Basic Information

Type: gene

Biological Identity

Species

rosa_samantha

Chromosome

Chr3C

Orthogroup ID

OG0011572

Physical Location & Seq

Genomic Coordinates Forward (+)

3446013 .. 3452079

Gene Structure 6067 bp

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UTR

Exon/CDS

Intron

Transcript / Protein ID

Rh3CG050800.1

Sequence Viewer

CDS Protein Promoter (2k)

Length: 930 bp

ATGACTCTCAGCAGTATTCCGTTGGCTACGTCGGATCTTCAAATCGGTCATGGAGCTCGAAGAAATTCGACACTAATCTGTGCGCCGGTAATGGGGGAATCAGTTGATCAGATGCTGCGTCAAGTGCGACAGGCAAAGGAACTTGGTGCTGACCTTGTTGAGATTCGGTTGGACTACATTAAGAACTTCAGTCCAAGACAAGATCTCGAAACTTTGATTAAGCGCAGCCCTTTGCCAACACTCGTCACTTACAGGCCAAAATGGGAAGGTGGTGAGTATGAAGGAGATGAAAATAAGCGACAAGAGGCACTCATTTTAGCCATGGAATTGGGAGCGGATTATATTGATGTTGAACTAAAGGTAGCAAATGACTTCTACAGTTCTATTCAAGGGAAGAAGCCAGAAAAGGTCAAAATCATAGTTTCTTCCCACAACTATGAGAATACTCCATCTGCTGAGGAAATTGGCAATCTTGTTGCAACGATACAAGCCATTGGAGCTGACATAGTCAAGGTCGCAACAACTGCCTTGGACATAACAGACAATGCAAGAATATTTCAAGTGCTAGCGCGTTCTCAAGTCCCAATGATAGGACTTTTGATGGGTGAGAAGGGTTTGATCTCTCGTGTACTTAGTGCAAAATATGGGTCATATGTCACATTTGGTACACTAGAGGCAGGTGAGGTATCAGCTCCTGGCCAGCCAACTGTAACGGATCTGTTGGAGTTATACAATTTTAGGCAGATTGGAGCCGATACCAAAGTACATGGTGTGATAGGAAATCCTATTGGTCACAGCAAAAGTCCTCATCTTTACAATGCAGCATTTAAAGCCAATAACTTCAATGGAATTTATCTGCCATTGCTGGTTGATAGCGTTGCAAACTTTATCAACACCTATAACTCCCCTGATTGGGTTGGATACAGGTAA

Functional Annotation

Gene Ontology

Molecular Function
Biological Process
Cellular Component

GO:0000003 GO:0003006 GO:0003674 GO:0003824 GO:0004764 GO:0005575 GO:0005622 GO:0005623 GO:0005737 GO:0006082 GO:0007275 GO:0008150 GO:0008152 GO:0009058 GO:0009423 GO:0009507 GO:0009532 GO:0009536 GO:0009570 GO:0009790 GO:0009791 GO:0009793 GO:0009987 GO:0010154 GO:0016053 GO:0016491 GO:0016614 GO:0016616 GO:0019632 GO:0019752 GO:0022414 GO:0032501 GO:0032502 GO:0032787 GO:0043226 GO:0043227 GO:0043229 GO:0043231 GO:0043436 GO:0043648 GO:0043650 GO:0044237 GO:0044249 GO:0044281 GO:0044283 GO:0044422 GO:0044424 GO:0044434 GO:0044435 GO:0044444 GO:0044446 GO:0044464 GO:0046394 GO:0046417 GO:0048316 GO:0048608 GO:0048731 GO:0048856 GO:0055114 GO:0061458 GO:0071704 GO:1901576 GO:1901615

KEGG Pathways

Metabolic & Signaling

ko00400 ko01100 ko01110 ko01130 ko01230 map00400 map01100 map01110 map01130 map01230

Pfam Domains

Protein Families

DHquinase_I Shikimate_DH Shikimate_dh_N

Protein Analysis

309

Amino Acids

33.93

Weight (kDa)

5.63

Isoelectric Point (pI)

26.38

Instability Index

Protein Domains (Pfam)

Domain Name	Pfam ID	Position	E-value	Description
DHquinase_I	PF01487	27 - 244	1.5e-70	Type I 3-dehydroquinase
Shikimate_dh_N	PF08501	258 - 308	2.6e-09	Shikimate dehydrogenase substrate binding domain

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: OG0011572)

Species	Orthologous Gene IDs
fragaria_vesca	FvH4_6g04670 FvH4_6g04670 FvH4_6g04670
malus_domestica	MD04G1213800.v1.1 MD12G1228800.v1.1
prunus_persica	Prupe.6G334000_v2.0.a1 Prupe.6G334000_v2.0.a1
pyrus_communis	pycom04g18930 pycom12g21340
rosa_chinensis	RchiOBHm_Chr3g0453141
rosa_laevigata	RLG00000025534
rosa_multiflora	Rmu_sc0007132.1_g000006 Rmu_sc0013481.1_g000002
rosa_roxburghii	Rroxscaffold_6G00430200
rosa_rugosa	Rorug02G0646800
rosa_samantha	Rh3AG049400 Rh3BG050600 Rh3CG050800 Rh3DG051400
rosa_wichuraiana	Rw3G003790

Restriction Enzyme Sites

1 / 10

Enzyme	Recognition Site	Cut Count	Positions (bp)
AarI	CACCTGC	1 cut(s)	668
Acc36I	ACCTGC	1 cut(s)	668
AccBSI	CCGCTC	1 cut(s)	335
AccII	CGCG	1 cut(s)	571
AciI	CCGC	1 cut(s)	335
AclWI	GGATC	2 cut(s)	42, 723
AcoI	YGGCCR	1 cut(s)	697
AcsI	RAATTY	2 cut(s)	64, 849
AcuI	CTGAAG	1 cut(s)	172
AfaI	GTAC	3 cut(s)	630, 667, 765
AfiI	CCNNNNNNNGG	4 cut(s)	92, 590, 912, 913
AgsI	TTSAA	5 cut(s)	41, 353, 389, 560, 844
AjnI	CCWGG	1 cut(s)	694
AluBI	AGCT	3 cut(s)	56, 500, 692
AluI	AGCT	3 cut(s)	56, 500, 692
Alw21I	GWGCWC	1 cut(s)	58
AlwI	GGATC	2 cut(s)	42, 723
AlwNI	CAGNNNCTG	2 cut(s)	115, 695
AoxI	GGCC	2 cut(s)	254, 697
ApeKI	GCWGC	3 cut(s)	115, 225, 821
ApoI	RAATTY	2 cut(s)	64, 849
ArsI	GACNNNNNNTTYG	2 cut(s)	632, 664
Asp700I	GAANNNNTTC	1 cut(s)	64
AspLEI	GCGC	3 cut(s)	85, 225, 571
AsuHPI	GGTGA	3 cut(s)	284, 617, 692
AsuNHI	GCTAGC	1 cut(s)	565
BaeI	ACNNNNGTAYC	2 cut(s)	747, 780
BalI	TGGCCA	1 cut(s)	699
BanII	GRGCYC	1 cut(s)	58
BauI	CACGAG	1 cut(s)	624
Bbv12I	GWGCWC	1 cut(s)	58
BbvCI	CCTCAGC	1 cut(s)	456
BbvI	GCAGC	3 cut(s)	102, 237, 833
BccI	CCATC	2 cut(s)	457, 595
BciT130I	CCWGG	1 cut(s)	696
BciVI	GTATCC	1 cut(s)	914
BclI	TGATCA	1 cut(s)	106
BfaI	CTAG	2 cut(s)	566, 671
BfmI	CTRYAG	1 cut(s)	376
BfuAI	ACCTGC	1 cut(s)	668
BfuI	GTATCC	1 cut(s)	914
BglII	AGATCT	1 cut(s)	202
BisI	GCNGC	3 cut(s)	116, 226, 822
BlsI	GCNGC	3 cut(s)	117, 227, 823
Bme1390I	CCNGG	1 cut(s)	696
BmiI	GGNNCC	1 cut(s)	751
BmrFI	CCNGG	1 cut(s)	696
BmsI	GCATC	1 cut(s)	102
BmtI	GCTAGC	1 cut(s)	569
Bpu10I	CCTNAGC	1 cut(s)	456
BpuEI	CTTGAG	1 cut(s)	561
BsaJI	CCNNGG	2 cut(s)	321, 528
Bsc4I	CCNNNNNNNGG	4 cut(s)	92, 590, 912, 913
Bse118I	RCCGGY	1 cut(s)	85
Bse3DI	GCAATG	1 cut(s)	860
BseBI	CCWGG	1 cut(s)	696
BseDI	CCNNGG	2 cut(s)	321, 528
BseLI	CCNNNNNNNGG	4 cut(s)	92, 590, 912, 913
BseMI	GCAATG	1 cut(s)	860
BseMII	CTCAG	2 cut(s)	22, 447
BseXI	GCAGC	3 cut(s)	102, 237, 833
Bsh1236I	CGCG	1 cut(s)	571
BshFI	GGCC	2 cut(s)	256, 699
BsiHKAI	GWGCWC	1 cut(s)	58
BsiSI	CCGG	1 cut(s)	86
BslFI	GGGAC	1 cut(s)	566
BslI	CCNNNNNNNGG	4 cut(s)	92, 590, 912, 913
BsmFI	GGGAC	1 cut(s)	566
BsnI	GGCC	2 cut(s)	256, 699
Bsp1286I	GDGCHC	1 cut(s)	58
Bsp143I	GATC	5 cut(s)	34, 106, 202, 618, 715
Bsp19I	CCATGG	1 cut(s)	321
BspACI	CCGC	1 cut(s)	335
BspANI	GGCC	2 cut(s)	256, 699
BspCNI	CTCAG	2 cut(s)	21, 448
BspFNI	CGCG	1 cut(s)	571
BspLI	GGNNCC	1 cut(s)	751
BspMI	ACCTGC	1 cut(s)	668
BspOI	GCTAGC	1 cut(s)	569
BspPI	GGATC	2 cut(s)	42, 723
BsrBI	CCGCTC	1 cut(s)	335
BsrDI	GCAATG	1 cut(s)	860
BsrFI	RCCGGY	1 cut(s)	85
BssAI	RCCGGY	1 cut(s)	85
BssECI	CCNNGG	2 cut(s)	321, 528
BssMI	GATC	5 cut(s)	34, 106, 202, 618, 715
BssSI	CACGAG	1 cut(s)	624
BssT1I	CCWWGG	2 cut(s)	321, 528
Bst2BI	CACGAG	1 cut(s)	624
Bst2UI	CCWGG	1 cut(s)	696
Bst4CI	ACNGT	2 cut(s)	380, 709
BstAPI	GCANNNNNTGC	1 cut(s)	524
BstC8I	GCNNGC	2 cut(s)	567, 701
BstDEI	CTNAG	3 cut(s)	8, 456, 632
BstDSI	CCRYGG	1 cut(s)	321
BstFNI	CGCG	1 cut(s)	571
BstHHI	GCGC	3 cut(s)	85, 225, 571
BstKTI	GATC	5 cut(s)	37, 109, 205, 621, 718
BstMBI	GATC	5 cut(s)	34, 106, 202, 618, 715
BstMWI	GCNNNNNNNGC	4 cut(s)	124, 497, 524, 830
BstNI	CCWGG	1 cut(s)	696
BstSCI	CCNGG	1 cut(s)	694
BstSFI	CTRYAG	1 cut(s)	376
BstUI	CGCG	1 cut(s)	571
BstV1I	GCAGC	3 cut(s)	102, 237, 833
BstX2I	RGATCY	3 cut(s)	34, 202, 715
BstXI	CCANNNNNNTGG	1 cut(s)	328
BstYI	RGATCY	3 cut(s)	34, 202, 715
BsuI	GTATCC	1 cut(s)	914
BsuRI	GGCC	2 cut(s)	256, 699
BtgI	CCRYGG	1 cut(s)	321
BveI	ACCTGC	1 cut(s)	668
Cac8I	GCNNGC	2 cut(s)	567, 701
CaiI	CAGNNNCTG	2 cut(s)	115, 695
CfoI	GCGC	3 cut(s)	85, 225, 571
Cfr10I	RCCGGY	1 cut(s)	85
CseI	GACGC	1 cut(s)	107
Csp6I	GTAC	3 cut(s)	629, 666, 764
CviAII	CATG	3 cut(s)	50, 322, 767
CviQI	GTAC	3 cut(s)	629, 666, 764
DdeI	CTNAG	3 cut(s)	8, 456, 632
DpnI	GATC	5 cut(s)	36, 108, 204, 620, 717
DpnII	GATC	5 cut(s)	34, 106, 202, 618, 715
DraI	TTTAAA	1 cut(s)	829
EaeI	YGGCCR	1 cut(s)	697
Ecl136II	GAGCTC	1 cut(s)	56
Eco130I	CCWWGG	2 cut(s)	321, 528
Eco24I	GRGCYC	1 cut(s)	58
Eco53kI	GAGCTC	1 cut(s)	56
Eco57I	CTGAAG	1 cut(s)	172
EcoICRI	GAGCTC	1 cut(s)	56
EcoRII	CCWGG	1 cut(s)	694
EcoT14I	CCWWGG	2 cut(s)	321, 528
EcoT38I	GRGCYC	1 cut(s)	58
ErhI	CCWWGG	2 cut(s)	321, 528
FaeI	CATG	3 cut(s)	53, 325, 770
FaqI	GGGAC	1 cut(s)	566
FatI	CATG	3 cut(s)	49, 321, 766
FauNDI	CATATG	1 cut(s)	652
FbaI	TGATCA	1 cut(s)	106
Fnu4HI	GCNGC	3 cut(s)	116, 226, 822
FriOI	GRGCYC	1 cut(s)	58
Fsp4HI	GCNGC	3 cut(s)	116, 226, 822
FspBI	CTAG	2 cut(s)	566, 671
GlaI	GCGC	3 cut(s)	84, 224, 570
GluI	GCNGC	3 cut(s)	116, 226, 822
HaeIII	GGCC	2 cut(s)	256, 699
HapII	CCGG	1 cut(s)	86
HgaI	GACGC	1 cut(s)	107
HhaI	GCGC	3 cut(s)	85, 225, 571
Hin1II	CATG	3 cut(s)	53, 325, 770
Hin6I	GCGC	3 cut(s)	83, 223, 569
HinP1I	GCGC	3 cut(s)	83, 223, 569
HinfI	GANTC	3 cut(s)	4, 98, 163
HpaII	CCGG	1 cut(s)	86
HphI	GGTGA	3 cut(s)	284, 617, 692
Hpy166II	GTNNAC	2 cut(s)	629, 668
Hpy188I	TCNGA	2 cut(s)	34, 111
Hpy188III	TCNNGA	1 cut(s)	206
Hpy8I	GTNNAC	2 cut(s)	629, 668
Hpy99I	CGWCG	1 cut(s)	34
HpyAV	CCTTC	3 cut(s)	260, 275, 604
HpyCH4III	ACNGT	2 cut(s)	380, 709
HpyCH4IV	ACGT	1 cut(s)	29
HpyCH4V	TGCA	5 cut(s)	479, 548, 638, 821, 881
HpyF10VI	GCNNNNNNNGC	4 cut(s)	124, 497, 524, 830
HpyF3I	CTNAG	3 cut(s)	8, 456, 632
HpySE526I	ACGT	1 cut(s)	29
Hsp92II	CATG	3 cut(s)	53, 325, 770
HspAI	GCGC	3 cut(s)	83, 223, 569
Ksp22I	TGATCA	1 cut(s)	106
Kzo9I	GATC	5 cut(s)	34, 106, 202, 618, 715
LmnI	GCTCC	5 cut(s)	53, 332, 497, 697, 749
Lsp1109I	GCAGC	3 cut(s)	102, 237, 833
LweI	GCATC	1 cut(s)	102
MaeI	CTAG	2 cut(s)	566, 671
MaeII	ACGT	1 cut(s)	29
MaeIII	GTNAC	4 cut(s)	244, 655, 709, 791
MalI	GATC	5 cut(s)	36, 108, 204, 620, 717
MbiI	CCGCTC	1 cut(s)	335
MboI	GATC	5 cut(s)	34, 106, 202, 618, 715
MboII	GAAGA	4 cut(s)	29, 72, 406, 417
MflI	RGATCY	3 cut(s)	34, 202, 715
MhlI	GDGCHC	1 cut(s)	58
MlsI	TGGCCA	1 cut(s)	699
MluCI	AATT	5 cut(s)	64, 326, 462, 733, 849
MluNI	TGGCCA	1 cut(s)	699
MmeI	TCCRAC	4 cut(s)	12, 150, 702, 898
MnlI	CCTC	5 cut(s)	298, 451, 667, 676, 816
Mox20I	TGGCCA	1 cut(s)	699
MroXI	GAANNNNTTC	1 cut(s)	64
MscI	TGGCCA	1 cut(s)	699
MseI	TTAA	3 cut(s)	180, 219, 828
MslI	CAYNNNNRTG	1 cut(s)	435
Msp20I	TGGCCA	1 cut(s)	699
MspI	CCGG	1 cut(s)	86
MspR9I	CCNGG	1 cut(s)	696
MvaI	CCWGG	1 cut(s)	696
MvnI	CGCG	1 cut(s)	571
MwoI	GCNNNNNNNGC	4 cut(s)	124, 497, 524, 830
NcoI	CCATGG	1 cut(s)	321
NdeI	CATATG	1 cut(s)	652
NdeII	GATC	5 cut(s)	34, 106, 202, 618, 715
NheI	GCTAGC	1 cut(s)	565
NlaIII	CATG	3 cut(s)	53, 325, 770
NlaIV	GGNNCC	1 cut(s)	751
NmuCI	GTSAC	3 cut(s)	244, 655, 791
PaqCI	CACCTGC	1 cut(s)	668
PdmI	GAANNNNTTC	1 cut(s)	64
PfeI	GAWTC	2 cut(s)	98, 163
PflFI	GACNNNGTC	1 cut(s)	506
PkrI	GCNGC	3 cut(s)	117, 227, 823
Psp124BI	GAGCTC	1 cut(s)	58
Psp6I	CCWGG	1 cut(s)	694
PspGI	CCWGG	1 cut(s)	694
PspN4I	GGNNCC	1 cut(s)	751
PstNI	CAGNNNCTG	2 cut(s)	115, 695
PsuI	RGATCY	3 cut(s)	34, 202, 715
PsyI	GACNNNGTC	1 cut(s)	506
RsaI	GTAC	3 cut(s)	630, 667, 765
RsaNI	GTAC	3 cut(s)	629, 666, 764
RseI	CAYNNNNRTG	1 cut(s)	435
SacI	GAGCTC	1 cut(s)	58
SaqAI	TTAA	3 cut(s)	180, 219, 828
SatI	GCNGC	3 cut(s)	116, 226, 822
Sau3AI	GATC	5 cut(s)	34, 106, 202, 618, 715
ScrFI	CCNGG	1 cut(s)	696
SduI	GDGCHC	1 cut(s)	58
SfaNI	GCATC	1 cut(s)	102
SfcI	CTRYAG	1 cut(s)	376
SmiMI	CAYNNNNRTG	1 cut(s)	435
SmlI	CTYRAG	1 cut(s)	576
SmoI	CTYRAG	1 cut(s)	576
Sse9I	AATT	5 cut(s)	64, 326, 462, 733, 849
SsiI	CCGC	1 cut(s)	335
SspI	AATATT	1 cut(s)	555
SspMI	CTAG	2 cut(s)	566, 671
SstI	GAGCTC	1 cut(s)	58
StyD4I	CCNGG	1 cut(s)	694
StyI	CCWWGG	2 cut(s)	321, 528
TaaI	ACNGT	2 cut(s)	380, 709
TaiI	ACGT	1 cut(s)	32
TaqI	TCGA	3 cut(s)	58, 68, 207
TaqII	GACCGA	1 cut(s)	35
TasI	AATT	5 cut(s)	64, 326, 462, 733, 849
TatI	WGTACW	2 cut(s)	628, 763
TfiI	GAWTC	2 cut(s)	98, 163
Tru1I	TTAA	3 cut(s)	180, 219, 828
Tru9I	TTAA	3 cut(s)	180, 219, 828
TseFI	GTSAC	3 cut(s)	244, 655, 791
TseI	GCWGC	3 cut(s)	115, 225, 821
Tsp45I	GTSAC	3 cut(s)	244, 655, 791
TspDTI	ATGAA	2 cut(s)	294, 303
TspGWI	ACGGA	2 cut(s)	9, 728
Tth111I	GACNNNGTC	1 cut(s)	506
XapI	RAATTY	2 cut(s)	64, 849
XmnI	GAANNNNTTC	1 cut(s)	64
XspI	CTAG	2 cut(s)	566, 671

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