Basic Information

Type: gene

Biological Identity

Species

rosa_laevigata

Chromosome

Chr7

Orthogroup ID

OG0001957

Physical Location & Seq

Genomic Coordinates Reverse (-)

67526059 .. 67531470

Gene Structure 5412 bp

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UTR

Exon/CDS

Intron

Transcript / Protein ID

RLM00000035486

Sequence Viewer

CDS Protein Promoter (2k)

Length: 807 bp

ATGCCATACAGATTGGATGAAACCACTGGTTACATTGACTATGGGCTGACCTATGCCACCAAAATATATCTGCAGTTGGAGAAAAGTGCCACACTATTCAGACCCAAATTAATAGTTGCTGGTGCCAGTGCATGTGCACGCTTGTACGACTATGCACTCATACGCAAGGTCTGTGATAAGCAGAAAGCTATTTTGTTAGCTAATATGGCACACATCAGTGGATTGGTTGGGGCAGATATTGTTACAACCACAACTCATAAGTCACTTCGTGGCCCTCGTGGGGCTATGATCTTCTTCAGGAAGGGGGTCATAGCCCCACGAGGCCACAACTCCAGAGTTCAAAGCTTACCAAGAACAAGTTCTCACTTGCTAGAGAAGGGCTATGATCTTGTCTCTGGTGGAACTGACAACCATTTAGTGTTGGTAAATTTGAGGGACAAGCCCCATTCCCATCACCGATCACCACCACAATCCCTACGCCCATCTCTAGATACCGTCCGGGGGCATAATCCCGACGTCGTCGGTGTAAAATCACCCACCTTGCAAATGTTTTCTCCAACATCCGACCCTTTCGCTTCACCTTCAAACCAGAATCCGAATCCACCGCATTTGCCTTTGTGGGCCCAACAGTTCTCACTCCTTGCCTCGCCTTCTCTATCACCGGAAACTTATTTCACTCTGACTTCCAGGGCCGGATCGGGTTGTACACCGGGTTTTCCATCACATTTGACTAGCATATTCTCTCCTCTTATTCTTCGAGCAAAGCTTCGTGCTCTCTTCCCGCATTCTCATCACAACCTCTTATGA

Functional Annotation

Gene Ontology

Molecular Function
Biological Process
Cellular Component

GO:0005575 GO:0005622 GO:0005623 GO:0005737 GO:0005739 GO:0043226 GO:0043227 GO:0043229 GO:0043231 GO:0044424 GO:0044444 GO:0044464

KEGG Pathways

Metabolic & Signaling

ko00260 ko00460 ko00630 ko00670 ko00680 ko01100 ko01110 ko01120 ko01130 ko01200 ko01230 ko01523 map00260 map00460 map00630 map00670 map00680 map01100 map01110 map01120 map01130 map01200 map01230 map01523

Pfam Domains

Protein Families

SHMT

Protein Analysis

269

Amino Acids

29.43

Weight (kDa)

9.97

Isoelectric Point (pI)

52.03

Instability Index

Protein Domains (Pfam)

Domain Name	Pfam ID	Position	E-value	Description
SHMT	PF00464	1 - 104	3.1e-33	Serine hydroxymethyltransferase
SHMT	PF00464	120 - 148	5.9e-07	Serine hydroxymethyltransferase

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)

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Tree File

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Publication-ready

iTOL Interactive Tree Of Life · Most popular EvolView Flexible annotations MEGA Desktop phylogenetics suite FigTree Desktop tree editor

Orthologous Genes (Group: OG0001957)

Species	Orthologous Gene IDs
arabidopsis_thaliana	AT5G26780 AT5G26780 AT5G26780 AT5G26780
fragaria_vesca	FvH4_5g34000 FvH4_5g34000 FvH4_5g34000
malus_domestica	MD08G1206800.v1.1 MD15G1390500.v1.1
prunus_persica	Prupe.1G539400_v2.0.a1 Prupe.1G539400_v2.0.a1 Prupe.1G539400_v2.0.a1 Prupe.1G539400_v2.0.a1
pyrus_communis	pycom08g17860
rosa_chinensis	RchiOBHm_Chr5g0052761 RchiOBHm_Chr7g0233441 RchiOBHm_Chr7g0235741
rosa_laevigata	RLG00000001270 RLG00000013832 RLG00000035486
rosa_multiflora	Rmu_sc0000029.1_g000053 Rmu_sc0006510.1_g000006
rosa_roxburghii	Rroxscaffold_3G00227300 Rroxscaffold_3G00241170
rosa_rugosa	Rorug07G0280700
rosa_samantha	Rh1CG020600 Rh1CG022300 Rh2AG156000 Rh2BG162300 Rh2BG221600 Rh2DG161400 Rh4DG362000 Rh5BG352800 Rh5CG247000 Rh5CG419500 Rh5DG369100 Rh7AG154700 Rh7AG436500 Rh7AG488000 Rh7BG409600 Rh7CG456400 Rh7DG425700
rosa_wichuraiana	Rw0G022490 Rw7G035990 Rw7G036020

Restriction Enzyme Sites

1 / 10

Enzyme	Recognition Site	Cut Count	Positions (bp)
AatII	GACGTC	1 cut(s)	519
AccB1I	GGYRCC	1 cut(s)	122
AciI	CCGC	2 cut(s)	605, 782
AclWI	GGATC	1 cut(s)	703
AcsI	RAATTY	1 cut(s)	427
AcuI	CTGAAG	1 cut(s)	280
AcyI	GRCGYC	1 cut(s)	516
AdeI	CACNNNGTG	1 cut(s)	269
AfaI	GTAC	2 cut(s)	146, 706
AfiI	CCNNNNNNNGG	2 cut(s)	280, 501
AgsI	TTSAA	2 cut(s)	341, 585
AjnI	CCWGG	1 cut(s)	686
AjuI	GAANNNNNNNTTGG	2 cut(s)	343, 375
AleI	CACNNNNGTG	1 cut(s)	216
AluBI	AGCT	4 cut(s)	188, 200, 345, 766
AluI	AGCT	4 cut(s)	188, 200, 345, 766
Alw21I	GWGCWC	2 cut(s)	139, 775
Alw26I	GTCTC	1 cut(s)	397
Alw44I	GTGCAC	1 cut(s)	135
AlwI	GGATC	1 cut(s)	703
AoxI	GGCC	4 cut(s)	271, 322, 621, 690
ApaI	GGGCCC	1 cut(s)	625
ApaLI	GTGCAC	1 cut(s)	135
ApoI	RAATTY	1 cut(s)	427
AseI	ATTAAT	1 cut(s)	110
Asp700I	GAANNNNTTC	1 cut(s)	358
AspS9I	GGNCC	4 cut(s)	272, 621, 622, 690
AsuC2I	CCSGG	2 cut(s)	500, 711
AsuHPI	GGTGA	5 cut(s)	446, 453, 525, 570, 651
BaeGI	GKGCMC	2 cut(s)	139, 625
BanI	GGYRCC	1 cut(s)	122
BanII	GRGCYC	1 cut(s)	625
BauI	CACGAG	2 cut(s)	276, 318
Bbv12I	GWGCWC	2 cut(s)	139, 775
BccI	CCATC	3 cut(s)	459, 490, 727
BciT130I	CCWGG	1 cut(s)	688
BcnI	CCSGG	2 cut(s)	500, 711
BcoDI	GTCTC	1 cut(s)	397
BfaI	CTAG	3 cut(s)	371, 488, 732
BfmI	CTRYAG	1 cut(s)	71
Bme1390I	CCNGG	3 cut(s)	500, 688, 711
BmgT120I	GGNCC	4 cut(s)	272, 621, 622, 690
BmiI	GGNNCC	2 cut(s)	124, 623
BmrFI	CCNGG	3 cut(s)	500, 688, 711
BpmI	CTGGAG	1 cut(s)	316
BpuMI	CCSGG	2 cut(s)	500, 711
BsaHI	GRCGYC	1 cut(s)	516
BsaJI	CCNNGG	2 cut(s)	499, 687
BsaWI	WCCGGW	1 cut(s)	661
Bsc4I	CCNNNNNNNGG	2 cut(s)	280, 501
Bse1I	ACTGG	2 cut(s)	31, 126
BseBI	CCWGG	1 cut(s)	688
BseDI	CCNNGG	2 cut(s)	499, 687
BseGI	GGATG	2 cut(s)	22, 560
BseLI	CCNNNNNNNGG	2 cut(s)	280, 501
BseNI	ACTGG	2 cut(s)	31, 126
BseRI	GAGGAG	1 cut(s)	735
BseSI	GKGCMC	2 cut(s)	139, 625
BshFI	GGCC	4 cut(s)	273, 324, 623, 692
BshNI	GGYRCC	1 cut(s)	122
BsiHKAI	GWGCWC	2 cut(s)	139, 775
BsiSI	CCGG	4 cut(s)	499, 662, 693, 710
BslFI	GGGAC	1 cut(s)	449
BslI	CCNNNNNNNGG	2 cut(s)	280, 501
BsmAI	GTCTC	1 cut(s)	397
BsmFI	GGGAC	1 cut(s)	449
BsmI	GAATGC	1 cut(s)	784
BsnI	GGCC	4 cut(s)	273, 324, 623, 692
Bsp120I	GGGCCC	1 cut(s)	621
Bsp1286I	GDGCHC	3 cut(s)	139, 625, 775
Bsp1407I	TGTACA	1 cut(s)	704
Bsp143I	GATC	4 cut(s)	288, 385, 458, 695
BspACI	CCGC	2 cut(s)	605, 782
BspANI	GGCC	4 cut(s)	273, 324, 623, 692
BspLI	GGNNCC	2 cut(s)	124, 623
BspMAI	CTGCAG	1 cut(s)	75
BspPI	GGATC	1 cut(s)	703
BspT107I	GGYRCC	1 cut(s)	122
BsrGI	TGTACA	1 cut(s)	704
BsrI	ACTGG	2 cut(s)	31, 126
BssECI	CCNNGG	2 cut(s)	499, 687
BssMI	GATC	4 cut(s)	288, 385, 458, 695
BssNI	GRCGYC	1 cut(s)	516
BssSI	CACGAG	2 cut(s)	276, 318
Bst2BI	CACGAG	2 cut(s)	276, 318
Bst2UI	CCWGG	1 cut(s)	688
Bst4CI	ACNGT	2 cut(s)	496, 630
Bst6I	CTCTTC	1 cut(s)	782
BstACI	GRCGYC	1 cut(s)	516
BstAUI	TGTACA	1 cut(s)	704
BstC8I	GCNNGC	1 cut(s)	139
BstF5I	GGATG	2 cut(s)	22, 560
BstKTI	GATC	4 cut(s)	291, 388, 461, 698
BstMAI	GTCTC	1 cut(s)	397
BstMBI	GATC	4 cut(s)	288, 385, 458, 695
BstMWI	GCNNNNNNNGC	1 cut(s)	206
BstNI	CCWGG	1 cut(s)	688
BstNSI	RCATGY	1 cut(s)	135
BstSCI	CCNGG	3 cut(s)	498, 686, 709
BstSFI	CTRYAG	1 cut(s)	71
BstSLI	GKGCMC	2 cut(s)	139, 625
BsuRI	GGCC	4 cut(s)	273, 324, 623, 692
BtsCI	GGATG	2 cut(s)	22, 560
BtsIMutI	CAGTG	3 cut(s)	24, 133, 223
Cac8I	GCNNGC	1 cut(s)	139
Cfr13I	GGNCC	4 cut(s)	272, 621, 622, 690
Csp6I	GTAC	2 cut(s)	145, 705
CspCI	CAANNNNNGTGG	2 cut(s)	591, 626
CviAII	CATG	1 cut(s)	132
CviQI	GTAC	2 cut(s)	145, 705
DpnI	GATC	4 cut(s)	290, 387, 460, 697
DpnII	GATC	4 cut(s)	288, 385, 458, 695
DraIII	CACNNNGTG	1 cut(s)	269
Eam1104I	CTCTTC	1 cut(s)	782
EarI	CTCTTC	1 cut(s)	782
Eco24I	GRGCYC	1 cut(s)	625
Eco57I	CTGAAG	1 cut(s)	280
EcoRII	CCWGG	1 cut(s)	686
EcoT38I	GRGCYC	1 cut(s)	625
FaeI	CATG	1 cut(s)	135
FaqI	GGGAC	1 cut(s)	449
FatI	CATG	1 cut(s)	131
FauI	CCCGC	1 cut(s)	789
FokI	GGATG	2 cut(s)	29, 547
FriOI	GRGCYC	1 cut(s)	625
FspBI	CTAG	3 cut(s)	371, 488, 732
GsuI	CTGGAG	1 cut(s)	316
HaeIII	GGCC	4 cut(s)	273, 324, 623, 692
HapII	CCGG	4 cut(s)	499, 662, 693, 710
Hin1I	GRCGYC	1 cut(s)	516
Hin1II	CATG	1 cut(s)	135
HindIII	AAGCTT	2 cut(s)	343, 764
HinfI	GANTC	2 cut(s)	592, 598
HpaII	CCGG	4 cut(s)	499, 662, 693, 710
HphI	GGTGA	5 cut(s)	446, 453, 525, 570, 651
Hpy166II	GTNNAC	2 cut(s)	137, 707
Hpy188I	TCNGA	4 cut(s)	101, 565, 597, 681
Hpy188III	TCNNGA	4 cut(s)	298, 333, 488, 512
Hpy8I	GTNNAC	2 cut(s)	137, 707
Hpy99I	CGWCG	3 cut(s)	518, 521, 524
HpyAV	CCTTC	4 cut(s)	295, 370, 591, 660
HpyCH4III	ACNGT	2 cut(s)	496, 630
HpyCH4IV	ACGT	1 cut(s)	516
HpyCH4V	TGCA	5 cut(s)	73, 131, 137, 155, 544
HpyF10VI	GCNNNNNNNGC	1 cut(s)	206
HpySE526I	ACGT	1 cut(s)	516
Hsp92I	GRCGYC	1 cut(s)	516
Hsp92II	CATG	1 cut(s)	135
Kzo9I	GATC	4 cut(s)	288, 385, 458, 695
MaeI	CTAG	3 cut(s)	371, 488, 732
MaeII	ACGT	1 cut(s)	516
MaeIII	GTNAC	3 cut(s)	29, 241, 261
MalI	GATC	4 cut(s)	290, 387, 460, 697
MboI	GATC	4 cut(s)	288, 385, 458, 695
MboII	GAAGA	4 cut(s)	283, 286, 746, 769
MhlI	GDGCHC	3 cut(s)	139, 625, 775
MluCI	AATT	2 cut(s)	107, 427
MmeI	TCCRAC	3 cut(s)	57, 581, 588
MnlI	CCTC	5 cut(s)	285, 314, 426, 655, 756
MroXI	GAANNNNTTC	1 cut(s)	358
MseI	TTAA	1 cut(s)	110
MslI	CAYNNNNRTG	1 cut(s)	216
MspI	CCGG	4 cut(s)	499, 662, 693, 710
MspR9I	CCNGG	3 cut(s)	500, 688, 711
Mva1269I	GAATGC	1 cut(s)	784
MvaI	CCWGG	1 cut(s)	688
MwoI	GCNNNNNNNGC	1 cut(s)	206
NciI	CCSGG	2 cut(s)	500, 711
NdeII	GATC	4 cut(s)	288, 385, 458, 695
NlaIII	CATG	1 cut(s)	135
NlaIV	GGNNCC	2 cut(s)	124, 623
NmuCI	GTSAC	1 cut(s)	261
NspI	RCATGY	1 cut(s)	135
OliI	CACNNNNGTG	1 cut(s)	216
PcsI	WCGNNNNNNNCGW	1 cut(s)	274
PctI	GAATGC	1 cut(s)	784
PdmI	GAANNNNTTC	1 cut(s)	358
PfeI	GAWTC	2 cut(s)	592, 598
PflFI	GACNNNGTC	1 cut(s)	518
PshBI	ATTAAT	1 cut(s)	110
Psp6I	CCWGG	1 cut(s)	686
PspGI	CCWGG	1 cut(s)	686
PspN4I	GGNNCC	2 cut(s)	124, 623
PspOMI	GGGCCC	1 cut(s)	621
PspPI	GGNCC	4 cut(s)	272, 621, 622, 690
PstI	CTGCAG	1 cut(s)	75
PsyI	GACNNNGTC	1 cut(s)	518
RsaI	GTAC	2 cut(s)	146, 706
RsaNI	GTAC	2 cut(s)	145, 705
RseI	CAYNNNNRTG	1 cut(s)	216
SaqAI	TTAA	1 cut(s)	110
Sau3AI	GATC	4 cut(s)	288, 385, 458, 695
Sau96I	GGNCC	4 cut(s)	272, 621, 622, 690
ScrFI	CCNGG	3 cut(s)	500, 688, 711
SduI	GDGCHC	3 cut(s)	139, 625, 775
SfcI	CTRYAG	1 cut(s)	71
SmiMI	CAYNNNNRTG	1 cut(s)	216
Sse9I	AATT	2 cut(s)	107, 427
SsiI	CCGC	2 cut(s)	605, 782
SspMI	CTAG	3 cut(s)	371, 488, 732
StyD4I	CCNGG	3 cut(s)	498, 686, 709
TaaI	ACNGT	2 cut(s)	496, 630
TaiI	ACGT	1 cut(s)	519
TaqI	TCGA	1 cut(s)	757
TasI	AATT	2 cut(s)	107, 427
TatI	WGTACW	1 cut(s)	704
TfiI	GAWTC	2 cut(s)	592, 598
Tru1I	TTAA	1 cut(s)	110
Tru9I	TTAA	1 cut(s)	110
TscAI	CASTG	3 cut(s)	31, 133, 223
TseFI	GTSAC	1 cut(s)	261
Tsp45I	GTSAC	1 cut(s)	261
TspDTI	ATGAA	1 cut(s)	33
TspRI	CASTG	3 cut(s)	31, 133, 223
Tth111I	GACNNNGTC	1 cut(s)	518
VneI	GTGCAC	1 cut(s)	135
VspI	ATTAAT	1 cut(s)	110
XapI	RAATTY	1 cut(s)	427
XbaI	TCTAGA	1 cut(s)	487
XceI	RCATGY	1 cut(s)	135
XmnI	GAANNNNTTC	1 cut(s)	358
XspI	CTAG	3 cut(s)	371, 488, 732
ZraI	GACGTC	1 cut(s)	517

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