Basic Information

Type: gene

Biological Identity

Species

rosa_samantha

Chromosome

Chr3A

Orthogroup ID

OG0006506

Physical Location & Seq

Genomic Coordinates Reverse (-)

11392152 .. 11396633

Gene Structure 4482 bp

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UTR

Exon/CDS

Intron

Transcript / Protein ID

Rh3AG131700.1

Sequence Viewer

CDS Protein Promoter (2k)

Length: 726 bp

ATGGAGTTTGAGTATTTCGGAGACTCTTTTGGTGAGCTATCTCGGAGAAATTCTAGCCCAATAACTCCTAGGTCAGCTTCGGCGAGCAATGCAGCTGCTTCTGAGAGTGTCCGGAGCTCCTCGAACAGTATGACTTTCCATTGTGACAGTACAAGTACACCAGATGTTGACAAAAATGCGGGAAAGAAGAAAAGGGGCTCAAGATATACAGCTGGAGGTCTACGTCAGTTCAGCGCCATAGTTTGCAGCAAGTTGAAGAGCAAGGGAAGAGCAACATATAATGAGGTTGCAGATGAGATCATTTCAGAGTTACCTGGAATTTACGGTGAAACAGAAGCTTTGAGTGAGTTTGATGAGAAAAACATACGACGACGAGTATATGATGCATTAAATGTTCTTATGGCAATGGATATCATCACCAAAGAGAAAAAACAAATCCAGTGGAAAGGACTTCCAGATACAAATGTTATTGATCTGGAAGGTATTAAGGCTCAGCGGGTTAAATTGATGGGCAGGATTGGTGCAAAAGAGGCTTACTTGAAAGACTTGGAAGAACAAATGGCAGATCTCCAGAATTTGATGTTGCGTAATAAGCAGTTGATCAAGAGTGGAAACAGTCGCCACAAAGGATTTTCTTTTCCATTTATACTGGCTCAGGTATATAGATCTTATTGGTTGTTTGCTGGCATTATGATGGTTAGAAATCAATTTTATAGTTCTAATTGA

Functional Annotation

Gene Ontology

Molecular Function
Biological Process
Cellular Component

GO:0000082 GO:0000278 GO:0000981 GO:0003674 GO:0003700 GO:0005488 GO:0005515 GO:0005575 GO:0005622 GO:0005623 GO:0005634 GO:0005737 GO:0006139 GO:0006259 GO:0006260 GO:0006261 GO:0006355 GO:0006357 GO:0006725 GO:0006807 GO:0007049 GO:0008150 GO:0008152 GO:0009058 GO:0009059 GO:0009889 GO:0009987 GO:0010468 GO:0010556 GO:0019219 GO:0019222 GO:0022402 GO:0031323 GO:0031326 GO:0034641 GO:0034645 GO:0042023 GO:0043170 GO:0043226 GO:0043227 GO:0043229 GO:0043231 GO:0044237 GO:0044238 GO:0044249 GO:0044260 GO:0044424 GO:0044464 GO:0044770 GO:0044772 GO:0044786 GO:0044843 GO:0046483 GO:0046982 GO:0046983 GO:0050789 GO:0050794 GO:0051171 GO:0051252 GO:0060255 GO:0065007 GO:0071704 GO:0080090 GO:0090304 GO:0140110 GO:1901360 GO:1901576 GO:1903047 GO:1903506 GO:2000112 GO:2001141

KEGG Pathways

Metabolic & Signaling

ko04110 ko04350 map04110 map04350

Pfam Domains

Protein Families

DP E2F_TDP

Protein Analysis

241

Amino Acids

27.15

Weight (kDa)

9.39

Isoelectric Point (pI)

47.05

Instability Index

Protein Domains (Pfam)

Domain Name	Pfam ID	Position	E-value	Description
WHD_E2F_TDP	PF02319	72 - 150	5.4e-17	E2F/DP family winged-helix DNA-binding domain
DP	PF08781	159 - 219	8.9e-09	Transcription factor DP

Hydrophobicity Profile (Kyte-Doolittle)

AI Structure Prediction Report

Calculating structure properties...

Genomic Context

Gene Family Tree

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Align Labels (Cladogram)

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Publication-ready

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Orthologous Genes (Group: OG0006506)

Species	Orthologous Gene IDs
arabidopsis_thaliana	AT5G02470 AT5G02470 AT5G02470
fragaria_vesca	FvH4_6g14010 FvH4_6g14010 FvH4_6g14010 FvH4_6g14010 FvH4_6g14010 FvH4_6g14010 FvH4_6g14010
malus_domestica	MD04G1126400.v1.1
prunus_persica	Prupe.6G253200_v2.0.a1 Prupe.6G253200_v2.0.a1
pyrus_communis	pycom04g11340
rosa_chinensis	RchiOBHm_Chr3g0466841
rosa_laevigata	RLG00000024547
rosa_multiflora	Rmu_sc0026100.1_g000001
rosa_roxburghii	Rroxscaffold_6G00414090
rosa_rugosa	Rorug03G0083900 Rorug03G0084000 Rorug03G0084100
rosa_samantha	Rh3AG131700 Rh3BG152800 Rh3CG153000 Rh3DG153900
rosa_wichuraiana	Rw3G012450

Restriction Enzyme Sites

1 / 10

Enzyme	Recognition Site	Cut Count	Positions (bp)
AccI	GTMKAC	1 cut(s)	220
AccIII	TCCGGA	1 cut(s)	111
AciI	CCGC	2 cut(s)	179, 496
AcsI	RAATTY	3 cut(s)	49, 318, 574
AfaI	GTAC	2 cut(s)	151, 157
AgsI	TTSAA	2 cut(s)	256, 541
AjnI	CCWGG	1 cut(s)	313
AluBI	AGCT	6 cut(s)	37, 77, 95, 117, 212, 338
AluI	AGCT	6 cut(s)	37, 77, 95, 117, 212, 338
Alw21I	GWGCWC	1 cut(s)	119
Alw26I	GTCTC	1 cut(s)	15
Aor13HI	TCCGGA	1 cut(s)	111
ApeKI	GCWGC	3 cut(s)	92, 95, 246
ApoI	RAATTY	3 cut(s)	49, 318, 574
AspA2I	CCTAGG	1 cut(s)	68
AspLEI	GCGC	1 cut(s)	236
AsuHPI	GGTGA	3 cut(s)	44, 338, 409
AvrII	CCTAGG	1 cut(s)	68
BaeI	ACNNNNGTAYC	2 cut(s)	450, 483
BanII	GRGCYC	2 cut(s)	119, 200
Bbv12I	GWGCWC	1 cut(s)	119
BbvI	GCAGC	3 cut(s)	82, 104, 258
BccI	CCATC	2 cut(s)	502, 688
BciT130I	CCWGG	1 cut(s)	315
BclI	TGATCA	1 cut(s)	600
BcoDI	GTCTC	1 cut(s)	15
BfaI	CTAG	2 cut(s)	54, 69
BfoI	RGCGCY	1 cut(s)	237
BglII	AGATCT	2 cut(s)	565, 665
BisI	GCNGC	3 cut(s)	93, 96, 247
BlnI	CCTAGG	1 cut(s)	68
BlpI	GCTNAGC	1 cut(s)	492
BlsI	GCNGC	3 cut(s)	94, 97, 248
Bme1390I	CCNGG	1 cut(s)	315
BmrFI	CCNGG	1 cut(s)	315
BmsI	GCATC	1 cut(s)	373
BpmI	CTGGAG	2 cut(s)	234, 554
Bpu10I	CCTNAGC	1 cut(s)	654
Bpu1102I	GCTNAGC	1 cut(s)	492
BpuEI	CTTGAG	1 cut(s)	184
BsaJI	CCNNGG	1 cut(s)	68
BsaWI	WCCGGW	1 cut(s)	111
BsaXI	ACNNNNNCTCC	1 cut(s)	26
Bse1I	ACTGG	2 cut(s)	439, 654
Bse3DI	GCAATG	2 cut(s)	94, 411
BseAI	TCCGGA	1 cut(s)	111
BseBI	CCWGG	1 cut(s)	315
BseDI	CCNNGG	1 cut(s)	68
BseMI	GCAATG	2 cut(s)	94, 411
BseMII	CTCAG	3 cut(s)	93, 506, 668
BseNI	ACTGG	2 cut(s)	439, 654
BseRI	GAGGAG	1 cut(s)	109
BseXI	GCAGC	3 cut(s)	82, 104, 258
BsiHKAI	GWGCWC	1 cut(s)	119
BsiSI	CCGG	1 cut(s)	112
BsmAI	GTCTC	1 cut(s)	15
Bsp1286I	GDGCHC	2 cut(s)	119, 200
Bsp13I	TCCGGA	1 cut(s)	111
Bsp143I	GATC	5 cut(s)	297, 472, 565, 600, 665
Bsp1720I	GCTNAGC	1 cut(s)	492
BspACI	CCGC	2 cut(s)	179, 496
BspCNI	CTCAG	3 cut(s)	94, 505, 667
BspEI	TCCGGA	1 cut(s)	111
BspQI	GCTCTTC	2 cut(s)	251, 262
BsrDI	GCAATG	2 cut(s)	94, 411
BsrI	ACTGG	2 cut(s)	439, 654
BssECI	CCNNGG	1 cut(s)	68
BssMI	GATC	5 cut(s)	297, 472, 565, 600, 665
BssT1I	CCWWGG	1 cut(s)	68
Bst2UI	CCWGG	1 cut(s)	315
Bst4CI	ACNGT	4 cut(s)	128, 149, 326, 617
Bst6I	CTCTTC	2 cut(s)	251, 262
BstC8I	GCNNGC	2 cut(s)	85, 685
BstDEI	CTNAG	3 cut(s)	102, 492, 654
BstH2I	RGCGCY	1 cut(s)	237
BstHHI	GCGC	1 cut(s)	236
BstKTI	GATC	5 cut(s)	300, 475, 568, 603, 668
BstMAI	GTCTC	1 cut(s)	15
BstMBI	GATC	5 cut(s)	297, 472, 565, 600, 665
BstMWI	GCNNNNNNNGC	3 cut(s)	89, 530, 592
BstNI	CCWGG	1 cut(s)	315
BstSCI	CCNGG	1 cut(s)	313
BstV1I	GCAGC	3 cut(s)	82, 104, 258
BstX2I	RGATCY	2 cut(s)	565, 665
BstYI	RGATCY	2 cut(s)	565, 665
BtsIMutI	CAGTG	1 cut(s)	446
Cac8I	GCNNGC	2 cut(s)	85, 685
CfoI	GCGC	1 cut(s)	236
Csp6I	GTAC	2 cut(s)	150, 156
CspCI	CAANNNNNGTGG	2 cut(s)	422, 457
CviQI	GTAC	2 cut(s)	150, 156
DdeI	CTNAG	3 cut(s)	102, 492, 654
DpnI	GATC	5 cut(s)	299, 474, 567, 602, 667
DpnII	GATC	5 cut(s)	297, 472, 565, 600, 665
Eam1104I	CTCTTC	2 cut(s)	251, 262
EarI	CTCTTC	2 cut(s)	251, 262
Ecl136II	GAGCTC	1 cut(s)	117
Eco130I	CCWWGG	1 cut(s)	68
Eco24I	GRGCYC	2 cut(s)	119, 200
Eco32I	GATATC	1 cut(s)	412
Eco53kI	GAGCTC	1 cut(s)	117
EcoICRI	GAGCTC	1 cut(s)	117
EcoRII	CCWGG	1 cut(s)	313
EcoRV	GATATC	1 cut(s)	412
EcoT14I	CCWWGG	1 cut(s)	68
EcoT22I	ATGCAT	1 cut(s)	388
EcoT38I	GRGCYC	2 cut(s)	119, 200
ErhI	CCWWGG	1 cut(s)	68
FauI	CCCGC	2 cut(s)	172, 489
FbaI	TGATCA	1 cut(s)	600
FblI	GTMKAC	1 cut(s)	220
Fnu4HI	GCNGC	3 cut(s)	93, 96, 247
FriOI	GRGCYC	2 cut(s)	119, 200
Fsp4HI	GCNGC	3 cut(s)	93, 96, 247
FspBI	CTAG	2 cut(s)	54, 69
GlaI	GCGC	1 cut(s)	235
GluI	GCNGC	3 cut(s)	93, 96, 247
GsuI	CTGGAG	2 cut(s)	234, 554
HaeII	RGCGCY	1 cut(s)	237
HapII	CCGG	1 cut(s)	112
HhaI	GCGC	1 cut(s)	236
Hin6I	GCGC	1 cut(s)	234
HinP1I	GCGC	1 cut(s)	234
HincII	GTYRAC	1 cut(s)	169
HindII	GTYRAC	1 cut(s)	169
HindIII	AAGCTT	1 cut(s)	336
HinfI	GANTC	1 cut(s)	23
HpaII	CCGG	1 cut(s)	112
HphI	GGTGA	3 cut(s)	44, 338, 409
Hpy166II	GTNNAC	3 cut(s)	158, 169, 221
Hpy188I	TCNGA	4 cut(s)	20, 45, 103, 307
Hpy188III	TCNNGA	6 cut(s)	112, 201, 455, 476, 571, 604
Hpy8I	GTNNAC	3 cut(s)	158, 169, 221
Hpy99I	CGWCG	2 cut(s)	372, 375
HpyAV	CCTTC	1 cut(s)	473
HpyCH4III	ACNGT	4 cut(s)	128, 149, 326, 617
HpyCH4IV	ACGT	1 cut(s)	223
HpyCH4V	TGCA	5 cut(s)	92, 246, 290, 386, 524
HpyF10VI	GCNNNNNNNGC	3 cut(s)	89, 530, 592
HpyF3I	CTNAG	3 cut(s)	102, 492, 654
HpySE526I	ACGT	1 cut(s)	223
HspAI	GCGC	1 cut(s)	234
Kpn2I	TCCGGA	1 cut(s)	111
Ksp22I	TGATCA	1 cut(s)	600
Kzo9I	GATC	5 cut(s)	297, 472, 565, 600, 665
LguI	GCTCTTC	2 cut(s)	251, 262
LmnI	GCTCC	2 cut(s)	114, 122
Lsp1109I	GCAGC	3 cut(s)	82, 104, 258
LweI	GCATC	1 cut(s)	373
MaeI	CTAG	2 cut(s)	54, 69
MaeII	ACGT	1 cut(s)	223
MaeIII	GTNAC	2 cut(s)	143, 309
MalI	GATC	5 cut(s)	299, 474, 567, 602, 667
MboI	GATC	5 cut(s)	297, 472, 565, 600, 665
MboII	GAAGA	4 cut(s)	199, 268, 279, 563
MflI	RGATCY	2 cut(s)	565, 665
MhlI	GDGCHC	2 cut(s)	119, 200
MluCI	AATT	6 cut(s)	49, 318, 503, 574, 707, 721
MlyI	GAGTC	1 cut(s)	17
MnlI	CCTC	4 cut(s)	130, 209, 277, 523
Mph1103I	ATGCAT	1 cut(s)	388
MroI	TCCGGA	1 cut(s)	111
MseI	TTAA	3 cut(s)	389, 486, 501
MslI	CAYNNNNRTG	1 cut(s)	692
MspA1I	CMGCKG	3 cut(s)	95, 212, 496
MspI	CCGG	1 cut(s)	112
MspR9I	CCNGG	1 cut(s)	315
MvaI	CCWGG	1 cut(s)	315
MwoI	GCNNNNNNNGC	3 cut(s)	89, 530, 592
NdeII	GATC	5 cut(s)	297, 472, 565, 600, 665
NmuCI	GTSAC	1 cut(s)	143
NsiI	ATGCAT	1 cut(s)	388
PciSI	GCTCTTC	2 cut(s)	251, 262
PkrI	GCNGC	3 cut(s)	94, 97, 248
PleI	GAGTC	1 cut(s)	17
PpsI	GAGTC	1 cut(s)	17
Psp124BI	GAGCTC	1 cut(s)	119
Psp6I	CCWGG	1 cut(s)	313
PspGI	CCWGG	1 cut(s)	313
PsuI	RGATCY	2 cut(s)	565, 665
PvuII	CAGCTG	2 cut(s)	95, 212
RsaI	GTAC	2 cut(s)	151, 157
RsaNI	GTAC	2 cut(s)	150, 156
RseI	CAYNNNNRTG	1 cut(s)	692
SacI	GAGCTC	1 cut(s)	119
SapI	GCTCTTC	2 cut(s)	251, 262
SaqAI	TTAA	3 cut(s)	389, 486, 501
SatI	GCNGC	3 cut(s)	93, 96, 247
Sau3AI	GATC	5 cut(s)	297, 472, 565, 600, 665
SchI	GAGTC	1 cut(s)	17
ScrFI	CCNGG	1 cut(s)	315
SduI	GDGCHC	2 cut(s)	119, 200
SfaNI	GCATC	1 cut(s)	373
SmiMI	CAYNNNNRTG	1 cut(s)	692
SmlI	CTYRAG	1 cut(s)	199
SmoI	CTYRAG	1 cut(s)	199
Sse9I	AATT	6 cut(s)	49, 318, 503, 574, 707, 721
SsiI	CCGC	2 cut(s)	179, 496
SspMI	CTAG	2 cut(s)	54, 69
SstI	GAGCTC	1 cut(s)	119
StyD4I	CCNGG	1 cut(s)	313
StyI	CCWWGG	1 cut(s)	68
TaaI	ACNGT	4 cut(s)	128, 149, 326, 617
TaiI	ACGT	1 cut(s)	226
TaqI	TCGA	1 cut(s)	122
TasI	AATT	6 cut(s)	49, 318, 503, 574, 707, 721
TatI	WGTACW	2 cut(s)	149, 155
Tru1I	TTAA	3 cut(s)	389, 486, 501
Tru9I	TTAA	3 cut(s)	389, 486, 501
TscAI	CASTG	1 cut(s)	446
TseFI	GTSAC	1 cut(s)	143
TseI	GCWGC	3 cut(s)	92, 95, 246
Tsp45I	GTSAC	1 cut(s)	143
TspRI	CASTG	1 cut(s)	446
XapI	RAATTY	3 cut(s)	49, 318, 574
XmaJI	CCTAGG	1 cut(s)	68
XmiI	GTMKAC	1 cut(s)	220
XspI	CTAG	2 cut(s)	54, 69
Zsp2I	ATGCAT	1 cut(s)	388

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