Basic Information

Type: gene

Biological Identity

Species

rosa_wichuraiana

Chromosome

Contig00108

Orthogroup ID

OG0001724

Physical Location & Seq

Genomic Coordinates Forward (+)

49805 .. 52418

Gene Structure 2614 bp

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UTR

Exon/CDS

Intron

Transcript / Protein ID

Rw0G003180.1

Sequence Viewer

CDS Protein Promoter (2k)

Length: 969 bp

ATGTTGCAAGGAAAGGAGTTTTCTGCTATTCCTGCTGGTTCGTGGTTCAACTTTAACAAGGTTGCACAATATAAGCAACTTACTCTAGAGGAAGCGGAAGAGAAGATGAACAATAGGAAAAAGACTCAAGATGGATATGAAAGATGGATGATGAAATTGGAACTAACGAACCTGGTCCACTTCGGACGCAAAAAAATGACTGGTGATGATGATGAGGGAAATTTCTCTGATAAAGGGGAGGAAGATGAGGAAGAAGAGACAGCAAGGAAAAATAGACTTGGTCTCAATAAAAAAGGTGGTGATGATGACGATGATGAAGGTGGAAATGAAGAAGATGACTTAGATGATGATAGCAGTGAGAAGGCAGGTGATGATTGGGAGCATGAAGAAATATTCACCGATGATGATGAAGCTGTTGGTATTAATCCTGAGGAGAGAGAAGAATTTGAACCTGAGGTTCCAGCTCCTCCAGAAATTAAGCAGATGGATGATGATATTGCCTTGCCTCAAGCGCTTGCACCAAAGCAGAAGGATGCACCCAAACAGGAACCAGTTGACAACAGTCCTATTAAACCCGGGACTTCTGGATCTGCTGCTAAAGCAAATCCATCTGCCTCCAAGTCGGCGAAGGGAAAGAGAAAATTAAATGGTGATGACGCTAAAGCGTCCAACAGTGCACCTCCCAAGAAGGTGAAGACTGAAAATGAGCAAAAATCAGTCAAAGAGGAGCCTGCTTCTGAAAGTAGTGTGCCTGCAAAAGGTACTGCTGCATCCTCGAAAACGGGTTCAACACCATCTGGTGGTCCTACAGGTCCTGTATCTGAGGAAGAAATTAGGGCAGTTTTGATGCAAAAGTCACCCATCACCACACGCGATCTTGAGAAGGATGCTTTTGCAGCAATCCTGAGGAAAATGTTTAGGATACAGAAGAACAATGGGATCAGCTATGTTGTATTAAGGGAGAAGTGA

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

322

Amino Acids

35.45

Weight (kDa)

4.73

Isoelectric Point (pI)

53.42

Instability Index

Protein Domains (Pfam)

Domain Name	Pfam ID	Position	E-value	Description
TFIIF_alpha	PF05793	3 - 165	1e-32	Transcription initiation factor IIF, alpha subunit (TFIIF-alpha)
TFIIF_alpha	PF05793	164 - 294	1e-16	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

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

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)
AarI	CACCTGC	1 cut(s)	356
Acc36I	ACCTGC	1 cut(s)	356
AccB7I	CCANNNNNTGG	1 cut(s)	800
AccII	CGCG	1 cut(s)	873
AciI	CCGC	1 cut(s)	95
AclWI	GGATC	2 cut(s)	595, 947
AcsI	RAATTY	2 cut(s)	220, 443
AfaI	GTAC	1 cut(s)	763
AfeI	AGCGCT	1 cut(s)	513
AfiI	CCNNNNNNNGG	2 cut(s)	758, 800
AgsI	TTSAA	3 cut(s)	49, 449, 789
AjnI	CCWGG	1 cut(s)	171
AluBI	AGCT	3 cut(s)	413, 464, 945
AluI	AGCT	3 cut(s)	413, 464, 945
Alw21I	GWGCWC	1 cut(s)	679
Alw26I	GTCTC	2 cut(s)	251, 287
Alw44I	GTGCAC	1 cut(s)	675
AlwI	GGATC	2 cut(s)	595, 947
AlwNI	CAGNNNCTG	1 cut(s)	815
Ama87I	CYCGRG	1 cut(s)	575
Aor51HI	AGCGCT	1 cut(s)	513
ApaLI	GTGCAC	1 cut(s)	675
ApeKI	GCWGC	3 cut(s)	593, 767, 896
ApoI	RAATTY	2 cut(s)	220, 443
AseI	ATTAAT	1 cut(s)	423
AspLEI	GCGC	1 cut(s)	514
AspS9I	GGNCC	3 cut(s)	175, 803, 812
AsuC2I	CCSGG	2 cut(s)	576, 577
AsuHPI	GGTGA	8 cut(s)	215, 311, 380, 388, 662, 703, 849, 856
AvaI	CYCGRG	1 cut(s)	575
AvaII	GGWCC	3 cut(s)	175, 803, 812
AxyI	CCTNAGG	3 cut(s)	429, 453, 905
BaeGI	GKGCMC	1 cut(s)	679
BbsI	GAAGAC	1 cut(s)	701
Bbv12I	GWGCWC	1 cut(s)	679
BbvI	GCAGC	3 cut(s)	580, 754, 908
BccI	CCATC	6 cut(s)	125, 138, 478, 616, 802, 869
BciT130I	CCWGG	1 cut(s)	173
BciVI	GTATCC	1 cut(s)	915
BcnI	CCSGG	2 cut(s)	576, 577
BcoDI	GTCTC	2 cut(s)	251, 287
BfaI	CTAG	1 cut(s)	86
BfmI	CTRYAG	1 cut(s)	807
BfoI	RGCGCY	1 cut(s)	515
BfuAI	ACCTGC	1 cut(s)	356
BfuI	GTATCC	1 cut(s)	915
BisI	GCNGC	3 cut(s)	594, 768, 897
BlsI	GCNGC	3 cut(s)	595, 769, 898
Bme1390I	CCNGG	3 cut(s)	173, 576, 577
Bme18I	GGWCC	3 cut(s)	175, 803, 812
BmeT110I	CYCGRG	1 cut(s)	575
BmgT120I	GGNCC	3 cut(s)	175, 803, 812
BmiI	GGNNCC	3 cut(s)	459, 549, 729
BmrFI	CCNGG	3 cut(s)	173, 576, 577
BmsI	GCATC	4 cut(s)	523, 779, 837, 877
BoxI	GACNNNNGTC	1 cut(s)	561
BpiI	GAAGAC	1 cut(s)	701
BpmI	CTGGAG	1 cut(s)	453
BpuEI	CTTGAG	3 cut(s)	111, 492, 899
BpuMI	CCSGG	2 cut(s)	576, 577
BsaI	GGTCTC	1 cut(s)	287
BsaJI	CCNNGG	1 cut(s)	575
Bsc4I	CCNNNNNNNGG	2 cut(s)	758, 800
Bse1I	ACTGG	2 cut(s)	205, 551
Bse21I	CCTNAGG	3 cut(s)	429, 453, 905
BseBI	CCWGG	1 cut(s)	173
BseDI	CCNNGG	1 cut(s)	575
BseGI	GGATG	5 cut(s)	153, 493, 538, 770, 892
BseLI	CCNNNNNNNGG	2 cut(s)	758, 800
BseMII	CTCAG	4 cut(s)	420, 444, 813, 896
BseNI	ACTGG	2 cut(s)	205, 551
BseRI	GAGGAG	3 cut(s)	446, 456, 740
BseSI	GKGCMC	1 cut(s)	679
BseXI	GCAGC	3 cut(s)	580, 754, 908
Bsh1236I	CGCG	1 cut(s)	873
BsiHKAI	GWGCWC	1 cut(s)	679
BsiHKCI	CYCGRG	1 cut(s)	575
BsiSI	CCGG	1 cut(s)	576
BslFI	GGGAC	1 cut(s)	592
BslI	CCNNNNNNNGG	2 cut(s)	758, 800
BsmAI	GTCTC	2 cut(s)	251, 287
BsmFI	GGGAC	1 cut(s)	592
Bso31I	GGTCTC	1 cut(s)	287
BsoBI	CYCGRG	1 cut(s)	575
Bsp1286I	GDGCHC	1 cut(s)	679
Bsp143I	GATC	3 cut(s)	587, 874, 939
BspACI	CCGC	1 cut(s)	95
BspCNI	CTCAG	4 cut(s)	421, 445, 814, 897
BspFNI	CGCG	1 cut(s)	873
BspLI	GGNNCC	3 cut(s)	459, 549, 729
BspMI	ACCTGC	1 cut(s)	356
BspPI	GGATC	2 cut(s)	595, 947
BspTNI	GGTCTC	1 cut(s)	287
BsrI	ACTGG	2 cut(s)	205, 551
BssECI	CCNNGG	1 cut(s)	575
BssMI	GATC	3 cut(s)	587, 874, 939
Bst2UI	CCWGG	1 cut(s)	173
Bst4CI	ACNGT	2 cut(s)	563, 674
Bst6I	CTCTTC	2 cut(s)	93, 249
BstC8I	GCNNGC	3 cut(s)	516, 732, 753
BstDEI	CTNAG	5 cut(s)	340, 429, 453, 822, 905
BstENI	CCTNNNNNAGG	1 cut(s)	756
BstF5I	GGATG	5 cut(s)	153, 493, 538, 770, 892
BstFNI	CGCG	1 cut(s)	873
BstH2I	RGCGCY	1 cut(s)	515
BstHHI	GCGC	1 cut(s)	514
BstKTI	GATC	3 cut(s)	590, 877, 942
BstMAI	GTCTC	2 cut(s)	251, 287
BstMBI	GATC	3 cut(s)	587, 874, 939
BstMWI	GCNNNNNNNGC	4 cut(s)	32, 511, 599, 896
BstNI	CCWGG	1 cut(s)	173
BstPAI	GACNNNNGTC	1 cut(s)	561
BstSCI	CCNGG	3 cut(s)	171, 574, 575
BstSFI	CTRYAG	1 cut(s)	807
BstSLI	GKGCMC	1 cut(s)	679
BstUI	CGCG	1 cut(s)	873
BstV1I	GCAGC	3 cut(s)	580, 754, 908
BstV2I	GAAGAC	1 cut(s)	701
BstX2I	RGATCY	1 cut(s)	587
BstYI	RGATCY	1 cut(s)	587
Bsu36I	CCTNAGG	3 cut(s)	429, 453, 905
BsuI	GTATCC	1 cut(s)	915
BtsCI	GGATG	5 cut(s)	153, 493, 538, 770, 892
BtsI	GCAGTG	1 cut(s)	361
BtsIMutI	CAGTG	2 cut(s)	361, 679
BveI	ACCTGC	1 cut(s)	356
Cac8I	GCNNGC	3 cut(s)	516, 732, 753
CaiI	CAGNNNCTG	1 cut(s)	815
CfoI	GCGC	1 cut(s)	514
Cfr13I	GGNCC	3 cut(s)	175, 803, 812
Cfr9I	CCCGGG	1 cut(s)	575
CseI	GACGC	3 cut(s)	195, 654, 665
CsiI	ACCWGGT	1 cut(s)	171
Csp6I	GTAC	1 cut(s)	762
CviAII	CATG	1 cut(s)	383
CviJI	RGCY	4 cut(s)	413, 464, 730, 945
CviKI_1	RGCY	4 cut(s)	413, 464, 730, 945
CviQI	GTAC	1 cut(s)	762
DdeI	CTNAG	5 cut(s)	340, 429, 453, 822, 905
DpnI	GATC	3 cut(s)	589, 876, 941
DpnII	GATC	3 cut(s)	587, 874, 939
Eam1104I	CTCTTC	2 cut(s)	93, 249
EarI	CTCTTC	2 cut(s)	93, 249
Eco31I	GGTCTC	1 cut(s)	287
Eco47I	GGWCC	3 cut(s)	175, 803, 812
Eco47III	AGCGCT	1 cut(s)	513
Eco81I	CCTNAGG	3 cut(s)	429, 453, 905
Eco88I	CYCGRG	1 cut(s)	575
EcoNI	CCTNNNNNAGG	1 cut(s)	756
EcoO109I	RGGNCCY	1 cut(s)	812
EcoRII	CCWGG	1 cut(s)	171
FaeI	CATG	1 cut(s)	386
FaiI	YATR	4 cut(s)	72, 138, 384, 948
FaqI	GGGAC	1 cut(s)	592
FatI	CATG	1 cut(s)	382
Fnu4HI	GCNGC	3 cut(s)	594, 768, 897
FokI	GGATG	5 cut(s)	160, 500, 545, 757, 899
Fsp4HI	GCNGC	3 cut(s)	594, 768, 897
FspBI	CTAG	1 cut(s)	86
GlaI	GCGC	1 cut(s)	513
GluI	GCNGC	3 cut(s)	594, 768, 897
GsuI	CTGGAG	1 cut(s)	453
HaeII	RGCGCY	1 cut(s)	515
HapII	CCGG	1 cut(s)	576
HgaI	GACGC	3 cut(s)	195, 654, 665
HhaI	GCGC	1 cut(s)	514
Hin1II	CATG	1 cut(s)	386
Hin6I	GCGC	1 cut(s)	512
HinP1I	GCGC	1 cut(s)	512
HincII	GTYRAC	1 cut(s)	556
HindII	GTYRAC	1 cut(s)	556
HinfI	GANTC	1 cut(s)	124
HpaII	CCGG	1 cut(s)	576
HphI	GGTGA	8 cut(s)	215, 311, 380, 388, 662, 703, 849, 856
Hpy166II	GTNNAC	3 cut(s)	178, 556, 677
Hpy188I	TCNGA	4 cut(s)	185, 229, 739, 823
Hpy188III	TCNNGA	7 cut(s)	86, 128, 428, 470, 585, 878, 904
Hpy8I	GTNNAC	3 cut(s)	178, 556, 677
HpyAV	CCTTC	6 cut(s)	311, 355, 523, 622, 682, 877
HpyCH4III	ACNGT	2 cut(s)	563, 674
HpyCH4V	TGCA	9 cut(s)	7, 65, 518, 536, 677, 755, 770, 850, 896
HpyF10VI	GCNNNNNNNGC	4 cut(s)	32, 511, 599, 896
HpyF3I	CTNAG	5 cut(s)	340, 429, 453, 822, 905
Hsp92II	CATG	1 cut(s)	386
HspAI	GCGC	1 cut(s)	512
Kzo9I	GATC	3 cut(s)	587, 874, 939
LmnI	GCTCC	3 cut(s)	379, 469, 727
Lsp1109I	GCAGC	3 cut(s)	580, 754, 908
LweI	GCATC	4 cut(s)	523, 779, 837, 877
MabI	ACCWGGT	1 cut(s)	171
MaeI	CTAG	1 cut(s)	86
MaeIII	GTNAC	1 cut(s)	855
MalI	GATC	3 cut(s)	589, 876, 941
MboI	GATC	3 cut(s)	587, 874, 939
MflI	RGATCY	1 cut(s)	587
MhlI	GDGCHC	1 cut(s)	679
MluCI	AATT	6 cut(s)	155, 220, 443, 474, 641, 831
MlyI	GAGTC	1 cut(s)	118
MmeI	TCCRAC	1 cut(s)	693
MseI	TTAA	6 cut(s)	54, 423, 477, 570, 644, 956
MspI	CCGG	1 cut(s)	576
MspR9I	CCNGG	3 cut(s)	173, 576, 577
MvaI	CCWGG	1 cut(s)	173
MvnI	CGCG	1 cut(s)	873
MwoI	GCNNNNNNNGC	4 cut(s)	32, 511, 599, 896
NciI	CCSGG	2 cut(s)	576, 577
NdeII	GATC	3 cut(s)	587, 874, 939
NlaIII	CATG	1 cut(s)	386
NlaIV	GGNNCC	3 cut(s)	459, 549, 729
NmuCI	GTSAC	1 cut(s)	855
PaqCI	CACCTGC	1 cut(s)	356
PflFI	GACNNNGTC	1 cut(s)	279
PflMI	CCANNNNNTGG	1 cut(s)	800
PkrI	GCNGC	3 cut(s)	595, 769, 898
PleI	GAGTC	1 cut(s)	118
PpsI	GAGTC	1 cut(s)	118
PpuMI	RGGWCCY	1 cut(s)	812
PshAI	GACNNNNGTC	1 cut(s)	561
PshBI	ATTAAT	1 cut(s)	423
Psp5II	RGGWCCY	1 cut(s)	812
Psp6I	CCWGG	1 cut(s)	171
PspGI	CCWGG	1 cut(s)	171
PspN4I	GGNNCC	3 cut(s)	459, 549, 729
PspPI	GGNCC	3 cut(s)	175, 803, 812
PspPPI	RGGWCCY	1 cut(s)	812
PstNI	CAGNNNCTG	1 cut(s)	815
PsuI	RGATCY	1 cut(s)	587
PsyI	GACNNNGTC	1 cut(s)	279
RsaI	GTAC	1 cut(s)	763
RsaNI	GTAC	1 cut(s)	762
SaqAI	TTAA	6 cut(s)	54, 423, 477, 570, 644, 956
SatI	GCNGC	3 cut(s)	594, 768, 897
Sau3AI	GATC	3 cut(s)	587, 874, 939
Sau96I	GGNCC	3 cut(s)	175, 803, 812
SchI	GAGTC	1 cut(s)	118
ScrFI	CCNGG	3 cut(s)	173, 576, 577
SduI	GDGCHC	1 cut(s)	679
SexAI	ACCWGGT	1 cut(s)	171
SfaNI	GCATC	4 cut(s)	523, 779, 837, 877
SfcI	CTRYAG	1 cut(s)	807
SinI	GGWCC	3 cut(s)	175, 803, 812
SmaI	CCCGGG	1 cut(s)	577
SmlI	CTYRAG	3 cut(s)	126, 507, 878
SmoI	CTYRAG	3 cut(s)	126, 507, 878
Sse9I	AATT	6 cut(s)	155, 220, 443, 474, 641, 831
SsiI	CCGC	1 cut(s)	95
SspI	AATATT	1 cut(s)	393
SspMI	CTAG	1 cut(s)	86
StyD4I	CCNGG	3 cut(s)	171, 574, 575
TaaI	ACNGT	2 cut(s)	563, 674
TaqI	TCGA	1 cut(s)	776
TasI	AATT	6 cut(s)	155, 220, 443, 474, 641, 831
Tru1I	TTAA	6 cut(s)	54, 423, 477, 570, 644, 956
Tru9I	TTAA	6 cut(s)	54, 423, 477, 570, 644, 956
TscAI	CASTG	2 cut(s)	361, 679
TseFI	GTSAC	1 cut(s)	855
TseI	GCWGC	3 cut(s)	593, 767, 896
Tsp45I	GTSAC	1 cut(s)	855
TspDTI	ATGAA	7 cut(s)	122, 153, 167, 330, 342, 399, 423
TspMI	CCCGGG	1 cut(s)	575
TspRI	CASTG	2 cut(s)	361, 679
Tth111I	GACNNNGTC	1 cut(s)	279
Van91I	CCANNNNNTGG	1 cut(s)	800
VneI	GTGCAC	1 cut(s)	675
VpaK11BI	GGWCC	3 cut(s)	175, 803, 812
VspI	ATTAAT	1 cut(s)	423
XagI	CCTNNNNNAGG	1 cut(s)	756
XapI	RAATTY	2 cut(s)	220, 443
XbaI	TCTAGA	1 cut(s)	85
XmaI	CCCGGG	1 cut(s)	575
XspI	CTAG	1 cut(s)	86

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