Basic Information

Type: gene

Biological Identity

Species

rosa_samantha

Chromosome

Chr5D

Orthogroup ID

OG0001856

Physical Location & Seq

Genomic Coordinates Reverse (-)

71289801 .. 71295356

Gene Structure 5556 bp

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UTR

Exon/CDS

Intron

Transcript / Protein ID

Rh5DG446900.1

Sequence Viewer

CDS Protein Promoter (2k)

Length: 816 bp

ATGAGAATCTTGGTTACTGGAGGAGCTGGATTCATTGGTTCTCACCTGGTTGACAGATTAATGGAAAATGAAAAGAATGAGGTTATTGTTGTTGATAACTACTTCACTGGCTCCAAGGACAATCTTAAAAAATGGATTGGTCATCCCAGATTTGAGCTTATTCGTCATGATGTCACTGAAACATTGTTGGTTGAGGTTGATCGGATATACCATCTTGCATGCCCAGCTTCTCCAATTTTCTACAAATATAATCCTGTAAAGACAATAAAAACAAATGTGATTGGCACTCTAAACATGCTTGGACTTGCCAAGCGAGTTGGAGCGAGGATTTTACTGACATCAACTTCAGAGGTATATGGAGACCCCCTTGTGCACCCACAACCTGAAAGCTATTGGGGTAATGTTAACCCAATTGGAGTGAGGAGCTGCTATGATGAGGGCAAGCGAGTTGCTGAGACCTTGATGTTTGACTATCATCGGCAACATGGGATAGAAATACGCATTGCCAGAATCTTCAACACATATGGCCCTCGCATGAATATTGATGATGGGCGTGTAGTGAGCAACTTTATAGCTCAAGCACTTCGAGATGAACCATTGACGGTCCAAAACCCTGGAACTCAAACTCGCAGTTTCTGTTACGTCTCTGACATGGTTGATGGCCTCATCCGTCTCATGGAAGGAGAGCACACTGGACCCATAAACATTGGAAACCCAGGTGAATTTACGATGCTTGAACTCGCAGAGACAGTGAAGGAGGTAAGTTTTATTGTTTCTCTTCCCTTCATAGGCTGTTATAAGATAGTTCTTAAGTAA

Functional Annotation

Gene Ontology

Molecular Function
Biological Process
Cellular Component

GO:0000166 GO:0003674 GO:0003824 GO:0005488 GO:0005515 GO:0005575 GO:0005622 GO:0005623 GO:0005737 GO:0005829 GO:0005886 GO:0005975 GO:0005996 GO:0008150 GO:0008152 GO:0009987 GO:0016020 GO:0016043 GO:0016829 GO:0016830 GO:0016831 GO:0019321 GO:0022607 GO:0036094 GO:0042732 GO:0042802 GO:0042803 GO:0043167 GO:0043168 GO:0043933 GO:0044085 GO:0044238 GO:0044281 GO:0044424 GO:0044444 GO:0044464 GO:0046983 GO:0048037 GO:0048040 GO:0050662 GO:0051259 GO:0051262 GO:0051287 GO:0065003 GO:0070403 GO:0071704 GO:0071840 GO:0071944 GO:0097159 GO:1901265 GO:1901363

KEGG Pathways

Metabolic & Signaling

ko00520 ko01100 map00520 map01100

Pfam Domains

Protein Families

GDP_Man_Dehyd

Protein Analysis

271

Amino Acids

30.56

Weight (kDa)

6.45

Isoelectric Point (pI)

25.64

Instability Index

Protein Domains (Pfam)

Domain Name	Pfam ID	Position	E-value	Description
RmlD_sub_bind	PF04321	1 - 252	7.8e-08	RmlD substrate binding domain
Epimerase	PF01370	3 - 237	5.3e-48	NAD dependent epimerase/dehydratase family
Polysacc_synt_2	PF02719	3 - 112	1.4e-08	Polysaccharide biosynthesis protein
GDP_Man_Dehyd	PF16363	4 - 250	8.6e-44	GDP-mannose 4,6 dehydratase
3Beta_HSD	PF01073	4 - 155	2e-12	3-beta hydroxysteroid dehydrogenase/isomerase family
NAD_binding_4	PF07993	57 - 173	4.2e-07	Male sterility protein

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: OG0001856)

Species	Orthologous Gene IDs
fragaria_vesca	FvH4_3g35550 FvH4_3g35550 FvH4_3g35550 FvH4_3g35550 FvH4_3g35550 FvH4_3g35550 FvH4_3g35550 FvH4_3g35550 FvH4_3g35550 FvH4_3g35550 FvH4_3g35550 FvH4_3g35550
malus_domestica	MD03G1096800.v1.1 MD11G1143300.v1.1
prunus_persica	Prupe.6G081100_v2.0.a1 Prupe.6G081100_v2.0.a1 Prupe.6G081100_v2.0.a1 Prupe.6G081100_v2.0.a1 Prupe.6G081100_v2.0.a1 Prupe.6G081100_v2.0.a1
pyrus_communis	pycom03g08000 pycom11g09310
rosa_chinensis	RchiOBHm_Chr5g0063761
rosa_laevigata	RLG00000035666
rosa_multiflora	Rmu_sc0002724.1_g000023
rosa_roxburghii	Rroxscaffold_1G00017090 Rroxscaffold_1G00037850 Rroxscaffold_3G00246740
rosa_rugosa	Rorug03G0248000 Rorug05G0359100 Rorug05G0359200 Rorug05G0359200 Rorug05G0359200 Rorug05G0359200 Rorug05G0359300 Rorug05G0359400
rosa_samantha	Rh2BG210700 Rh5AG128600 Rh5AG389400 Rh5BG433300 Rh5CG456500 Rh5DG446900 Rh5DG449700 Rh6AG145900
rosa_wichuraiana	Rw4G004490 Rw5G039270

Restriction Enzyme Sites

1 / 10

Enzyme	Recognition Site	Cut Count	Positions (bp)
AanI	TTATAA	1 cut(s)	798
AcsI	RAATTY	1 cut(s)	722
AcuI	CTGAAG	1 cut(s)	330
AfiI	CCNNNNNNNGG	2 cut(s)	676, 788
AflII	CTTAAG	1 cut(s)	809
AgsI	TTSAA	2 cut(s)	517, 737
AjnI	CCWGG	3 cut(s)	45, 613, 715
AluBI	AGCT	6 cut(s)	26, 157, 227, 390, 426, 575
AluI	AGCT	6 cut(s)	26, 157, 227, 390, 426, 575
Alw21I	GWGCWC	2 cut(s)	375, 690
Alw26I	GTCTC	5 cut(s)	354, 449, 649, 677, 740
Alw44I	GTGCAC	1 cut(s)	371
AlwNI	CAGNNNCTG	1 cut(s)	636
AoxI	GGCC	2 cut(s)	526, 661
ApaLI	GTGCAC	1 cut(s)	371
ApeKI	GCWGC	1 cut(s)	426
ApoI	RAATTY	1 cut(s)	722
AseI	ATTAAT	1 cut(s)	59
AspS9I	GGNCC	3 cut(s)	527, 604, 695
AsuHPI	GGTGA	2 cut(s)	35, 731
AvaII	GGWCC	2 cut(s)	604, 695
BaeGI	GKGCMC	1 cut(s)	375
Bbv12I	GWGCWC	2 cut(s)	375, 690
BbvI	GCAGC	1 cut(s)	413
BccI	CCATC	3 cut(s)	219, 542, 653
BciT130I	CCWGG	3 cut(s)	47, 615, 717
BcoDI	GTCTC	5 cut(s)	354, 449, 649, 677, 740
BfrI	CTTAAG	1 cut(s)	809
BisI	GCNGC	1 cut(s)	427
BlsI	GCNGC	1 cut(s)	428
Bme1390I	CCNGG	3 cut(s)	47, 615, 717
Bme18I	GGWCC	2 cut(s)	604, 695
BmgT120I	GGNCC	3 cut(s)	527, 604, 695
BmiI	GGNNCC	2 cut(s)	112, 697
BmrFI	CCNGG	3 cut(s)	47, 615, 717
BmsI	GCATC	1 cut(s)	720
BpmI	CTGGAG	1 cut(s)	39
BpuEI	CTTGAG	1 cut(s)	561
BsaI	GGTCTC	2 cut(s)	354, 449
BsaJI	CCNNGG	3 cut(s)	114, 613, 715
Bsc4I	CCNNNNNNNGG	2 cut(s)	676, 788
Bse1I	ACTGG	3 cut(s)	22, 112, 697
Bse3DI	GCAATG	1 cut(s)	501
BseBI	CCWGG	3 cut(s)	47, 615, 717
BseDI	CCNNGG	3 cut(s)	114, 613, 715
BseGI	GGATG	2 cut(s)	142, 666
BseLI	CCNNNNNNNGG	2 cut(s)	676, 788
BseMI	GCAATG	1 cut(s)	501
BseMII	CTCAG	1 cut(s)	444
BseNI	ACTGG	3 cut(s)	22, 112, 697
BseRI	GAGGAG	2 cut(s)	36, 436
BseSI	GKGCMC	1 cut(s)	375
BseXI	GCAGC	1 cut(s)	413
BseYI	CCCAGC	1 cut(s)	223
BshFI	GGCC	2 cut(s)	528, 663
BsiHKAI	GWGCWC	2 cut(s)	375, 690
BslI	CCNNNNNNNGG	2 cut(s)	676, 788
BsmAI	GTCTC	5 cut(s)	354, 449, 649, 677, 740
BsmBI	CGTCTC	2 cut(s)	649, 677
BsnI	GGCC	2 cut(s)	528, 663
Bso31I	GGTCTC	2 cut(s)	354, 449
Bsp1286I	GDGCHC	2 cut(s)	375, 690
Bsp143I	GATC	1 cut(s)	199
BspANI	GGCC	2 cut(s)	528, 663
BspCNI	CTCAG	1 cut(s)	445
BspHI	TCATGA	1 cut(s)	166
BspLI	GGNNCC	2 cut(s)	112, 697
BspTI	CTTAAG	1 cut(s)	809
BspTNI	GGTCTC	2 cut(s)	354, 449
BsrDI	GCAATG	1 cut(s)	501
BsrI	ACTGG	3 cut(s)	22, 112, 697
BssECI	CCNNGG	3 cut(s)	114, 613, 715
BssMI	GATC	1 cut(s)	199
BssT1I	CCWWGG	1 cut(s)	114
Bst2UI	CCWGG	3 cut(s)	47, 615, 717
Bst4CI	ACNGT	2 cut(s)	604, 751
Bst6I	CTCTTC	1 cut(s)	783
BstAFI	CTTAAG	1 cut(s)	809
BstC8I	GCNNGC	2 cut(s)	220, 443
BstDEI	CTNAG	1 cut(s)	453
BstF5I	GGATG	2 cut(s)	142, 666
BstKTI	GATC	1 cut(s)	202
BstMAI	GTCTC	5 cut(s)	354, 449, 649, 677, 740
BstMBI	GATC	1 cut(s)	199
BstMWI	GCNNNNNNNGC	1 cut(s)	224
BstNI	CCWGG	3 cut(s)	47, 615, 717
BstNSI	RCATGY	2 cut(s)	222, 298
BstSCI	CCNGG	3 cut(s)	45, 613, 715
BstSLI	GKGCMC	1 cut(s)	375
BstV1I	GCAGC	1 cut(s)	413
BstXI	CCANNNNNNTGG	1 cut(s)	614
BsuRI	GGCC	2 cut(s)	528, 663
BtsCI	GGATG	2 cut(s)	142, 666
BtsIMutI	CAGTG	4 cut(s)	105, 174, 690, 756
Cac8I	GCNNGC	2 cut(s)	220, 443
CaiI	CAGNNNCTG	1 cut(s)	636
CciI	TCATGA	1 cut(s)	166
Cfr13I	GGNCC	3 cut(s)	527, 604, 695
CsiI	ACCWGGT	1 cut(s)	45
CviAII	CATG	7 cut(s)	167, 219, 295, 485, 535, 652, 676
DdeI	CTNAG	1 cut(s)	453
DpnI	GATC	1 cut(s)	201
DpnII	GATC	1 cut(s)	199
Eam1104I	CTCTTC	1 cut(s)	783
EarI	CTCTTC	1 cut(s)	783
Eco130I	CCWWGG	1 cut(s)	114
Eco31I	GGTCTC	2 cut(s)	354, 449
Eco47I	GGWCC	2 cut(s)	604, 695
Eco57I	CTGAAG	1 cut(s)	330
EcoRII	CCWGG	3 cut(s)	45, 613, 715
EcoT14I	CCWWGG	1 cut(s)	114
ErhI	CCWWGG	1 cut(s)	114
Esp3I	CGTCTC	2 cut(s)	649, 677
FaeI	CATG	7 cut(s)	170, 222, 298, 488, 538, 655, 679
FatI	CATG	7 cut(s)	166, 218, 294, 484, 534, 651, 675
FauNDI	CATATG	1 cut(s)	523
Fnu4HI	GCNGC	1 cut(s)	427
FokI	GGATG	2 cut(s)	129, 653
Fsp4HI	GCNGC	1 cut(s)	427
GluI	GCNGC	1 cut(s)	427
GsaI	CCCAGC	1 cut(s)	227
GsuI	CTGGAG	1 cut(s)	39
HaeIII	GGCC	2 cut(s)	528, 663
Hin1II	CATG	7 cut(s)	170, 222, 298, 488, 538, 655, 679
HincII	GTYRAC	2 cut(s)	52, 406
HindII	GTYRAC	2 cut(s)	52, 406
HinfI	GANTC	3 cut(s)	6, 30, 510
HpaI	GTTAAC	1 cut(s)	406
HphI	GGTGA	2 cut(s)	35, 731
Hpy166II	GTNNAC	3 cut(s)	52, 373, 406
Hpy188I	TCNGA	3 cut(s)	204, 349, 649
Hpy188III	TCNNGA	2 cut(s)	167, 587
Hpy8I	GTNNAC	3 cut(s)	52, 373, 406
HpyAV	CCTTC	3 cut(s)	674, 748, 793
HpyCH4III	ACNGT	2 cut(s)	604, 751
HpyCH4IV	ACGT	1 cut(s)	642
HpyCH4V	TGCA	2 cut(s)	218, 373
HpyF10VI	GCNNNNNNNGC	1 cut(s)	224
HpyF3I	CTNAG	1 cut(s)	453
HpySE526I	ACGT	1 cut(s)	642
Hsp92II	CATG	7 cut(s)	170, 222, 298, 488, 538, 655, 679
KspAI	GTTAAC	1 cut(s)	406
Kzo9I	GATC	1 cut(s)	199
LmnI	GCTCC	4 cut(s)	23, 116, 320, 423
Lsp1109I	GCAGC	1 cut(s)	413
LweI	GCATC	1 cut(s)	720
MabI	ACCWGGT	1 cut(s)	45
MaeII	ACGT	1 cut(s)	642
MaeIII	GTNAC	3 cut(s)	13, 172, 638
MalI	GATC	1 cut(s)	201
MboI	GATC	1 cut(s)	199
MboII	GAAGA	2 cut(s)	505, 770
MfeI	CAATTG	1 cut(s)	411
MhlI	GDGCHC	2 cut(s)	375, 690
MluCI	AATT	3 cut(s)	234, 411, 722
MmeI	TCCRAC	1 cut(s)	298
MseI	TTAA	4 cut(s)	59, 126, 405, 810
MspCI	CTTAAG	1 cut(s)	809
MspR9I	CCNGG	3 cut(s)	47, 615, 717
MunI	CAATTG	1 cut(s)	411
MvaI	CCWGG	3 cut(s)	47, 615, 717
MwoI	GCNNNNNNNGC	1 cut(s)	224
NdeI	CATATG	1 cut(s)	523
NdeII	GATC	1 cut(s)	199
NlaIII	CATG	7 cut(s)	170, 222, 298, 488, 538, 655, 679
NlaIV	GGNNCC	2 cut(s)	112, 697
NmuCI	GTSAC	1 cut(s)	172
NspI	RCATGY	2 cut(s)	222, 298
PaeI	GCATGC	1 cut(s)	222
PagI	TCATGA	1 cut(s)	166
PfeI	GAWTC	3 cut(s)	6, 30, 510
PkrI	GCNGC	1 cut(s)	428
PshBI	ATTAAT	1 cut(s)	59
PsiI	TTATAA	1 cut(s)	798
Psp6I	CCWGG	3 cut(s)	45, 613, 715
PspFI	CCCAGC	1 cut(s)	223
PspGI	CCWGG	3 cut(s)	45, 613, 715
PspN4I	GGNNCC	2 cut(s)	112, 697
PspPI	GGNCC	3 cut(s)	527, 604, 695
PstNI	CAGNNNCTG	1 cut(s)	636
SaqAI	TTAA	4 cut(s)	59, 126, 405, 810
SatI	GCNGC	1 cut(s)	427
Sau3AI	GATC	1 cut(s)	199
Sau96I	GGNCC	3 cut(s)	527, 604, 695
ScrFI	CCNGG	3 cut(s)	47, 615, 717
SduI	GDGCHC	2 cut(s)	375, 690
SexAI	ACCWGGT	1 cut(s)	45
SfaNI	GCATC	1 cut(s)	720
SinI	GGWCC	2 cut(s)	604, 695
SmlI	CTYRAG	2 cut(s)	576, 809
SmoI	CTYRAG	2 cut(s)	576, 809
SphI	GCATGC	1 cut(s)	222
Sse9I	AATT	3 cut(s)	234, 411, 722
SspI	AATATT	1 cut(s)	541
StyD4I	CCNGG	3 cut(s)	45, 613, 715
StyI	CCWWGG	1 cut(s)	114
TaaI	ACNGT	2 cut(s)	604, 751
TaiI	ACGT	1 cut(s)	645
TaqI	TCGA	1 cut(s)	586
TasI	AATT	3 cut(s)	234, 411, 722
TfiI	GAWTC	3 cut(s)	6, 30, 510
Tru1I	TTAA	4 cut(s)	59, 126, 405, 810
Tru9I	TTAA	4 cut(s)	59, 126, 405, 810
TscAI	CASTG	4 cut(s)	112, 181, 697, 756
TseFI	GTSAC	1 cut(s)	172
TseI	GCWGC	1 cut(s)	426
Tsp45I	GTSAC	1 cut(s)	172
TspDTI	ATGAA	5 cut(s)	22, 84, 551, 606, 775
TspGWI	ACGGA	1 cut(s)	659
TspRI	CASTG	4 cut(s)	112, 181, 697, 756
Vha464I	CTTAAG	1 cut(s)	809
VneI	GTGCAC	1 cut(s)	371
VpaK11BI	GGWCC	2 cut(s)	604, 695
VspI	ATTAAT	1 cut(s)	59
XapI	RAATTY	1 cut(s)	722
XceI	RCATGY	2 cut(s)	222, 298

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