Basic Information

Type: gene

Biological Identity

Species

rosa_samantha

Chromosome

Chr5A

Orthogroup ID

OG0009056

Physical Location & Seq

Genomic Coordinates Reverse (-)

17780531 .. 17783862

Gene Structure 3332 bp

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UTR

Exon/CDS

Intron

Transcript / Protein ID

Rh5AG165000.1

Sequence Viewer

CDS Protein Promoter (2k)

Length: 918 bp

ATGGTTGCTAGGGGGGCCATGCTTGGCCCTGATCAGCCTGTGATTCTGCACATGCTTGATATTCCTCCTGCAGCTGAGGCCTTGAATGGGGTAAAAATGGAACTGATTGATGCCGCCTTTCCTCTTCTCAAAGGTGTCGTGGCTACAACAGATGTTGAGGAAGCTTGTAAAGGTGTCAACATTGCTGTTATGGTTGGTGGATTCCCAAGGAAGGAAGGTATGGAAAGAAAGGATGTGATGTCAAAAAATGTATCAATCTACAAGGGTCAAGCTTCAGCATTGGAAAAGCACGCTGCTTCAGATGTCAAGGTTCTGGTGGTTGCTAACCCAGCAAACACCAATGCACTCATCTTGAAAGAATATGCACCTTCAATTCCAGAGAAAAACATCACATGTCTTACACGACTAGATCATAACCGAGCATTGGGGCAAATCTCTCAGAGGCTAAATGTTCATGTTGGTGATGTAAAGAATGTTATCATCTGGGGAAATCATTCTTCAACTCAGTATCCTGATGTCAATCATGCAACTGTTGGAGACAAACCTGTCAGACAACTTGTAGCTGATGATCAATGGTTGAATACTGAGTTCATCACCACTGTGCAGCAGCGTGGTGCAGCCATTATCAAAGCTCGGAAACTATCAAGTGCTTTGTCTGCTGCAAGTTCTGCCTGTGATCACATACGCGATTGGGTTCTTGGGACTCCTAAGGGGACACATGTTTCCATGGGTGTGTATTCTGATGGTTCTTATGGAATCCAGGAAGGCCTCATTTACTCTTTCCCTGTCACCTGTGAGAAAGGGGAATGGAAAATTGTGCAAGGACTGAAGATCGACGAGTTCTCGAGGAAAAAGCTTGATGCAACTGCACAAGAGCTCATTGAAGAGAAATCGTTGGCCCATTCATGTCTCAACTGA

Functional Annotation

Gene Ontology

Molecular Function
Biological Process
Cellular Component

GO:0003674 GO:0003824 GO:0005575 GO:0005622 GO:0005623 GO:0005737 GO:0006082 GO:0006091 GO:0006099 GO:0006101 GO:0006107 GO:0006108 GO:0006139 GO:0006725 GO:0006732 GO:0006733 GO:0006734 GO:0006753 GO:0006793 GO:0006796 GO:0006807 GO:0008150 GO:0008152 GO:0009060 GO:0009117 GO:0009987 GO:0015980 GO:0016020 GO:0016491 GO:0016614 GO:0016615 GO:0016616 GO:0016999 GO:0017144 GO:0019362 GO:0019637 GO:0019674 GO:0019752 GO:0030060 GO:0034641 GO:0043436 GO:0043648 GO:0044237 GO:0044238 GO:0044281 GO:0044424 GO:0044464 GO:0045333 GO:0046483 GO:0046496 GO:0051186 GO:0055086 GO:0055114 GO:0071704 GO:0072350 GO:0072524 GO:1901360 GO:1901564

KEGG Pathways

Metabolic & Signaling

ko00020 ko00270 ko00620 ko00630 ko00710 ko01100 ko01110 ko01120 ko01130 ko01200 ko04964 map00020 map00270 map00620 map00630 map00710 map01100 map01110 map01120 map01130 map01200 map04964

Pfam Domains

Protein Families

Ldh_1_C Ldh_1_N

Protein Analysis

305

Amino Acids

33.06

Weight (kDa)

6.76

Isoelectric Point (pI)

30.89

Instability Index

Protein Domains (Pfam)

Domain Name	Pfam ID	Position	E-value	Description
Ldh_1_N	PF00056	16 - 130	9.1e-25	lactate/malate dehydrogenase, NAD binding domain
Ldh_1_C	PF02866	134 - 298	2.9e-45	lactate/malate dehydrogenase, alpha/beta C-terminal 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: OG0009056)

Species	Orthologous Gene IDs
arabidopsis_thaliana	AT5G56720
fragaria_vesca	FvH4_3g14020 FvH4_3g14020 FvH4_3g14020
malus_domestica	MD05G1238800.v1.1 MD10G1216900.v1.1
prunus_persica	Prupe.4G127500_v2.0.a1 Prupe.4G127500_v2.0.a1
pyrus_communis	pycom05g21480 pycom10g18290
rosa_chinensis	RchiOBHm_Chr5g0023331
rosa_laevigata	RLG00000032714
rosa_multiflora	Rmu_sc0004693.1_g000004 Rmu_sc0009954.1_g000015
rosa_roxburghii	Rroxscaffold_1G00056000
rosa_rugosa	Rorug05G0078400 Rorug05G0078500
rosa_samantha	Rh5AG165000 Rh5BG164500 Rh5CG179400 Rh5DG166000
rosa_wichuraiana	Rw5G014870

Restriction Enzyme Sites

1 / 10

Enzyme	Recognition Site	Cut Count	Positions (bp)
AasI	GACNNNNNNGTC	1 cut(s)	545
AccII	CGCG	1 cut(s)	687
AciI	CCGC	1 cut(s)	114
AcuI	CTGAAG	3 cut(s)	258, 282, 848
AfiI	CCNNNNNNNGG	3 cut(s)	87, 211, 424
AflIII	ACRYGT	2 cut(s)	392, 718
AgsI	TTSAA	6 cut(s)	85, 355, 372, 501, 580, 884
AjnI	CCWGG	1 cut(s)	759
AleI	CACNNNNGTG	1 cut(s)	599
AluBI	AGCT	7 cut(s)	74, 164, 272, 563, 632, 856, 877
AluI	AGCT	7 cut(s)	74, 164, 272, 563, 632, 856, 877
Alw21I	GWGCWC	1 cut(s)	879
Alw26I	GTCTC	2 cut(s)	531, 914
Ama87I	CYCGRG	1 cut(s)	844
AoxI	GGCC	5 cut(s)	15, 25, 78, 766, 897
ApeKI	GCWGC	6 cut(s)	71, 293, 604, 607, 617, 659
Asp700I	GAANNNNTTC	1 cut(s)	493
AspS9I	GGNCC	3 cut(s)	15, 26, 898
AsuHPI	GGTGA	3 cut(s)	473, 586, 781
AvaI	CYCGRG	1 cut(s)	844
AxyI	CCTNAGG	1 cut(s)	708
BanII	GRGCYC	1 cut(s)	879
Bbv12I	GWGCWC	1 cut(s)	879
BbvCI	CCTCAGC	1 cut(s)	75
BbvI	GCAGC	6 cut(s)	83, 280, 616, 619, 629, 646
BccI	CCATC	1 cut(s)	737
BciT130I	CCWGG	1 cut(s)	761
BciVI	GTATCC	1 cut(s)	519
BclI	TGATCA	3 cut(s)	31, 568, 676
BcoDI	GTCTC	2 cut(s)	531, 914
BfaI	CTAG	2 cut(s)	9, 407
BfmI	CTRYAG	1 cut(s)	69
BfuI	GTATCC	1 cut(s)	519
BisI	GCNGC	7 cut(s)	72, 114, 294, 605, 608, 618, 660
BlsI	GCNGC	7 cut(s)	73, 115, 295, 606, 609, 619, 661
Bme1390I	CCNGG	1 cut(s)	761
BmeT110I	CYCGRG	1 cut(s)	844
BmgT120I	GGNCC	3 cut(s)	15, 26, 898
BmiI	GGNNCC	1 cut(s)	16
BmrFI	CCNGG	1 cut(s)	761
BmsI	GCATC	2 cut(s)	100, 850
Bpu10I	CCTNAGC	1 cut(s)	75
BsaBI	GATNNNNATC	1 cut(s)	519
BsaJI	CCNNGG	2 cut(s)	206, 726
Bsc4I	CCNNNNNNNGG	3 cut(s)	87, 211, 424
Bse21I	CCTNAGG	1 cut(s)	708
Bse3DI	GCAATG	1 cut(s)	180
Bse8I	GATNNNNATC	1 cut(s)	519
BseBI	CCWGG	1 cut(s)	761
BseDI	CCNNGG	2 cut(s)	206, 726
BseGI	GGATG	1 cut(s)	238
BseJI	GATNNNNATC	1 cut(s)	519
BseLI	CCNNNNNNNGG	3 cut(s)	87, 211, 424
BseMI	GCAATG	1 cut(s)	180
BseMII	CTCAG	4 cut(s)	66, 452, 518, 576
BseXI	GCAGC	6 cut(s)	83, 280, 616, 619, 629, 646
BseYI	CCCAGC	1 cut(s)	328
BsgI	GTGCAG	4 cut(s)	32, 623, 636, 852
Bsh1236I	CGCG	1 cut(s)	687
BshFI	GGCC	5 cut(s)	17, 27, 80, 768, 899
BsiHKAI	GWGCWC	1 cut(s)	879
BsiHKCI	CYCGRG	1 cut(s)	844
BslFI	GGGAC	2 cut(s)	715, 727
BslI	CCNNNNNNNGG	3 cut(s)	87, 211, 424
BsmAI	GTCTC	2 cut(s)	531, 914
BsmFI	GGGAC	2 cut(s)	715, 727
BsnI	GGCC	5 cut(s)	17, 27, 80, 768, 899
BsoBI	CYCGRG	1 cut(s)	844
Bsp1286I	GDGCHC	1 cut(s)	879
Bsp143I	GATC	5 cut(s)	31, 409, 568, 676, 831
Bsp19I	CCATGG	1 cut(s)	726
BspACI	CCGC	1 cut(s)	114
BspANI	GGCC	5 cut(s)	17, 27, 80, 768, 899
BspCNI	CTCAG	4 cut(s)	67, 451, 517, 577
BspFNI	CGCG	1 cut(s)	687
BspLI	GGNNCC	1 cut(s)	16
BspMAI	CTGCAG	1 cut(s)	73
BsrDI	GCAATG	1 cut(s)	180
BssECI	CCNNGG	2 cut(s)	206, 726
BssMI	GATC	5 cut(s)	31, 409, 568, 676, 831
BssT1I	CCWWGG	2 cut(s)	206, 726
Bst2UI	CCWGG	1 cut(s)	761
Bst4CI	ACNGT	2 cut(s)	532, 601
Bst6I	CTCTTC	2 cut(s)	129, 879
BstAPI	GCANNNNNTGC	1 cut(s)	668
BstC8I	GCNNGC	1 cut(s)	291
BstDEI	CTNAG	5 cut(s)	75, 438, 504, 585, 708
BstDSI	CCRYGG	1 cut(s)	726
BstF5I	GGATG	1 cut(s)	238
BstFNI	CGCG	1 cut(s)	687
BstKTI	GATC	5 cut(s)	34, 412, 571, 679, 834
BstMAI	GTCTC	2 cut(s)	531, 914
BstMBI	GATC	5 cut(s)	31, 409, 568, 676, 831
BstMWI	GCNNNNNNNGC	5 cut(s)	14, 77, 329, 656, 668
BstNI	CCWGG	1 cut(s)	761
BstNSI	RCATGY	3 cut(s)	55, 396, 722
BstSCI	CCNGG	1 cut(s)	759
BstSFI	CTRYAG	1 cut(s)	69
BstUI	CGCG	1 cut(s)	687
BstV1I	GCAGC	6 cut(s)	83, 280, 616, 619, 629, 646
Bsu36I	CCTNAGG	1 cut(s)	708
BsuI	GTATCC	1 cut(s)	519
BsuRI	GGCC	5 cut(s)	17, 27, 80, 768, 899
BtgI	CCRYGG	1 cut(s)	726
BtsCI	GGATG	1 cut(s)	238
BtsIMutI	CAGTG	1 cut(s)	597
Cac8I	GCNNGC	1 cut(s)	291
Cfr13I	GGNCC	3 cut(s)	15, 26, 898
CviAII	CATG	8 cut(s)	19, 52, 393, 455, 524, 719, 727, 906
DdeI	CTNAG	5 cut(s)	75, 438, 504, 585, 708
DpnI	GATC	5 cut(s)	33, 411, 570, 678, 833
DpnII	GATC	5 cut(s)	31, 409, 568, 676, 831
DrdI	GACNNNNNNGTC	1 cut(s)	545
DseDI	GACNNNNNNGTC	1 cut(s)	545
Eam1104I	CTCTTC	2 cut(s)	129, 879
EarI	CTCTTC	2 cut(s)	129, 879
Ecl136II	GAGCTC	1 cut(s)	877
Eco130I	CCWWGG	2 cut(s)	206, 726
Eco147I	AGGCCT	2 cut(s)	80, 768
Eco24I	GRGCYC	1 cut(s)	879
Eco53kI	GAGCTC	1 cut(s)	877
Eco57I	CTGAAG	3 cut(s)	258, 282, 848
Eco81I	CCTNAGG	1 cut(s)	708
Eco88I	CYCGRG	1 cut(s)	844
EcoICRI	GAGCTC	1 cut(s)	877
EcoRII	CCWGG	1 cut(s)	759
EcoT14I	CCWWGG	2 cut(s)	206, 726
EcoT38I	GRGCYC	1 cut(s)	879
ErhI	CCWWGG	2 cut(s)	206, 726
FaeI	CATG	8 cut(s)	22, 55, 396, 458, 527, 722, 730, 909
FaqI	GGGAC	2 cut(s)	715, 727
FatI	CATG	8 cut(s)	18, 51, 392, 454, 523, 718, 726, 905
FbaI	TGATCA	3 cut(s)	31, 568, 676
Fnu4HI	GCNGC	7 cut(s)	72, 114, 294, 605, 608, 618, 660
FokI	GGATG	1 cut(s)	245
FriOI	GRGCYC	1 cut(s)	879
Fsp4HI	GCNGC	7 cut(s)	72, 114, 294, 605, 608, 618, 660
FspBI	CTAG	2 cut(s)	9, 407
GluI	GCNGC	7 cut(s)	72, 114, 294, 605, 608, 618, 660
GsaI	CCCAGC	1 cut(s)	332
HaeIII	GGCC	5 cut(s)	17, 27, 80, 768, 899
Hin1II	CATG	8 cut(s)	22, 55, 396, 458, 527, 722, 730, 909
HincII	GTYRAC	1 cut(s)	178
HindII	GTYRAC	1 cut(s)	178
HindIII	AAGCTT	3 cut(s)	162, 270, 854
HinfI	GANTC	4 cut(s)	43, 201, 703, 756
HphI	GGTGA	3 cut(s)	473, 586, 781
Hpy166II	GTNNAC	1 cut(s)	178
Hpy188I	TCNGA	5 cut(s)	301, 441, 551, 636, 742
Hpy188III	TCNNGA	4 cut(s)	352, 377, 512, 844
Hpy8I	GTNNAC	1 cut(s)	178
Hpy99I	CGWCG	1 cut(s)	839
HpyAV	CCTTC	4 cut(s)	205, 209, 378, 758
HpyCH4III	ACNGT	2 cut(s)	532, 601
HpyF10VI	GCNNNNNNNGC	5 cut(s)	14, 77, 329, 656, 668
HpyF3I	CTNAG	5 cut(s)	75, 438, 504, 585, 708
Hsp92II	CATG	8 cut(s)	22, 55, 396, 458, 527, 722, 730, 909
Ksp22I	TGATCA	3 cut(s)	31, 568, 676
Kzo9I	GATC	5 cut(s)	31, 409, 568, 676, 831
Lsp1109I	GCAGC	6 cut(s)	83, 280, 616, 619, 629, 646
LweI	GCATC	2 cut(s)	100, 850
MaeI	CTAG	2 cut(s)	9, 407
MaeIII	GTNAC	1 cut(s)	787
MalI	GATC	5 cut(s)	33, 411, 570, 678, 833
MboI	GATC	5 cut(s)	31, 409, 568, 676, 831
MboII	GAAGA	4 cut(s)	116, 489, 841, 896
MhlI	GDGCHC	1 cut(s)	879
MluCI	AATT	2 cut(s)	372, 813
MlyI	GAGTC	1 cut(s)	697
MmeI	TCCRAC	1 cut(s)	514
MnlI	CCTC	7 cut(s)	70, 75, 132, 151, 435, 779, 840
MroXI	GAANNNNTTC	1 cut(s)	493
MslI	CAYNNNNRTG	3 cut(s)	459, 599, 731
MspA1I	CMGCKG	1 cut(s)	74
MspR9I	CCNGG	1 cut(s)	761
MvaI	CCWGG	1 cut(s)	761
MvnI	CGCG	1 cut(s)	687
MwoI	GCNNNNNNNGC	5 cut(s)	14, 77, 329, 656, 668
NcoI	CCATGG	1 cut(s)	726
NdeII	GATC	5 cut(s)	31, 409, 568, 676, 831
NlaIII	CATG	8 cut(s)	22, 55, 396, 458, 527, 722, 730, 909
NlaIV	GGNNCC	1 cut(s)	16
NmuCI	GTSAC	1 cut(s)	787
NspI	RCATGY	3 cut(s)	55, 396, 722
OliI	CACNNNNGTG	1 cut(s)	599
PaeR7I	CTCGAG	1 cut(s)	844
PceI	AGGCCT	2 cut(s)	80, 768
PciI	ACATGT	2 cut(s)	392, 718
PdmI	GAANNNNTTC	1 cut(s)	493
PfeI	GAWTC	3 cut(s)	43, 201, 756
PfoI	TCCNGGA	1 cut(s)	759
PkrI	GCNGC	7 cut(s)	73, 115, 295, 606, 609, 619, 661
PleI	GAGTC	1 cut(s)	697
PpsI	GAGTC	1 cut(s)	697
PscI	ACATGT	2 cut(s)	392, 718
Psp124BI	GAGCTC	1 cut(s)	879
Psp6I	CCWGG	1 cut(s)	759
PspFI	CCCAGC	1 cut(s)	328
PspGI	CCWGG	1 cut(s)	759
PspN4I	GGNNCC	1 cut(s)	16
PspPI	GGNCC	3 cut(s)	15, 26, 898
PstI	CTGCAG	1 cut(s)	73
PvuII	CAGCTG	1 cut(s)	74
RseI	CAYNNNNRTG	3 cut(s)	459, 599, 731
SacI	GAGCTC	1 cut(s)	879
SatI	GCNGC	7 cut(s)	72, 114, 294, 605, 608, 618, 660
Sau3AI	GATC	5 cut(s)	31, 409, 568, 676, 831
Sau96I	GGNCC	3 cut(s)	15, 26, 898
SchI	GAGTC	1 cut(s)	697
ScrFI	CCNGG	1 cut(s)	761
SduI	GDGCHC	1 cut(s)	879
SfaNI	GCATC	2 cut(s)	100, 850
SfcI	CTRYAG	1 cut(s)	69
Sfr274I	CTCGAG	1 cut(s)	844
SlaI	CTCGAG	1 cut(s)	844
SmiMI	CAYNNNNRTG	3 cut(s)	459, 599, 731
SmlI	CTYRAG	1 cut(s)	844
SmoI	CTYRAG	1 cut(s)	844
Sse9I	AATT	2 cut(s)	372, 813
SseBI	AGGCCT	2 cut(s)	80, 768
SsiI	CCGC	1 cut(s)	114
SspMI	CTAG	2 cut(s)	9, 407
SstI	GAGCTC	1 cut(s)	879
StuI	AGGCCT	2 cut(s)	80, 768
StyD4I	CCNGG	1 cut(s)	759
StyI	CCWWGG	2 cut(s)	206, 726
TaaI	ACNGT	2 cut(s)	532, 601
TaqI	TCGA	2 cut(s)	834, 845
TasI	AATT	2 cut(s)	372, 813
TauI	GCSGC	1 cut(s)	116
TfiI	GAWTC	3 cut(s)	43, 201, 756
TscAI	CASTG	1 cut(s)	604
TseFI	GTSAC	1 cut(s)	787
TseI	GCWGC	6 cut(s)	71, 293, 604, 607, 617, 659
Tsp45I	GTSAC	1 cut(s)	787
TspDTI	ATGAA	3 cut(s)	443, 580, 894
TspRI	CASTG	1 cut(s)	604
XceI	RCATGY	3 cut(s)	55, 396, 722
XhoI	CTCGAG	1 cut(s)	844
XmnI	GAANNNNTTC	1 cut(s)	493
XspI	CTAG	2 cut(s)	9, 407

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