Rroxscaffold_4G00292900

General transcription factor IIF subunit

Design Primers CRISPR Design

Basic Information

Type: gene
Biological Identity
rosa_roxburghii
GWHEROQ00000004
OG0013034
Physical Location & Seq
Forward (+)
13097205 .. 13100544
3340 bp
Loading structure...
UTR
Exon/CDS
Intron
Rroxscaffold_4G00292900.1

Sequence Viewer

Length: 903 bp
ATGGCGCCAAGCCAAATAGCAATGGAAGACCAAAAACCACAACGAAACAGTAGCACTAGTAATTGTGGCGGCAACAACAACAACAACAGCAACAAAAATTTGAGGGGGCATTTGGAGACGAAAAGCAAAGAAAATTGGGGGCATTTGGAGACGACCAAAGCAGCGGAGCCAGTGTGGCTCATGAAATGCCCACCCAACGTGGCCAAATCGTTTAAGCCTGACGCCGCCGACGATGGCTCCGTCGCCGCAGAGGAGCCTTGTCCTTCCGGCCCTGTCGCCAAGGTCATCCTCTCCCTTGACCCTCTCAACTCCAATAACGAACCTAAGTTTACCATGGAACTGGCGGCCACTGAATCTGCAAATACCCCCAAGTGTTACGTTTTGGATATGTCCAGGGACTTCATTCCAATGTCTGTGTTTTCAGAGTCGTCAGAAGGAAAGTTATCTGTGGAGGGGAAAATCTTCAACAAATTTGACATGAAGCCCCATGATGAGAATCTTGAGAATTATGGGAAACTTTGCCGTGAACGAACAAAAAAGCATATGAAAAGTAGAAAGATTCAGGTGATCGACAATGACAACGGGGCACATATGAGGCCTATGCCAGGGATGATTGGTTTTGTGGCTCCTGGACCCAGTGACAAGAAGAAAGCGCCAACTAAGGGATCAGAAATGAAGAGAACAAGGAGGGACCGTGGAGAAATGGAACATATTATGTTTAAGCTCTTTGAAAGGCAACCTAATTGGACTTTAAGACAATTGATCCAAGAGACAGATCAACCCGAACAATTTCTGAAAGACATACTTAAGGACCTCTCTGTTTACAACAACAAGGGAGCTAATCAAGGCACTTACGAGCTGAAACCTGAATACAGGAGAACAGGCCAGGAGCCAGCTCACTAA
Functional Annotation
Gene Ontology
Molecular Function
Biological Process
Cellular Component
GO:0000375 GO:0000377 GO:0000398 GO:0000428 GO:0000988 GO:0000990 GO:0000991 GO:0003674 GO:0005575 GO:0005622 GO:0005623 GO:0005634 GO:0005654 GO:0005667 GO:0005674 GO:0005856 GO:0006139 GO:0006351 GO:0006352 GO:0006354 GO:0006355 GO:0006357 GO:0006366 GO:0006367 GO:0006368 GO:0006370 GO:0006396 GO:0006397 GO:0006725 GO:0006807 GO:0007154 GO:0007165 GO:0007166 GO:0007167 GO:0007169 GO:0008150 GO:0008152 GO:0008380 GO:0008543 GO:0009058 GO:0009059 GO:0009301 GO:0009452 GO:0009719 GO:0009889 GO:0009891 GO:0009893 GO:0009987 GO:0010033 GO:0010467 GO:0010468 GO:0010556 GO:0010557 GO:0010604 GO:0010628 GO:0015630 GO:0016070 GO:0016071 GO:0016073 GO:0016591 GO:0018130 GO:0019219 GO:0019222 GO:0019438 GO:0023052 GO:0030880 GO:0031323 GO:0031325 GO:0031326 GO:0031328 GO:0031334 GO:0031974 GO:0031981 GO:0032774 GO:0032784 GO:0032786 GO:0032968 GO:0032991 GO:0032993 GO:0034243 GO:0034641 GO:0034645 GO:0034654 GO:0034660 GO:0036260 GO:0042221 GO:0042795 GO:0043170 GO:0043226 GO:0043227 GO:0043228 GO:0043229 GO:0043231 GO:0043232 GO:0043233 GO:0043254 GO:0044087 GO:0044089 GO:0044237 GO:0044238 GO:0044249 GO:0044260 GO:0044271 GO:0044344 GO:0044422 GO:0044424 GO:0044428 GO:0044446 GO:0044451 GO:0044464 GO:0044798 GO:0045893 GO:0045935 GO:0045944 GO:0046483 GO:0048518 GO:0048522 GO:0050789 GO:0050794 GO:0050896 GO:0051128 GO:0051130 GO:0051171 GO:0051173 GO:0051252 GO:0051254 GO:0051716 GO:0055029 GO:0060255 GO:0060260 GO:0060261 GO:0061695 GO:0065007 GO:0070013 GO:0070848 GO:0070887 GO:0071310 GO:0071363 GO:0071495 GO:0071704 GO:0071774 GO:0080090 GO:0090304 GO:0090575 GO:0097550 GO:0097659 GO:0098781 GO:0140110 GO:1901360 GO:1901362 GO:1901576 GO:1902494 GO:1902680 GO:1903506 GO:1903508 GO:1990234 GO:2000112 GO:2000142 GO:2000144 GO:2001141
KEGG Pathways
Metabolic & Signaling
ko03022 map03022
Pfam Domains
Protein Families
TFIIF_beta

Protein Analysis

300

Amino Acids

33.82

Weight (kDa)

8.65

Isoelectric Point (pI)

37.76

Instability Index
Protein Domains (Pfam)
Domain Name Pfam ID Position E-value Description
TFIIF_beta PF02270 229 - 292 3.6e-18 TFIIF, beta subunit HTH domain
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: OG0013034)

Species Orthologous Gene IDs
arabidopsis_thaliana AT3G52270
fragaria_vesca FvH4_7g19881
malus_domestica MD01G1111000.v1.1 MD07G1177200.v1.1
prunus_persica Prupe.2G215900_v2.0.a1
pyrus_communis pycom07g17120
rosa_chinensis RchiOBHm_Chr1g0363871
rosa_laevigata RLG00000027539
rosa_multiflora Rmu_sc0002483.1_g000003
rosa_roxburghii Rroxscaffold_4G00292900
rosa_rugosa Rorug01G0310400 Rorug01G0310500 Rorug01G0310600
rosa_samantha Rh1AG318500 Rh1BG281700 Rh1CG298100 Rh1DG313000
rosa_wichuraiana Rw1G028270

Restriction Enzyme Sites

1 / 10
Enzyme Recognition Site Cut Count Positions (bp)
AccB1I GGYRCC 1 cut(s) 4
AciI CCGC 5 cut(s) 69, 164, 225, 246, 344
AclWI GGATC 2 cut(s) 673, 757
AcoI YGGCCR 2 cut(s) 201, 345
AcsI RAATTY 2 cut(s) 97, 470
AcyI GRCGYC 2 cut(s) 5, 222
AfiI CCNNNNNNNGG 2 cut(s) 605, 662
AflII CTTAAG 1 cut(s) 806
AgsI TTSAA 2 cut(s) 466, 731
AhlI ACTAGT 1 cut(s) 56
AjnI CCWGG 4 cut(s) 392, 604, 628, 885
AluBI AGCT 4 cut(s) 724, 839, 859, 896
AluI AGCT 4 cut(s) 724, 839, 859, 896
Alw26I GTCTC 3 cut(s) 110, 143, 764
AlwI GGATC 2 cut(s) 673, 757
AoxI GGCC 5 cut(s) 201, 268, 345, 596, 883
ApeKI GCWGC 1 cut(s) 161
ApoI RAATTY 2 cut(s) 97, 470
Asp700I GAANNNNTTC 2 cut(s) 461, 789
AspLEI GCGC 2 cut(s) 7, 655
AspS9I GGNCC 4 cut(s) 269, 632, 691, 811
AsuHPI GGTGA 1 cut(s) 577
AvaII GGWCC 3 cut(s) 632, 691, 811
BaeGI GKGCMC 1 cut(s) 589
BalI TGGCCA 1 cut(s) 203
BanI GGYRCC 1 cut(s) 4
BbsI GAAGAC 1 cut(s) 33
BbvI GCAGC 1 cut(s) 173
BccI CCATC 1 cut(s) 227
BceAI ACGGC 1 cut(s) 507
BciT130I CCWGG 4 cut(s) 394, 606, 630, 887
BcoDI GTCTC 3 cut(s) 110, 143, 764
BcuI ACTAGT 1 cut(s) 56
BfaI CTAG 1 cut(s) 57
BfoI RGCGCY 2 cut(s) 8, 656
BfrI CTTAAG 1 cut(s) 806
BglI GCCNNNNNGGC 1 cut(s) 175
BisI GCNGC 5 cut(s) 70, 162, 225, 246, 345
BlsI GCNGC 5 cut(s) 71, 163, 226, 247, 346
Bme1390I CCNGG 4 cut(s) 394, 606, 630, 887
Bme18I GGWCC 3 cut(s) 632, 691, 811
BmgT120I GGNCC 4 cut(s) 269, 632, 691, 811
BmiI GGNNCC 8 cut(s) 6, 168, 238, 255, 627, 634, 692, 891
BmrFI CCNGG 4 cut(s) 394, 606, 630, 887
BmrI ACTGGG 1 cut(s) 630
BmuI ACTGGG 1 cut(s) 630
BpiI GAAGAC 1 cut(s) 33
BpuEI CTTGAG 1 cut(s) 521
BsaBI GATNNNNATC 1 cut(s) 495
BsaHI GRCGYC 2 cut(s) 5, 222
BsaJI CCNNGG 5 cut(s) 279, 333, 393, 605, 694
BsaXI ACNNNNNCTCC 6 cut(s) 158, 188, 221, 251, 679, 709
Bsc4I CCNNNNNNNGG 2 cut(s) 605, 662
Bse1I ACTGG 3 cut(s) 170, 345, 636
Bse3DI GCAATG 1 cut(s) 27
Bse8I GATNNNNATC 1 cut(s) 495
BseBI CCWGG 4 cut(s) 394, 606, 630, 887
BseDI CCNNGG 5 cut(s) 279, 333, 393, 605, 694
BseGI GGATG 2 cut(s) 285, 615
BseJI GATNNNNATC 1 cut(s) 495
BseLI CCNNNNNNNGG 2 cut(s) 605, 662
BseMI GCAATG 1 cut(s) 27
BseNI ACTGG 3 cut(s) 170, 345, 636
BseRI GAGGAG 1 cut(s) 266
BseSI GKGCMC 1 cut(s) 589
BseXI GCAGC 1 cut(s) 173
BshFI GGCC 5 cut(s) 203, 270, 347, 598, 885
BshNI GGYRCC 1 cut(s) 4
BsiSI CCGG 1 cut(s) 267
BslFI GGGAC 2 cut(s) 410, 704
BslI CCNNNNNNNGG 2 cut(s) 605, 662
BsmAI GTCTC 3 cut(s) 110, 143, 764
BsmBI CGTCTC 2 cut(s) 110, 143
BsmFI GGGAC 2 cut(s) 410, 704
BsnI GGCC 5 cut(s) 203, 270, 347, 598, 885
Bsp1286I GDGCHC 1 cut(s) 589
Bsp143I GATC 4 cut(s) 567, 665, 762, 775
Bsp19I CCATGG 1 cut(s) 333
BspACI CCGC 5 cut(s) 69, 164, 225, 246, 344
BspANI GGCC 5 cut(s) 203, 270, 347, 598, 885
BspHI TCATGA 1 cut(s) 180
BspLI GGNNCC 8 cut(s) 6, 168, 238, 255, 627, 634, 692, 891
BspPI GGATC 2 cut(s) 673, 757
BspT107I GGYRCC 1 cut(s) 4
BspTI CTTAAG 1 cut(s) 806
BsrDI GCAATG 1 cut(s) 27
BsrI ACTGG 3 cut(s) 170, 345, 636
BssECI CCNNGG 5 cut(s) 279, 333, 393, 605, 694
BssMI GATC 4 cut(s) 567, 665, 762, 775
BssNI GRCGYC 2 cut(s) 5, 222
BssT1I CCWWGG 2 cut(s) 279, 333
Bst2UI CCWGG 4 cut(s) 394, 606, 630, 887
Bst4CI ACNGT 2 cut(s) 50, 695
Bst6I CTCTTC 1 cut(s) 671
BstACI GRCGYC 2 cut(s) 5, 222
BstAFI CTTAAG 1 cut(s) 806
BstC8I GCNNGC 1 cut(s) 894
BstDEI CTNAG 2 cut(s) 324, 660
BstDSI CCRYGG 2 cut(s) 333, 694
BstENI CCTNNNNNAGG 1 cut(s) 603
BstF5I GGATG 2 cut(s) 285, 615
BstH2I RGCGCY 2 cut(s) 8, 656
BstHHI GCGC 2 cut(s) 7, 655
BstKTI GATC 4 cut(s) 570, 668, 765, 778
BstMAI GTCTC 3 cut(s) 110, 143, 764
BstMBI GATC 4 cut(s) 567, 665, 762, 775
BstMWI GCNNNNNNNGC 1 cut(s) 175
BstNI CCWGG 4 cut(s) 394, 606, 630, 887
BstSCI CCNGG 4 cut(s) 392, 604, 628, 885
BstSLI GKGCMC 1 cut(s) 589
BstV1I GCAGC 1 cut(s) 173
BstV2I GAAGAC 1 cut(s) 33
BstXI CCANNNNNNTGG 1 cut(s) 340
BsuRI GGCC 5 cut(s) 203, 270, 347, 598, 885
BtgI CCRYGG 2 cut(s) 333, 694
BtsCI GGATG 2 cut(s) 285, 615
BtsIMutI CAGTG 3 cut(s) 177, 348, 643
Cac8I GCNNGC 1 cut(s) 894
CciI TCATGA 1 cut(s) 180
CfoI GCGC 2 cut(s) 7, 655
Cfr13I GGNCC 4 cut(s) 269, 632, 691, 811
CseI GACGC 1 cut(s) 230
CviAII CATG 4 cut(s) 181, 334, 478, 488
DdeI CTNAG 2 cut(s) 324, 660
DinI GGCGCC 1 cut(s) 6
DpnI GATC 4 cut(s) 569, 667, 764, 777
DpnII GATC 4 cut(s) 567, 665, 762, 775
EaeI YGGCCR 2 cut(s) 201, 345
Eam1104I CTCTTC 1 cut(s) 671
EarI CTCTTC 1 cut(s) 671
Eco130I CCWWGG 2 cut(s) 279, 333
Eco147I AGGCCT 1 cut(s) 598
Eco47I GGWCC 3 cut(s) 632, 691, 811
EcoNI CCTNNNNNAGG 1 cut(s) 603
EcoO109I RGGNCCY 1 cut(s) 811
EcoRII CCWGG 4 cut(s) 392, 604, 628, 885
EcoT14I CCWWGG 2 cut(s) 279, 333
EgeI GGCGCC 1 cut(s) 6
EheI GGCGCC 1 cut(s) 6
ErhI CCWWGG 2 cut(s) 279, 333
Esp3I CGTCTC 2 cut(s) 110, 143
FaeI CATG 4 cut(s) 184, 337, 481, 491
FalI AAGNNNNNCTT 2 cut(s) 789, 821
FaqI GGGAC 2 cut(s) 410, 704
FatI CATG 4 cut(s) 180, 333, 477, 487
FauNDI CATATG 2 cut(s) 543, 591
Fnu4HI GCNGC 5 cut(s) 70, 162, 225, 246, 345
FokI GGATG 2 cut(s) 272, 622
Fsp4HI GCNGC 5 cut(s) 70, 162, 225, 246, 345
FspBI CTAG 1 cut(s) 57
GlaI GCGC 2 cut(s) 6, 654
GluI GCNGC 5 cut(s) 70, 162, 225, 246, 345
HaeII RGCGCY 2 cut(s) 8, 656
HaeIII GGCC 5 cut(s) 203, 270, 347, 598, 885
HapII CCGG 1 cut(s) 267
HgaI GACGC 1 cut(s) 230
HhaI GCGC 2 cut(s) 7, 655
Hin1I GRCGYC 2 cut(s) 5, 222
Hin1II CATG 4 cut(s) 184, 337, 481, 491
Hin6I GCGC 2 cut(s) 5, 653
HinP1I GCGC 2 cut(s) 5, 653
HinfI GANTC 4 cut(s) 353, 425, 496, 559
HpaII CCGG 1 cut(s) 267
HphI GGTGA 1 cut(s) 577
Hpy166II GTNNAC 3 cut(s) 330, 527, 823
Hpy188I TCNGA 4 cut(s) 424, 433, 670, 795
Hpy188III TCNNGA 2 cut(s) 181, 500
Hpy8I GTNNAC 3 cut(s) 330, 527, 823
Hpy99I CGWCG 2 cut(s) 233, 245
HpyAV CCTTC 2 cut(s) 273, 428
HpyCH4III ACNGT 2 cut(s) 50, 695
HpyCH4IV ACGT 2 cut(s) 198, 378
HpyCH4V TGCA 1 cut(s) 359
HpyF10VI GCNNNNNNNGC 1 cut(s) 175
HpyF3I CTNAG 2 cut(s) 324, 660
HpySE526I ACGT 2 cut(s) 198, 378
Hsp92I GRCGYC 2 cut(s) 5, 222
Hsp92II CATG 4 cut(s) 184, 337, 481, 491
HspAI GCGC 2 cut(s) 5, 653
KasI GGCGCC 1 cut(s) 4
Kzo9I GATC 4 cut(s) 567, 665, 762, 775
LmnI GCTCC 6 cut(s) 166, 242, 253, 631, 836, 889
Lsp1109I GCAGC 1 cut(s) 173
MaeI CTAG 1 cut(s) 57
MaeII ACGT 2 cut(s) 198, 378
MaeIII GTNAC 2 cut(s) 374, 638
MalI GATC 4 cut(s) 569, 667, 764, 777
MboI GATC 4 cut(s) 567, 665, 762, 775
MboII GAAGA 4 cut(s) 38, 454, 658, 688
MfeI CAATTG 1 cut(s) 758
MhlI GDGCHC 1 cut(s) 589
MlsI TGGCCA 1 cut(s) 203
MluCI AATT 8 cut(s) 61, 97, 133, 470, 505, 742, 758, 788
MluNI TGGCCA 1 cut(s) 203
Mly113I GGCGCC 1 cut(s) 5
MlyI GAGTC 1 cut(s) 434
MnlI CCTC 8 cut(s) 96, 244, 299, 312, 445, 588, 681, 824
Mox20I TGGCCA 1 cut(s) 203
MroXI GAANNNNTTC 2 cut(s) 461, 789
MscI TGGCCA 1 cut(s) 203
MseI TTAA 4 cut(s) 213, 720, 752, 807
MslI CAYNNNNRTG 1 cut(s) 407
Msp20I TGGCCA 1 cut(s) 203
MspA1I CMGCKG 1 cut(s) 164
MspCI CTTAAG 1 cut(s) 806
MspI CCGG 1 cut(s) 267
MspR9I CCNGG 4 cut(s) 394, 606, 630, 887
MunI CAATTG 1 cut(s) 758
MvaI CCWGG 4 cut(s) 394, 606, 630, 887
MwoI GCNNNNNNNGC 1 cut(s) 175
NarI GGCGCC 1 cut(s) 5
NcoI CCATGG 1 cut(s) 333
NdeI CATATG 2 cut(s) 543, 591
NdeII GATC 4 cut(s) 567, 665, 762, 775
NlaIII CATG 4 cut(s) 184, 337, 481, 491
NlaIV GGNNCC 8 cut(s) 6, 168, 238, 255, 627, 634, 692, 891
NmuCI GTSAC 1 cut(s) 638
PagI TCATGA 1 cut(s) 180
PceI AGGCCT 1 cut(s) 598
PcsI WCGNNNNNNNCGW 2 cut(s) 228, 237
PdmI GAANNNNTTC 2 cut(s) 461, 789
PfeI GAWTC 3 cut(s) 353, 496, 559
PfoI TCCNGGA 1 cut(s) 628
PkrI GCNGC 5 cut(s) 71, 163, 226, 247, 346
PleI GAGTC 1 cut(s) 433
PluTI GGCGCC 1 cut(s) 8
PpsI GAGTC 1 cut(s) 433
PpuMI RGGWCCY 1 cut(s) 811
Psp5II RGGWCCY 1 cut(s) 811
Psp6I CCWGG 4 cut(s) 392, 604, 628, 885
PspGI CCWGG 4 cut(s) 392, 604, 628, 885
PspN4I GGNNCC 8 cut(s) 6, 168, 238, 255, 627, 634, 692, 891
PspPI GGNCC 4 cut(s) 269, 632, 691, 811
PspPPI RGGWCCY 1 cut(s) 811
RseI CAYNNNNRTG 1 cut(s) 407
SaqAI TTAA 4 cut(s) 213, 720, 752, 807
SatI GCNGC 5 cut(s) 70, 162, 225, 246, 345
Sau3AI GATC 4 cut(s) 567, 665, 762, 775
Sau96I GGNCC 4 cut(s) 269, 632, 691, 811
SchI GAGTC 1 cut(s) 434
ScrFI CCNGG 4 cut(s) 394, 606, 630, 887
SduI GDGCHC 1 cut(s) 589
SfoI GGCGCC 1 cut(s) 6
SinI GGWCC 3 cut(s) 632, 691, 811
SmiMI CAYNNNNRTG 1 cut(s) 407
SmlI CTYRAG 2 cut(s) 500, 806
SmoI CTYRAG 2 cut(s) 500, 806
SpeI ACTAGT 1 cut(s) 56
Sse9I AATT 8 cut(s) 61, 97, 133, 470, 505, 742, 758, 788
SseBI AGGCCT 1 cut(s) 598
SsiI CCGC 5 cut(s) 69, 164, 225, 246, 344
SspDI GGCGCC 1 cut(s) 4
SspMI CTAG 1 cut(s) 57
StuI AGGCCT 1 cut(s) 598
StyD4I CCNGG 4 cut(s) 392, 604, 628, 885
StyI CCWWGG 2 cut(s) 279, 333
TaaI ACNGT 2 cut(s) 50, 695
TaiI ACGT 2 cut(s) 201, 381
TaqI TCGA 1 cut(s) 570
TasI AATT 8 cut(s) 61, 97, 133, 470, 505, 742, 758, 788
TauI GCSGC 4 cut(s) 72, 227, 248, 347
TfiI GAWTC 3 cut(s) 353, 496, 559
Tru1I TTAA 4 cut(s) 213, 720, 752, 807
Tru9I TTAA 4 cut(s) 213, 720, 752, 807
TscAI CASTG 3 cut(s) 177, 355, 643
TseFI GTSAC 1 cut(s) 638
TseI GCWGC 1 cut(s) 161
Tsp45I GTSAC 1 cut(s) 638
TspDTI ATGAA 5 cut(s) 197, 391, 494, 560, 689
TspGWI ACGGA 1 cut(s) 229
TspRI CASTG 3 cut(s) 177, 355, 643
Vha464I CTTAAG 1 cut(s) 806
VpaK11BI GGWCC 3 cut(s) 632, 691, 811
XagI CCTNNNNNAGG 1 cut(s) 603
XapI RAATTY 2 cut(s) 97, 470
XmnI GAANNNNTTC 2 cut(s) 461, 789
XspI CTAG 1 cut(s) 57
Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.