Basic Information

Type: gene

Biological Identity

Species

rosa_samantha

Chromosome

Chr5D

Orthogroup ID

OG0001957

Physical Location & Seq

Genomic Coordinates Forward (+)

55365571 .. 55379520

Gene Structure 13950 bp

Loading structure...

UTR

Exon/CDS

Intron

Transcript / Protein ID

Rh5DG369100.1

Sequence Viewer

CDS Protein Promoter (2k)

Length: 420 bp

ATGGCACACATCAGTGGATTGGTTGCGGCAGGTGTTATTCCATCTCCTTTTGAGTATGCAGATATTGTTACAACCACAACTCACAAGTCACTTCGTGGCCCTCGTGGGGCTATGATCTTCTTCAGGAAGGGGGTCAAAAATGTAAACAAGCAAGGACAAGAAGTTGTCTTTCCTGGACTCCAAGGTGGTCCACACAATCACACCATAGCTGGGTTAGCAGTTGCACTCAAGCAGGCCACAACTCCAGAGTTCAAAGCTTACCAAGAACAAGTTCTCAGTAATTCCGCAAAATTTGCAGAGAGCTTGCTAGAGAAGGGCTATGATCTTGTCTCTGGTGGAACTGACAACCATTTAGTGTTGGTAAATTTGAGGGACAAGGACACAAACATGGGTCAGCCGACAATTCAACCGAATAAATAG

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

139

Amino Acids

14.94

Weight (kDa)

9.26

Isoelectric Point (pI)

38.15

Instability Index

Protein Domains (Pfam)

Domain Name	Pfam ID	Position	E-value	Description
SHMT	PF00464	1 - 129	2.3e-63	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)	20
Acc36I	ACCTGC	1 cut(s)	20
AciI	CCGC	2 cut(s)	26, 285
AcsI	RAATTY	2 cut(s)	290, 364
AcuI	CTGAAG	1 cut(s)	106
AdeI	CACNNNGTG	1 cut(s)	95
AfiI	CCNNNNNNNGG	2 cut(s)	106, 210
AgsI	TTSAA	2 cut(s)	253, 407
AjnI	CCWGG	1 cut(s)	172
AjuI	GAANNNNNNNTTGG	2 cut(s)	255, 287
AleI	CACNNNNGTG	1 cut(s)	12
AluBI	AGCT	3 cut(s)	209, 257, 303
AluI	AGCT	3 cut(s)	209, 257, 303
Alw26I	GTCTC	1 cut(s)	334
AoxI	GGCC	2 cut(s)	97, 234
ApoI	RAATTY	2 cut(s)	290, 364
Asp700I	GAANNNNTTC	1 cut(s)	270
AspS9I	GGNCC	2 cut(s)	98, 188
AvaII	GGWCC	1 cut(s)	188
BauI	CACGAG	1 cut(s)	102
BccI	CCATC	1 cut(s)	49
BciT130I	CCWGG	1 cut(s)	174
BcoDI	GTCTC	1 cut(s)	334
BfaI	CTAG	1 cut(s)	308
BfuAI	ACCTGC	1 cut(s)	20
BisI	GCNGC	1 cut(s)	27
BlsI	GCNGC	1 cut(s)	28
Bme1390I	CCNGG	1 cut(s)	174
Bme18I	GGWCC	1 cut(s)	188
BmgT120I	GGNCC	2 cut(s)	98, 188
BmrFI	CCNGG	1 cut(s)	174
BpmI	CTGGAG	1 cut(s)	228
BpuEI	CTTGAG	1 cut(s)	212
BsaJI	CCNNGG	1 cut(s)	181
Bsc4I	CCNNNNNNNGG	2 cut(s)	106, 210
BseBI	CCWGG	1 cut(s)	174
BseDI	CCNNGG	1 cut(s)	181
BseLI	CCNNNNNNNGG	2 cut(s)	106, 210
BseMII	CTCAG	1 cut(s)	289
BseYI	CCCAGC	1 cut(s)	209
BshFI	GGCC	2 cut(s)	99, 236
BslFI	GGGAC	1 cut(s)	386
BslI	CCNNNNNNNGG	2 cut(s)	106, 210
BsmAI	GTCTC	1 cut(s)	334
BsmFI	GGGAC	1 cut(s)	386
BsnI	GGCC	2 cut(s)	99, 236
Bsp143I	GATC	2 cut(s)	114, 322
BspACI	CCGC	2 cut(s)	26, 285
BspANI	GGCC	2 cut(s)	99, 236
BspCNI	CTCAG	1 cut(s)	288
BspMI	ACCTGC	1 cut(s)	20
BssECI	CCNNGG	1 cut(s)	181
BssMI	GATC	2 cut(s)	114, 322
BssSI	CACGAG	1 cut(s)	102
BssT1I	CCWWGG	1 cut(s)	181
Bst2BI	CACGAG	1 cut(s)	102
Bst2UI	CCWGG	1 cut(s)	174
BstAPI	GCANNNNNTGC	1 cut(s)	293
BstC8I	GCNNGC	2 cut(s)	234, 305
BstDEI	CTNAG	1 cut(s)	275
BstKTI	GATC	2 cut(s)	117, 325
BstMAI	GTCTC	1 cut(s)	334
BstMBI	GATC	2 cut(s)	114, 322
BstMWI	GCNNNNNNNGC	2 cut(s)	215, 293
BstNI	CCWGG	1 cut(s)	174
BstSCI	CCNGG	1 cut(s)	172
BsuRI	GGCC	2 cut(s)	99, 236
BtsIMutI	CAGTG	1 cut(s)	19
BveI	ACCTGC	1 cut(s)	20
Cac8I	GCNNGC	2 cut(s)	234, 305
Cfr13I	GGNCC	2 cut(s)	98, 188
CviAII	CATG	1 cut(s)	388
CviJI	RGCY	8 cut(s)	99, 110, 209, 236, 257, 303, 318, 397
CviKI_1	RGCY	8 cut(s)	99, 110, 209, 236, 257, 303, 318, 397
DdeI	CTNAG	1 cut(s)	275
DpnI	GATC	2 cut(s)	116, 324
DpnII	GATC	2 cut(s)	114, 322
DraIII	CACNNNGTG	1 cut(s)	95
Eco130I	CCWWGG	1 cut(s)	181
Eco47I	GGWCC	1 cut(s)	188
Eco57I	CTGAAG	1 cut(s)	106
EcoRII	CCWGG	1 cut(s)	172
EcoT14I	CCWWGG	1 cut(s)	181
ErhI	CCWWGG	1 cut(s)	181
FaeI	CATG	1 cut(s)	391
FaiI	YATR	5 cut(s)	57, 113, 206, 321, 389
FaqI	GGGAC	1 cut(s)	386
FatI	CATG	1 cut(s)	387
Fnu4HI	GCNGC	1 cut(s)	27
Fsp4HI	GCNGC	1 cut(s)	27
FspBI	CTAG	1 cut(s)	308
GluI	GCNGC	1 cut(s)	27
GsaI	CCCAGC	1 cut(s)	213
GsuI	CTGGAG	1 cut(s)	228
HaeIII	GGCC	2 cut(s)	99, 236
Hin1II	CATG	1 cut(s)	391
HindIII	AAGCTT	1 cut(s)	255
HinfI	GANTC	1 cut(s)	177
Hpy166II	GTNNAC	2 cut(s)	145, 191
Hpy188III	TCNNGA	2 cut(s)	124, 245
Hpy8I	GTNNAC	2 cut(s)	145, 191
HpyAV	CCTTC	2 cut(s)	121, 307
HpyCH4V	TGCA	3 cut(s)	59, 224, 296
HpyF10VI	GCNNNNNNNGC	2 cut(s)	215, 293
HpyF3I	CTNAG	1 cut(s)	275
Hsp92II	CATG	1 cut(s)	391
Kzo9I	GATC	2 cut(s)	114, 322
LpnPI	CCDG	8 cut(s)	15, 109, 159, 186, 195, 218, 258, 318
MaeI	CTAG	1 cut(s)	308
MaeIII	GTNAC	2 cut(s)	67, 87
MalI	GATC	2 cut(s)	116, 324
MboI	GATC	2 cut(s)	114, 322
MboII	GAAGA	2 cut(s)	109, 112
MluCI	AATT	4 cut(s)	280, 290, 364, 402
MlyI	GAGTC	1 cut(s)	171
MnlI	CCTC	2 cut(s)	111, 363
MroXI	GAANNNNTTC	1 cut(s)	270
MslI	CAYNNNNRTG	2 cut(s)	12, 386
MspR9I	CCNGG	1 cut(s)	174
MvaI	CCWGG	1 cut(s)	174
MwoI	GCNNNNNNNGC	2 cut(s)	215, 293
NdeII	GATC	2 cut(s)	114, 322
NlaIII	CATG	1 cut(s)	391
NmuCI	GTSAC	1 cut(s)	87
OliI	CACNNNNGTG	1 cut(s)	12
PaqCI	CACCTGC	1 cut(s)	20
PcsI	WCGNNNNNNNCGW	1 cut(s)	100
PdmI	GAANNNNTTC	1 cut(s)	270
PfoI	TCCNGGA	1 cut(s)	172
PkrI	GCNGC	1 cut(s)	28
PleI	GAGTC	1 cut(s)	171
PpsI	GAGTC	1 cut(s)	171
Psp6I	CCWGG	1 cut(s)	172
PspFI	CCCAGC	1 cut(s)	209
PspGI	CCWGG	1 cut(s)	172
PspPI	GGNCC	2 cut(s)	98, 188
RseI	CAYNNNNRTG	2 cut(s)	12, 386
SatI	GCNGC	1 cut(s)	27
Sau3AI	GATC	2 cut(s)	114, 322
Sau96I	GGNCC	2 cut(s)	98, 188
SchI	GAGTC	1 cut(s)	171
ScrFI	CCNGG	1 cut(s)	174
SetI	ASST	5 cut(s)	34, 187, 211, 259, 305
SinI	GGWCC	1 cut(s)	188
SmiMI	CAYNNNNRTG	2 cut(s)	12, 386
SmlI	CTYRAG	1 cut(s)	227
SmoI	CTYRAG	1 cut(s)	227
Sse9I	AATT	4 cut(s)	280, 290, 364, 402
SsiI	CCGC	2 cut(s)	26, 285
SspMI	CTAG	1 cut(s)	308
StyD4I	CCNGG	1 cut(s)	172
StyI	CCWWGG	1 cut(s)	181
TasI	AATT	4 cut(s)	280, 290, 364, 402
TauI	GCSGC	1 cut(s)	29
TscAI	CASTG	1 cut(s)	19
TseFI	GTSAC	1 cut(s)	87
Tsp45I	GTSAC	1 cut(s)	87
TspRI	CASTG	1 cut(s)	19
VpaK11BI	GGWCC	1 cut(s)	188
XapI	RAATTY	2 cut(s)	290, 364
XmnI	GAANNNNTTC	1 cut(s)	270
XspI	CTAG	1 cut(s)	308

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