Basic Information

Type: gene

Biological Identity

Species

rosa_samantha

Chromosome

Chr3C

Orthogroup ID

OG0006506

Physical Location & Seq

Genomic Coordinates Reverse (-)

12781737 .. 12786016

Gene Structure 4280 bp

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UTR

Exon/CDS

Intron

Transcript / Protein ID

Rh3CG153000.1

Sequence Viewer

CDS Protein Promoter (2k)

Length: 906 bp

ATGGAGGTTGAGTATTTCGGAGACTCTTTTGGTGAGCTATCTCGGAGAAATTCTAGCCCAACAACTCCTAGGTCAGCTTCGGCGAGCAATGCAGCTGCTTCTGAGAGTGTCCGGAGCTCCTCGAACAGTATGACTTTCCATTGTGACAGTACAAGTACACCAGATGTTGACAAAAATGCGGGAAAGAAGAAAAGAGGCTCAAGATATACAGCTGGAGGTCTACGTCAGTTCAGTGCCATAGTTTGCAGCAAGTTGAAGAGCAAGGGAAGAGCAACATATAATGAGGTTGCAGATGAGATCATTTCAGAGTTACCTGGAATTTACGGTGAAACAGAAGCTTTGAGTGAGTTTGATGAGAAAAACATACGACGACGAGTATATGATGCATTAAATGTTCTTATGGCAATGGATATCATCACCAAAGAGAAAAAACAAATCCAGTGGAAAGGACTTCCAGATACAAATGTTATTGATCTGGAAGGTATTAAGGCTCAGCGGGTTAAATTGATGGGTAGGATTGGTGCAAAAGAGGCTTACTTGAAAGACTTGGAAGAACAAATGGCAGATCTCCAGAATTTGATGTTGCGTAATAAGCAGTTGATCAAGAGTGGAAACAGTCACCACAAAGGATTTTCTTTTCCATTTATACTGGCTCAGACAAGCAATAATGCTACGGTTGAGATTGAGATTTCTGAAGATATGCAGTTGGTGCACTGTGACTTCAATAGTACCCCTTTCTCCTTGCACGATGATACTTCCATTCTGAAGCTATTGCGGTGCCACCAATTGCCAGAAAGTAGAAATGTGTCTCAAAGTTCTTCTGTTTACTCGTCTTCAAGTTCTGGCATGGCTTCTGGAGGCACCAGACCCTTTCTTTGGAACTCTGAAACAGAAACTCCAAAATGA

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

301

Amino Acids

33.36

Weight (kDa)

7.02

Isoelectric Point (pI)

55.65

Instability Index

Protein Domains (Pfam)

Domain Name	Pfam ID	Position	E-value	Description
WHD_E2F_TDP	PF02319	72 - 150	8.3e-17	E2F/DP family winged-helix DNA-binding domain
DP	PF08781	159 - 269	2.7e-27	Transcription factor DP

Hydrophobicity Profile (Kyte-Doolittle)

AI Structure Prediction Report

Calculating structure properties...

Genomic Context

Gene Family Tree

Species Filter

Style Settings

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Align Labels (Cladogram)

Image

Tree File

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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)
AccB1I	GGYRCC	2 cut(s)	777, 860
AccI	GTMKAC	1 cut(s)	220
AccIII	TCCGGA	1 cut(s)	111
AciI	CCGC	3 cut(s)	179, 496, 775
AcsI	RAATTY	3 cut(s)	49, 318, 574
AcuI	CTGAAG	2 cut(s)	714, 785
AfaI	GTAC	3 cut(s)	151, 157, 730
AfiI	CCNNNNNNNGG	1 cut(s)	876
AgsI	TTSAA	4 cut(s)	256, 541, 724, 837
AjnI	CCWGG	1 cut(s)	313
AluBI	AGCT	7 cut(s)	37, 77, 95, 117, 212, 338, 769
AluI	AGCT	7 cut(s)	37, 77, 95, 117, 212, 338, 769
Alw21I	GWGCWC	2 cut(s)	119, 714
Alw26I	GTCTC	2 cut(s)	15, 813
Alw44I	GTGCAC	1 cut(s)	710
Aor13HI	TCCGGA	1 cut(s)	111
ApaLI	GTGCAC	1 cut(s)	710
ApeKI	GCWGC	3 cut(s)	92, 95, 246
ApoI	RAATTY	3 cut(s)	49, 318, 574
ArsI	GACNNNNNNTTYG	2 cut(s)	858, 890
AspA2I	CCTAGG	1 cut(s)	68
AsuHPI	GGTGA	4 cut(s)	44, 338, 409, 611
AvrII	CCTAGG	1 cut(s)	68
BaeGI	GKGCMC	1 cut(s)	714
BaeI	ACNNNNGTAYC	2 cut(s)	450, 483
BanI	GGYRCC	2 cut(s)	777, 860
BanII	GRGCYC	1 cut(s)	119
BbsI	GAAGAC	1 cut(s)	825
Bbv12I	GWGCWC	2 cut(s)	119, 714
BbvI	GCAGC	3 cut(s)	82, 104, 258
BccI	CCATC	1 cut(s)	502
BciT130I	CCWGG	1 cut(s)	315
BclI	TGATCA	1 cut(s)	600
BcoDI	GTCTC	2 cut(s)	15, 813
BfaI	CTAG	2 cut(s)	54, 69
BglII	AGATCT	1 cut(s)	565
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
BmiI	GGNNCC	2 cut(s)	779, 862
BmrFI	CCNGG	1 cut(s)	315
BmsI	GCATC	1 cut(s)	373
BpiI	GAAGAC	1 cut(s)	825
BpmI	CTGGAG	3 cut(s)	234, 554, 876
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	2 cut(s)	26, 880
Bsc4I	CCNNNNNNNGG	1 cut(s)	876
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
BseLI	CCNNNNNNNGG	1 cut(s)	876
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
BseSI	GKGCMC	1 cut(s)	714
BseXI	GCAGC	3 cut(s)	82, 104, 258
BshNI	GGYRCC	2 cut(s)	777, 860
BsiHKAI	GWGCWC	2 cut(s)	119, 714
BsiSI	CCGG	1 cut(s)	112
BslI	CCNNNNNNNGG	1 cut(s)	876
BsmAI	GTCTC	2 cut(s)	15, 813
Bsp1286I	GDGCHC	2 cut(s)	119, 714
Bsp13I	TCCGGA	1 cut(s)	111
Bsp143I	GATC	4 cut(s)	297, 472, 565, 600
Bsp1720I	GCTNAGC	1 cut(s)	492
BspACI	CCGC	3 cut(s)	179, 496, 775
BspCNI	CTCAG	3 cut(s)	94, 505, 667
BspEI	TCCGGA	1 cut(s)	111
BspLI	GGNNCC	2 cut(s)	779, 862
BspQI	GCTCTTC	2 cut(s)	251, 262
BspT107I	GGYRCC	2 cut(s)	777, 860
BsrDI	GCAATG	2 cut(s)	94, 411
BsrI	ACTGG	2 cut(s)	439, 654
BssECI	CCNNGG	1 cut(s)	68
BssMI	GATC	4 cut(s)	297, 472, 565, 600
BssT1I	CCWWGG	1 cut(s)	68
Bst2UI	CCWGG	1 cut(s)	315
Bst4CI	ACNGT	6 cut(s)	128, 149, 326, 617, 676, 716
Bst6I	CTCTTC	2 cut(s)	251, 262
BstAPI	GCANNNNNTGC	1 cut(s)	709
BstC8I	GCNNGC	1 cut(s)	85
BstDEI	CTNAG	3 cut(s)	102, 492, 654
BstKTI	GATC	4 cut(s)	300, 475, 568, 603
BstMAI	GTCTC	2 cut(s)	15, 813
BstMBI	GATC	4 cut(s)	297, 472, 565, 600
BstMWI	GCNNNNNNNGC	4 cut(s)	89, 530, 592, 709
BstNI	CCWGG	1 cut(s)	315
BstSCI	CCNGG	1 cut(s)	313
BstSLI	GKGCMC	1 cut(s)	714
BstV1I	GCAGC	3 cut(s)	82, 104, 258
BstV2I	GAAGAC	1 cut(s)	825
BstX2I	RGATCY	1 cut(s)	565
BstYI	RGATCY	1 cut(s)	565
BtsIMutI	CAGTG	3 cut(s)	238, 446, 712
Cac8I	GCNNGC	1 cut(s)	85
Csp6I	GTAC	3 cut(s)	150, 156, 729
CspCI	CAANNNNNGTGG	2 cut(s)	422, 457
CviAII	CATG	1 cut(s)	847
CviQI	GTAC	3 cut(s)	150, 156, 729
DdeI	CTNAG	3 cut(s)	102, 492, 654
DpnI	GATC	4 cut(s)	299, 474, 567, 602
DpnII	GATC	4 cut(s)	297, 472, 565, 600
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	1 cut(s)	119
Eco32I	GATATC	1 cut(s)	412
Eco53kI	GAGCTC	1 cut(s)	117
Eco57I	CTGAAG	2 cut(s)	714, 785
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	1 cut(s)	119
ErhI	CCWWGG	1 cut(s)	68
FaeI	CATG	1 cut(s)	850
FatI	CATG	1 cut(s)	846
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	1 cut(s)	119
Fsp4HI	GCNGC	3 cut(s)	93, 96, 247
FspBI	CTAG	2 cut(s)	54, 69
GluI	GCNGC	3 cut(s)	93, 96, 247
GsuI	CTGGAG	3 cut(s)	234, 554, 876
HapII	CCGG	1 cut(s)	112
Hin1II	CATG	1 cut(s)	850
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	4 cut(s)	44, 338, 409, 611
Hpy166II	GTNNAC	5 cut(s)	158, 169, 221, 712, 826
Hpy188I	TCNGA	8 cut(s)	20, 45, 103, 307, 657, 694, 765, 886
Hpy188III	TCNNGA	7 cut(s)	112, 201, 455, 476, 571, 604, 855
Hpy8I	GTNNAC	5 cut(s)	158, 169, 221, 712, 826
Hpy99I	CGWCG	2 cut(s)	372, 375
HpyAV	CCTTC	1 cut(s)	473
HpyCH4III	ACNGT	6 cut(s)	128, 149, 326, 617, 676, 716
HpyCH4IV	ACGT	1 cut(s)	223
HpyCH4V	TGCA	8 cut(s)	92, 246, 290, 386, 524, 703, 712, 745
HpyF10VI	GCNNNNNNNGC	4 cut(s)	89, 530, 592, 709
HpyF3I	CTNAG	3 cut(s)	102, 492, 654
HpySE526I	ACGT	1 cut(s)	223
Hsp92II	CATG	1 cut(s)	850
Kpn2I	TCCGGA	1 cut(s)	111
Ksp22I	TGATCA	1 cut(s)	600
Kzo9I	GATC	4 cut(s)	297, 472, 565, 600
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	4 cut(s)	143, 309, 617, 716
MalI	GATC	4 cut(s)	299, 474, 567, 602
MboI	GATC	4 cut(s)	297, 472, 565, 600
MboII	GAAGA	7 cut(s)	199, 268, 279, 563, 707, 810, 825
MfeI	CAATTG	1 cut(s)	785
MflI	RGATCY	1 cut(s)	565
MhlI	GDGCHC	2 cut(s)	119, 714
MluCI	AATT	5 cut(s)	49, 318, 503, 574, 785
MlyI	GAGTC	1 cut(s)	17
MnlI	CCTC	6 cut(s)	130, 188, 209, 277, 523, 851
Mph1103I	ATGCAT	1 cut(s)	388
MroI	TCCGGA	1 cut(s)	111
MseI	TTAA	3 cut(s)	389, 486, 501
MspA1I	CMGCKG	3 cut(s)	95, 212, 496
MspI	CCGG	1 cut(s)	112
MspR9I	CCNGG	1 cut(s)	315
MunI	CAATTG	1 cut(s)	785
MvaI	CCWGG	1 cut(s)	315
MwoI	GCNNNNNNNGC	4 cut(s)	89, 530, 592, 709
NdeII	GATC	4 cut(s)	297, 472, 565, 600
NlaIII	CATG	1 cut(s)	850
NlaIV	GGNNCC	2 cut(s)	779, 862
NmuCI	GTSAC	3 cut(s)	143, 617, 716
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
PspN4I	GGNNCC	2 cut(s)	779, 862
PsuI	RGATCY	1 cut(s)	565
PvuII	CAGCTG	2 cut(s)	95, 212
RsaI	GTAC	3 cut(s)	151, 157, 730
RsaNI	GTAC	3 cut(s)	150, 156, 729
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	4 cut(s)	297, 472, 565, 600
SchI	GAGTC	1 cut(s)	17
ScrFI	CCNGG	1 cut(s)	315
SduI	GDGCHC	2 cut(s)	119, 714
SfaNI	GCATC	1 cut(s)	373
SmlI	CTYRAG	1 cut(s)	199
SmoI	CTYRAG	1 cut(s)	199
Sse9I	AATT	5 cut(s)	49, 318, 503, 574, 785
SsiI	CCGC	3 cut(s)	179, 496, 775
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	6 cut(s)	128, 149, 326, 617, 676, 716
TaiI	ACGT	1 cut(s)	226
TaqI	TCGA	1 cut(s)	122
TasI	AATT	5 cut(s)	49, 318, 503, 574, 785
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	3 cut(s)	238, 446, 719
TseFI	GTSAC	3 cut(s)	143, 617, 716
TseI	GCWGC	3 cut(s)	92, 95, 246
Tsp45I	GTSAC	3 cut(s)	143, 617, 716
TspRI	CASTG	3 cut(s)	238, 446, 719
VneI	GTGCAC	1 cut(s)	710
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.