Rh5AG475300

Transcription initiation factor

Design Primers CRISPR Design

Basic Information

Type: gene
Biological Identity
rosa_samantha
Chr5A
OG0000387
Physical Location & Seq
Reverse (-)
81569010 .. 81572407
3398 bp
Loading structure...
UTR
Exon/CDS
Intron
Rh5AG475300.1

Sequence Viewer

Length: 585 bp
ATGTTTTCACATACTGCAATCAGTTCCCCAGATTACAAACTTATCATCATGTTTGTATATAAGGAATATGTTATCTCATTCATGGATTTATTTCACTATGATCCGGCCAATGACATATATAAGAAGATGACTGATCAAAAACCTCTCAGATTTAGGACTCCAGACGCAATTGCGGCTCCTTCCGTCTTCATTGCCTGTAGACATGAAAATAAGCCACGTAGTGTGAAAGAAAACATTCCAAACTTTGCCAACATTTGGGAATCTCAGACAATTGAACTTGGATTAGTAAAAGTGAGGAAGTTTGGTGACCTTTTAACTACTGGAATACTAACAATTTTATCTCTGCATTCATATGGATCAGCACTTACTTATTCTGAAAACACAATTGGAAAGATTGATTTGCTTTACAGACTGCTGCACATAAAGGCCTTGTTGTGCCAGTTATCCGCAATGCTGATAAAGATGAAATGTGGTGAGATAGAGGAGATCAATTCGCTTGCAAAGAAGGCAAATGAGGGACGTCTTTCAATTGATGATATGGCTGGGGGTTCATTTCCAATGGTGGAGTTTATGGAAGCCTTATAA
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

194

Amino Acids

22.01

Weight (kDa)

6.96

Isoelectric Point (pI)

42.48

Instability Index
Protein Domains (Pfam)
Domain Name Pfam ID Position E-value Description
TFIIB PF00382 34 - 77 1.3e-06 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: OG0000387)

Species Orthologous Gene IDs
arabidopsis_thaliana AT4G26910 AT4G26910 AT4G26910 AT5G55070 AT5G55070
fragaria_vesca FvH4_3g23070 FvH4_3g23070 FvH4_3g23070 FvH4_3g23070 FvH4_6g42960 FvH4_6g42960 FvH4_6g42960 FvH4_6g42960
malus_domestica MD03G1198100.v1.1 MD09G1110700.v1.1 MD17G1098600.v1.1
prunus_persica Prupe.3G215800_v2.0.a1 Prupe.4G216900_v2.0.a1 Prupe.4G216900_v2.0.a1
pyrus_communis pycom03g14960 pycom09g03320 pycom17g09400
rosa_chinensis RchiOBHm_Chr2g0119431 RchiOBHm_Chr2g0119441 RchiOBHm_Chr2g0158941 RchiOBHm_Chr5g0040581 RchiOBHm_Chr5g0052421 RchiOBHm_Chr5g0052431
rosa_laevigata RLG00000002270 RLG00000012296 RLG00000021125 RLG00000031115 RLG00000033989
rosa_multiflora Rmu_co8099772.1_g000001 Rmu_co8181026.1_g000001 Rmu_co8403685.1_g000001 Rmu_sc0001893.1_g000003 Rmu_sc0004787.1_g000003 Rmu_sc0007967.1_g000007 Rmu_sc0010369.1_g000001 Rmu_ssc0000174.1_g000008
rosa_roxburghii Rroxscaffold_1G00040090 Rroxscaffold_1G00040800 Rroxscaffold_1G00049000 Rroxscaffold_2G00090860 Rroxscaffold_2G00122640 Rroxscaffold_2G00127540 Rroxscaffold_2G00128360 Rroxscaffold_3G00249890 Rroxscaffold_4G00314140 Rroxscaffold_5G00345820 Rroxscaffold_5G00345830 Rroxscaffold_5G00371680 Rroxscaffold_7G00164980 Rroxscaffold_7G00209200
rosa_rugosa Rorug01G0153500.1 Rorug02G0473100 Rorug02G0473200 Rorug02G0473200 Rorug03G0343200 Rorug05G0185800
rosa_samantha Rh1AG155300 Rh1AG275400 Rh1BG123600 Rh1CG026200 Rh1CG145600 Rh2AG539600 Rh2BG510900 Rh2BG552500 Rh2CG522900 Rh2DG522600 Rh2DG522700 Rh2DG562200 Rh3CG234300 Rh3CG302000 Rh3CG302100 Rh4DG305100 Rh5AG250900 Rh5AG272600 Rh5AG475300 Rh5BG276800 Rh5BG355700 Rh5CG308700 Rh5DG285400 Rh6BG136500 Rh6BG167900 Rh6BG220000 Rh7AG327600 Rh7AG349200 Rh7AG349300 Rh7AG349400 Rh7AG353200 Rh7CG344900 Rh7CG366500 Rh7CG366600
rosa_wichuraiana Rw1G002110 Rw2G044660 Rw3G008210 Rw4G016310 Rw4G019560 Rw5G025520 Rw5G030020

Restriction Enzyme Sites

1 / 10
Enzyme Recognition Site Cut Count Positions (bp)
AanI TTATAA 1 cut(s) 583
AatII GACGTC 1 cut(s) 523
AccB7I CCANNNNNTGG 1 cut(s) 255
AccI GTMKAC 1 cut(s) 199
AciI CCGC 2 cut(s) 173, 447
AclWI GGATC 2 cut(s) 95, 364
AcoI YGGCCR 1 cut(s) 105
AcyI GRCGYC 1 cut(s) 520
AdeI CACNNNGTG 1 cut(s) 221
AfiI CCNNNNNNNGG 1 cut(s) 255
AgsI TTSAA 2 cut(s) 275, 528
AjuI GAANNNNNNNTTGG 2 cut(s) 369, 401
AlwI GGATC 2 cut(s) 95, 364
AoxI GGCC 2 cut(s) 105, 426
ApeKI GCWGC 1 cut(s) 415
Asp700I GAANNNNTTC 1 cut(s) 234
AsuHPI GGTGA 2 cut(s) 317, 485
BbsI GAAGAC 1 cut(s) 178
BbvI GCAGC 1 cut(s) 402
BclI TGATCA 1 cut(s) 133
BfmI CTRYAG 1 cut(s) 196
BisI GCNGC 2 cut(s) 174, 416
BlsI GCNGC 2 cut(s) 175, 417
BmiI GGNNCC 1 cut(s) 177
BpiI GAAGAC 1 cut(s) 178
BpmI CTGGAG 1 cut(s) 144
BsaAI YACGTR 1 cut(s) 218
BsaHI GRCGYC 1 cut(s) 520
Bsc4I CCNNNNNNNGG 1 cut(s) 255
Bse1I ACTGG 2 cut(s) 325, 439
Bse3DI GCAATG 2 cut(s) 189, 456
BseLI CCNNNNNNNGG 1 cut(s) 255
BseMI GCAATG 2 cut(s) 189, 456
BseMII CTCAG 2 cut(s) 160, 278
BseNI ACTGG 2 cut(s) 325, 439
BseRI GAGGAG 1 cut(s) 497
BseXI GCAGC 1 cut(s) 402
BseYI CCCAGC 1 cut(s) 542
BsgI GTGCAG 1 cut(s) 401
BshFI GGCC 2 cut(s) 107, 428
BsiSI CCGG 1 cut(s) 104
BslFI GGGAC 1 cut(s) 531
BslI CCNNNNNNNGG 1 cut(s) 255
BsmFI GGGAC 1 cut(s) 531
BsmI GAATGC 1 cut(s) 346
BsnI GGCC 2 cut(s) 107, 428
Bsp143I GATC 4 cut(s) 100, 133, 356, 486
BspACI CCGC 2 cut(s) 173, 447
BspANI GGCC 2 cut(s) 107, 428
BspCNI CTCAG 2 cut(s) 159, 277
BspLI GGNNCC 1 cut(s) 177
BspPI GGATC 2 cut(s) 95, 364
BsrDI GCAATG 2 cut(s) 189, 456
BsrI ACTGG 2 cut(s) 325, 439
BssMI GATC 4 cut(s) 100, 133, 356, 486
BssNI GRCGYC 1 cut(s) 520
BstACI GRCGYC 1 cut(s) 520
BstBAI YACGTR 1 cut(s) 218
BstC8I GCNNGC 1 cut(s) 498
BstDEI CTNAG 2 cut(s) 146, 264
BstEII GGTNACC 1 cut(s) 305
BstKTI GATC 4 cut(s) 103, 136, 359, 489
BstMBI GATC 4 cut(s) 100, 133, 356, 486
BstMWI GCNNNNNNNGC 2 cut(s) 173, 506
BstPI GGTNACC 1 cut(s) 305
BstSFI CTRYAG 1 cut(s) 196
BstV1I GCAGC 1 cut(s) 402
BstV2I GAAGAC 1 cut(s) 178
BsuRI GGCC 2 cut(s) 107, 428
Cac8I GCNNGC 1 cut(s) 498
CseI GACGC 1 cut(s) 173
CviAII CATG 3 cut(s) 49, 82, 203
CviJI RGCY 6 cut(s) 107, 176, 214, 428, 542, 578
CviKI_1 RGCY 6 cut(s) 107, 176, 214, 428, 542, 578
DdeI CTNAG 2 cut(s) 146, 264
DpnI GATC 4 cut(s) 102, 135, 358, 488
DpnII GATC 4 cut(s) 100, 133, 356, 486
DraIII CACNNNGTG 1 cut(s) 221
EaeI YGGCCR 1 cut(s) 105
Eco147I AGGCCT 1 cut(s) 428
Eco91I GGTNACC 1 cut(s) 305
EcoO65I GGTNACC 1 cut(s) 305
FaeI CATG 3 cut(s) 52, 85, 206
FaqI GGGAC 1 cut(s) 531
FatI CATG 3 cut(s) 48, 81, 202
FauNDI CATATG 1 cut(s) 352
FbaI TGATCA 1 cut(s) 133
FblI GTMKAC 1 cut(s) 199
Fnu4HI GCNGC 2 cut(s) 174, 416
Fsp4HI GCNGC 2 cut(s) 174, 416
GluI GCNGC 2 cut(s) 174, 416
GsaI CCCAGC 1 cut(s) 546
GsuI CTGGAG 1 cut(s) 144
HaeIII GGCC 2 cut(s) 107, 428
HapII CCGG 1 cut(s) 104
HgaI GACGC 1 cut(s) 173
Hin1I GRCGYC 1 cut(s) 520
Hin1II CATG 3 cut(s) 52, 85, 206
HinfI GANTC 2 cut(s) 157, 260
HpaII CCGG 1 cut(s) 104
HphI GGTGA 2 cut(s) 317, 485
Hpy166II GTNNAC 1 cut(s) 200
Hpy188I TCNGA 3 cut(s) 149, 267, 376
Hpy188III TCNNGA 1 cut(s) 161
Hpy8I GTNNAC 1 cut(s) 200
HpyAV CCTTC 2 cut(s) 189, 499
HpyCH4IV ACGT 2 cut(s) 217, 520
HpyCH4V TGCA 4 cut(s) 17, 346, 418, 500
HpyF10VI GCNNNNNNNGC 2 cut(s) 173, 506
HpyF3I CTNAG 2 cut(s) 146, 264
HpySE526I ACGT 2 cut(s) 217, 520
Hsp92I GRCGYC 1 cut(s) 520
Hsp92II CATG 3 cut(s) 52, 85, 206
Ksp22I TGATCA 1 cut(s) 133
Kzo9I GATC 4 cut(s) 100, 133, 356, 486
LmnI GCTCC 1 cut(s) 181
LpnPI CCDG 7 cut(s) 42, 117, 174, 208, 306, 452, 528
Lsp1109I GCAGC 1 cut(s) 402
MaeII ACGT 2 cut(s) 217, 520
MaeIII GTNAC 1 cut(s) 305
MalI GATC 4 cut(s) 102, 135, 358, 488
MboI GATC 4 cut(s) 100, 133, 356, 486
MboII GAAGA 2 cut(s) 136, 178
MfeI CAATTG 4 cut(s) 168, 270, 384, 528
MluCI AATT 6 cut(s) 168, 270, 333, 384, 490, 528
MlyI GAGTC 1 cut(s) 151
MnlI CCTC 4 cut(s) 153, 288, 475, 508
MroXI GAANNNNTTC 1 cut(s) 234
MseI TTAA 1 cut(s) 314
MslI CAYNNNNRTG 1 cut(s) 351
MspI CCGG 1 cut(s) 104
MunI CAATTG 4 cut(s) 168, 270, 384, 528
Mva1269I GAATGC 1 cut(s) 346
MwoI GCNNNNNNNGC 2 cut(s) 173, 506
NdeI CATATG 1 cut(s) 352
NdeII GATC 4 cut(s) 100, 133, 356, 486
NlaIII CATG 3 cut(s) 52, 85, 206
NlaIV GGNNCC 1 cut(s) 177
NmuCI GTSAC 1 cut(s) 305
PceI AGGCCT 1 cut(s) 428
PctI GAATGC 1 cut(s) 346
PdmI GAANNNNTTC 1 cut(s) 234
PfeI GAWTC 1 cut(s) 260
PflMI CCANNNNNTGG 1 cut(s) 255
PkrI GCNGC 2 cut(s) 175, 417
PleI GAGTC 1 cut(s) 151
PpsI GAGTC 1 cut(s) 151
Ppu21I YACGTR 1 cut(s) 218
PsiI TTATAA 1 cut(s) 583
PspEI GGTNACC 1 cut(s) 305
PspFI CCCAGC 1 cut(s) 542
PspN4I GGNNCC 1 cut(s) 177
RseI CAYNNNNRTG 1 cut(s) 351
SaqAI TTAA 1 cut(s) 314
SatI GCNGC 2 cut(s) 174, 416
Sau3AI GATC 4 cut(s) 100, 133, 356, 486
SchI GAGTC 1 cut(s) 151
SetI ASST 4 cut(s) 145, 220, 312, 523
SfcI CTRYAG 1 cut(s) 196
SmiMI CAYNNNNRTG 1 cut(s) 351
Sse9I AATT 6 cut(s) 168, 270, 333, 384, 490, 528
SseBI AGGCCT 1 cut(s) 428
SsiI CCGC 2 cut(s) 173, 447
StuI AGGCCT 1 cut(s) 428
TaiI ACGT 2 cut(s) 220, 523
TasI AATT 6 cut(s) 168, 270, 333, 384, 490, 528
TauI GCSGC 1 cut(s) 176
TfiI GAWTC 1 cut(s) 260
Tru1I TTAA 1 cut(s) 314
Tru9I TTAA 1 cut(s) 314
TseFI GTSAC 1 cut(s) 305
TseI GCWGC 1 cut(s) 415
Tsp45I GTSAC 1 cut(s) 305
TspDTI ATGAA 6 cut(s) 70, 178, 219, 339, 479, 540
TspGWI ACGGA 1 cut(s) 172
Van91I CCANNNNNTGG 1 cut(s) 255
XmiI GTMKAC 1 cut(s) 199
XmnI GAANNNNTTC 1 cut(s) 234
ZraI GACGTC 1 cut(s) 521
Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.