Rroxscaffold_3G00227010

TFIIA is a component of the transcription machinery of RNA polymerase II and plays an important role in transcriptional activation

Design Primers CRISPR Design

Basic Information

Type: gene
Biological Identity
rosa_roxburghii
GWHEROQ00000003
OG0008441
Physical Location & Seq
Reverse (-)
10885555 .. 10889183
3629 bp
Loading structure...
UTR
Exon/CDS
Intron
Rroxscaffold_3G00227010.1

Sequence Viewer

Length: 321 bp
ATGGCGACGTTTGAGCTCTACAGGAGGTCAACGATCGGAATGTGTCTGACTGAGACTTTGGATGAGATGGTTCAGAACGGGACTCTCAGTCCTGAGCTTGCCATTCAGGTTCTGGTCCAGTTCGATAAGTCTATGACTGAAGCTCTGGAAACCCAAGTGAAGAGCAAGGTCTCCATCAAGGGACATCTGCACACCTACAGATTCTGTGACAATGTTTGGACCTTTATCTTACAGGATGCTTTGTTTAAGAATGAGGATAATCAGGAAAATGTTGGCCGGGTTAAAATAGTGGCATGTGACTCAAAGCTGCTCTCACAATGA
Functional Annotation
Gene Ontology
Molecular Function
Biological Process
Cellular Component
GO:0000428 GO:0003674 GO:0003712 GO:0003713 GO:0005488 GO:0005515 GO:0005575 GO:0005622 GO:0005623 GO:0005634 GO:0005654 GO:0005667 GO:0005672 GO:0006139 GO:0006351 GO:0006352 GO:0006355 GO:0006357 GO:0006366 GO:0006367 GO:0006725 GO:0006807 GO:0008134 GO:0008150 GO:0008152 GO:0009058 GO:0009059 GO:0009889 GO:0009891 GO:0009893 GO:0009987 GO:0010467 GO:0010468 GO:0010556 GO:0010557 GO:0010604 GO:0010628 GO:0016043 GO:0016070 GO:0016591 GO:0017025 GO:0018130 GO:0019219 GO:0019222 GO:0019438 GO:0022607 GO:0030880 GO:0031323 GO:0031325 GO:0031326 GO:0031328 GO:0031974 GO:0031981 GO:0032774 GO:0032991 GO:0034622 GO:0034641 GO:0034645 GO:0034654 GO:0043170 GO:0043226 GO:0043227 GO:0043229 GO:0043231 GO:0043233 GO:0043933 GO:0044085 GO:0044093 GO:0044237 GO:0044238 GO:0044249 GO:0044260 GO:0044271 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:0051090 GO:0051091 GO:0051123 GO:0051171 GO:0051173 GO:0051252 GO:0051254 GO:0055029 GO:0060255 GO:0061695 GO:0065003 GO:0065004 GO:0065007 GO:0065009 GO:0070013 GO:0070897 GO:0071704 GO:0071824 GO:0071840 GO:0080090 GO:0090304 GO:0090575 GO:0097659 GO:0140110 GO:1901360 GO:1901362 GO:1901576 GO:1902494 GO:1902680 GO:1903506 GO:1903508 GO:1990234 GO:2000112 GO:2001141
KEGG Pathways
Metabolic & Signaling
ko03022 ko05203 map03022 map05203
Pfam Domains
Protein Families
TFIIA_gamma_C TFIIA_gamma_N

Protein Analysis

106

Amino Acids

12.1

Weight (kDa)

5.29

Isoelectric Point (pI)

37.37

Instability Index
Protein Domains (Pfam)
Domain Name Pfam ID Position E-value Description
TFIIA_gamma_N PF02268 4 - 49 1.8e-22 Transcription initiation factor IIA, gamma subunit, helical domain
TFIIA_gamma_C PF02751 60 - 101 4.1e-22 Transcription initiation factor IIA, gamma subunit
Hydrophobicity Profile (Kyte-Doolittle)
AI Structure Prediction Report
Calculating structure properties...

Genomic Context

Gene Family Tree

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Restriction Enzyme Sites

1 / 10
Enzyme Recognition Site Cut Count Positions (bp)
AcoI YGGCCR 1 cut(s) 274
AcuI CTGAAG 1 cut(s) 159
AhdI GACNNNNNGTC 1 cut(s) 87
AluBI AGCT 4 cut(s) 16, 97, 143, 307
AluI AGCT 4 cut(s) 16, 97, 143, 307
Alw21I GWGCWC 1 cut(s) 18
Alw26I GTCTC 2 cut(s) 47, 175
AlwNI CAGNNNCTG 2 cut(s) 112, 204
AoxI GGCC 1 cut(s) 274
ApeKI GCWGC 1 cut(s) 307
ArsI GACNNNNNNTTYG 2 cut(s) 40, 72
AspS9I GGNCC 2 cut(s) 115, 219
AsuC2I CCSGG 1 cut(s) 278
AvaII GGWCC 2 cut(s) 115, 219
BanII GRGCYC 1 cut(s) 18
Bbv12I GWGCWC 1 cut(s) 18
BbvI GCAGC 1 cut(s) 294
BccI CCATC 2 cut(s) 61, 182
BcnI CCSGG 1 cut(s) 278
BcoDI GTCTC 2 cut(s) 47, 175
BfmI CTRYAG 2 cut(s) 19, 196
BisI GCNGC 1 cut(s) 308
BlsI GCNGC 1 cut(s) 309
Bme1390I CCNGG 1 cut(s) 278
Bme18I GGWCC 2 cut(s) 115, 219
BmeRI GACNNNNNGTC 1 cut(s) 87
BmgT120I GGNCC 2 cut(s) 115, 219
BmrFI CCNGG 1 cut(s) 278
BmsI GCATC 1 cut(s) 226
Bpu10I CCTNAGC 1 cut(s) 93
BpuMI CCSGG 1 cut(s) 278
BsaI GGTCTC 1 cut(s) 175
Bse1I ACTGG 1 cut(s) 118
BseGI GGATG 2 cut(s) 67, 241
BseMII CTCAG 3 cut(s) 42, 84, 100
BseNI ACTGG 1 cut(s) 118
BseXI GCAGC 1 cut(s) 294
BsgI GTGCAG 1 cut(s) 173
Bsh1285I CGRYCG 1 cut(s) 36
BshFI GGCC 1 cut(s) 276
BsiEI CGRYCG 1 cut(s) 36
BsiHKAI GWGCWC 1 cut(s) 18
BsiSI CCGG 1 cut(s) 277
BslFI GGGAC 2 cut(s) 94, 195
BsmAI GTCTC 2 cut(s) 47, 175
BsmFI GGGAC 2 cut(s) 94, 195
BsnI GGCC 1 cut(s) 276
Bso31I GGTCTC 1 cut(s) 175
Bsp1286I GDGCHC 1 cut(s) 18
Bsp143I GATC 1 cut(s) 33
BspANI GGCC 1 cut(s) 276
BspCNI CTCAG 3 cut(s) 43, 85, 99
BspQI GCTCTTC 1 cut(s) 155
BspTNI GGTCTC 1 cut(s) 175
BsrI ACTGG 1 cut(s) 118
BssMI GATC 1 cut(s) 33
Bst6I CTCTTC 1 cut(s) 155
BstC8I GCNNGC 1 cut(s) 99
BstDEI CTNAG 3 cut(s) 51, 86, 93
BstF5I GGATG 2 cut(s) 67, 241
BstKTI GATC 1 cut(s) 36
BstMAI GTCTC 2 cut(s) 47, 175
BstMBI GATC 1 cut(s) 33
BstMCI CGRYCG 1 cut(s) 36
BstNSI RCATGY 1 cut(s) 297
BstSCI CCNGG 1 cut(s) 276
BstSFI CTRYAG 2 cut(s) 19, 196
BstV1I GCAGC 1 cut(s) 294
BsuRI GGCC 1 cut(s) 276
BtsCI GGATG 2 cut(s) 67, 241
Cac8I GCNNGC 1 cut(s) 99
CaiI CAGNNNCTG 2 cut(s) 112, 204
Cfr13I GGNCC 2 cut(s) 115, 219
CviAII CATG 1 cut(s) 294
CviJI RGCY 5 cut(s) 16, 97, 143, 276, 307
CviKI_1 RGCY 5 cut(s) 16, 97, 143, 276, 307
DdeI CTNAG 3 cut(s) 51, 86, 93
DpnI GATC 1 cut(s) 35
DpnII GATC 1 cut(s) 33
DriI GACNNNNNGTC 1 cut(s) 87
EaeI YGGCCR 1 cut(s) 274
Eam1104I CTCTTC 1 cut(s) 155
Eam1105I GACNNNNNGTC 1 cut(s) 87
EarI CTCTTC 1 cut(s) 155
Ecl136II GAGCTC 1 cut(s) 16
Eco24I GRGCYC 1 cut(s) 18
Eco31I GGTCTC 1 cut(s) 175
Eco47I GGWCC 2 cut(s) 115, 219
Eco53kI GAGCTC 1 cut(s) 16
Eco57I CTGAAG 1 cut(s) 159
EcoICRI GAGCTC 1 cut(s) 16
EcoT38I GRGCYC 1 cut(s) 18
FaeI CATG 1 cut(s) 297
FaiI YATR 2 cut(s) 134, 295
FaqI GGGAC 2 cut(s) 94, 195
FatI CATG 1 cut(s) 293
Fnu4HI GCNGC 1 cut(s) 308
FokI GGATG 2 cut(s) 74, 248
FriOI GRGCYC 1 cut(s) 18
Fsp4HI GCNGC 1 cut(s) 308
GluI GCNGC 1 cut(s) 308
HaeIII GGCC 1 cut(s) 276
HapII CCGG 1 cut(s) 277
Hin1II CATG 1 cut(s) 297
HincII GTYRAC 1 cut(s) 30
HindII GTYRAC 1 cut(s) 30
HinfI GANTC 3 cut(s) 82, 201, 299
HpaII CCGG 1 cut(s) 277
Hpy166II GTNNAC 1 cut(s) 30
Hpy188I TCNGA 3 cut(s) 38, 48, 75
Hpy188III TCNNGA 3 cut(s) 92, 146, 263
Hpy8I GTNNAC 1 cut(s) 30
Hpy99I CGWCG 1 cut(s) 10
HpyCH4IV ACGT 1 cut(s) 8
HpyCH4V TGCA 1 cut(s) 190
HpyF3I CTNAG 3 cut(s) 51, 86, 93
HpySE526I ACGT 1 cut(s) 8
Hsp92II CATG 1 cut(s) 297
Kzo9I GATC 1 cut(s) 33
LguI GCTCTTC 1 cut(s) 155
LpnPI CCDG 9 cut(s) 7, 92, 98, 105, 131, 131, 218, 248, 290
Lsp1109I GCAGC 1 cut(s) 294
LweI GCATC 1 cut(s) 226
MaeII ACGT 1 cut(s) 8
MaeIII GTNAC 2 cut(s) 206, 296
MalI GATC 1 cut(s) 35
MboI GATC 1 cut(s) 33
MboII GAAGA 1 cut(s) 172
MhlI GDGCHC 1 cut(s) 18
MlyI GAGTC 2 cut(s) 76, 293
MnlI CCTC 2 cut(s) 18, 247
MseI TTAA 2 cut(s) 246, 282
MspI CCGG 1 cut(s) 277
MspR9I CCNGG 1 cut(s) 278
NciI CCSGG 1 cut(s) 278
NdeII GATC 1 cut(s) 33
NlaIII CATG 1 cut(s) 297
NmuCI GTSAC 2 cut(s) 206, 296
NspI RCATGY 1 cut(s) 297
PciSI GCTCTTC 1 cut(s) 155
PfeI GAWTC 1 cut(s) 201
PkrI GCNGC 1 cut(s) 309
Ple19I CGATCG 1 cut(s) 36
PleI GAGTC 2 cut(s) 76, 293
PpsI GAGTC 2 cut(s) 76, 293
Psp124BI GAGCTC 1 cut(s) 18
PspPI GGNCC 2 cut(s) 115, 219
PstNI CAGNNNCTG 2 cut(s) 112, 204
PvuI CGATCG 1 cut(s) 36
SacI GAGCTC 1 cut(s) 18
SapI GCTCTTC 1 cut(s) 155
SaqAI TTAA 2 cut(s) 246, 282
SatI GCNGC 1 cut(s) 308
Sau3AI GATC 1 cut(s) 33
Sau96I GGNCC 2 cut(s) 115, 219
SchI GAGTC 2 cut(s) 76, 293
ScrFI CCNGG 1 cut(s) 278
SduI GDGCHC 1 cut(s) 18
SfaNI GCATC 1 cut(s) 226
SfcI CTRYAG 2 cut(s) 19, 196
SinI GGWCC 2 cut(s) 115, 219
SstI GAGCTC 1 cut(s) 18
StyD4I CCNGG 1 cut(s) 276
TaiI ACGT 1 cut(s) 11
TaqI TCGA 1 cut(s) 123
TfiI GAWTC 1 cut(s) 201
Tru1I TTAA 2 cut(s) 246, 282
Tru9I TTAA 2 cut(s) 246, 282
TseFI GTSAC 2 cut(s) 206, 296
TseI GCWGC 1 cut(s) 307
Tsp45I GTSAC 2 cut(s) 206, 296
VpaK11BI GGWCC 2 cut(s) 115, 219
XceI RCATGY 1 cut(s) 297
XcmI CCANNNNNNNNNTGG 1 cut(s) 109
Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.