Basic Information

Type: gene

Biological Identity

Species

rosa_samantha

Chromosome

Chr2D

Orthogroup ID

OG0001957

Physical Location & Seq

Genomic Coordinates Reverse (-)

13828545 .. 13834900

Gene Structure 6356 bp

Loading structure...

UTR

Exon/CDS

Intron

Transcript / Protein ID

Rh2DG161400.1

Sequence Viewer

CDS Protein Promoter (2k)

Length: 561 bp

ATGTTGGAGAAAAGTGCCACACTATTCAGACCCAAATTAATAGTTGCTGGTGCCAATGCTTGTGCATGTTTGTACGACTATGCACACATACGCAAGGTCTGTGATAAGCAGAAAGCTATTTTGTTAGCTGATATGGCACACATCAGTGGATTGGTTGCGGCAGGTGTTATTCCATCTCCTTTTGAGTATGCAGATATTGTTACAACCACAACTCACAAGTCACTTCGTAGCCCTCGTGGGGCTATGATCTTCTTCAGGAAGGGGGTCAAAAATGTAAACAAGCAAGGACAAGAAGCTGTCTTTCCTGGACTCCAAGGTGGTCCACACAATCACACCATAGCTGGGTTAGCAGTTGCACTCAAGCAGGCCACAACTCCAGAGTTCAAAGCTTACCAAGAGCAAGTTCTCAGTAATTCCGCAAAATTTGTAGAGAGCTTGCTAGAGAAGGGCTATGATCTTGTCTCTGGTGGAACTGACAACCATTTAGTATTGGTAAATTTGAGGGACAAGTGGGCTGAAGACTATTTTAACCAAAAGAGATTGGGTTGTGTGGGGGCTTAA

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

186

Amino Acids

20.23

Weight (kDa)

9.16

Isoelectric Point (pI)

46.6

Instability Index

Protein Domains (Pfam)

Domain Name	Pfam ID	Position	E-value	Description
SHMT	PF00464	2 - 171	6.7e-81	Serine hydroxymethyltransferase

Hydrophobicity Profile (Kyte-Doolittle)

AI Structure Prediction Report

Calculating structure properties...

Genomic Context

Gene Family Tree

Species Filter

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Publication-ready

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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)
AarI	CACCTGC	1 cut(s)	152
Acc36I	ACCTGC	1 cut(s)	152
AccB1I	GGYRCC	1 cut(s)	50
AciI	CCGC	2 cut(s)	158, 417
AcsI	RAATTY	2 cut(s)	422, 496
AcuI	CTGAAG	2 cut(s)	238, 537
AfaI	GTAC	1 cut(s)	74
AfiI	CCNNNNNNNGG	2 cut(s)	238, 342
AgsI	TTSAA	1 cut(s)	385
AjnI	CCWGG	1 cut(s)	304
AjuI	GAANNNNNNNTTGG	2 cut(s)	387, 419
AleI	CACNNNNGTG	1 cut(s)	144
AluBI	AGCT	6 cut(s)	116, 128, 296, 341, 389, 435
AluI	AGCT	6 cut(s)	116, 128, 296, 341, 389, 435
Alw26I	GTCTC	1 cut(s)	466
AoxI	GGCC	1 cut(s)	366
ApoI	RAATTY	2 cut(s)	422, 496
AseI	ATTAAT	1 cut(s)	38
AspS9I	GGNCC	1 cut(s)	320
AvaII	GGWCC	1 cut(s)	320
BanI	GGYRCC	1 cut(s)	50
BauI	CACGAG	1 cut(s)	234
BbsI	GAAGAC	1 cut(s)	525
BccI	CCATC	1 cut(s)	181
BciT130I	CCWGG	1 cut(s)	306
BcoDI	GTCTC	1 cut(s)	466
BfaI	CTAG	1 cut(s)	440
BfuAI	ACCTGC	1 cut(s)	152
BisI	GCNGC	1 cut(s)	159
BlsI	GCNGC	1 cut(s)	160
Bme1390I	CCNGG	1 cut(s)	306
Bme18I	GGWCC	1 cut(s)	320
BmgT120I	GGNCC	1 cut(s)	320
BmiI	GGNNCC	1 cut(s)	52
BmrFI	CCNGG	1 cut(s)	306
BpiI	GAAGAC	1 cut(s)	525
BpmI	CTGGAG	1 cut(s)	360
BpuEI	CTTGAG	1 cut(s)	344
BsaJI	CCNNGG	1 cut(s)	313
Bsc4I	CCNNNNNNNGG	2 cut(s)	238, 342
BseBI	CCWGG	1 cut(s)	306
BseDI	CCNNGG	1 cut(s)	313
BseLI	CCNNNNNNNGG	2 cut(s)	238, 342
BseMII	CTCAG	1 cut(s)	421
BseYI	CCCAGC	1 cut(s)	341
BshFI	GGCC	1 cut(s)	368
BshNI	GGYRCC	1 cut(s)	50
BslFI	GGGAC	1 cut(s)	518
BslI	CCNNNNNNNGG	2 cut(s)	238, 342
BsmAI	GTCTC	1 cut(s)	466
BsmFI	GGGAC	1 cut(s)	518
BsnI	GGCC	1 cut(s)	368
Bsp143I	GATC	2 cut(s)	246, 454
BspACI	CCGC	2 cut(s)	158, 417
BspANI	GGCC	1 cut(s)	368
BspCNI	CTCAG	1 cut(s)	420
BspLI	GGNNCC	1 cut(s)	52
BspMI	ACCTGC	1 cut(s)	152
BspT107I	GGYRCC	1 cut(s)	50
BssECI	CCNNGG	1 cut(s)	313
BssMI	GATC	2 cut(s)	246, 454
BssSI	CACGAG	1 cut(s)	234
BssT1I	CCWWGG	1 cut(s)	313
Bst2BI	CACGAG	1 cut(s)	234
Bst2UI	CCWGG	1 cut(s)	306
BstC8I	GCNNGC	2 cut(s)	366, 437
BstDEI	CTNAG	1 cut(s)	407
BstKTI	GATC	2 cut(s)	249, 457
BstMAI	GTCTC	1 cut(s)	466
BstMBI	GATC	2 cut(s)	246, 454
BstMWI	GCNNNNNNNGC	2 cut(s)	134, 347
BstNI	CCWGG	1 cut(s)	306
BstNSI	RCATGY	1 cut(s)	69
BstSCI	CCNGG	1 cut(s)	304
BstV2I	GAAGAC	1 cut(s)	525
BsuRI	GGCC	1 cut(s)	368
BtsIMutI	CAGTG	1 cut(s)	151
BveI	ACCTGC	1 cut(s)	152
Cac8I	GCNNGC	2 cut(s)	366, 437
Cfr13I	GGNCC	1 cut(s)	320
Csp6I	GTAC	1 cut(s)	73
CviAII	CATG	1 cut(s)	66
CviQI	GTAC	1 cut(s)	73
DdeI	CTNAG	1 cut(s)	407
DpnI	GATC	2 cut(s)	248, 456
DpnII	GATC	2 cut(s)	246, 454
Eco130I	CCWWGG	1 cut(s)	313
Eco47I	GGWCC	1 cut(s)	320
Eco57I	CTGAAG	2 cut(s)	238, 537
EcoRII	CCWGG	1 cut(s)	304
EcoT14I	CCWWGG	1 cut(s)	313
ErhI	CCWWGG	1 cut(s)	313
FaeI	CATG	1 cut(s)	69
FaiI	YATR	8 cut(s)	67, 81, 89, 134, 189, 245, 338, 453
FaqI	GGGAC	1 cut(s)	518
FatI	CATG	1 cut(s)	65
Fnu4HI	GCNGC	1 cut(s)	159
Fsp4HI	GCNGC	1 cut(s)	159
FspBI	CTAG	1 cut(s)	440
GluI	GCNGC	1 cut(s)	159
GsaI	CCCAGC	1 cut(s)	345
GsuI	CTGGAG	1 cut(s)	360
HaeIII	GGCC	1 cut(s)	368
Hin1II	CATG	1 cut(s)	69
HindIII	AAGCTT	1 cut(s)	387
HinfI	GANTC	1 cut(s)	309
Hpy166II	GTNNAC	2 cut(s)	277, 323
Hpy188I	TCNGA	1 cut(s)	29
Hpy188III	TCNNGA	2 cut(s)	256, 377
Hpy8I	GTNNAC	2 cut(s)	277, 323
HpyAV	CCTTC	2 cut(s)	253, 439
HpyCH4V	TGCA	4 cut(s)	65, 83, 191, 356
HpyF10VI	GCNNNNNNNGC	2 cut(s)	134, 347
HpyF3I	CTNAG	1 cut(s)	407
Hsp92II	CATG	1 cut(s)	69
Kzo9I	GATC	2 cut(s)	246, 454
LpnPI	CCDG	9 cut(s)	33, 147, 241, 291, 318, 327, 350, 390, 450
MaeI	CTAG	1 cut(s)	440
MaeIII	GTNAC	2 cut(s)	199, 219
MalI	GATC	2 cut(s)	248, 456
MboI	GATC	2 cut(s)	246, 454
MboII	GAAGA	3 cut(s)	241, 244, 530
MluCI	AATT	4 cut(s)	35, 412, 422, 496
MlyI	GAGTC	1 cut(s)	303
MnlI	CCTC	2 cut(s)	243, 495
MseI	TTAA	3 cut(s)	38, 528, 559
MslI	CAYNNNNRTG	1 cut(s)	144
MspR9I	CCNGG	1 cut(s)	306
MvaI	CCWGG	1 cut(s)	306
MwoI	GCNNNNNNNGC	2 cut(s)	134, 347
NdeII	GATC	2 cut(s)	246, 454
NlaIII	CATG	1 cut(s)	69
NlaIV	GGNNCC	1 cut(s)	52
NmuCI	GTSAC	1 cut(s)	219
NspI	RCATGY	1 cut(s)	69
OliI	CACNNNNGTG	1 cut(s)	144
PaqCI	CACCTGC	1 cut(s)	152
PcsI	WCGNNNNNNNCGW	1 cut(s)	232
PfoI	TCCNGGA	1 cut(s)	304
PkrI	GCNGC	1 cut(s)	160
PleI	GAGTC	1 cut(s)	303
PpsI	GAGTC	1 cut(s)	303
PshBI	ATTAAT	1 cut(s)	38
Psp6I	CCWGG	1 cut(s)	304
PspFI	CCCAGC	1 cut(s)	341
PspGI	CCWGG	1 cut(s)	304
PspN4I	GGNNCC	1 cut(s)	52
PspPI	GGNCC	1 cut(s)	320
RsaI	GTAC	1 cut(s)	74
RsaNI	GTAC	1 cut(s)	73
RseI	CAYNNNNRTG	1 cut(s)	144
SaqAI	TTAA	3 cut(s)	38, 528, 559
SatI	GCNGC	1 cut(s)	159
Sau3AI	GATC	2 cut(s)	246, 454
Sau96I	GGNCC	1 cut(s)	320
SchI	GAGTC	1 cut(s)	303
ScrFI	CCNGG	1 cut(s)	306
SetI	ASST	9 cut(s)	99, 118, 130, 166, 298, 319, 343, 391, 437
SinI	GGWCC	1 cut(s)	320
SmiMI	CAYNNNNRTG	1 cut(s)	144
SmlI	CTYRAG	1 cut(s)	359
SmoI	CTYRAG	1 cut(s)	359
Sse9I	AATT	4 cut(s)	35, 412, 422, 496
SsiI	CCGC	2 cut(s)	158, 417
SspMI	CTAG	1 cut(s)	440
StyD4I	CCNGG	1 cut(s)	304
StyI	CCWWGG	1 cut(s)	313
TasI	AATT	4 cut(s)	35, 412, 422, 496
TauI	GCSGC	1 cut(s)	161
Tru1I	TTAA	3 cut(s)	38, 528, 559
Tru9I	TTAA	3 cut(s)	38, 528, 559
TscAI	CASTG	1 cut(s)	151
TseFI	GTSAC	1 cut(s)	219
Tsp45I	GTSAC	1 cut(s)	219
TspRI	CASTG	1 cut(s)	151
VpaK11BI	GGWCC	1 cut(s)	320
VspI	ATTAAT	1 cut(s)	38
XapI	RAATTY	2 cut(s)	422, 496
XceI	RCATGY	1 cut(s)	69
XspI	CTAG	1 cut(s)	440

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