Basic Information

Type: gene

Biological Identity

Species

rosa_samantha

Chromosome

Chr5B

Orthogroup ID

OG0009056

Physical Location & Seq

Genomic Coordinates Reverse (-)

17195425 .. 17198602

Gene Structure 3178 bp

Loading structure...

UTR

Exon/CDS

Intron

Transcript / Protein ID

Rh5BG164500.1

Sequence Viewer

CDS Protein Promoter (2k)

Length: 987 bp

ATGGGGAAAAACCCAGTTCGAGTTCTTGTAACTGGTGCTGCTGGGCAAATAGGCTATGCTATCGTTCCGATGGTTGCTAGGGGGGCCATGCTTGGCCCTGATCAGCCTGTGATTCTGCACATGCTTGATATTCCTCCTGCAGCTGAGGCCTTGAATGGGGTAAAAATGGAACTGATTGATGCCGCCTTTCCTCTTCTCAAAGGTGTTGTGGCTACAACAGATGTTGAGGAAGCTTGTAAAGGTGTCAACATTGCTGTTATGGTTGGTGGATTCCCAAGGAAGGAAGGTATGGAAAGAAAGGATGTGATGTCAAAAAATGTATCAATCTACAAGGGTCAAGCTTCAGCATTGGAAAAGCACGCTGCTTCAGATGTCAAGGTTCTGGTGGTTGCTAACCCAGCAAACACCAATGCACTCATCTTGAAAGAATACGCACCTTCAATTCCAGAGAAAAACATCACATGTCTTACACGACTAGATCATAACCGAGCATTGGGGCAAATCTCTCAGAGGCTAAATGTTCATGTTGGTGATGTAAAGAATGTTATCATCTGGGGAAATCATTCTTCAACTCAGTATCCTGATGTCAATCATGCAACTGTTGGAGACAAACCTGTCAGACAACTTGTAGCTGATGATCAATGGTTGAATACTGAGTTCATCACCACTGTGCAGCAGCGTGGCGCAGCCATTATCAAAGCTCGGAAACTATCAAGTGCTTTGTCTGCTGCAAGTTCTGCCTGTGATCACATACGCGATTGGGTTCTTGGGACTCCTAAGGGGACACATGTTTCCATGGGCGTGTATTCTGATGGTTCTTATGGAATCCAGGAAGGCCTCATTTATTCTTTCCCTGTTACCTGTGAGAAAGGGGAATGGAAAATTGTGCAAGGACTGAAGATTGACGAGTTCTCGAGGAAAAAGCTTGATGCAACTGCACAAGAGCTCATTGAAGAGAAATCGTTGGCCCATTCATGTCTCAACTGA

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

328

Amino Acids

35.35

Weight (kDa)

7.67

Isoelectric Point (pI)

29.45

Instability Index

Protein Domains (Pfam)

Domain Name	Pfam ID	Position	E-value	Description
Ldh_1_N	PF00056	6 - 153	2.1e-30	lactate/malate dehydrogenase, NAD binding domain
Ldh_1_C	PF02866	157 - 321	3.5e-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

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: 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)	614
AccII	CGCG	1 cut(s)	756
AciI	CCGC	1 cut(s)	183
AcuI	CTGAAG	3 cut(s)	327, 351, 917
AfiI	CCNNNNNNNGG	3 cut(s)	156, 280, 493
AflIII	ACRYGT	2 cut(s)	461, 787
AgsI	TTSAA	6 cut(s)	154, 424, 441, 570, 649, 953
AjnI	CCWGG	1 cut(s)	828
AleI	CACNNNNGTG	1 cut(s)	668
AluBI	AGCT	7 cut(s)	143, 233, 341, 632, 701, 925, 946
AluI	AGCT	7 cut(s)	143, 233, 341, 632, 701, 925, 946
Alw21I	GWGCWC	1 cut(s)	948
Alw26I	GTCTC	2 cut(s)	600, 983
Ama87I	CYCGRG	1 cut(s)	913
AoxI	GGCC	5 cut(s)	84, 94, 147, 835, 966
ApeKI	GCWGC	7 cut(s)	38, 140, 362, 673, 676, 686, 728
Asp700I	GAANNNNTTC	1 cut(s)	562
AspLEI	GCGC	1 cut(s)	686
AspS9I	GGNCC	3 cut(s)	84, 95, 967
AsuHPI	GGTGA	2 cut(s)	542, 655
AvaI	CYCGRG	1 cut(s)	913
AxyI	CCTNAGG	1 cut(s)	777
BanII	GRGCYC	1 cut(s)	948
Bbv12I	GWGCWC	1 cut(s)	948
BbvCI	CCTCAGC	1 cut(s)	144
BbvI	GCAGC	7 cut(s)	25, 152, 349, 685, 688, 698, 715
BccI	CCATC	2 cut(s)	64, 806
BciT130I	CCWGG	1 cut(s)	830
BciVI	GTATCC	1 cut(s)	588
BclI	TGATCA	3 cut(s)	100, 637, 745
BcoDI	GTCTC	2 cut(s)	600, 983
BfaI	CTAG	2 cut(s)	78, 476
BfmI	CTRYAG	1 cut(s)	138
BfuI	GTATCC	1 cut(s)	588
BisI	GCNGC	8 cut(s)	39, 141, 183, 363, 674, 677, 687, 729
BlsI	GCNGC	8 cut(s)	40, 142, 184, 364, 675, 678, 688, 730
Bme1390I	CCNGG	1 cut(s)	830
BmeT110I	CYCGRG	1 cut(s)	913
BmgT120I	GGNCC	3 cut(s)	84, 95, 967
BmiI	GGNNCC	1 cut(s)	85
BmrFI	CCNGG	1 cut(s)	830
BmrI	ACTGGG	1 cut(s)	8
BmsI	GCATC	2 cut(s)	169, 919
BmuI	ACTGGG	1 cut(s)	8
Bpu10I	CCTNAGC	1 cut(s)	144
BsaBI	GATNNNNATC	1 cut(s)	588
BsaJI	CCNNGG	2 cut(s)	275, 795
Bsc4I	CCNNNNNNNGG	3 cut(s)	156, 280, 493
Bse1I	ACTGG	2 cut(s)	14, 37
Bse21I	CCTNAGG	1 cut(s)	777
Bse3DI	GCAATG	1 cut(s)	249
Bse8I	GATNNNNATC	1 cut(s)	588
BseBI	CCWGG	1 cut(s)	830
BseDI	CCNNGG	2 cut(s)	275, 795
BseGI	GGATG	1 cut(s)	307
BseJI	GATNNNNATC	1 cut(s)	588
BseLI	CCNNNNNNNGG	3 cut(s)	156, 280, 493
BseMI	GCAATG	1 cut(s)	249
BseMII	CTCAG	4 cut(s)	135, 521, 587, 645
BseNI	ACTGG	2 cut(s)	14, 37
BseXI	GCAGC	7 cut(s)	25, 152, 349, 685, 688, 698, 715
BseYI	CCCAGC	2 cut(s)	41, 397
BsgI	GTGCAG	3 cut(s)	101, 692, 921
Bsh1236I	CGCG	1 cut(s)	756
BshFI	GGCC	5 cut(s)	86, 96, 149, 837, 968
BsiHKAI	GWGCWC	1 cut(s)	948
BsiHKCI	CYCGRG	1 cut(s)	913
BslFI	GGGAC	2 cut(s)	784, 796
BslI	CCNNNNNNNGG	3 cut(s)	156, 280, 493
BsmAI	GTCTC	2 cut(s)	600, 983
BsmFI	GGGAC	2 cut(s)	784, 796
BsnI	GGCC	5 cut(s)	86, 96, 149, 837, 968
BsoBI	CYCGRG	1 cut(s)	913
Bsp1286I	GDGCHC	1 cut(s)	948
Bsp143I	GATC	4 cut(s)	100, 478, 637, 745
Bsp19I	CCATGG	1 cut(s)	795
BspACI	CCGC	1 cut(s)	183
BspANI	GGCC	5 cut(s)	86, 96, 149, 837, 968
BspCNI	CTCAG	4 cut(s)	136, 520, 586, 646
BspFNI	CGCG	1 cut(s)	756
BspLI	GGNNCC	1 cut(s)	85
BspMAI	CTGCAG	1 cut(s)	142
BsrDI	GCAATG	1 cut(s)	249
BsrI	ACTGG	2 cut(s)	14, 37
BssECI	CCNNGG	2 cut(s)	275, 795
BssMI	GATC	4 cut(s)	100, 478, 637, 745
BssT1I	CCWWGG	2 cut(s)	275, 795
Bst2UI	CCWGG	1 cut(s)	830
Bst4CI	ACNGT	2 cut(s)	601, 670
Bst6I	CTCTTC	2 cut(s)	198, 948
BstAPI	GCANNNNNTGC	1 cut(s)	737
BstC8I	GCNNGC	1 cut(s)	360
BstDEI	CTNAG	5 cut(s)	144, 507, 573, 654, 777
BstDSI	CCRYGG	1 cut(s)	795
BstF5I	GGATG	1 cut(s)	307
BstFNI	CGCG	1 cut(s)	756
BstHHI	GCGC	1 cut(s)	686
BstKTI	GATC	4 cut(s)	103, 481, 640, 748
BstMAI	GTCTC	2 cut(s)	600, 983
BstMBI	GATC	4 cut(s)	100, 478, 637, 745
BstMWI	GCNNNNNNNGC	5 cut(s)	83, 146, 398, 725, 737
BstNI	CCWGG	1 cut(s)	830
BstNSI	RCATGY	3 cut(s)	124, 465, 791
BstSCI	CCNGG	1 cut(s)	828
BstSFI	CTRYAG	1 cut(s)	138
BstUI	CGCG	1 cut(s)	756
BstV1I	GCAGC	7 cut(s)	25, 152, 349, 685, 688, 698, 715
Bsu36I	CCTNAGG	1 cut(s)	777
BsuI	GTATCC	1 cut(s)	588
BsuRI	GGCC	5 cut(s)	86, 96, 149, 837, 968
BtgI	CCRYGG	1 cut(s)	795
BtsCI	GGATG	1 cut(s)	307
BtsIMutI	CAGTG	1 cut(s)	666
Cac8I	GCNNGC	1 cut(s)	360
CfoI	GCGC	1 cut(s)	686
Cfr13I	GGNCC	3 cut(s)	84, 95, 967
CviAII	CATG	8 cut(s)	88, 121, 462, 524, 593, 788, 796, 975
DdeI	CTNAG	5 cut(s)	144, 507, 573, 654, 777
DpnI	GATC	4 cut(s)	102, 480, 639, 747
DpnII	GATC	4 cut(s)	100, 478, 637, 745
DrdI	GACNNNNNNGTC	1 cut(s)	614
DseDI	GACNNNNNNGTC	1 cut(s)	614
Eam1104I	CTCTTC	2 cut(s)	198, 948
EarI	CTCTTC	2 cut(s)	198, 948
Ecl136II	GAGCTC	1 cut(s)	946
Eco130I	CCWWGG	2 cut(s)	275, 795
Eco147I	AGGCCT	2 cut(s)	149, 837
Eco24I	GRGCYC	1 cut(s)	948
Eco53kI	GAGCTC	1 cut(s)	946
Eco57I	CTGAAG	3 cut(s)	327, 351, 917
Eco81I	CCTNAGG	1 cut(s)	777
Eco88I	CYCGRG	1 cut(s)	913
EcoICRI	GAGCTC	1 cut(s)	946
EcoRII	CCWGG	1 cut(s)	828
EcoT14I	CCWWGG	2 cut(s)	275, 795
EcoT38I	GRGCYC	1 cut(s)	948
ErhI	CCWWGG	2 cut(s)	275, 795
FaeI	CATG	8 cut(s)	91, 124, 465, 527, 596, 791, 799, 978
FaqI	GGGAC	2 cut(s)	784, 796
FatI	CATG	8 cut(s)	87, 120, 461, 523, 592, 787, 795, 974
FbaI	TGATCA	3 cut(s)	100, 637, 745
Fnu4HI	GCNGC	8 cut(s)	39, 141, 183, 363, 674, 677, 687, 729
FokI	GGATG	1 cut(s)	314
FriOI	GRGCYC	1 cut(s)	948
Fsp4HI	GCNGC	8 cut(s)	39, 141, 183, 363, 674, 677, 687, 729
FspBI	CTAG	2 cut(s)	78, 476
GlaI	GCGC	1 cut(s)	685
GluI	GCNGC	8 cut(s)	39, 141, 183, 363, 674, 677, 687, 729
GsaI	CCCAGC	2 cut(s)	45, 401
HaeIII	GGCC	5 cut(s)	86, 96, 149, 837, 968
HhaI	GCGC	1 cut(s)	686
Hin1II	CATG	8 cut(s)	91, 124, 465, 527, 596, 791, 799, 978
Hin6I	GCGC	1 cut(s)	684
HinP1I	GCGC	1 cut(s)	684
HincII	GTYRAC	1 cut(s)	247
HindII	GTYRAC	1 cut(s)	247
HindIII	AAGCTT	3 cut(s)	231, 339, 923
HinfI	GANTC	4 cut(s)	112, 270, 772, 825
HphI	GGTGA	2 cut(s)	542, 655
Hpy166II	GTNNAC	1 cut(s)	247
Hpy188I	TCNGA	6 cut(s)	69, 370, 510, 620, 705, 811
Hpy188III	TCNNGA	4 cut(s)	421, 446, 581, 913
Hpy8I	GTNNAC	1 cut(s)	247
HpyAV	CCTTC	4 cut(s)	274, 278, 447, 827
HpyCH4III	ACNGT	2 cut(s)	601, 670
HpyCH4V	TGCA	9 cut(s)	118, 140, 413, 596, 673, 731, 889, 932, 938
HpyF10VI	GCNNNNNNNGC	5 cut(s)	83, 146, 398, 725, 737
HpyF3I	CTNAG	5 cut(s)	144, 507, 573, 654, 777
Hsp92II	CATG	8 cut(s)	91, 124, 465, 527, 596, 791, 799, 978
HspAI	GCGC	1 cut(s)	684
Ksp22I	TGATCA	3 cut(s)	100, 637, 745
Kzo9I	GATC	4 cut(s)	100, 478, 637, 745
Lsp1109I	GCAGC	7 cut(s)	25, 152, 349, 685, 688, 698, 715
LweI	GCATC	2 cut(s)	169, 919
MaeI	CTAG	2 cut(s)	78, 476
MaeIII	GTNAC	2 cut(s)	28, 856
MalI	GATC	4 cut(s)	102, 480, 639, 747
MboI	GATC	4 cut(s)	100, 478, 637, 745
MboII	GAAGA	4 cut(s)	185, 558, 910, 965
MhlI	GDGCHC	1 cut(s)	948
MluCI	AATT	2 cut(s)	441, 882
MlyI	GAGTC	1 cut(s)	766
MmeI	TCCRAC	1 cut(s)	583
MnlI	CCTC	7 cut(s)	139, 144, 201, 220, 504, 848, 909
MroXI	GAANNNNTTC	1 cut(s)	562
MslI	CAYNNNNRTG	3 cut(s)	528, 668, 800
MspA1I	CMGCKG	1 cut(s)	143
MspR9I	CCNGG	1 cut(s)	830
MvaI	CCWGG	1 cut(s)	830
MvnI	CGCG	1 cut(s)	756
MwoI	GCNNNNNNNGC	5 cut(s)	83, 146, 398, 725, 737
NcoI	CCATGG	1 cut(s)	795
NdeII	GATC	4 cut(s)	100, 478, 637, 745
NlaIII	CATG	8 cut(s)	91, 124, 465, 527, 596, 791, 799, 978
NlaIV	GGNNCC	1 cut(s)	85
NspI	RCATGY	3 cut(s)	124, 465, 791
OliI	CACNNNNGTG	1 cut(s)	668
PaeR7I	CTCGAG	1 cut(s)	913
PceI	AGGCCT	2 cut(s)	149, 837
PciI	ACATGT	2 cut(s)	461, 787
PdmI	GAANNNNTTC	1 cut(s)	562
PfeI	GAWTC	3 cut(s)	112, 270, 825
PfoI	TCCNGGA	1 cut(s)	828
PkrI	GCNGC	8 cut(s)	40, 142, 184, 364, 675, 678, 688, 730
PleI	GAGTC	1 cut(s)	766
PpsI	GAGTC	1 cut(s)	766
PscI	ACATGT	2 cut(s)	461, 787
Psp124BI	GAGCTC	1 cut(s)	948
Psp6I	CCWGG	1 cut(s)	828
PspFI	CCCAGC	2 cut(s)	41, 397
PspGI	CCWGG	1 cut(s)	828
PspN4I	GGNNCC	1 cut(s)	85
PspPI	GGNCC	3 cut(s)	84, 95, 967
PstI	CTGCAG	1 cut(s)	142
PvuII	CAGCTG	1 cut(s)	143
RseI	CAYNNNNRTG	3 cut(s)	528, 668, 800
SacI	GAGCTC	1 cut(s)	948
SatI	GCNGC	8 cut(s)	39, 141, 183, 363, 674, 677, 687, 729
Sau3AI	GATC	4 cut(s)	100, 478, 637, 745
Sau96I	GGNCC	3 cut(s)	84, 95, 967
SchI	GAGTC	1 cut(s)	766
ScrFI	CCNGG	1 cut(s)	830
SduI	GDGCHC	1 cut(s)	948
SfaNI	GCATC	2 cut(s)	169, 919
SfcI	CTRYAG	1 cut(s)	138
Sfr274I	CTCGAG	1 cut(s)	913
SlaI	CTCGAG	1 cut(s)	913
SmiMI	CAYNNNNRTG	3 cut(s)	528, 668, 800
SmlI	CTYRAG	1 cut(s)	913
SmoI	CTYRAG	1 cut(s)	913
Sse9I	AATT	2 cut(s)	441, 882
SseBI	AGGCCT	2 cut(s)	149, 837
SsiI	CCGC	1 cut(s)	183
SspMI	CTAG	2 cut(s)	78, 476
SstI	GAGCTC	1 cut(s)	948
StuI	AGGCCT	2 cut(s)	149, 837
StyD4I	CCNGG	1 cut(s)	828
StyI	CCWWGG	2 cut(s)	275, 795
TaaI	ACNGT	2 cut(s)	601, 670
TaqI	TCGA	2 cut(s)	19, 914
TasI	AATT	2 cut(s)	441, 882
TauI	GCSGC	1 cut(s)	185
TfiI	GAWTC	3 cut(s)	112, 270, 825
TscAI	CASTG	1 cut(s)	673
TseI	GCWGC	7 cut(s)	38, 140, 362, 673, 676, 686, 728
TspDTI	ATGAA	3 cut(s)	512, 649, 963
TspRI	CASTG	1 cut(s)	673
XceI	RCATGY	3 cut(s)	124, 465, 791
XhoI	CTCGAG	1 cut(s)	913
XmnI	GAANNNNTTC	1 cut(s)	562
XspI	CTAG	2 cut(s)	78, 476

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