Basic Information

Type: gene

Biological Identity

Species

rosa_samantha

Chromosome

Chr5C

Orthogroup ID

OG0009056

Physical Location & Seq

Genomic Coordinates Reverse (-)

17512142 .. 17515471

Gene Structure 3330 bp

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UTR

Exon/CDS

Intron

Transcript / Protein ID

Rh5CG179400.1

Sequence Viewer

CDS Protein Promoter (2k)

Length: 828 bp

ATGGTTGCTAGGGGGGCCATGCTTGGCCCTGATCAGCCTGTGATTCTGCACATGCTTGATATTCCTCCTGCAGCTGAGGCCTTGAATGGGGTAAAAATGGAACTGATTGATGCTGCCTTTCCTCTTCTCAAAGGTGTCGTGGCTACAACAGATGTTGAGGAAGCTTGTAAAGGTGTCAACATTGCTGTTATGGTTGGTGGATTCCCAAGGAAGGAAGGTATGGAAAGAAAGGATGTGATGTCAAAAAATGTATCAATCTACAAGGGTCAAGCTTCAGCATTGGAAAAGCACGCTGCTTCAGATGTCAAGGTTCTGGTGGTTGCTAACCCAGCAAACACCAATGCACTCATCTTGAAAGAATATGCACCTTCAATTCCAGAGAAAAACATCACATGTCTTACACGACTAGATCATAACCGAGCATTGGGGCAAATCTCTCAGAGGCTAAATGTTCATGTTGGTGATGTAAAGAATGTTATCATCTGGGGAAATCATTCTTCAACTCAGTATCCTGATGTCAATCATGCAACTGTTGGAGACAAACCCGTCAGACAACTTGTAGCTGATGATCAATGGTTGAATACCGAGTTCATCACCACCGTGCAGCAGCGTGGCGCTGCCATTATCAAAGCTCGGAAACTATCAAGTGCTTTGTCTGCTGCAAGTTCTGCCTGTGATCACATACGCGATTGGGTTCTTGGGACTCCTAAGGGGACACATGTTTCCATGGGTGTGTATTCTGATGGTTCTTATGGAATCCAGGAAGGCCTCATTTACTCTTTCCCTGTCACCTGTGAGAAAGGGGAATGGAAAATTGTGCAAGGTTAG

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

275

Amino Acids

29.65

Weight (kDa)

7.09

Isoelectric Point (pI)

28.33

Instability Index

Protein Domains (Pfam)

Domain Name	Pfam ID	Position	E-value	Description
Ldh_1_N	PF00056	16 - 130	7.1e-25	lactate/malate dehydrogenase, NAD binding domain
Ldh_1_C	PF02866	134 - 274	1.9e-38	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
AcuI	CTGAAG	2 cut(s)	258, 282
AfiI	CCNNNNNNNGG	3 cut(s)	87, 211, 424
AflIII	ACRYGT	2 cut(s)	392, 718
AgsI	TTSAA	5 cut(s)	85, 355, 372, 501, 580
AjnI	CCWGG	1 cut(s)	759
AleI	CACNNNNGTG	1 cut(s)	599
AluBI	AGCT	5 cut(s)	74, 164, 272, 563, 632
AluI	AGCT	5 cut(s)	74, 164, 272, 563, 632
Alw26I	GTCTC	1 cut(s)	531
AoxI	GGCC	4 cut(s)	15, 25, 78, 766
ApeKI	GCWGC	7 cut(s)	71, 113, 293, 604, 607, 617, 659
Asp700I	GAANNNNTTC	1 cut(s)	493
AspLEI	GCGC	1 cut(s)	617
AspS9I	GGNCC	2 cut(s)	15, 26
AsuHPI	GGTGA	3 cut(s)	473, 586, 781
AxyI	CCTNAGG	1 cut(s)	708
BbvCI	CCTCAGC	1 cut(s)	75
BbvI	GCAGC	7 cut(s)	83, 100, 280, 604, 616, 619, 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	1 cut(s)	531
BfaI	CTAG	2 cut(s)	9, 407
BfmI	CTRYAG	1 cut(s)	69
BfoI	RGCGCY	1 cut(s)	618
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
BmgT120I	GGNCC	2 cut(s)	15, 26
BmiI	GGNNCC	1 cut(s)	16
BmrFI	CCNGG	1 cut(s)	761
BmsI	GCATC	1 cut(s)	100
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	3 cut(s)	66, 452, 518
BseXI	GCAGC	7 cut(s)	83, 100, 280, 604, 616, 619, 646
BseYI	CCCAGC	1 cut(s)	328
BsgI	GTGCAG	2 cut(s)	32, 623
Bsh1236I	CGCG	1 cut(s)	687
BshFI	GGCC	4 cut(s)	17, 27, 80, 768
BslFI	GGGAC	2 cut(s)	715, 727
BslI	CCNNNNNNNGG	3 cut(s)	87, 211, 424
BsmAI	GTCTC	1 cut(s)	531
BsmFI	GGGAC	2 cut(s)	715, 727
BsnI	GGCC	4 cut(s)	17, 27, 80, 768
Bsp143I	GATC	4 cut(s)	31, 409, 568, 676
Bsp19I	CCATGG	1 cut(s)	726
BspANI	GGCC	4 cut(s)	17, 27, 80, 768
BspCNI	CTCAG	3 cut(s)	67, 451, 517
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	4 cut(s)	31, 409, 568, 676
BssT1I	CCWWGG	2 cut(s)	206, 726
Bst2UI	CCWGG	1 cut(s)	761
Bst4CI	ACNGT	2 cut(s)	532, 601
Bst6I	CTCTTC	1 cut(s)	129
BstAPI	GCANNNNNTGC	1 cut(s)	668
BstC8I	GCNNGC	1 cut(s)	291
BstDEI	CTNAG	4 cut(s)	75, 438, 504, 708
BstDSI	CCRYGG	1 cut(s)	726
BstF5I	GGATG	1 cut(s)	238
BstFNI	CGCG	1 cut(s)	687
BstH2I	RGCGCY	1 cut(s)	618
BstHHI	GCGC	1 cut(s)	617
BstKTI	GATC	4 cut(s)	34, 412, 571, 679
BstMAI	GTCTC	1 cut(s)	531
BstMBI	GATC	4 cut(s)	31, 409, 568, 676
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	7 cut(s)	83, 100, 280, 604, 616, 619, 646
Bsu36I	CCTNAGG	1 cut(s)	708
BsuI	GTATCC	1 cut(s)	519
BsuRI	GGCC	4 cut(s)	17, 27, 80, 768
BtgI	CCRYGG	1 cut(s)	726
BtsCI	GGATG	1 cut(s)	238
Cac8I	GCNNGC	1 cut(s)	291
CfoI	GCGC	1 cut(s)	617
Cfr13I	GGNCC	2 cut(s)	15, 26
CviAII	CATG	7 cut(s)	19, 52, 393, 455, 524, 719, 727
DdeI	CTNAG	4 cut(s)	75, 438, 504, 708
DpnI	GATC	4 cut(s)	33, 411, 570, 678
DpnII	GATC	4 cut(s)	31, 409, 568, 676
DrdI	GACNNNNNNGTC	1 cut(s)	545
DseDI	GACNNNNNNGTC	1 cut(s)	545
Eam1104I	CTCTTC	1 cut(s)	129
EarI	CTCTTC	1 cut(s)	129
Eco130I	CCWWGG	2 cut(s)	206, 726
Eco147I	AGGCCT	2 cut(s)	80, 768
Eco57I	CTGAAG	2 cut(s)	258, 282
Eco81I	CCTNAGG	1 cut(s)	708
EcoRII	CCWGG	1 cut(s)	759
EcoT14I	CCWWGG	2 cut(s)	206, 726
ErhI	CCWWGG	2 cut(s)	206, 726
FaeI	CATG	7 cut(s)	22, 55, 396, 458, 527, 722, 730
FaqI	GGGAC	2 cut(s)	715, 727
FatI	CATG	7 cut(s)	18, 51, 392, 454, 523, 718, 726
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
Fsp4HI	GCNGC	7 cut(s)	72, 114, 294, 605, 608, 618, 660
FspBI	CTAG	2 cut(s)	9, 407
GlaI	GCGC	1 cut(s)	616
GluI	GCNGC	7 cut(s)	72, 114, 294, 605, 608, 618, 660
GsaI	CCCAGC	1 cut(s)	332
HaeII	RGCGCY	1 cut(s)	618
HaeIII	GGCC	4 cut(s)	17, 27, 80, 768
HhaI	GCGC	1 cut(s)	617
Hin1II	CATG	7 cut(s)	22, 55, 396, 458, 527, 722, 730
Hin6I	GCGC	1 cut(s)	615
HinP1I	GCGC	1 cut(s)	615
HincII	GTYRAC	1 cut(s)	178
HindII	GTYRAC	1 cut(s)	178
HindIII	AAGCTT	2 cut(s)	162, 270
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	3 cut(s)	352, 377, 512
Hpy8I	GTNNAC	1 cut(s)	178
HpyAV	CCTTC	4 cut(s)	205, 209, 378, 758
HpyCH4III	ACNGT	2 cut(s)	532, 601
HpyCH4V	TGCA	8 cut(s)	49, 71, 344, 365, 527, 604, 662, 820
HpyF10VI	GCNNNNNNNGC	5 cut(s)	14, 77, 329, 656, 668
HpyF3I	CTNAG	4 cut(s)	75, 438, 504, 708
Hsp92II	CATG	7 cut(s)	22, 55, 396, 458, 527, 722, 730
HspAI	GCGC	1 cut(s)	615
Ksp22I	TGATCA	3 cut(s)	31, 568, 676
Kzo9I	GATC	4 cut(s)	31, 409, 568, 676
Lsp1109I	GCAGC	7 cut(s)	83, 100, 280, 604, 616, 619, 646
LweI	GCATC	1 cut(s)	100
MaeI	CTAG	2 cut(s)	9, 407
MaeIII	GTNAC	1 cut(s)	787
MalI	GATC	4 cut(s)	33, 411, 570, 678
MboI	GATC	4 cut(s)	31, 409, 568, 676
MboII	GAAGA	2 cut(s)	116, 489
MluCI	AATT	2 cut(s)	372, 813
MlyI	GAGTC	1 cut(s)	697
MmeI	TCCRAC	1 cut(s)	514
MnlI	CCTC	6 cut(s)	70, 75, 132, 151, 435, 779
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	4 cut(s)	31, 409, 568, 676
NlaIII	CATG	7 cut(s)	22, 55, 396, 458, 527, 722, 730
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
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
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	2 cut(s)	15, 26
PstI	CTGCAG	1 cut(s)	73
PvuII	CAGCTG	1 cut(s)	74
RseI	CAYNNNNRTG	3 cut(s)	459, 599, 731
SatI	GCNGC	7 cut(s)	72, 114, 294, 605, 608, 618, 660
Sau3AI	GATC	4 cut(s)	31, 409, 568, 676
Sau96I	GGNCC	2 cut(s)	15, 26
SchI	GAGTC	1 cut(s)	697
ScrFI	CCNGG	1 cut(s)	761
SfaNI	GCATC	1 cut(s)	100
SfcI	CTRYAG	1 cut(s)	69
SmiMI	CAYNNNNRTG	3 cut(s)	459, 599, 731
Sse9I	AATT	2 cut(s)	372, 813
SseBI	AGGCCT	2 cut(s)	80, 768
SspMI	CTAG	2 cut(s)	9, 407
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
TasI	AATT	2 cut(s)	372, 813
TfiI	GAWTC	3 cut(s)	43, 201, 756
TseFI	GTSAC	1 cut(s)	787
TseI	GCWGC	7 cut(s)	71, 113, 293, 604, 607, 617, 659
Tsp45I	GTSAC	1 cut(s)	787
TspDTI	ATGAA	2 cut(s)	443, 580
XceI	RCATGY	3 cut(s)	55, 396, 722
XmnI	GAANNNNTTC	1 cut(s)	493
XspI	CTAG	2 cut(s)	9, 407

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