(s) 510, 546, 716
MlyI GAGTC 2 cut(s) 110, 158
MmeI TCCRAC 3 cut(s) 45, 678, 690
Mph1103I ATGCAT 1 cut(s) 448
MroI TCCGGA 1 cut(s) 301
MseI TTAA 1 cut(s) 800
MspA1I CMGCKG 4 cut(s) 62, 291, 580, 755
MspI CCGG 4 cut(s) 153, 249, 302, 627
MspR9I CCNGG 1 cut(s) 628
MvnI CGCG 1 cut(s) 291
MwoI GCNNNNNNNGC 6 cut(s) 24, 84, 452, 530, 683, 695
NciI CCSGG 1 cut(s) 628
NdeII GATC 5 cut(s) 52, 304, 379, 412, 913
NlaIII CATG 3 cut(s) 346, 626, 875
NlaIV GGNNCC 4 cut(s) 184, 295, 532, 734
NmeAIII GCCGAG 1 cut(s) 578
NsiI ATGCAT 1 cut(s) 448
NspI RCATGY 1 cut(s) 626
PaeR7I CTCGAG 1 cut(s) 98
PaqCI CACCTGC 1 cut(s) 267
PcsI WCGNNNNNNNCGW 2 cut(s) 123, 153
PflFI GACNNNGTC 2 cut(s) 71, 167
PkrI GCNGC 7 cut(s) 89, 293, 457, 688, 751, 754, 932
PleI GAGTC 2 cut(s) 109, 157
PpsI GAGTC 2 cut(s) 109, 157
PsiI TTATAA 1 cut(s) 770
PspFI CCCAGC 1 cut(s) 580
PspN4I GGNNCC 4 cut(s) 184, 295, 532, 734
PspOMI GGGCCC 1 cut(s) 182
PspPI GGNCC 3 cut(s) 182, 183, 358
PspXI VCTCGAGB 1 cut(s) 98
PstNI CAGNNNCTG 1 cut(s) 755
PsuI RGATCY 1 cut(s) 913
PsyI GACNNNGTC 2 cut(s) 71, 167
PvuII CAGCTG 2 cut(s) 580, 755
SacII CCGCGG 1 cut(s) 292
SalI GTCGAC 1 cut(s) 477
SaqAI TTAA 1 cut(s) 800
SatI GCNGC 7 cut(s) 88, 292, 456, 687, 750, 753, 931
Sau3AI GATC 5 cut(s) 52, 304, 379, 412, 913
Sau96I GGNCC 3 cut(s) 182, 183, 358
SchI GAGTC 2 cut(s) 110, 158
ScrFI CCNGG 1 cut(s) 628
SduI GDGCHC 2 cut(s) 186, 737
SfaNI GCATC 1 cut(s) 433
Sfr274I CTCGAG 1 cut(s) 98
Sfr303I CCGCGG 1 cut(s) 292
SgrBI CCGCGG 1 cut(s) 292
SlaI CTCGAG 1 cut(s) 98
SmlI CTYRAG 2 cut(s) 98, 690
SmoI CTYRAG 2 cut(s) 98, 690
Sse9I AATT 3 cut(s) 510, 546, 716
SsiI CCGC 8 cut(s) 60, 87, 194, 210, 289, 291, 496, 677
SspMI CTAG 1 cut(s) 423
StyD4I CCNGG 1 cut(s) 626
StyI CCWWGG 2 cut(s) 658, 903
TaaI ACNGT 3 cut(s) 73, 223, 502
TaiI ACGT 1 cut(s) 125
TaqI TCGA 5 cut(s) 51, 99, 114, 382, 478
TasI AATT 3 cut(s) 510, 546, 716
TauI GCSGC 2 cut(s) 90, 294
Tru1I TTAA 1 cut(s) 800
Tru9I TTAA 1 cut(s) 800
TscAI CASTG 2 cut(s) 505, 609
TseI GCWGC 5 cut(s) 455, 686, 749, 752, 930
TspDTI ATGAA 1 cut(s) 680
TspGWI ACGGA 3 cut(s) 53, 161, 508
TspRI CASTG 2 cut(s) 505, 609
Tth111I GACNNNGTC 2 cut(s) 71, 167
XapI RAATTY 2 cut(s) 510, 716
XceI RCATGY 1 cut(s) 626
XcmI CCANNNNNNNNNTGG 1 cut(s) 196
XhoI CTCGAG 1 cut(s) 98
XmiI GTMKAC 1 cut(s) 478
XspI CTAG 1 cut(s) 423
ZraI GACGTC 1 cut(s) 123
Zsp2I ATGCAT 1 cut(s) 448
Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.