Rh5CG065400

Transcription initiation factor IIF subunit

Design Primers CRISPR Design

Basic Information

Type: gene
Biological Identity
rosa_samantha
Chr5C
OG0019209
Physical Location & Seq
Reverse (-)
4994425 .. 4996056
1632 bp
Loading structure...
UTR
Exon/CDS
Intron
Rh5CG065400.1

Sequence Viewer

Length: 1500 bp
ATGTCAACCGATTTATTGTTAAAGCCGTCGTGCCAAGTCCGCGGATGTGGATCGACTTCTGACTTGTACGGAAGCAACTGTAAGCACATGACTCTGTGCTTCTCATGTGGCAAGTCCATGGCAGAGAACAAAGCCAAATGCATCCAATGCGACGCCATTGTCACTCGCTTAATTCGCGAGTACAATGTTCGGCGGGAAAGTACTGTCAACAACAAGAACTACTTCATTGGCAGATTCGGGACGGGTTTGCCAAACTTTTCGAAAACGAAGAATCCTTCTCAGAATAAATGGTCTCTTCGTAAGGATCTTCAAGACCCAAGAAAGAACAAGGAAGAGCAGAAAACTAAACCATGGGTCTTGGATGAACTAACGGGCCAGTCTCGGTATCAGGGTCATCAAGAAGGTGCACAGTCTGCAAGTTACTACCTACTAATGAAGCAAGGGAAGGAGTTTGCGGCTGTTCCGGCTGGTTCTTGGTTCAACTTCAACAAGGTTGCACAATATAAGCAACTTACTCTAGAGGAAGCGGAAGAGAAGATGAATAATAGGCAAAAGACTAATCGAGATGGATATAAAAGATGGATTATGAAATTTGGAAACGGACCTGAAAAAGTTACTGGTGATGGTGGTGGTGGTGGTGAAGGAAACTTCTCCGACAATGAGGAAGAAGAAACAACCAGAGAAAGATATAGACTTGGATCACTCAACAAAATAGGCGGGGATGGTGATGATGATGAGGATAATCTTATAGGTGGAAACGAAGATGGTGACTTAAATGATGATGGTAGTGACAAGGGTAGTGATTGGGAGCACGAAGAAATTTTCAGTGATGATGATGAAGCTGTAGGTAATCCTGATGAACGAGAAGATTTCGAACATGAGGCTCCAGCTCCACCGGAAACTAAGCAGGATGATGATGGTAATGAAGAGGAGGCCGGGCTGAGTGAATCAGGGAGAGAGTTGAAGAAGCTACTTGGGAGAAGTGGTGGCCTGAATGGTATTGATGAGGAAGAGGAAGATGAAGACGACGATGATGAGGATGATATGGATGAGGATATTTGCTTATTGCCTCCGGCACCAAAGCAGAAGGATGCGCCCAAACAGCTGGAACCATTTGACAACAGATCCACAAAACCAGTTACGAAGGGAAAGAGAAAACTAGATAGTGATCAGGCTAATAAGGCATCTAACACAGCACCTCCGAAGAAGATGAAGACTGAAAATGAACAAAAATCATCTGTCAGAGCTTCTGAAATTAGTGTGCACGCCAAAGTTACTCCATCCTTGAAAACTGGTTCTTCTAGTCCGGTATCTGAGGAAGAAATTAGGGCTCTATTGATGCAAAAGGCACCAATCGCCCTACCTGATTTTGTTAATAACTTCCCGGAAAGACGCAAATATTCCAAAGAGCAGAAGGATGCTTTTACAGCAATCGTTAAGAAAGTATCTGAGCTAGAGAAGAAGAACGGGATCAGCTATGTTGTATTGAGAAAGAAGTGA
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

499

Amino Acids

55.87

Weight (kDa)

5.02

Isoelectric Point (pI)

51.23

Instability Index
Protein Domains (Pfam)
Domain Name Pfam ID Position E-value Description
TFIIF_alpha PF05793 50 - 497 6.9e-61 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) 1075, 1348
AccII CGCG 2 cut(s) 42, 177
AciI CCGC 6 cut(s) 40, 42, 193, 455, 527, 717
AclWI GGATC 5 cut(s) 58, 312, 706, 1119, 1478
AcsI RAATTY 2 cut(s) 590, 819
AcyI GRCGYC 1 cut(s) 153
AfaI GTAC 3 cut(s) 68, 182, 202
AgsI TTSAA 5 cut(s) 311, 481, 487, 964, 1288
AluBI AGCT 7 cut(s) 842, 890, 970, 1105, 1247, 1453, 1476
AluI AGCT 7 cut(s) 842, 890, 970, 1105, 1247, 1453, 1476
Alw21I GWGCWC 3 cut(s) 409, 813, 1266
Alw26I GTCTC 2 cut(s) 297, 384
Alw44I GTGCAC 2 cut(s) 405, 1262
AlwI GGATC 5 cut(s) 58, 312, 706, 1119, 1478
AoxI GGCC 3 cut(s) 373, 933, 988
ApaLI GTGCAC 2 cut(s) 405, 1262
ApoI RAATTY 2 cut(s) 590, 819
Asp700I GAANNNNTTC 1 cut(s) 221
AspLEI GCGC 1 cut(s) 1096
AspS9I GGNCC 2 cut(s) 373, 602
AsuC2I CCSGG 2 cut(s) 937, 1385
AsuHPI GGTGA 4 cut(s) 632, 650, 737, 779
AsuII TTCGAA 2 cut(s) 260, 873
AvaII GGWCC 1 cut(s) 602
BaeGI GKGCMC 2 cut(s) 409, 1266
BanI GGYRCC 2 cut(s) 1075, 1348
BanII GRGCYC 1 cut(s) 1333
BbsI GAAGAC 2 cut(s) 1029, 1220
Bbv12I GWGCWC 3 cut(s) 409, 813, 1266
BccI CCATC 8 cut(s) 560, 573, 617, 716, 758, 776, 911, 1288
BceAI ACGGC 1 cut(s) 10
BclI TGATCA 1 cut(s) 1168
BcnI CCSGG 2 cut(s) 937, 1385
BcoDI GTCTC 2 cut(s) 297, 384
BfaI CTAG 4 cut(s) 518, 1160, 1302, 1454
BfmI CTRYAG 1 cut(s) 843
BisI GCNGC 1 cut(s) 456
BlsI GCNGC 1 cut(s) 457
BmcAI AGTACT 1 cut(s) 202
Bme1390I CCNGG 2 cut(s) 937, 1385
Bme18I GGWCC 1 cut(s) 602
BmgT120I GGNCC 2 cut(s) 373, 602
BmiI GGNNCC 4 cut(s) 885, 1077, 1110, 1350
BmrFI CCNGG 2 cut(s) 937, 1385
BmsI GCATC 5 cut(s) 150, 1081, 1193, 1329, 1408
BpiI GAAGAC 2 cut(s) 1029, 1220
BpmI CTGGAG 1 cut(s) 870
Bpu14I TTCGAA 2 cut(s) 260, 873
BpuMI CCSGG 2 cut(s) 937, 1385
BsaBI GATNNNNATC 2 cut(s) 49, 1167
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) 895, 1306
BsaXI ACNNNNNCTCC 4 cut(s) 970, 1000, 1183, 1213
Bse1I ACTGG 4 cut(s) 376, 622, 1136, 1297
Bse8I GATNNNNATC 2 cut(s) 49, 1167
BseDI CCNNGG 3 cut(s) 40, 117, 350
BseJI GATNNNNATC 2 cut(s) 49, 1167
BseMII CTCAG 4 cut(s) 293, 932, 1305, 1440
BseNI ACTGG 4 cut(s) 376, 622, 1136, 1297
BseRI GAGGAG 1 cut(s) 944
BseSI GKGCMC 2 cut(s) 409, 1266
Bsh1236I CGCG 2 cut(s) 42, 177
BshFI GGCC 3 cut(s) 375, 935, 990
BshNI GGYRCC 2 cut(s) 1075, 1348
BsiHKAI GWGCWC 3 cut(s) 409, 813, 1266
BsiSI CCGG 6 cut(s) 464, 896, 936, 1073, 1307, 1385
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, 935, 990
Bso31I GGTCTC 1 cut(s) 297
Bsp119I TTCGAA 2 cut(s) 260, 873
Bsp1286I GDGCHC 4 cut(s) 409, 813, 1266, 1333
Bsp143I GATC 6 cut(s) 50, 304, 698, 1124, 1168, 1470
Bsp19I CCATGG 2 cut(s) 117, 350
Bsp68I TCGCGA 1 cut(s) 177
BspACI CCGC 6 cut(s) 40, 42, 193, 455, 527, 717
BspANI GGCC 3 cut(s) 375, 935, 990
BspCNI CTCAG 4 cut(s) 292, 933, 1306, 1441
BspFNI CGCG 2 cut(s) 42, 177
BspLI GGNNCC 4 cut(s) 885, 1077, 1110, 1350
BspPI GGATC 5 cut(s) 58, 312, 706, 1119, 1478
BspQI GCTCTTC 1 cut(s) 327
BspT104I TTCGAA 2 cut(s) 260, 873
BspT107I GGYRCC 2 cut(s) 1075, 1348
BspTNI GGTCTC 1 cut(s) 297
BsrI ACTGG 4 cut(s) 376, 622, 1136, 1297
BssECI CCNNGG 3 cut(s) 40, 117, 350
BssMI GATC 6 cut(s) 50, 304, 698, 1124, 1168, 1470
BssNI GRCGYC 1 cut(s) 153
BssT1I CCWWGG 2 cut(s) 117, 350
Bst4CI ACNGT 3 cut(s) 80, 205, 411
Bst6I CTCTTC 5 cut(s) 300, 327, 525, 921, 1005
BstACI GRCGYC 1 cut(s) 153
BstAPI GCANNNNNTGC 2 cut(s) 147, 413
BstBI TTCGAA 2 cut(s) 260, 873
BstC8I GCNNGC 1 cut(s) 1266
BstDEI CTNAG 5 cut(s) 279, 903, 941, 1314, 1449
BstDSI CCRYGG 3 cut(s) 40, 117, 350
BstFNI CGCG 2 cut(s) 42, 177
BstHHI GCGC 1 cut(s) 1096
BstKTI GATC 6 cut(s) 53, 307, 701, 1127, 1171, 1473
BstMAI GTCTC 2 cut(s) 297, 384
BstMBI GATC 6 cut(s) 50, 304, 698, 1124, 1168, 1470
BstMWI GCNNNNNNNGC 9 cut(s) 39, 147, 174, 413, 464, 1102, 1181, 1355, 1427
BstSCI CCNGG 2 cut(s) 935, 1383
BstSFI CTRYAG 1 cut(s) 843
BstSLI GKGCMC 2 cut(s) 409, 1266
BstUI CGCG 2 cut(s) 42, 177
BstV2I GAAGAC 2 cut(s) 1029, 1220
BstX2I RGATCY 2 cut(s) 304, 1124
BstXI CCANNNNNNTGG 1 cut(s) 1105
BstYI RGATCY 2 cut(s) 304, 1124
BsuRI GGCC 3 cut(s) 375, 935, 990
BtgI CCRYGG 3 cut(s) 40, 117, 350
BtsIMutI CAGTG 1 cut(s) 832
BtuMI TCGCGA 1 cut(s) 177
Cac8I GCNNGC 1 cut(s) 1266
CfoI GCGC 1 cut(s) 1096
Cfr13I GGNCC 2 cut(s) 373, 602
Cfr42I CCGCGG 1 cut(s) 43
CseI GACGC 2 cut(s) 161, 1401
Csp6I GTAC 3 cut(s) 67, 181, 201
CviAII CATG 5 cut(s) 88, 105, 118, 351, 878
CviQI GTAC 3 cut(s) 67, 181, 201
DdeI CTNAG 5 cut(s) 279, 903, 941, 1314, 1449
DpnI GATC 6 cut(s) 52, 306, 700, 1126, 1170, 1472
DpnII GATC 6 cut(s) 50, 304, 698, 1124, 1168, 1470
DrdI GACNNNNNNGTC 1 cut(s) 158
DseDI GACNNNNNNGTC 1 cut(s) 158
Eam1104I CTCTTC 5 cut(s) 300, 327, 525, 921, 1005
EarI CTCTTC 5 cut(s) 300, 327, 525, 921, 1005
Eco130I CCWWGG 2 cut(s) 117, 350
Eco24I GRGCYC 1 cut(s) 1333
Eco31I GGTCTC 1 cut(s) 297
Eco47I GGWCC 1 cut(s) 602
EcoT14I CCWWGG 2 cut(s) 117, 350
EcoT22I ATGCAT 1 cut(s) 143
EcoT38I GRGCYC 1 cut(s) 1333
ErhI CCWWGG 2 cut(s) 117, 350
FaeI CATG 5 cut(s) 91, 108, 121, 354, 881
FalI AAGNNNNNCTT 2 cut(s) 206, 238
FaqI GGGAC 1 cut(s) 253
FatI CATG 5 cut(s) 87, 104, 117, 350, 877
FauI CCCGC 2 cut(s) 186, 710
FbaI TGATCA 1 cut(s) 1168
Fnu4HI GCNGC 1 cut(s) 456
FriOI GRGCYC 1 cut(s) 1333
Fsp4HI GCNGC 1 cut(s) 456
FspBI CTAG 4 cut(s) 518, 1160, 1302, 1454
GlaI GCGC 1 cut(s) 1095
GluI GCNGC 1 cut(s) 456
GsuI CTGGAG 1 cut(s) 870
HaeIII GGCC 3 cut(s) 375, 935, 990
HapII CCGG 6 cut(s) 464, 896, 936, 1073, 1307, 1385
HgaI GACGC 2 cut(s) 161, 1401
HhaI GCGC 1 cut(s) 1096
Hin1I GRCGYC 1 cut(s) 153
Hin1II CATG 5 cut(s) 91, 108, 121, 354, 881
Hin6I GCGC 1 cut(s) 1094
HinP1I GCGC 1 cut(s) 1094
HincII GTYRAC 2 cut(s) 6, 208
HindII GTYRAC 2 cut(s) 6, 208
HinfI GANTC 4 cut(s) 91, 234, 271, 947
HpaII CCGG 6 cut(s) 464, 896, 936, 1073, 1307, 1385
HphI GGTGA 4 cut(s) 632, 650, 737, 779
Hpy166II GTNNAC 4 cut(s) 6, 208, 407, 1264
Hpy188I TCNGA 8 cut(s) 61, 282, 655, 1203, 1244, 1252, 1315, 1450
Hpy188III TCNNGA 7 cut(s) 176, 238, 311, 398, 518, 563, 854
Hpy8I GTNNAC 4 cut(s) 6, 208, 407, 1264
Hpy99I CGWCG 3 cut(s) 31, 155, 1031
HpyAV CCTTC 7 cut(s) 285, 395, 439, 635, 1081, 1138, 1408
HpyCH4III ACNGT 3 cut(s) 80, 205, 411
HpyCH4V TGCA 6 cut(s) 141, 407, 416, 497, 1264, 1342
HpyF10VI GCNNNNNNNGC 9 cut(s) 39, 147, 174, 413, 464, 1102, 1181, 1355, 1427
HpyF3I CTNAG 5 cut(s) 279, 903, 941, 1314, 1449
Hsp92I GRCGYC 1 cut(s) 153
Hsp92II CATG 5 cut(s) 91, 108, 121, 354, 881
HspAI GCGC 1 cut(s) 1094
Ksp22I TGATCA 1 cut(s) 1168
KspI CCGCGG 1 cut(s) 43
Kzo9I GATC 6 cut(s) 50, 304, 698, 1124, 1168, 1470
LguI GCTCTTC 1 cut(s) 327
LmnI GCTCC 3 cut(s) 808, 889, 895
LweI GCATC 5 cut(s) 150, 1081, 1193, 1329, 1408
MaeI CTAG 4 cut(s) 518, 1160, 1302, 1454
MaeIII GTNAC 7 cut(s) 160, 419, 613, 767, 788, 1138, 1273
MalI GATC 6 cut(s) 52, 306, 700, 1126, 1170, 1472
MboI GATC 6 cut(s) 50, 304, 698, 1124, 1168, 1470
MflI RGATCY 2 cut(s) 304, 1124
MhlI GDGCHC 4 cut(s) 409, 813, 1266, 1333
MluCI AATT 5 cut(s) 171, 590, 819, 1254, 1323
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 5 cut(s) 20, 170, 773, 1374, 1437
MspA1I CMGCKG 2 cut(s) 42, 1105
MspI CCGG 6 cut(s) 464, 896, 936, 1073, 1307, 1385
MspR9I CCNGG 2 cut(s) 937, 1385
MvnI CGCG 2 cut(s) 42, 177
MwoI GCNNNNNNNGC 9 cut(s) 39, 147, 174, 413, 464, 1102, 1181, 1355, 1427
NciI CCSGG 2 cut(s) 937, 1385
NcoI CCATGG 2 cut(s) 117, 350
NdeII GATC 6 cut(s) 50, 304, 698, 1124, 1168, 1470
NlaIII CATG 5 cut(s) 91, 108, 121, 354, 881
NlaIV GGNNCC 4 cut(s) 885, 1077, 1110, 1350
NmuCI GTSAC 3 cut(s) 160, 767, 788
NruI TCGCGA 1 cut(s) 177
NsiI ATGCAT 1 cut(s) 143
NspV TTCGAA 2 cut(s) 260, 873
PciSI GCTCTTC 1 cut(s) 327
PdmI GAANNNNTTC 1 cut(s) 221
PfeI GAWTC 3 cut(s) 234, 271, 947
PfoI TCCNGGA 1 cut(s) 1383
PkrI GCNGC 1 cut(s) 457
PleI GAGTC 1 cut(s) 85
PpsI GAGTC 1 cut(s) 85
PspN4I GGNNCC 4 cut(s) 885, 1077, 1110, 1350
PspPI GGNCC 2 cut(s) 373, 602
PsuI RGATCY 2 cut(s) 304, 1124
PvuII CAGCTG 1 cut(s) 1105
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, 773, 1374, 1437
SatI GCNGC 1 cut(s) 456
Sau3AI GATC 6 cut(s) 50, 304, 698, 1124, 1168, 1470
Sau96I GGNCC 2 cut(s) 373, 602
ScaI AGTACT 1 cut(s) 202
SchI GAGTC 1 cut(s) 85
ScrFI CCNGG 2 cut(s) 937, 1385
SduI GDGCHC 4 cut(s) 409, 813, 1266, 1333
SfaNI GCATC 5 cut(s) 150, 1081, 1193, 1329, 1408
SfcI CTRYAG 1 cut(s) 843
Sfr303I CCGCGG 1 cut(s) 43
SfuI TTCGAA 2 cut(s) 260, 873
SgrBI CCGCGG 1 cut(s) 43
SinI GGWCC 1 cut(s) 602
Sse9I AATT 5 cut(s) 171, 590, 819, 1254, 1323
SsiI CCGC 6 cut(s) 40, 42, 193, 455, 527, 717
SspI AATATT 1 cut(s) 1400
SspMI CTAG 4 cut(s) 518, 1160, 1302, 1454
StyD4I CCNGG 2 cut(s) 935, 1383
StyI CCWWGG 2 cut(s) 117, 350
TaaI ACNGT 3 cut(s) 80, 205, 411
TaqI TCGA 4 cut(s) 53, 260, 562, 873
TasI AATT 5 cut(s) 171, 590, 819, 1254, 1323
TatI WGTACW 2 cut(s) 180, 200
TauI GCSGC 1 cut(s) 458
TfiI GAWTC 3 cut(s) 234, 271, 947
Tru1I TTAA 5 cut(s) 20, 170, 773, 1374, 1437
Tru9I TTAA 5 cut(s) 20, 170, 773, 1374, 1437
TscAI CASTG 1 cut(s) 832
TseFI GTSAC 3 cut(s) 160, 767, 788
Tsp45I GTSAC 3 cut(s) 160, 767, 788
TspGWI ACGGA 2 cut(s) 84, 615
TspRI CASTG 1 cut(s) 832
VneI GTGCAC 2 cut(s) 405, 1262
VpaK11BI GGWCC 1 cut(s) 602
XapI RAATTY 2 cut(s) 590, 819
XbaI TCTAGA 1 cut(s) 517
XmnI GAANNNNTTC 1 cut(s) 221
XspI CTAG 4 cut(s) 518, 1160, 1302, 1454
ZrmI AGTACT 1 cut(s) 202
Zsp2I ATGCAT 1 cut(s) 143
Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.