RchiOBHm_Chr5g0007791

Transcription initiation factor IIF subunit

Design Primers CRISPR Design

Basic Information

Type: gene
Biological Identity
rosa_chinensis
5
OG0019209
Physical Location & Seq
Reverse (-)
4963481 .. 4964986
1506 bp
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UTR
Exon/CDS
Intron
PRQ28881

Sequence Viewer

Length: 1506 bp
ATGTCAACCGATTTGTTGTTAAAGCCGTCGTGCCAAGTCCGCGGATGTGGATCGACTTCTGACTTGTACGGAAGCAACTGTAAGCACATGACTCTGTGCTTCTCATGTGGCAAGTCCATGGCAGAGAACAAAGCCAAATGCATCCAATGCGACGCCATTGTCACTCGCTTAGTTCGCGAGTACAATGTTCGGCGGGAAAGTACTGTCAACAACAAGAACTACTTCATTGGCAGATTCGGAACGGGTTTGCCAAACTTTTCGAAAACGAAGAATCCTTCTCAGAATAAATGGTCTCTTCGTAAGGATCTTCAAGACCCAAGAAAGAACAAGGAAGAGCAGAAAACTAAACCATGGGTCTTGGATGAACTAACGGGCCAGTCTCGGTATCAGGGTCATCAAGAAGGTGCACAGTCTGCAAGTTACTACCTACTAATGAAGCAAGGAAAGGAGTTTTCGGCTGTTCCGGCTGGTTCTTGGTTCAACTTCAACAAGGTTGCACAATATAAGCAACTTACTCTAGAGGAAGCGGAAGAGAAGATGAATAATAGGCAAAAGACTAATCGAGATGGATATAAAAGATGGATTATGAAATTTGGAAACGGACCTGAAAAAGTTACTGGTGATGGTGGTGGTGGTGGAGAAGGAAACTTCTCCGACAATGAGGAAGAAGAAACAACCAGGAAAAGATATAGACTTGGATCACTCAACAAAATAGGCGGGGATGGTGATGATGATGAGGATAATCTTATAGGTGCAGATGGTGACTTAAATGATGATGGTAGTGACAAGGGTAGTGATTGGGAGCACGAAGAAATTTTCAGTGATGATGATGAAGCTGTAGGTAATCCTGATGAACGAGAAGATTTCGAACATGAGGCTGCAGCTCCACCGGAAACTAAGCAGGATGATGATGGTAATGAAGAGGAGGCCGGGCTGAGTGAATCAGGGAGAGAGTTGAAGAAGCTACTTGGGAGAAGTGGTGGCCTGAATGGTATTGATAAGGAAGAGGAAGATGAAGACGACGACGATGAGGATGATATGGATGAGGATATTTGCTTATTGCCTCCGGCACCAAAGCAGAAGGATGCGCCCAAACAGCTGGAACCATTTGACAACAGATCCACAAAAGCAGTTACGAAGGGAAAGAGAAAACTAGATAGTGATCAGGCTAATAAGGCATCTAACACTGCACCTCCGAAGAAGATGAAGACTGAAAATGAACAAAAATCATCTGTCAGAGAGAAGCCAGCTGCTTCTGAAATTAGTGTGCACGCCAAAGTTATTCCATCCTTGAAAACTGGTTCTGCTAGTCCGGTAGCTGAGGAAGAAATTAGGGCTCTATTGATGCAAAAGGCACCAATCGCCCTACCTGATTTTGTTAATAACTTCCCGGAAAGACGCAAATATTCCAAAGAGCAGAAGGATGCTTTTACAGCAATCGTTAAGAAAGTATCTGAGCTAGAGAAGAAGAACGGGATCAGCTATGTTGTATTGAGAAAGAAGTGA
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

501

Amino Acids

55.99

Weight (kDa)

5.2

Isoelectric Point (pI)

48.29

Instability Index
Protein Domains (Pfam)
Domain Name Pfam ID Position E-value Description
TFIIF_alpha PF05793 114 - 204 7.6e-30 Transcription initiation factor IIF, alpha subunit (TFIIF-alpha)
TFIIF_alpha PF05793 218 - 499 1.6e-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
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Publication-ready
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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) 1069, 1354
AccII CGCG 2 cut(s) 42, 177
AciI CCGC 5 cut(s) 40, 42, 193, 527, 717
AclWI GGATC 5 cut(s) 58, 312, 706, 1113, 1484
AcsI RAATTY 2 cut(s) 590, 813
AcyI GRCGYC 1 cut(s) 153
AfaI GTAC 3 cut(s) 68, 182, 202
AgsI TTSAA 5 cut(s) 311, 481, 487, 958, 1294
AjnI CCWGG 1 cut(s) 677
AluBI AGCT 8 cut(s) 836, 884, 964, 1099, 1250, 1319, 1459, 1482
AluI AGCT 8 cut(s) 836, 884, 964, 1099, 1250, 1319, 1459, 1482
Alw21I GWGCWC 3 cut(s) 409, 807, 1272
Alw26I GTCTC 2 cut(s) 297, 384
Alw44I GTGCAC 2 cut(s) 405, 1268
AlwI GGATC 5 cut(s) 58, 312, 706, 1113, 1484
AoxI GGCC 3 cut(s) 373, 927, 982
ApaLI GTGCAC 2 cut(s) 405, 1268
ApeKI GCWGC 3 cut(s) 878, 881, 1250
ApoI RAATTY 2 cut(s) 590, 813
Asp700I GAANNNNTTC 1 cut(s) 221
AspLEI GCGC 1 cut(s) 1090
AspS9I GGNCC 2 cut(s) 373, 602
AsuC2I CCSGG 2 cut(s) 931, 1391
AsuHPI GGTGA 3 cut(s) 632, 737, 773
AsuII TTCGAA 2 cut(s) 260, 867
AvaII GGWCC 1 cut(s) 602
BaeGI GKGCMC 2 cut(s) 409, 1272
BanI GGYRCC 2 cut(s) 1069, 1354
BanII GRGCYC 1 cut(s) 1339
BbsI GAAGAC 2 cut(s) 1023, 1214
Bbv12I GWGCWC 3 cut(s) 409, 807, 1272
BbvCI CCTCAGC 1 cut(s) 1320
BbvI GCAGC 3 cut(s) 865, 893, 1237
BccI CCATC 8 cut(s) 560, 573, 617, 716, 752, 770, 905, 1294
BceAI ACGGC 1 cut(s) 10
BciT130I CCWGG 1 cut(s) 679
BclI TGATCA 1 cut(s) 1162
BcnI CCSGG 2 cut(s) 931, 1391
BcoDI GTCTC 2 cut(s) 297, 384
BfaI CTAG 4 cut(s) 518, 1154, 1308, 1460
BfmI CTRYAG 2 cut(s) 837, 879
BisI GCNGC 3 cut(s) 879, 882, 1251
BlsI GCNGC 3 cut(s) 880, 883, 1252
BmcAI AGTACT 1 cut(s) 202
Bme1390I CCNGG 3 cut(s) 679, 931, 1391
Bme18I GGWCC 1 cut(s) 602
BmgT120I GGNCC 2 cut(s) 373, 602
BmiI GGNNCC 3 cut(s) 1071, 1104, 1356
BmrFI CCNGG 3 cut(s) 679, 931, 1391
BmsI GCATC 5 cut(s) 150, 1075, 1187, 1335, 1414
BpiI GAAGAC 2 cut(s) 1023, 1214
Bpu10I CCTNAGC 1 cut(s) 1320
Bpu14I TTCGAA 2 cut(s) 260, 867
BpuMI CCSGG 2 cut(s) 931, 1391
BsaBI GATNNNNATC 2 cut(s) 49, 1161
BsaHI GRCGYC 1 cut(s) 153
BsaI GGTCTC 1 cut(s) 297
BsaJI CCNNGG 3 cut(s) 40, 117, 350
BsaWI WCCGGW 2 cut(s) 889, 1312
BsaXI ACNNNNNCTCC 4 cut(s) 964, 994, 1177, 1207
Bse1I ACTGG 3 cut(s) 376, 622, 1303
Bse8I GATNNNNATC 2 cut(s) 49, 1161
BseBI CCWGG 1 cut(s) 679
BseDI CCNNGG 3 cut(s) 40, 117, 350
BseJI GATNNNNATC 2 cut(s) 49, 1161
BseMII CTCAG 4 cut(s) 293, 926, 1311, 1446
BseNI ACTGG 3 cut(s) 376, 622, 1303
BseRI GAGGAG 1 cut(s) 938
BseSI GKGCMC 2 cut(s) 409, 1272
BseXI GCAGC 3 cut(s) 865, 893, 1237
BsgI GTGCAG 2 cut(s) 774, 1173
Bsh1236I CGCG 2 cut(s) 42, 177
BshFI GGCC 3 cut(s) 375, 929, 984
BshNI GGYRCC 2 cut(s) 1069, 1354
BsiHKAI GWGCWC 3 cut(s) 409, 807, 1272
BsiSI CCGG 6 cut(s) 464, 890, 930, 1067, 1313, 1391
BsmAI GTCTC 2 cut(s) 297, 384
BsnI GGCC 3 cut(s) 375, 929, 984
Bso31I GGTCTC 1 cut(s) 297
Bsp119I TTCGAA 2 cut(s) 260, 867
Bsp1286I GDGCHC 4 cut(s) 409, 807, 1272, 1339
Bsp143I GATC 6 cut(s) 50, 304, 698, 1118, 1162, 1476
Bsp19I CCATGG 2 cut(s) 117, 350
Bsp68I TCGCGA 1 cut(s) 177
BspACI CCGC 5 cut(s) 40, 42, 193, 527, 717
BspANI GGCC 3 cut(s) 375, 929, 984
BspCNI CTCAG 4 cut(s) 292, 927, 1312, 1447
BspFNI CGCG 2 cut(s) 42, 177
BspLI GGNNCC 3 cut(s) 1071, 1104, 1356
BspMAI CTGCAG 1 cut(s) 883
BspPI GGATC 5 cut(s) 58, 312, 706, 1113, 1484
BspQI GCTCTTC 1 cut(s) 327
BspT104I TTCGAA 2 cut(s) 260, 867
BspT107I GGYRCC 2 cut(s) 1069, 1354
BspTNI GGTCTC 1 cut(s) 297
BsrI ACTGG 3 cut(s) 376, 622, 1303
BssECI CCNNGG 3 cut(s) 40, 117, 350
BssMI GATC 6 cut(s) 50, 304, 698, 1118, 1162, 1476
BssNI GRCGYC 1 cut(s) 153
BssT1I CCWWGG 2 cut(s) 117, 350
Bst2UI CCWGG 1 cut(s) 679
Bst4CI ACNGT 3 cut(s) 80, 205, 411
Bst6I CTCTTC 5 cut(s) 300, 327, 525, 915, 999
BstACI GRCGYC 1 cut(s) 153
BstAPI GCANNNNNTGC 2 cut(s) 147, 413
BstBI TTCGAA 2 cut(s) 260, 867
BstC8I GCNNGC 2 cut(s) 1248, 1272
BstDEI CTNAG 6 cut(s) 169, 279, 897, 935, 1320, 1455
BstDSI CCRYGG 3 cut(s) 40, 117, 350
BstFNI CGCG 2 cut(s) 42, 177
BstHHI GCGC 1 cut(s) 1090
BstKTI GATC 6 cut(s) 53, 307, 701, 1121, 1165, 1479
BstMAI GTCTC 2 cut(s) 297, 384
BstMBI GATC 6 cut(s) 50, 304, 698, 1118, 1162, 1476
BstMWI GCNNNNNNNGC 9 cut(s) 39, 147, 174, 413, 464, 1096, 1175, 1361, 1433
BstNI CCWGG 1 cut(s) 679
BstSCI CCNGG 3 cut(s) 677, 929, 1389
BstSFI CTRYAG 2 cut(s) 837, 879
BstSLI GKGCMC 2 cut(s) 409, 1272
BstUI CGCG 2 cut(s) 42, 177
BstV1I GCAGC 3 cut(s) 865, 893, 1237
BstV2I GAAGAC 2 cut(s) 1023, 1214
BstX2I RGATCY 2 cut(s) 304, 1118
BstXI CCANNNNNNTGG 1 cut(s) 1099
BstYI RGATCY 2 cut(s) 304, 1118
BsuRI GGCC 3 cut(s) 375, 929, 984
BtgI CCRYGG 3 cut(s) 40, 117, 350
BtsI GCAGTG 1 cut(s) 1185
BtsIMutI CAGTG 2 cut(s) 826, 1185
BtuMI TCGCGA 1 cut(s) 177
Cac8I GCNNGC 2 cut(s) 1248, 1272
CfoI GCGC 1 cut(s) 1090
Cfr13I GGNCC 2 cut(s) 373, 602
Cfr42I CCGCGG 1 cut(s) 43
CseI GACGC 2 cut(s) 161, 1407
Csp6I GTAC 3 cut(s) 67, 181, 201
CviAII CATG 5 cut(s) 88, 105, 118, 351, 872
CviQI GTAC 3 cut(s) 67, 181, 201
DdeI CTNAG 6 cut(s) 169, 279, 897, 935, 1320, 1455
DpnI GATC 6 cut(s) 52, 306, 700, 1120, 1164, 1478
DpnII GATC 6 cut(s) 50, 304, 698, 1118, 1162, 1476
DrdI GACNNNNNNGTC 1 cut(s) 158
DseDI GACNNNNNNGTC 1 cut(s) 158
Eam1104I CTCTTC 5 cut(s) 300, 327, 525, 915, 999
EarI CTCTTC 5 cut(s) 300, 327, 525, 915, 999
Eco130I CCWWGG 2 cut(s) 117, 350
Eco24I GRGCYC 1 cut(s) 1339
Eco31I GGTCTC 1 cut(s) 297
Eco47I GGWCC 1 cut(s) 602
EcoRII CCWGG 1 cut(s) 677
EcoT14I CCWWGG 2 cut(s) 117, 350
EcoT22I ATGCAT 1 cut(s) 143
EcoT38I GRGCYC 1 cut(s) 1339
ErhI CCWWGG 2 cut(s) 117, 350
FaeI CATG 5 cut(s) 91, 108, 121, 354, 875
FalI AAGNNNNNCTT 2 cut(s) 206, 238
FatI CATG 5 cut(s) 87, 104, 117, 350, 871
FauI CCCGC 2 cut(s) 186, 710
FbaI TGATCA 1 cut(s) 1162
Fnu4HI GCNGC 3 cut(s) 879, 882, 1251
FriOI GRGCYC 1 cut(s) 1339
Fsp4HI GCNGC 3 cut(s) 879, 882, 1251
FspBI CTAG 4 cut(s) 518, 1154, 1308, 1460
GlaI GCGC 1 cut(s) 1089
GluI GCNGC 3 cut(s) 879, 882, 1251
HaeIII GGCC 3 cut(s) 375, 929, 984
HapII CCGG 6 cut(s) 464, 890, 930, 1067, 1313, 1391
HgaI GACGC 2 cut(s) 161, 1407
HhaI GCGC 1 cut(s) 1090
Hin1I GRCGYC 1 cut(s) 153
Hin1II CATG 5 cut(s) 91, 108, 121, 354, 875
Hin6I GCGC 1 cut(s) 1088
HinP1I GCGC 1 cut(s) 1088
HincII GTYRAC 2 cut(s) 6, 208
HindII GTYRAC 2 cut(s) 6, 208
HinfI GANTC 4 cut(s) 91, 234, 271, 941
HpaII CCGG 6 cut(s) 464, 890, 930, 1067, 1313, 1391
HphI GGTGA 3 cut(s) 632, 737, 773
Hpy166II GTNNAC 4 cut(s) 6, 208, 407, 1270
Hpy188I TCNGA 8 cut(s) 61, 239, 282, 655, 1197, 1238, 1258, 1456
Hpy188III TCNNGA 6 cut(s) 176, 311, 398, 518, 563, 848
Hpy8I GTNNAC 4 cut(s) 6, 208, 407, 1270
Hpy99I CGWCG 4 cut(s) 31, 155, 1025, 1028
HpyAV CCTTC 6 cut(s) 285, 395, 635, 1075, 1132, 1414
HpyCH4III ACNGT 3 cut(s) 80, 205, 411
HpyCH4V TGCA 9 cut(s) 141, 407, 416, 497, 755, 881, 1190, 1270, 1348
HpyF10VI GCNNNNNNNGC 9 cut(s) 39, 147, 174, 413, 464, 1096, 1175, 1361, 1433
HpyF3I CTNAG 6 cut(s) 169, 279, 897, 935, 1320, 1455
Hsp92I GRCGYC 1 cut(s) 153
Hsp92II CATG 5 cut(s) 91, 108, 121, 354, 875
HspAI GCGC 1 cut(s) 1088
Ksp22I TGATCA 1 cut(s) 1162
KspI CCGCGG 1 cut(s) 43
Kzo9I GATC 6 cut(s) 50, 304, 698, 1118, 1162, 1476
LguI GCTCTTC 1 cut(s) 327
LmnI GCTCC 2 cut(s) 802, 889
Lsp1109I GCAGC 3 cut(s) 865, 893, 1237
LweI GCATC 5 cut(s) 150, 1075, 1187, 1335, 1414
MaeI CTAG 4 cut(s) 518, 1154, 1308, 1460
MaeIII GTNAC 6 cut(s) 160, 419, 613, 761, 782, 1132
MalI GATC 6 cut(s) 52, 306, 700, 1120, 1164, 1478
MboI GATC 6 cut(s) 50, 304, 698, 1118, 1162, 1476
MflI RGATCY 2 cut(s) 304, 1118
MhlI GDGCHC 4 cut(s) 409, 807, 1272, 1339
MluCI AATT 4 cut(s) 590, 813, 1260, 1329
MlyI GAGTC 1 cut(s) 85
MmeI TCCRAC 1 cut(s) 678
Mph1103I ATGCAT 1 cut(s) 143
MroXI GAANNNNTTC 1 cut(s) 221
MseI TTAA 4 cut(s) 20, 767, 1380, 1443
MspA1I CMGCKG 3 cut(s) 42, 1099, 1250
MspI CCGG 6 cut(s) 464, 890, 930, 1067, 1313, 1391
MspR9I CCNGG 3 cut(s) 679, 931, 1391
MvaI CCWGG 1 cut(s) 679
MvnI CGCG 2 cut(s) 42, 177
MwoI GCNNNNNNNGC 9 cut(s) 39, 147, 174, 413, 464, 1096, 1175, 1361, 1433
NciI CCSGG 2 cut(s) 931, 1391
NcoI CCATGG 2 cut(s) 117, 350
NdeII GATC 6 cut(s) 50, 304, 698, 1118, 1162, 1476
NlaIII CATG 5 cut(s) 91, 108, 121, 354, 875
NlaIV GGNNCC 3 cut(s) 1071, 1104, 1356
NmuCI GTSAC 3 cut(s) 160, 761, 782
NruI TCGCGA 1 cut(s) 177
NsiI ATGCAT 1 cut(s) 143
NspV TTCGAA 2 cut(s) 260, 867
PciSI GCTCTTC 1 cut(s) 327
PdmI GAANNNNTTC 1 cut(s) 221
PfeI GAWTC 3 cut(s) 234, 271, 941
PfoI TCCNGGA 1 cut(s) 1389
PkrI GCNGC 3 cut(s) 880, 883, 1252
PleI GAGTC 1 cut(s) 85
PpsI GAGTC 1 cut(s) 85
Psp6I CCWGG 1 cut(s) 677
PspGI CCWGG 1 cut(s) 677
PspN4I GGNNCC 3 cut(s) 1071, 1104, 1356
PspPI GGNCC 2 cut(s) 373, 602
PstI CTGCAG 1 cut(s) 883
PsuI RGATCY 2 cut(s) 304, 1118
PvuII CAGCTG 2 cut(s) 1099, 1250
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 4 cut(s) 20, 767, 1380, 1443
SatI GCNGC 3 cut(s) 879, 882, 1251
Sau3AI GATC 6 cut(s) 50, 304, 698, 1118, 1162, 1476
Sau96I GGNCC 2 cut(s) 373, 602
ScaI AGTACT 1 cut(s) 202
SchI GAGTC 1 cut(s) 85
ScrFI CCNGG 3 cut(s) 679, 931, 1391
SduI GDGCHC 4 cut(s) 409, 807, 1272, 1339
SfaNI GCATC 5 cut(s) 150, 1075, 1187, 1335, 1414
SfcI CTRYAG 2 cut(s) 837, 879
Sfr303I CCGCGG 1 cut(s) 43
SfuI TTCGAA 2 cut(s) 260, 867
SgrBI CCGCGG 1 cut(s) 43
SinI GGWCC 1 cut(s) 602
Sse9I AATT 4 cut(s) 590, 813, 1260, 1329
SsiI CCGC 5 cut(s) 40, 42, 193, 527, 717
SspI AATATT 1 cut(s) 1406
SspMI CTAG 4 cut(s) 518, 1154, 1308, 1460
StyD4I CCNGG 3 cut(s) 677, 929, 1389
StyI CCWWGG 2 cut(s) 117, 350
TaaI ACNGT 3 cut(s) 80, 205, 411
TaqI TCGA 4 cut(s) 53, 260, 562, 867
TasI AATT 4 cut(s) 590, 813, 1260, 1329
TatI WGTACW 2 cut(s) 180, 200
TfiI GAWTC 3 cut(s) 234, 271, 941
Tru1I TTAA 4 cut(s) 20, 767, 1380, 1443
Tru9I TTAA 4 cut(s) 20, 767, 1380, 1443
TscAI CASTG 2 cut(s) 826, 1192
TseFI GTSAC 3 cut(s) 160, 761, 782
TseI GCWGC 3 cut(s) 878, 881, 1250
Tsp45I GTSAC 3 cut(s) 160, 761, 782
TspGWI ACGGA 2 cut(s) 84, 615
TspRI CASTG 2 cut(s) 826, 1192
VneI GTGCAC 2 cut(s) 405, 1268
VpaK11BI GGWCC 1 cut(s) 602
XapI RAATTY 2 cut(s) 590, 813
XbaI TCTAGA 1 cut(s) 517
XmnI GAANNNNTTC 1 cut(s) 221
XspI CTAG 4 cut(s) 518, 1154, 1308, 1460
ZrmI AGTACT 1 cut(s) 202
Zsp2I ATGCAT 1 cut(s) 143
Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.