Rw5G006090

Transcription initiation factor IIF subunit

Design Primers CRISPR Design

Basic Information

Type: gene
Biological Identity
rosa_wichuraiana
Chr5
OG0019209
Physical Location & Seq
Forward (+)
6296385 .. 6297899
1515 bp
Loading structure...
UTR
Exon/CDS
Intron
Rw5G006090.1

Sequence Viewer

Length: 1515 bp
ATGTCAACCGATTTGTTGTTAAAGCCGTCGTGCCAAGTCCGCGGATGTGGATCGACTTCTGACTTGTACGGAAGCAACTGTAAGCACATGACTCTGTGCTTCTCATGTGGCAAGTCCATGGCAGAGAACAAAGCCAAATGCATCCAATGCGACGCCATTGTCACTCGCTTAATTCGCGAGTACAATGTTCGGCGGGAAAGTACTGTCAACAACAGGAACTACTTCATTGGTAGATTCGGGACGGGTTTGCCAAACTTTTCGAAAACGAAGAATCCTTCTCAGAATAAATTGTCTCTTCGTAAGGATCTTCAAGACCCAAGAAAGAACAAGGAAGAGCAGAAAACTAAACCATGGGTCTTGGATGAACTAACGGGCCAGTCTCGGTATCAGGGTCATCAAGAAGGTGCACAGTCTGCAAGTTACTACCTACTAATGAAGCAAGGAAAGGAGTTTTCGGCTGTTCCGGCTGGTTCTTGGTTCAACTTCAACAAGGTTGCACAATATAAGCAATTTACTCTAGAGGAAGCGGAAGAGAAGATGAATAATAGGCAAAAGACTAATCGAGATGGATATAAAAGATGGATTATGAAATTTGGAAACGGACCTGAAAAAGTTACTGGTGATGGTGGTGGTGGTGGTGGTGAAGGAAACTTCTCCGACAATGAGGAAGAAGAAACAACCAGGAAAAGATATAGACTTGGATCACTCAACAAAATAGGCGGGGATGGTGATGATGATGAGGATAATCTTATAGGTGCAAACGAAGATGGTGACTTAAATGATGATGGTAGTGACAAGGGTAGTGATTGGGAGCACGAAGAAATTTTCAGTGATGATGATGAAGCTGTAGGTAATCCTGATGAACGAGAAGATTTCGAACATGAGGCTCCAGCTCCACCGGAAACTAAGCAGGATGATGATGGTAATGAAGAGGAGGCCGGGCTGAGTGAATCAGGGAGAGAGTTGAAGAAGCTACTTGGGAGAAGTGGTGGCCTGAATGGTATTGATGAGGAAGAGGAAGATGAAGACGACGATGATGAGGATGATATGGATGAGGATATTTGCTTATTGCCTCCGGCACCAAAGCAGAAGGATGCGTCCAAACAGCTGGAACCATTTGACAACAGATCCACAAAACCAGTTACGAAGGGAAAGAGAAAACTAGATAGTGATCAGGCTAATAAGGCATCTAACACTGCACCTCCGAAGAAGATGAAGACTGAAAATGAACAAAAATCATCTGTCAGAGAGAAGCCAGCTGCTTCTGAAATTAGTGTGCACGCCAAAGTTACTCCATCCTTGAAAACTGGTTCTGCTAGTCCGGTATCTGAGGAAGAAATTAGGGCTCTATTGATGCAAAAGGCACCAATCGCCCTACCTGATTTTGTTAATAACTTCCCGGAAAGACGCAAATATTCCAAAGAGCAGAAGGATGCTTTTACAGCAATCGTTAAGAAAGTATCTGAGCTAGAGAAGAAGAACGGGATCAGCTATGTTGTATTGAGAAAGAAGTGA
Functional Annotation
Gene Ontology
Molecular Function
Biological Process
Cellular Component
GO:0003674 GO:0005488 GO:0005515 GO:0008022
KEGG Pathways
Metabolic & Signaling
ko03022 map03022
Pfam Domains
Protein Families
TFIIF_alpha

Protein Analysis

504

Amino Acids

56.34

Weight (kDa)

5.09

Isoelectric Point (pI)

50.01

Instability Index
Protein Domains (Pfam)
Domain Name Pfam ID Position E-value Description
TFIIF_alpha PF05793 50 - 204 1.7e-31 Transcription initiation factor IIF, alpha subunit (TFIIF-alpha)
TFIIF_alpha PF05793 218 - 502 8e-30 Transcription initiation factor IIF, alpha subunit (TFIIF-alpha)
Hydrophobicity Profile (Kyte-Doolittle)
AI Structure Prediction Report
Calculating structure properties...

Genomic Context

Gene Family Tree

Species Filter
Loading...
Style Settings
Image
Tree File
Tip: Beautify your tree with professional tools

Download the Full Tree (.nwk) file, then upload it to any of the following tools to customize colors, fonts, annotations, clades, and branch support.

Publication-ready
iTOL Interactive Tree Of Life · Most popular EvolView Flexible annotations MEGA Desktop phylogenetics suite FigTree Desktop tree editor

Orthologous Genes (Group: OG0019209)

Species Orthologous Gene IDs
fragaria_vesca FvH4_3g04782
rosa_chinensis RchiOBHm_Chr5g0007791
rosa_laevigata RLG00000031489
rosa_multiflora Rmu_sc0005098.1_g000015
rosa_roxburghii Rroxscaffold_1G00068620
rosa_rugosa Rorug04G0430500
rosa_samantha Rh5CG065400
rosa_wichuraiana Rw5G006090

Restriction Enzyme Sites

1 / 10
Enzyme Recognition Site Cut Count Positions (bp)
AasI GACNNNNNNGTC 1 cut(s) 158
AccB1I GGYRCC 2 cut(s) 1078, 1363
AccII CGCG 2 cut(s) 42, 177
AciI CCGC 5 cut(s) 40, 42, 193, 527, 720
AclWI GGATC 5 cut(s) 58, 312, 709, 1122, 1493
AcsI RAATTY 2 cut(s) 590, 822
AcyI GRCGYC 1 cut(s) 153
AfaI GTAC 3 cut(s) 68, 182, 202
AgsI TTSAA 5 cut(s) 311, 481, 487, 967, 1303
AjnI CCWGG 1 cut(s) 680
AluBI AGCT 7 cut(s) 845, 893, 973, 1108, 1259, 1468, 1491
AluI AGCT 7 cut(s) 845, 893, 973, 1108, 1259, 1468, 1491
Alw21I GWGCWC 3 cut(s) 409, 816, 1281
Alw26I GTCTC 2 cut(s) 297, 384
Alw44I GTGCAC 2 cut(s) 405, 1277
AlwI GGATC 5 cut(s) 58, 312, 709, 1122, 1493
AoxI GGCC 3 cut(s) 373, 936, 991
ApaLI GTGCAC 2 cut(s) 405, 1277
ApeKI GCWGC 1 cut(s) 1259
ApoI RAATTY 2 cut(s) 590, 822
Asp700I GAANNNNTTC 1 cut(s) 221
AspS9I GGNCC 2 cut(s) 373, 602
AsuC2I CCSGG 2 cut(s) 940, 1400
AsuHPI GGTGA 4 cut(s) 632, 653, 740, 782
AsuII TTCGAA 2 cut(s) 260, 876
AvaII GGWCC 1 cut(s) 602
BaeGI GKGCMC 2 cut(s) 409, 1281
BanI GGYRCC 2 cut(s) 1078, 1363
BanII GRGCYC 1 cut(s) 1348
BbsI GAAGAC 2 cut(s) 1032, 1223
Bbv12I GWGCWC 3 cut(s) 409, 816, 1281
BbvI GCAGC 1 cut(s) 1246
BccI CCATC 8 cut(s) 560, 573, 617, 719, 761, 779, 914, 1303
BceAI ACGGC 1 cut(s) 10
BciT130I CCWGG 1 cut(s) 682
BclI TGATCA 1 cut(s) 1171
BcnI CCSGG 2 cut(s) 940, 1400
BcoDI GTCTC 2 cut(s) 297, 384
BfaI CTAG 4 cut(s) 518, 1163, 1317, 1469
BfmI CTRYAG 1 cut(s) 846
BisI GCNGC 1 cut(s) 1260
BlsI GCNGC 1 cut(s) 1261
BmcAI AGTACT 1 cut(s) 202
Bme1390I CCNGG 3 cut(s) 682, 940, 1400
Bme18I GGWCC 1 cut(s) 602
BmgT120I GGNCC 2 cut(s) 373, 602
BmiI GGNNCC 4 cut(s) 888, 1080, 1113, 1365
BmrFI CCNGG 3 cut(s) 682, 940, 1400
BmsI GCATC 5 cut(s) 150, 1084, 1196, 1344, 1423
BpiI GAAGAC 2 cut(s) 1032, 1223
BpmI CTGGAG 1 cut(s) 873
Bpu14I TTCGAA 2 cut(s) 260, 876
BpuMI CCSGG 2 cut(s) 940, 1400
BsaBI GATNNNNATC 2 cut(s) 49, 1170
BsaHI GRCGYC 1 cut(s) 153
BsaJI CCNNGG 3 cut(s) 40, 117, 350
BsaWI WCCGGW 2 cut(s) 898, 1321
BsaXI ACNNNNNCTCC 4 cut(s) 973, 1003, 1186, 1216
Bse1I ACTGG 4 cut(s) 376, 622, 1139, 1312
Bse8I GATNNNNATC 2 cut(s) 49, 1170
BseBI CCWGG 1 cut(s) 682
BseDI CCNNGG 3 cut(s) 40, 117, 350
BseJI GATNNNNATC 2 cut(s) 49, 1170
BseMII CTCAG 4 cut(s) 293, 935, 1320, 1455
BseNI ACTGG 4 cut(s) 376, 622, 1139, 1312
BseRI GAGGAG 1 cut(s) 947
BseSI GKGCMC 2 cut(s) 409, 1281
BseXI GCAGC 1 cut(s) 1246
BsgI GTGCAG 1 cut(s) 1182
Bsh1236I CGCG 2 cut(s) 42, 177
BshFI GGCC 3 cut(s) 375, 938, 993
BshNI GGYRCC 2 cut(s) 1078, 1363
BsiHKAI GWGCWC 3 cut(s) 409, 816, 1281
BsiSI CCGG 6 cut(s) 464, 899, 939, 1076, 1322, 1400
BslFI GGGAC 1 cut(s) 253
BsmAI GTCTC 2 cut(s) 297, 384
BsmFI GGGAC 1 cut(s) 253
BsnI GGCC 3 cut(s) 375, 938, 993
Bsp119I TTCGAA 2 cut(s) 260, 876
Bsp1286I GDGCHC 4 cut(s) 409, 816, 1281, 1348
Bsp143I GATC 6 cut(s) 50, 304, 701, 1127, 1171, 1485
Bsp19I CCATGG 2 cut(s) 117, 350
Bsp68I TCGCGA 1 cut(s) 177
BspACI CCGC 5 cut(s) 40, 42, 193, 527, 720
BspANI GGCC 3 cut(s) 375, 938, 993
BspCNI CTCAG 4 cut(s) 292, 936, 1321, 1456
BspFNI CGCG 2 cut(s) 42, 177
BspLI GGNNCC 4 cut(s) 888, 1080, 1113, 1365
BspPI GGATC 5 cut(s) 58, 312, 709, 1122, 1493
BspQI GCTCTTC 1 cut(s) 327
BspT104I TTCGAA 2 cut(s) 260, 876
BspT107I GGYRCC 2 cut(s) 1078, 1363
BsrI ACTGG 4 cut(s) 376, 622, 1139, 1312
BssECI CCNNGG 3 cut(s) 40, 117, 350
BssMI GATC 6 cut(s) 50, 304, 701, 1127, 1171, 1485
BssNI GRCGYC 1 cut(s) 153
BssT1I CCWWGG 2 cut(s) 117, 350
Bst2UI CCWGG 1 cut(s) 682
Bst4CI ACNGT 3 cut(s) 80, 205, 411
Bst6I CTCTTC 5 cut(s) 300, 327, 525, 924, 1008
BstACI GRCGYC 1 cut(s) 153
BstAPI GCANNNNNTGC 2 cut(s) 147, 413
BstBI TTCGAA 2 cut(s) 260, 876
BstC8I GCNNGC 2 cut(s) 1257, 1281
BstDEI CTNAG 5 cut(s) 279, 906, 944, 1329, 1464
BstDSI CCRYGG 3 cut(s) 40, 117, 350
BstFNI CGCG 2 cut(s) 42, 177
BstKTI GATC 6 cut(s) 53, 307, 704, 1130, 1174, 1488
BstMAI GTCTC 2 cut(s) 297, 384
BstMBI GATC 6 cut(s) 50, 304, 701, 1127, 1171, 1485
BstMWI GCNNNNNNNGC 8 cut(s) 39, 147, 174, 413, 464, 1184, 1370, 1442
BstNI CCWGG 1 cut(s) 682
BstSCI CCNGG 3 cut(s) 680, 938, 1398
BstSFI CTRYAG 1 cut(s) 846
BstSLI GKGCMC 2 cut(s) 409, 1281
BstUI CGCG 2 cut(s) 42, 177
BstV1I GCAGC 1 cut(s) 1246
BstV2I GAAGAC 2 cut(s) 1032, 1223
BstX2I RGATCY 2 cut(s) 304, 1127
BstXI CCANNNNNNTGG 1 cut(s) 1108
BstYI RGATCY 2 cut(s) 304, 1127
BsuRI GGCC 3 cut(s) 375, 938, 993
BtgI CCRYGG 3 cut(s) 40, 117, 350
BtsI GCAGTG 1 cut(s) 1194
BtsIMutI CAGTG 2 cut(s) 835, 1194
BtuMI TCGCGA 1 cut(s) 177
Cac8I GCNNGC 2 cut(s) 1257, 1281
Cfr13I GGNCC 2 cut(s) 373, 602
Cfr42I CCGCGG 1 cut(s) 43
CseI GACGC 3 cut(s) 161, 1086, 1416
Csp6I GTAC 3 cut(s) 67, 181, 201
CviAII CATG 5 cut(s) 88, 105, 118, 351, 881
CviQI GTAC 3 cut(s) 67, 181, 201
DdeI CTNAG 5 cut(s) 279, 906, 944, 1329, 1464
DpnI GATC 6 cut(s) 52, 306, 703, 1129, 1173, 1487
DpnII GATC 6 cut(s) 50, 304, 701, 1127, 1171, 1485
DrdI GACNNNNNNGTC 1 cut(s) 158
DseDI GACNNNNNNGTC 1 cut(s) 158
Eam1104I CTCTTC 5 cut(s) 300, 327, 525, 924, 1008
EarI CTCTTC 5 cut(s) 300, 327, 525, 924, 1008
Eco130I CCWWGG 2 cut(s) 117, 350
Eco24I GRGCYC 1 cut(s) 1348
Eco47I GGWCC 1 cut(s) 602
EcoRII CCWGG 1 cut(s) 680
EcoT14I CCWWGG 2 cut(s) 117, 350
EcoT22I ATGCAT 1 cut(s) 143
EcoT38I GRGCYC 1 cut(s) 1348
ErhI CCWWGG 2 cut(s) 117, 350
FaeI CATG 5 cut(s) 91, 108, 121, 354, 884
FaqI GGGAC 1 cut(s) 253
FatI CATG 5 cut(s) 87, 104, 117, 350, 880
FauI CCCGC 2 cut(s) 186, 713
FbaI TGATCA 1 cut(s) 1171
Fnu4HI GCNGC 1 cut(s) 1260
FriOI GRGCYC 1 cut(s) 1348
Fsp4HI GCNGC 1 cut(s) 1260
FspBI CTAG 4 cut(s) 518, 1163, 1317, 1469
GluI GCNGC 1 cut(s) 1260
GsuI CTGGAG 1 cut(s) 873
HaeIII GGCC 3 cut(s) 375, 938, 993
HapII CCGG 6 cut(s) 464, 899, 939, 1076, 1322, 1400
HgaI GACGC 3 cut(s) 161, 1086, 1416
Hin1I GRCGYC 1 cut(s) 153
Hin1II CATG 5 cut(s) 91, 108, 121, 354, 884
HincII GTYRAC 2 cut(s) 6, 208
HindII GTYRAC 2 cut(s) 6, 208
HinfI GANTC 4 cut(s) 91, 234, 271, 950
HpaII CCGG 6 cut(s) 464, 899, 939, 1076, 1322, 1400
HphI GGTGA 4 cut(s) 632, 653, 740, 782
Hpy166II GTNNAC 4 cut(s) 6, 208, 407, 1279
Hpy188I TCNGA 8 cut(s) 61, 282, 658, 1206, 1247, 1267, 1330, 1465
Hpy188III TCNNGA 7 cut(s) 176, 238, 311, 398, 518, 563, 857
Hpy8I GTNNAC 4 cut(s) 6, 208, 407, 1279
Hpy99I CGWCG 3 cut(s) 31, 155, 1034
HpyAV CCTTC 6 cut(s) 285, 395, 638, 1084, 1141, 1423
HpyCH4III ACNGT 3 cut(s) 80, 205, 411
HpyCH4V TGCA 8 cut(s) 141, 407, 416, 497, 758, 1199, 1279, 1357
HpyF10VI GCNNNNNNNGC 8 cut(s) 39, 147, 174, 413, 464, 1184, 1370, 1442
HpyF3I CTNAG 5 cut(s) 279, 906, 944, 1329, 1464
Hsp92I GRCGYC 1 cut(s) 153
Hsp92II CATG 5 cut(s) 91, 108, 121, 354, 884
Ksp22I TGATCA 1 cut(s) 1171
KspI CCGCGG 1 cut(s) 43
Kzo9I GATC 6 cut(s) 50, 304, 701, 1127, 1171, 1485
LguI GCTCTTC 1 cut(s) 327
LmnI GCTCC 3 cut(s) 811, 892, 898
Lsp1109I GCAGC 1 cut(s) 1246
LweI GCATC 5 cut(s) 150, 1084, 1196, 1344, 1423
MaeI CTAG 4 cut(s) 518, 1163, 1317, 1469
MaeIII GTNAC 7 cut(s) 160, 419, 613, 770, 791, 1141, 1288
MalI GATC 6 cut(s) 52, 306, 703, 1129, 1173, 1487
MboI GATC 6 cut(s) 50, 304, 701, 1127, 1171, 1485
MflI RGATCY 2 cut(s) 304, 1127
MhlI GDGCHC 4 cut(s) 409, 816, 1281, 1348
MluCI AATT 7 cut(s) 171, 287, 509, 590, 822, 1269, 1338
MlyI GAGTC 1 cut(s) 85
MmeI TCCRAC 1 cut(s) 681
Mph1103I ATGCAT 1 cut(s) 143
MroXI GAANNNNTTC 1 cut(s) 221
MseI TTAA 5 cut(s) 20, 170, 776, 1389, 1452
MspA1I CMGCKG 3 cut(s) 42, 1108, 1259
MspI CCGG 6 cut(s) 464, 899, 939, 1076, 1322, 1400
MspR9I CCNGG 3 cut(s) 682, 940, 1400
MvaI CCWGG 1 cut(s) 682
MvnI CGCG 2 cut(s) 42, 177
MwoI GCNNNNNNNGC 8 cut(s) 39, 147, 174, 413, 464, 1184, 1370, 1442
NciI CCSGG 2 cut(s) 940, 1400
NcoI CCATGG 2 cut(s) 117, 350
NdeII GATC 6 cut(s) 50, 304, 701, 1127, 1171, 1485
NlaIII CATG 5 cut(s) 91, 108, 121, 354, 884
NlaIV GGNNCC 4 cut(s) 888, 1080, 1113, 1365
NmuCI GTSAC 3 cut(s) 160, 770, 791
NruI TCGCGA 1 cut(s) 177
NsiI ATGCAT 1 cut(s) 143
NspV TTCGAA 2 cut(s) 260, 876
PciSI GCTCTTC 1 cut(s) 327
PdmI GAANNNNTTC 1 cut(s) 221
PfeI GAWTC 3 cut(s) 234, 271, 950
PfoI TCCNGGA 1 cut(s) 1398
PkrI GCNGC 1 cut(s) 1261
PleI GAGTC 1 cut(s) 85
PpsI GAGTC 1 cut(s) 85
Psp6I CCWGG 1 cut(s) 680
PspGI CCWGG 1 cut(s) 680
PspN4I GGNNCC 4 cut(s) 888, 1080, 1113, 1365
PspPI GGNCC 2 cut(s) 373, 602
PsuI RGATCY 2 cut(s) 304, 1127
PvuII CAGCTG 2 cut(s) 1108, 1259
RruI TCGCGA 1 cut(s) 177
RsaI GTAC 3 cut(s) 68, 182, 202
RsaNI GTAC 3 cut(s) 67, 181, 201
SacII CCGCGG 1 cut(s) 43
SapI GCTCTTC 1 cut(s) 327
SaqAI TTAA 5 cut(s) 20, 170, 776, 1389, 1452
SatI GCNGC 1 cut(s) 1260
Sau3AI GATC 6 cut(s) 50, 304, 701, 1127, 1171, 1485
Sau96I GGNCC 2 cut(s) 373, 602
ScaI AGTACT 1 cut(s) 202
SchI GAGTC 1 cut(s) 85
ScrFI CCNGG 3 cut(s) 682, 940, 1400
SduI GDGCHC 4 cut(s) 409, 816, 1281, 1348
SfaNI GCATC 5 cut(s) 150, 1084, 1196, 1344, 1423
SfcI CTRYAG 1 cut(s) 846
Sfr303I CCGCGG 1 cut(s) 43
SfuI TTCGAA 2 cut(s) 260, 876
SgrBI CCGCGG 1 cut(s) 43
SinI GGWCC 1 cut(s) 602
Sse9I AATT 7 cut(s) 171, 287, 509, 590, 822, 1269, 1338
SsiI CCGC 5 cut(s) 40, 42, 193, 527, 720
SspI AATATT 1 cut(s) 1415
SspMI CTAG 4 cut(s) 518, 1163, 1317, 1469
StyD4I CCNGG 3 cut(s) 680, 938, 1398
StyI CCWWGG 2 cut(s) 117, 350
TaaI ACNGT 3 cut(s) 80, 205, 411
TaqI TCGA 4 cut(s) 53, 260, 562, 876
TasI AATT 7 cut(s) 171, 287, 509, 590, 822, 1269, 1338
TatI WGTACW 2 cut(s) 180, 200
TfiI GAWTC 3 cut(s) 234, 271, 950
Tru1I TTAA 5 cut(s) 20, 170, 776, 1389, 1452
Tru9I TTAA 5 cut(s) 20, 170, 776, 1389, 1452
TscAI CASTG 2 cut(s) 835, 1201
TseFI GTSAC 3 cut(s) 160, 770, 791
TseI GCWGC 1 cut(s) 1259
Tsp45I GTSAC 3 cut(s) 160, 770, 791
TspGWI ACGGA 2 cut(s) 84, 615
TspRI CASTG 2 cut(s) 835, 1201
VneI GTGCAC 2 cut(s) 405, 1277
VpaK11BI GGWCC 1 cut(s) 602
XapI RAATTY 2 cut(s) 590, 822
XbaI TCTAGA 1 cut(s) 517
XmnI GAANNNNTTC 1 cut(s) 221
XspI CTAG 4 cut(s) 518, 1163, 1317, 1469
ZrmI AGTACT 1 cut(s) 202
Zsp2I ATGCAT 1 cut(s) 143
Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.