FvH4_3g04782

Transcription initiation factor IIF subunit

Design Primers CRISPR Design

Basic Information

Type: gene
Biological Identity
fragaria_vesca
Fvb3
OG0019209
Physical Location & Seq
Reverse (-)
2746660 .. 2748129
1470 bp
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UTR
Exon/CDS
Intron
FvH4_3g04782.t1

Sequence Viewer

Length: 1470 bp
ATGTCAACCGATTTGTTGCTAAAGCCGTCGTGCGAAGTCCGGGGATGTGGATCGACTTCTGACTTGTATGGAAGCAACTGTAAGCACATGACTCTGTGCATCTCATGCGGCAAGACCATGGCAGAGAACAAAGCCAAATGCTCTCAATGCGACGCCATTGTCACTCGCTTAATTCGAGAGTACAATGTTCGGCGGGAAAGTACTATCGGTGACAAGAACTACTTCATTGGCAAATTCGGGACGGGTTTGCCAAGCTTTTTGAAAACGAAGAATCCTTCTCAGAATAAATGGTCTCTTCGTAAGGATCTTCAAGACTCGAGGAAGAACAAGAATGAGGTGAAATCTAAAGCATGGATATTGGATGAACAAAGGGGCCAGTCTCGGTATCAGGGTCATCAAGAATGTGCACAGTCATCAAGTTACTACCTACTAATGAAGGCAGGGAAGGAGTTTTCGGCTGTTCCGGCTGGTTCTTGGTTCAACTTCAACAAGGTTGCACAATATAAGCAACTAACTCTAGAGGAAGCGGAGGAGAAGATGAACAATAGGCAAAAGACTAATCGAGATGGATATAAAAGATGGATTATGAAACTTGGAAACGGACCTGAAAAAGTTACTGGTGAGAATGATGGTAGTGGTGAAGGAAAGTTCTCCAATAATGAGGAAGAAGAGACAAGGAAAGGAGATGGTTTTGATGAGGAGGGTGATATTGGAGGTGCTAGTGAAGATGGGGACTTGCATGATGATGGTAGTGACAAGGGTAGTGATTGGGAGCATGAAGAAATTTTCAGTGATGATGATGAGGCTGTAGGTAATCCTGATGAAAGAGAAGATTTGGAACATGAGGCTCCATCTCCTCCGGAAAGCAAGCACGATGAAGATGGTAATGAAGAACAGGTCAGGCTGAGCGAATCGGGGAGAGAGTTGAAGAAGCTACTTGGGAGAAGTGGTGGCCTGAATGGTATTGATGGAGAGGAAGAGGAAGATGAAGACGACGATGATGAGGATGATATGGACGAGGACATTGGCTTATTGCCTCCGGCACCAAAGCAGAAGGTTGCACCCAAACAGCTGGAAGGATTTTTCAACAGTCACACAAAACCAGTTCCGAAGGAAAAGAGAAAATTAGATGGTGATGAGGCTAATAAGCAGGCATCTAACACTGCATCGAAGAAGATGAAGACCGAAAATGAACAAAACTCACATGTGAGAGATAATGCAGCTGCTTCTATGCATCCACAAGCTTCTCCATCCATGAAAATTGGTTCTGCTAGTAGTCCGGTATCTGAGGACCAAATTAGGGCTCTGTTGATGAAGAAGGCACCAATCCCTTTGTCTGACTTTGTTAACAACTTCCCAGAAAGACGAAAATATTCCAAAGAGGAGAAGGACGCTTTTTCAAAAATAATGAAGAAAGTATCTACGCTGCAGAATAAGAACGGGATCAGCTATCTTTTATTGAAGAAGTAA
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

490

Amino Acids

54.73

Weight (kDa)

5.21

Isoelectric Point (pI)

52.44

Instability Index
Protein Domains (Pfam)
Domain Name Pfam ID Position E-value Description
TFIIF_alpha PF05793 111 - 229 7.9e-27 Transcription initiation factor IIF, alpha subunit (TFIIF-alpha)
TFIIF_alpha PF05793 207 - 487 1.8e-24 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) 1042, 1321
AccIII TCCGGA 1 cut(s) 859
AciI CCGC 3 cut(s) 108, 193, 527
AclWI GGATC 3 cut(s) 58, 312, 1451
AcsI RAATTY 2 cut(s) 233, 783
AcyI GRCGYC 1 cut(s) 153
AfaI GTAC 2 cut(s) 182, 202
AfiI CCNNNNNNNGG 1 cut(s) 1300
AflIII ACRYGT 1 cut(s) 1204
AgsI TTSAA 8 cut(s) 262, 311, 481, 487, 928, 1087, 1401, 1462
AluBI AGCT 6 cut(s) 255, 934, 1072, 1223, 1244, 1449
AluI AGCT 6 cut(s) 255, 934, 1072, 1223, 1244, 1449
Alw21I GWGCWC 1 cut(s) 409
Alw26I GTCTC 3 cut(s) 297, 384, 665
Alw44I GTGCAC 1 cut(s) 405
AlwI GGATC 3 cut(s) 58, 312, 1451
Ama87I CYCGRG 1 cut(s) 316
Aor13HI TCCGGA 1 cut(s) 859
AoxI GGCC 2 cut(s) 373, 952
ApaLI GTGCAC 1 cut(s) 405
ApeKI GCWGC 3 cut(s) 1220, 1223, 1426
ApoI RAATTY 2 cut(s) 233, 783
Asp700I GAANNNNTTC 2 cut(s) 221, 1372
AspS9I GGNCC 3 cut(s) 373, 602, 1291
AsuC2I CCSGG 1 cut(s) 41
AsuHPI GGTGA 6 cut(s) 221, 349, 632, 650, 716, 1145
AvaI CYCGRG 1 cut(s) 316
AvaII GGWCC 2 cut(s) 602, 1291
BaeGI GKGCMC 1 cut(s) 409
BanI GGYRCC 2 cut(s) 1042, 1321
BanII GRGCYC 1 cut(s) 1306
BbsI GAAGAC 2 cut(s) 996, 1187
Bbv12I GWGCWC 1 cut(s) 409
BbvI GCAGC 3 cut(s) 1210, 1232, 1413
BceAI ACGGC 1 cut(s) 10
BcnI CCSGG 1 cut(s) 41
BcoDI GTCTC 3 cut(s) 297, 384, 665
BfaI CTAG 3 cut(s) 518, 720, 1272
BfmI CTRYAG 2 cut(s) 807, 1427
BisI GCNGC 4 cut(s) 109, 1221, 1224, 1427
BlpI GCTNAGC 1 cut(s) 905
BlsI GCNGC 4 cut(s) 110, 1222, 1225, 1428
BmcAI AGTACT 1 cut(s) 202
Bme1390I CCNGG 1 cut(s) 41
Bme18I GGWCC 2 cut(s) 602, 1291
BmeT110I CYCGRG 1 cut(s) 316
BmgT120I GGNCC 3 cut(s) 373, 602, 1291
BmiI GGNNCC 4 cut(s) 374, 849, 1044, 1323
BmrFI CCNGG 1 cut(s) 41
BmsI GCATC 4 cut(s) 108, 1163, 1175, 1243
BpiI GAAGAC 2 cut(s) 996, 1187
Bpu1102I GCTNAGC 1 cut(s) 905
BpuMI CCSGG 1 cut(s) 41
BsaBI GATNNNNATC 1 cut(s) 49
BsaHI GRCGYC 1 cut(s) 153
BsaI GGTCTC 1 cut(s) 297
BsaJI CCNNGG 2 cut(s) 40, 117
BsaWI WCCGGW 2 cut(s) 859, 1279
BsaXI ACNNNNNCTCC 2 cut(s) 934, 964
Bsc4I CCNNNNNNNGG 1 cut(s) 1300
Bse1I ACTGG 3 cut(s) 376, 622, 1103
Bse8I GATNNNNATC 1 cut(s) 49
BseAI TCCGGA 1 cut(s) 859
BseDI CCNNGG 2 cut(s) 40, 117
BseGI GGATG 5 cut(s) 50, 367, 1012, 1234, 1250
BseJI GATNNNNATC 1 cut(s) 49
BseLI CCNNNNNNNGG 1 cut(s) 1300
BseMII CTCAG 3 cut(s) 293, 896, 1278
BseNI ACTGG 3 cut(s) 376, 622, 1103
BseRI GAGGAG 4 cut(s) 545, 713, 846, 1397
BseSI GKGCMC 1 cut(s) 409
BseXI GCAGC 3 cut(s) 1210, 1232, 1413
BshFI GGCC 2 cut(s) 375, 954
BshNI GGYRCC 2 cut(s) 1042, 1321
BsiHKAI GWGCWC 1 cut(s) 409
BsiHKCI CYCGRG 1 cut(s) 316
BsiSI CCGG 5 cut(s) 40, 464, 860, 1040, 1280
BslFI GGGAC 2 cut(s) 253, 746
BslI CCNNNNNNNGG 1 cut(s) 1300
BsmAI GTCTC 3 cut(s) 297, 384, 665
BsmFI GGGAC 2 cut(s) 253, 746
BsnI GGCC 2 cut(s) 375, 954
Bso31I GGTCTC 1 cut(s) 297
BsoBI CYCGRG 1 cut(s) 316
Bsp1286I GDGCHC 2 cut(s) 409, 1306
Bsp13I TCCGGA 1 cut(s) 859
Bsp143I GATC 3 cut(s) 50, 304, 1443
Bsp1720I GCTNAGC 1 cut(s) 905
Bsp19I CCATGG 1 cut(s) 117
BspACI CCGC 3 cut(s) 108, 193, 527
BspANI GGCC 2 cut(s) 375, 954
BspCNI CTCAG 3 cut(s) 292, 897, 1279
BspEI TCCGGA 1 cut(s) 859
BspLI GGNNCC 4 cut(s) 374, 849, 1044, 1323
BspMAI CTGCAG 1 cut(s) 1431
BspPI GGATC 3 cut(s) 58, 312, 1451
BspT107I GGYRCC 2 cut(s) 1042, 1321
BspTNI GGTCTC 1 cut(s) 297
BsrI ACTGG 3 cut(s) 376, 622, 1103
BssECI CCNNGG 2 cut(s) 40, 117
BssMI GATC 3 cut(s) 50, 304, 1443
BssNI GRCGYC 1 cut(s) 153
BssT1I CCWWGG 1 cut(s) 117
Bst4CI ACNGT 3 cut(s) 80, 411, 1091
Bst6I CTCTTC 3 cut(s) 300, 663, 972
BstACI GRCGYC 1 cut(s) 153
BstAPI GCANNNNNTGC 1 cut(s) 105
BstC8I GCNNGC 2 cut(s) 869, 1152
BstDEI CTNAG 3 cut(s) 279, 905, 1287
BstDSI CCRYGG 1 cut(s) 117
BstF5I GGATG 5 cut(s) 50, 367, 1012, 1234, 1250
BstKTI GATC 3 cut(s) 53, 307, 1446
BstMAI GTCTC 3 cut(s) 297, 384, 665
BstMBI GATC 3 cut(s) 50, 304, 1443
BstMWI GCNNNNNNNGC 3 cut(s) 105, 147, 464
BstNSI RCATGY 1 cut(s) 1208
BstSCI CCNGG 1 cut(s) 39
BstSFI CTRYAG 2 cut(s) 807, 1427
BstSLI GKGCMC 1 cut(s) 409
BstV1I GCAGC 3 cut(s) 1210, 1232, 1413
BstV2I GAAGAC 2 cut(s) 996, 1187
BstX2I RGATCY 1 cut(s) 304
BstXI CCANNNNNNTGG 1 cut(s) 1072
BstYI RGATCY 1 cut(s) 304
BsuRI GGCC 2 cut(s) 375, 954
BtgI CCRYGG 1 cut(s) 117
BtsCI GGATG 5 cut(s) 50, 367, 1012, 1234, 1250
BtsI GCAGTG 1 cut(s) 1161
BtsIMutI CAGTG 2 cut(s) 796, 1161
Cac8I GCNNGC 2 cut(s) 869, 1152
Cfr13I GGNCC 3 cut(s) 373, 602, 1291
CseI GACGC 2 cut(s) 161, 1400
Csp6I GTAC 2 cut(s) 181, 201
CviAII CATG 9 cut(s) 88, 105, 118, 351, 740, 776, 842, 1205, 1255
CviQI GTAC 2 cut(s) 181, 201
DdeI CTNAG 3 cut(s) 279, 905, 1287
DpnI GATC 3 cut(s) 52, 306, 1445
DpnII GATC 3 cut(s) 50, 304, 1443
DrdI GACNNNNNNGTC 1 cut(s) 158
DseDI GACNNNNNNGTC 1 cut(s) 158
Eam1104I CTCTTC 3 cut(s) 300, 663, 972
EarI CTCTTC 3 cut(s) 300, 663, 972
Eco130I CCWWGG 1 cut(s) 117
Eco24I GRGCYC 1 cut(s) 1306
Eco31I GGTCTC 1 cut(s) 297
Eco47I GGWCC 2 cut(s) 602, 1291
Eco88I CYCGRG 1 cut(s) 316
EcoT14I CCWWGG 1 cut(s) 117
EcoT22I ATGCAT 1 cut(s) 1236
EcoT38I GRGCYC 1 cut(s) 1306
ErhI CCWWGG 1 cut(s) 117
FaeI CATG 9 cut(s) 91, 108, 121, 354, 743, 779, 845, 1208, 1258
FalI AAGNNNNNCTT 2 cut(s) 206, 238
FaqI GGGAC 2 cut(s) 253, 746
FatI CATG 9 cut(s) 87, 104, 117, 350, 739, 775, 841, 1204, 1254
FauI CCCGC 1 cut(s) 186
Fnu4HI GCNGC 4 cut(s) 109, 1221, 1224, 1427
FokI GGATG 5 cut(s) 57, 374, 1019, 1221, 1237
FriOI GRGCYC 1 cut(s) 1306
Fsp4HI GCNGC 4 cut(s) 109, 1221, 1224, 1427
FspBI CTAG 3 cut(s) 518, 720, 1272
GluI GCNGC 4 cut(s) 109, 1221, 1224, 1427
HaeIII GGCC 2 cut(s) 375, 954
HapII CCGG 5 cut(s) 40, 464, 860, 1040, 1280
HgaI GACGC 2 cut(s) 161, 1400
Hin1I GRCGYC 1 cut(s) 153
Hin1II CATG 9 cut(s) 91, 108, 121, 354, 743, 779, 845, 1208, 1258
HincII GTYRAC 2 cut(s) 6, 1348
HindII GTYRAC 2 cut(s) 6, 1348
HindIII AAGCTT 2 cut(s) 253, 1242
HinfI GANTC 4 cut(s) 91, 271, 314, 911
HpaI GTTAAC 1 cut(s) 1348
HpaII CCGG 5 cut(s) 40, 464, 860, 1040, 1280
HphI GGTGA 6 cut(s) 221, 349, 632, 650, 716, 1145
Hpy166II GTNNAC 3 cut(s) 6, 407, 1348
Hpy188I TCNGA 5 cut(s) 61, 282, 1110, 1288, 1339
Hpy188III TCNNGA 8 cut(s) 176, 238, 311, 398, 518, 563, 818, 860
Hpy8I GTNNAC 3 cut(s) 6, 407, 1348
Hpy99I CGWCG 3 cut(s) 31, 155, 998
HpyAV CCTTC 9 cut(s) 285, 430, 439, 635, 1048, 1070, 1105, 1312, 1381
HpyCH4III ACNGT 3 cut(s) 80, 411, 1091
HpyCH4V TGCA 9 cut(s) 99, 407, 497, 739, 1061, 1166, 1220, 1234, 1429
HpyF10VI GCNNNNNNNGC 3 cut(s) 105, 147, 464
HpyF3I CTNAG 3 cut(s) 279, 905, 1287
Hsp92I GRCGYC 1 cut(s) 153
Hsp92II CATG 9 cut(s) 91, 108, 121, 354, 743, 779, 845, 1208, 1258
Kpn2I TCCGGA 1 cut(s) 859
KspAI GTTAAC 1 cut(s) 1348
Kzo9I GATC 3 cut(s) 50, 304, 1443
LmnI GCTCC 2 cut(s) 772, 853
Lsp1109I GCAGC 3 cut(s) 1210, 1232, 1413
LweI GCATC 4 cut(s) 108, 1163, 1175, 1243
MaeI CTAG 3 cut(s) 518, 720, 1272
MaeIII GTNAC 6 cut(s) 160, 209, 419, 613, 752, 1091
MalI GATC 3 cut(s) 52, 306, 1445
MboI GATC 3 cut(s) 50, 304, 1443
MflI RGATCY 1 cut(s) 304
MhlI GDGCHC 2 cut(s) 409, 1306
MluCI AATT 6 cut(s) 171, 233, 783, 1124, 1260, 1296
MlyI GAGTC 2 cut(s) 85, 308
Mph1103I ATGCAT 1 cut(s) 1236
MroI TCCGGA 1 cut(s) 859
MroXI GAANNNNTTC 2 cut(s) 221, 1372
MseI TTAA 2 cut(s) 170, 1347
MslI CAYNNNNRTG 1 cut(s) 744
MspA1I CMGCKG 2 cut(s) 1072, 1223
MspI CCGG 5 cut(s) 40, 464, 860, 1040, 1280
MspR9I CCNGG 1 cut(s) 41
MwoI GCNNNNNNNGC 3 cut(s) 105, 147, 464
NciI CCSGG 1 cut(s) 41
NcoI CCATGG 1 cut(s) 117
NdeII GATC 3 cut(s) 50, 304, 1443
NlaIII CATG 9 cut(s) 91, 108, 121, 354, 743, 779, 845, 1208, 1258
NlaIV GGNNCC 4 cut(s) 374, 849, 1044, 1323
NmuCI GTSAC 4 cut(s) 160, 209, 752, 1091
NsiI ATGCAT 1 cut(s) 1236
NspI RCATGY 1 cut(s) 1208
PaeR7I CTCGAG 1 cut(s) 316
PciI ACATGT 1 cut(s) 1204
PcsI WCGNNNNNNNCGW 1 cut(s) 172
PdmI GAANNNNTTC 2 cut(s) 221, 1372
PfeI GAWTC 2 cut(s) 271, 911
PkrI GCNGC 4 cut(s) 110, 1222, 1225, 1428
PleI GAGTC 2 cut(s) 85, 308
PpsI GAGTC 2 cut(s) 85, 308
PscI ACATGT 1 cut(s) 1204
PspN4I GGNNCC 4 cut(s) 374, 849, 1044, 1323
PspPI GGNCC 3 cut(s) 373, 602, 1291
PspXI VCTCGAGB 1 cut(s) 316
PstI CTGCAG 1 cut(s) 1431
PsuI RGATCY 1 cut(s) 304
PvuII CAGCTG 2 cut(s) 1072, 1223
RsaI GTAC 2 cut(s) 182, 202
RsaNI GTAC 2 cut(s) 181, 201
RseI CAYNNNNRTG 1 cut(s) 744
SaqAI TTAA 2 cut(s) 170, 1347
SatI GCNGC 4 cut(s) 109, 1221, 1224, 1427
Sau3AI GATC 3 cut(s) 50, 304, 1443
Sau96I GGNCC 3 cut(s) 373, 602, 1291
ScaI AGTACT 1 cut(s) 202
SchI GAGTC 2 cut(s) 85, 308
ScrFI CCNGG 1 cut(s) 41
SduI GDGCHC 2 cut(s) 409, 1306
SfaNI GCATC 4 cut(s) 108, 1163, 1175, 1243
SfcI CTRYAG 2 cut(s) 807, 1427
Sfr274I CTCGAG 1 cut(s) 316
SinI GGWCC 2 cut(s) 602, 1291
SlaI CTCGAG 1 cut(s) 316
SmiMI CAYNNNNRTG 1 cut(s) 744
SmlI CTYRAG 1 cut(s) 316
SmoI CTYRAG 1 cut(s) 316
Sse9I AATT 6 cut(s) 171, 233, 783, 1124, 1260, 1296
SsiI CCGC 3 cut(s) 108, 193, 527
SspI AATATT 1 cut(s) 1373
SspMI CTAG 3 cut(s) 518, 720, 1272
StyD4I CCNGG 1 cut(s) 39
StyI CCWWGG 1 cut(s) 117
TaaI ACNGT 3 cut(s) 80, 411, 1091
TaqI TCGA 5 cut(s) 53, 175, 317, 562, 1169
TaqII GACCGA 1 cut(s) 1199
TasI AATT 6 cut(s) 171, 233, 783, 1124, 1260, 1296
TatI WGTACW 2 cut(s) 180, 200
TauI GCSGC 1 cut(s) 111
TfiI GAWTC 2 cut(s) 271, 911
Tru1I TTAA 2 cut(s) 170, 1347
Tru9I TTAA 2 cut(s) 170, 1347
TscAI CASTG 2 cut(s) 796, 1168
TseFI GTSAC 4 cut(s) 160, 209, 752, 1091
TseI GCWGC 3 cut(s) 1220, 1223, 1426
Tsp45I GTSAC 4 cut(s) 160, 209, 752, 1091
TspGWI ACGGA 1 cut(s) 615
TspRI CASTG 2 cut(s) 796, 1168
VneI GTGCAC 1 cut(s) 405
VpaK11BI GGWCC 2 cut(s) 602, 1291
XapI RAATTY 2 cut(s) 233, 783
XbaI TCTAGA 1 cut(s) 517
XceI RCATGY 1 cut(s) 1208
XhoI CTCGAG 1 cut(s) 316
XmnI GAANNNNTTC 2 cut(s) 221, 1372
XspI CTAG 3 cut(s) 518, 720, 1272
ZrmI AGTACT 1 cut(s) 202
Zsp2I ATGCAT 1 cut(s) 1236
Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.