Basic Information

Type: gene

Biological Identity

Species

rosa_wichuraiana

Chromosome

Chr6

Orthogroup ID

OG0001724

Physical Location & Seq

Genomic Coordinates Reverse (-)

50715467 .. 50719919

Gene Structure 4453 bp

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UTR

Exon/CDS

Intron

Transcript / Protein ID

Rw6G027030.1

Sequence Viewer

CDS Protein Promoter (2k)

Length: 1329 bp

ATGACAATGGATTTGGTGCTCAAGCTTTCATGTATCGACCGCGGTTTATCCTCCGACTTGTACGGAAGTGGCTGCAAGCACTTGACTATCTCCAAGTGCTCTCACTGTGGTGCTGTTCTCACCCGCTTGATTCGATATGATGTTGTGCGTGCAAACAATGATGACAAGAACTACTTCATCGGTAGATTCTTGACAGGACTGCCCAACTTCTCCAAGAACAAAACCTTATTTTCATTGACCTATCCACCGTGGGTCTTGGAGGATGAGACTGGATGGTCCGAGTACCAGGGCCATCTTCAAGAATTATTTTCAGCTTACTACCTACAAATGCAAGAAGGAGAGGAGATTTTTGCTGTTCCCGCTGGTTCCTGGTATTATAATAAGCAACTTACTTTCGAGGAAGCGGAAGCAAAGATGATCAATAAGAAAAAGACACAAGATTTATATCAAAGAAGGCTTATGAAAGCTGCAACTAATGGAGCTGTTGCATTTGGAAAAGTGAACAAATTTGGGGCAAGCATAGCAAACAAAAAACTTGTTTTGATGATGATGATGATGAAGGGAACATCTCAGATAATGATGATGAGGAACAAGAGGGAGCAAGGAAAAATAGACTTGGACCCAAGAGAAGAGATGGCCGGTGATAATGAAGGAAACATCTCAGATAATAGTGATGAGGAAGAAGATGTAGCAAGGAAAAACATACTTGAACTCGAGAGAATAGGTGGCGATGATGAAGGTACAAATGATGACTGGAAGCTTGAGGAGATTTTTAGCGATGATGATGAAAATAATACCAAGGAAATAGAAGACTTTGTAACCGAGGTTCCAGTTCCACCAGAACTTACGCATTTGACATGTTCGTTTAATATGAGGTTTCTTTGGTATATATGTGATGATGAGGAAGATGATAATAATGAAGAGGAGGGTGGGCTTAGTGAATCCGGAAAAGAGTTGAAGAAGCTACTTGGGCACCTCATTGATCATTCTAGATCGGCTCAGACTACCCCATCTCCCTCCAAGCCATCCAAAAGTATGAGAAAACGATATGATGATGATACCGAGACATTTAGTTGTGCACCTCCCCATAAGTTGAAGACTGAAAATGATAAAAAACCTTCCATAAAAGAAGAGTCTGCATTTGCTAGTCCTATCAGTGAGGAAGAAATCAGGGCTGTTCTTGAGAAAGAACTAGCGATTTCCTTACAAGACCTTGTTGACCACTATCCAGGAAGAGTCGAATCGAATGAGAACTCAAATAATATAAAACCTATTTATATGCATTTATTTAAAGGGAACAATAATAAATCTTTATGGATTTTTGAATAA

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

442

Amino Acids

50.54

Weight (kDa)

4.93

Isoelectric Point (pI)

52.93

Instability Index

Protein Domains (Pfam)

Domain Name	Pfam ID	Position	E-value	Description
TFIIF_alpha	PF05793	78 - 325	2.7e-20	Transcription initiation factor IIF, alpha subunit (TFIIF-alpha)
TFIIF_alpha	PF05793	331 - 425	1e-05	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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Align Labels (Cladogram)

Image

Tree File

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Publication-ready

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Orthologous Genes (Group: OG0001724)

Species	Orthologous Gene IDs
arabidopsis_thaliana	AT4G12610 AT4G12610
fragaria_vesca	FvH4_2g22070 FvH4_2g22070 FvH4_2g22070 FvH4_3g01042
malus_domestica	MD05G1357300.v1.1 MD10G1331000.v1.1
prunus_persica	Prupe.4G011300_v2.0.a1 Prupe.4G011300_v2.0.a1
pyrus_communis	pycom05g32330 pycom10g28050
rosa_chinensis	RchiOBHm_Chr5g0001581 RchiOBHm_Chr6g0288941
rosa_laevigata	RLG00000009133 RLG00000012342 RLG00000012344 RLG00000030944
rosa_multiflora	Rmu_sc0003749.1_g000001 Rmu_sc0006320.1_g000007 Rmu_sc0007182.1_g000001
rosa_roxburghii	Rroxscaffold_1G00074740 Rroxscaffold_7G00179460 Rroxscaffold_7G00179470 Rroxscaffold_7G00179490
rosa_rugosa	Rorug04G0391100 Rorug06G0199700 Rorug06G0201700
rosa_samantha	Rh2BG455300 Rh2DG465300 Rh5AG012500 Rh5BG015400 Rh5CG013500 Rh5CG313700 Rh5DG013300 Rh6AG312800 Rh6BG317400 Rh6BG319600 Rh6CG326300 Rh6DG312400
rosa_wichuraiana	Rw0G003180 Rw0G005580 Rw1G016380 Rw2G040560 Rw5G001200 Rw6G027030 Rw7G019510 Rw7G019540

Restriction Enzyme Sites

1 / 10

Enzyme	Recognition Site	Cut Count	Positions (bp)
AanI	TTATAA	1 cut(s)	378
AasI	GACNNNNNNGTC	1 cut(s)	274
AccB1I	GGYRCC	1 cut(s)	972
AccII	CGCG	1 cut(s)	42
AccIII	TCCGGA	1 cut(s)	944
AciI	CCGC	5 cut(s)	40, 42, 124, 360, 404
AcoI	YGGCCR	1 cut(s)	636
AcsI	RAATTY	1 cut(s)	506
AfaI	GTAC	3 cut(s)	62, 284, 742
AflIII	ACRYGT	1 cut(s)	857
AgsI	TTSAA	5 cut(s)	299, 710, 958, 1096, 1325
AjnI	CCWGG	3 cut(s)	285, 368, 1228
AleI	CACNNNNGTG	1 cut(s)	108
AluBI	AGCT	6 cut(s)	25, 314, 467, 482, 760, 964
AluI	AGCT	6 cut(s)	25, 314, 467, 482, 760, 964
Alw21I	GWGCWC	3 cut(s)	21, 101, 1081
Alw26I	GTCTC	2 cut(s)	260, 1058
Alw44I	GTGCAC	1 cut(s)	1077
Ama87I	CYCGRG	1 cut(s)	713
Aor13HI	TCCGGA	1 cut(s)	944
AoxI	GGCC	2 cut(s)	289, 636
ApaLI	GTGCAC	1 cut(s)	1077
ApeKI	GCWGC	2 cut(s)	72, 467
ApoI	RAATTY	1 cut(s)	506
ArsI	GACNNNNNNTTYG	1 cut(s)	27
Asp700I	GAANNNNTTC	1 cut(s)	173
AspS9I	GGNCC	3 cut(s)	276, 289, 619
AsuHPI	GGTGA	2 cut(s)	112, 653
AvaI	CYCGRG	1 cut(s)	713
AvaII	GGWCC	2 cut(s)	276, 619
BaeGI	GKGCMC	2 cut(s)	975, 1081
BanI	GGYRCC	1 cut(s)	972
BbsI	GAAGAC	2 cut(s)	816, 1103
Bbv12I	GWGCWC	3 cut(s)	21, 101, 1081
BbvI	GCAGC	2 cut(s)	59, 454
BccI	CCATC	5 cut(s)	267, 300, 628, 1018, 1033
BciT130I	CCWGG	3 cut(s)	287, 370, 1230
BclI	TGATCA	2 cut(s)	417, 982
BcoDI	GTCTC	2 cut(s)	260, 1058
BfaI	CTAG	3 cut(s)	990, 1146, 1193
BisI	GCNGC	2 cut(s)	73, 468
BlsI	GCNGC	2 cut(s)	74, 469
Bme1390I	CCNGG	3 cut(s)	287, 370, 1230
Bme18I	GGWCC	2 cut(s)	276, 619
BmeT110I	CYCGRG	1 cut(s)	713
BmgT120I	GGNCC	3 cut(s)	276, 289, 619
BmiI	GGNNCC	4 cut(s)	367, 621, 828, 974
BmrFI	CCNGG	3 cut(s)	287, 370, 1230
BpiI	GAAGAC	2 cut(s)	816, 1103
BpuEI	CTTGAG	3 cut(s)	5, 782, 1202
BsaBI	GATNNNNATC	1 cut(s)	444
BsaJI	CCNNGG	5 cut(s)	40, 248, 286, 798, 822
BsaWI	WCCGGW	1 cut(s)	944
BsaXI	ACNNNNNCTCC	2 cut(s)	997, 1027
Bse118I	RCCGGY	1 cut(s)	638
Bse1I	ACTGG	3 cut(s)	274, 758, 830
Bse8I	GATNNNNATC	1 cut(s)	444
BseAI	TCCGGA	1 cut(s)	944
BseBI	CCWGG	3 cut(s)	287, 370, 1230
BseDI	CCNNGG	5 cut(s)	40, 248, 286, 798, 822
BseGI	GGATG	3 cut(s)	268, 278, 1025
BseJI	GATNNNNATC	1 cut(s)	444
BseMII	CTCAG	3 cut(s)	584, 675, 1013
BseNI	ACTGG	3 cut(s)	274, 758, 830
BseRI	GAGGAG	3 cut(s)	356, 779, 938
BseSI	GKGCMC	2 cut(s)	975, 1081
BseXI	GCAGC	2 cut(s)	59, 454
Bsh1236I	CGCG	1 cut(s)	42
Bsh1285I	CGRYCG	1 cut(s)	40
BshFI	GGCC	2 cut(s)	291, 638
BshNI	GGYRCC	1 cut(s)	972
BsiEI	CGRYCG	1 cut(s)	40
BsiHKAI	GWGCWC	3 cut(s)	21, 101, 1081
BsiHKCI	CYCGRG	1 cut(s)	713
BsiSI	CCGG	2 cut(s)	639, 945
BsmAI	GTCTC	2 cut(s)	260, 1058
BsnI	GGCC	2 cut(s)	291, 638
BsoBI	CYCGRG	1 cut(s)	713
Bsp1286I	GDGCHC	4 cut(s)	21, 101, 975, 1081
Bsp13I	TCCGGA	1 cut(s)	944
Bsp143I	GATC	3 cut(s)	417, 982, 992
BspACI	CCGC	5 cut(s)	40, 42, 124, 360, 404
BspANI	GGCC	2 cut(s)	291, 638
BspCNI	CTCAG	3 cut(s)	583, 674, 1012
BspEI	TCCGGA	1 cut(s)	944
BspFNI	CGCG	1 cut(s)	42
BspLI	GGNNCC	4 cut(s)	367, 621, 828, 974
BspT107I	GGYRCC	1 cut(s)	972
BsrFI	RCCGGY	1 cut(s)	638
BsrI	ACTGG	3 cut(s)	274, 758, 830
BssAI	RCCGGY	1 cut(s)	638
BssECI	CCNNGG	5 cut(s)	40, 248, 286, 798, 822
BssMI	GATC	3 cut(s)	417, 982, 992
BssT1I	CCWWGG	1 cut(s)	798
Bst2UI	CCWGG	3 cut(s)	287, 370, 1230
Bst4CI	ACNGT	2 cut(s)	107, 249
Bst6I	CTCTTC	4 cut(s)	624, 915, 1125, 1228
BstC8I	GCNNGC	3 cut(s)	77, 150, 517
BstDEI	CTNAG	4 cut(s)	570, 661, 935, 999
BstDSI	CCRYGG	2 cut(s)	40, 248
BstF5I	GGATG	3 cut(s)	268, 278, 1025
BstFNI	CGCG	1 cut(s)	42
BstKTI	GATC	3 cut(s)	420, 985, 995
BstMAI	GTCTC	2 cut(s)	260, 1058
BstMBI	GATC	3 cut(s)	417, 982, 992
BstMCI	CGRYCG	1 cut(s)	40
BstMWI	GCNNNNNNNGC	3 cut(s)	359, 521, 970
BstNI	CCWGG	3 cut(s)	287, 370, 1230
BstNSI	RCATGY	1 cut(s)	861
BstSCI	CCNGG	3 cut(s)	285, 368, 1228
BstSLI	GKGCMC	2 cut(s)	975, 1081
BstUI	CGCG	1 cut(s)	42
BstV1I	GCAGC	2 cut(s)	59, 454
BstV2I	GAAGAC	2 cut(s)	816, 1103
BsuRI	GGCC	2 cut(s)	291, 638
BtgI	CCRYGG	2 cut(s)	40, 248
BtgZI	GCGATG	2 cut(s)	744, 792
BtsCI	GGATG	3 cut(s)	268, 278, 1025
BtsIMutI	CAGTG	2 cut(s)	103, 1162
Cac8I	GCNNGC	3 cut(s)	77, 150, 517
Cfr10I	RCCGGY	1 cut(s)	638
Cfr13I	GGNCC	3 cut(s)	276, 289, 619
Cfr42I	CCGCGG	1 cut(s)	43
Csp6I	GTAC	3 cut(s)	61, 283, 741
CviAII	CATG	2 cut(s)	30, 858
CviQI	GTAC	3 cut(s)	61, 283, 741
DdeI	CTNAG	4 cut(s)	570, 661, 935, 999
DpnI	GATC	3 cut(s)	419, 984, 994
DpnII	GATC	3 cut(s)	417, 982, 992
DraI	TTTAAA	1 cut(s)	1291
DrdI	GACNNNNNNGTC	1 cut(s)	274
DseDI	GACNNNNNNGTC	1 cut(s)	274
EaeI	YGGCCR	1 cut(s)	636
Eam1104I	CTCTTC	4 cut(s)	624, 915, 1125, 1228
EarI	CTCTTC	4 cut(s)	624, 915, 1125, 1228
Eco130I	CCWWGG	1 cut(s)	798
Eco47I	GGWCC	2 cut(s)	276, 619
Eco88I	CYCGRG	1 cut(s)	713
EcoRII	CCWGG	3 cut(s)	285, 368, 1228
EcoT14I	CCWWGG	1 cut(s)	798
EcoT22I	ATGCAT	1 cut(s)	1284
ErhI	CCWWGG	1 cut(s)	798
FaeI	CATG	2 cut(s)	33, 861
FalI	AAGNNNNNCTT	2 cut(s)	158, 190
FatI	CATG	2 cut(s)	29, 857
FauI	CCCGC	2 cut(s)	131, 367
FbaI	TGATCA	2 cut(s)	417, 982
Fnu4HI	GCNGC	2 cut(s)	73, 468
FokI	GGATG	3 cut(s)	275, 285, 1012
Fsp4HI	GCNGC	2 cut(s)	73, 468
FspBI	CTAG	3 cut(s)	990, 1146, 1193
GluI	GCNGC	2 cut(s)	73, 468
HaeIII	GGCC	2 cut(s)	291, 638
HapII	CCGG	2 cut(s)	639, 945
Hin1II	CATG	2 cut(s)	33, 861
HincII	GTYRAC	1 cut(s)	1219
HindII	GTYRAC	1 cut(s)	1219
HindIII	AAGCTT	2 cut(s)	23, 758
HinfI	GANTC	6 cut(s)	130, 186, 941, 1133, 1236, 1241
HpaII	CCGG	2 cut(s)	639, 945
HphI	GGTGA	2 cut(s)	112, 653
Hpy166II	GTNNAC	3 cut(s)	502, 1079, 1219
Hpy188I	TCNGA	5 cut(s)	55, 280, 573, 664, 1002
Hpy188III	TCNNGA	6 cut(s)	190, 299, 715, 945, 990, 1181
Hpy8I	GTNNAC	3 cut(s)	502, 1079, 1219
HpyAV	CCTTC	6 cut(s)	329, 447, 553, 644, 731, 1128
HpyCH4III	ACNGT	2 cut(s)	107, 249
HpyCH4V	TGCA	8 cut(s)	75, 152, 331, 470, 488, 1079, 1139, 1282
HpyF10VI	GCNNNNNNNGC	3 cut(s)	359, 521, 970
HpyF3I	CTNAG	4 cut(s)	570, 661, 935, 999
Hsp92II	CATG	2 cut(s)	33, 861
Kpn2I	TCCGGA	1 cut(s)	944
Ksp22I	TGATCA	2 cut(s)	417, 982
KspI	CCGCGG	1 cut(s)	43
Kzo9I	GATC	3 cut(s)	417, 982, 992
LmnI	GCTCC	2 cut(s)	479, 598
Lsp1109I	GCAGC	2 cut(s)	59, 454
MaeI	CTAG	3 cut(s)	990, 1146, 1193
MaeIII	GTNAC	1 cut(s)	817
MalI	GATC	3 cut(s)	419, 984, 994
MboI	GATC	3 cut(s)	417, 982, 992
MhlI	GDGCHC	4 cut(s)	21, 101, 975, 1081
MluCI	AATT	2 cut(s)	302, 506
MlyI	GAGTC	2 cut(s)	1142, 1245
MmeI	TCCRAC	1 cut(s)	78
Mph1103I	ATGCAT	1 cut(s)	1284
MroI	TCCGGA	1 cut(s)	944
MroXI	GAANNNNTTC	1 cut(s)	173
MseI	TTAA	2 cut(s)	867, 1290
MslI	CAYNNNNRTG	1 cut(s)	108
MspA1I	CMGCKG	2 cut(s)	42, 362
MspI	CCGG	2 cut(s)	639, 945
MspR9I	CCNGG	3 cut(s)	287, 370, 1230
MvaI	CCWGG	3 cut(s)	287, 370, 1230
MvnI	CGCG	1 cut(s)	42
MwoI	GCNNNNNNNGC	3 cut(s)	359, 521, 970
NdeII	GATC	3 cut(s)	417, 982, 992
NlaIII	CATG	2 cut(s)	33, 861
NlaIV	GGNNCC	4 cut(s)	367, 621, 828, 974
NsiI	ATGCAT	1 cut(s)	1284
NspI	RCATGY	1 cut(s)	861
OliI	CACNNNNGTG	1 cut(s)	108
PaeR7I	CTCGAG	1 cut(s)	713
PciI	ACATGT	1 cut(s)	857
PdmI	GAANNNNTTC	1 cut(s)	173
PfeI	GAWTC	4 cut(s)	130, 186, 941, 1241
PfoI	TCCNGGA	1 cut(s)	1228
PkrI	GCNGC	2 cut(s)	74, 469
PleI	GAGTC	2 cut(s)	1141, 1244
PpsI	GAGTC	2 cut(s)	1141, 1244
PscI	ACATGT	1 cut(s)	857
PsiI	TTATAA	1 cut(s)	378
Psp6I	CCWGG	3 cut(s)	285, 368, 1228
PspGI	CCWGG	3 cut(s)	285, 368, 1228
PspN4I	GGNNCC	4 cut(s)	367, 621, 828, 974
PspPI	GGNCC	3 cut(s)	276, 289, 619
PsrI	GAACNNNNNNTAC	2 cut(s)	810, 842
RsaI	GTAC	3 cut(s)	62, 284, 742
RsaNI	GTAC	3 cut(s)	61, 283, 741
RseI	CAYNNNNRTG	1 cut(s)	108
SacII	CCGCGG	1 cut(s)	43
SaqAI	TTAA	2 cut(s)	867, 1290
SatI	GCNGC	2 cut(s)	73, 468
Sau3AI	GATC	3 cut(s)	417, 982, 992
Sau96I	GGNCC	3 cut(s)	276, 289, 619
SchI	GAGTC	2 cut(s)	1142, 1245
ScrFI	CCNGG	3 cut(s)	287, 370, 1230
SduI	GDGCHC	4 cut(s)	21, 101, 975, 1081
Sfr274I	CTCGAG	1 cut(s)	713
Sfr303I	CCGCGG	1 cut(s)	43
SgrBI	CCGCGG	1 cut(s)	43
SinI	GGWCC	2 cut(s)	276, 619
SlaI	CTCGAG	1 cut(s)	713
SmiMI	CAYNNNNRTG	1 cut(s)	108
SmlI	CTYRAG	4 cut(s)	20, 713, 761, 1181
SmoI	CTYRAG	4 cut(s)	20, 713, 761, 1181
Sse9I	AATT	2 cut(s)	302, 506
SsiI	CCGC	5 cut(s)	40, 42, 124, 360, 404
SspMI	CTAG	3 cut(s)	990, 1146, 1193
StyD4I	CCNGG	3 cut(s)	285, 368, 1228
StyI	CCWWGG	1 cut(s)	798
TaaI	ACNGT	2 cut(s)	107, 249
TaqI	TCGA	6 cut(s)	36, 133, 396, 714, 1239, 1244
TasI	AATT	2 cut(s)	302, 506
TfiI	GAWTC	4 cut(s)	130, 186, 941, 1241
Tru1I	TTAA	2 cut(s)	867, 1290
Tru9I	TTAA	2 cut(s)	867, 1290
TscAI	CASTG	2 cut(s)	110, 1162
TseI	GCWGC	2 cut(s)	72, 467
TspDTI	ATGAA	9 cut(s)	18, 166, 222, 476, 572, 663, 750, 801, 933
TspGWI	ACGGA	1 cut(s)	78
TspRI	CASTG	2 cut(s)	110, 1162
VneI	GTGCAC	1 cut(s)	1077
VpaK11BI	GGWCC	2 cut(s)	276, 619
XapI	RAATTY	1 cut(s)	506
XbaI	TCTAGA	1 cut(s)	989
XceI	RCATGY	1 cut(s)	861
XhoI	CTCGAG	1 cut(s)	713
XmnI	GAANNNNTTC	1 cut(s)	173
XspI	CTAG	3 cut(s)	990, 1146, 1193
Zsp2I	ATGCAT	1 cut(s)	1284

Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.