SHMT1 (serine hydroxymethyltransferase 1) - Rat Genome Database

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Gene: SHMT1 (serine hydroxymethyltransferase 1) Canis lupus familiaris
Analyze
Symbol: SHMT1
Name: serine hydroxymethyltransferase 1
RGD ID: 12290979
Description: ENCODES a protein that exhibits aldehyde-lyase activity (ortholog); amino acid binding (ortholog); glycine hydroxymethyltransferase activity (ortholog); INVOLVED IN cellular response to leukemia inhibitory factor (ortholog); cellular response to tetrahydrofolate (ortholog); dTMP biosynthetic process (ortholog); PARTICIPATES IN carnitine biosynthetic pathway; dihydropyrimidine dehydrogenase deficiency pathway; dimethylglycine dehydrogenase deficiency pathway; ASSOCIATED WITH Animal Disease Models (ortholog); autistic disorder (ortholog); breast cancer (ortholog); FOUND IN cytosol (ortholog); nucleoplasm (ortholog); nucleus (ortholog); INTERACTS WITH clofibrate
Type: protein-coding
RefSeq Status: MODEL
Previously known as: serine hydroxymethyltransferase, cytosolic
RGD Orthologs
Human
Mouse
Rat
Chinchilla
Bonobo
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Orthologs
More Info more info ...
Latest Assembly: CanFam3.1 - Dog CanFam3.1 Assembly
Position:
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1541,221,531 - 41,248,653 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl541,221,562 - 41,253,166 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha541,361,842 - 41,388,892 (+)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.0541,329,062 - 41,356,290 (+)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl541,329,080 - 41,356,907 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1541,296,632 - 41,323,803 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0541,244,262 - 41,272,073 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0541,435,940 - 41,463,042 (+)NCBIUU_Cfam_GSD_1.0
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
clofibrate  (EXP)

References
Additional References at PubMed
PMID:22301074   PMID:30032202  


Genomics

Comparative Map Data
SHMT1
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1541,221,531 - 41,248,653 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl541,221,562 - 41,253,166 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha541,361,842 - 41,388,892 (+)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.0541,329,062 - 41,356,290 (+)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl541,329,080 - 41,356,907 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1541,296,632 - 41,323,803 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0541,244,262 - 41,272,073 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0541,435,940 - 41,463,042 (+)NCBIUU_Cfam_GSD_1.0
SHMT1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh381718,327,873 - 18,363,550 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl1718,327,873 - 18,363,550 (-)EnsemblGRCh38hg38GRCh38
GRCh371718,231,187 - 18,266,864 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 361718,171,912 - 18,207,581 (-)NCBINCBI36Build 36hg18NCBI36
Build 341718,171,912 - 18,207,581NCBI
Celera1719,172,258 - 19,207,893 (-)NCBICelera
Cytogenetic Map17p11.2NCBI
HuRef1717,984,719 - 18,020,240 (-)NCBIHuRef
CHM1_11718,239,946 - 18,275,839 (-)NCBICHM1_1
T2T-CHM13v2.01718,274,679 - 18,310,356 (-)NCBIT2T-CHM13v2.0
Shmt1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391160,679,723 - 60,702,062 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1160,678,930 - 60,702,544 (-)EnsemblGRCm39 Ensembl
GRCm381160,788,897 - 60,811,265 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1160,788,104 - 60,811,718 (-)EnsemblGRCm38mm10GRCm38
MGSCv371160,602,399 - 60,624,767 (-)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv361161,219,982 - 61,242,350 (-)NCBIMGSCv36mm8
MGSCv361160,605,092 - 60,627,460 (-)NCBIMGSCv36mm8
Cytogenetic Map11B2NCBI
cM Map1137.84NCBI
Shmt1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81045,968,959 - 45,990,341 (-)NCBIGRCr8
mRatBN7.21045,468,698 - 45,490,833 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1045,468,700 - 45,497,820 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx1050,170,944 - 50,199,114 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01049,661,340 - 49,689,514 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01045,164,929 - 45,193,103 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.01047,030,813 - 47,059,216 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1047,031,050 - 47,059,216 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01046,802,986 - 46,831,051 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41046,936,605 - 46,964,779 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.11046,948,782 - 46,971,713 (-)NCBI
Celera1044,724,251 - 44,752,341 (-)NCBICelera
Cytogenetic Map10q22NCBI
Shmt1
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495547810,978,139 - 11,001,202 (+)EnsemblChiLan1.0
ChiLan1.0NW_00495547810,972,791 - 11,001,535 (+)NCBIChiLan1.0ChiLan1.0
SHMT1
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v21952,905,330 - 52,940,088 (+)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan11757,616,479 - 57,650,574 (+)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v01732,870,949 - 32,905,690 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.11737,849,206 - 37,884,220 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1737,849,206 - 37,884,220 (+)Ensemblpanpan1.1panPan2
Shmt1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440560260,989,489 - 61,018,689 (+)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049367411,849,609 - 1,877,727 (-)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_0049367411,849,239 - 1,877,724 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
SHMT1
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1260,416,463 - 60,435,450 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.11260,414,421 - 60,435,451 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
SHMT1
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11617,371,704 - 17,408,499 (-)NCBIChlSab1.1ChlSab1.1chlSab2
Vero_WHO_p1.0NW_0236660593,494,856 - 3,535,333 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Shmt1
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_0046248493,114,876 - 3,146,248 (+)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_0046248493,108,875 - 3,146,669 (+)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in SHMT1
237 total Variants

Expression

RNA-SEQ Expression

adipose tissue
alimentary part of gastrointestinal system
circulatory system
ectoderm
endocrine system
endoderm
exocrine system
hemolymphoid system
hepatobiliary system
integumental system
mesenchyme
mesoderm
nervous system
reproductive system
respiratory system
6 5 5 23 22 16 6 6 6 6 33 22 12 14 10

Sequence


Ensembl Acc Id: ENSCAFT00000028996   ⟹   ENSCAFP00000026966
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
CanFam3.1 Ensembl541,221,562 - 41,249,073 (+)Ensembl
Ensembl Acc Id: ENSCAFT00000064633   ⟹   ENSCAFP00000044478
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
CanFam3.1 Ensembl541,221,562 - 41,249,073 (+)Ensembl
Ensembl Acc Id: ENSCAFT00000085743   ⟹   ENSCAFP00000047028
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
CanFam3.1 Ensembl541,221,562 - 41,249,073 (+)Ensembl
Ensembl Acc Id: ENSCAFT00000089953   ⟹   ENSCAFP00000060399
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
CanFam3.1 Ensembl541,221,562 - 41,253,166 (+)Ensembl
Ensembl Acc Id: ENSCAFT00845035493   ⟹   ENSCAFP00845027772
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
ROS_Cfam_1.0 Ensembl541,329,080 - 41,356,907 (+)Ensembl
Ensembl Acc Id: ENSCAFT00845035582   ⟹   ENSCAFP00845027835
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
ROS_Cfam_1.0 Ensembl541,329,080 - 41,356,907 (+)Ensembl
RefSeq Acc Id: XM_005620143   ⟹   XP_005620200
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
CanFam3.1541,222,546 - 41,248,653 (+)NCBI
Dog10K_Boxer_Tasha541,362,858 - 41,388,892 (+)NCBI
Sequence:
RefSeq Acc Id: XM_038475903   ⟹   XP_038331831
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
UMICH_Zoey_3.1541,296,632 - 41,323,803 (+)NCBI
RefSeq Acc Id: XM_038475904   ⟹   XP_038331832
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
UMICH_Zoey_3.1541,297,651 - 41,323,803 (+)NCBI
RefSeq Acc Id: XM_038537093   ⟹   XP_038393021
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
UU_Cfam_GSD_1.0541,435,940 - 41,463,042 (+)NCBI
RefSeq Acc Id: XM_038537094   ⟹   XP_038393022
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
UU_Cfam_GSD_1.0541,436,956 - 41,463,042 (+)NCBI
RefSeq Acc Id: XM_038601224   ⟹   XP_038457152
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
UNSW_CanFamBas_1.0541,244,262 - 41,272,073 (+)NCBI
RefSeq Acc Id: XM_038601225   ⟹   XP_038457153
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
UNSW_CanFamBas_1.0541,245,289 - 41,272,073 (+)NCBI
RefSeq Acc Id: XM_038665786   ⟹   XP_038521714
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
ROS_Cfam_1.0541,329,062 - 41,356,290 (+)NCBI
RefSeq Acc Id: XM_846726   ⟹   XP_851819
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
CanFam3.1541,221,531 - 41,248,653 (+)NCBI
Dog10K_Boxer_Tasha541,361,842 - 41,388,892 (+)NCBI
Sequence:
RefSeq Acc Id: XP_851819   ⟸   XM_846726
- Peptide Label: isoform X5
- UniProtKB: A0A8I3PGW1 (UniProtKB/TrEMBL),   A0A8C0LY66 (UniProtKB/TrEMBL),   A0A8C0RW38 (UniProtKB/TrEMBL),   A0A8C0R542 (UniProtKB/TrEMBL),   A0A8I3S1J1 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_005620200   ⟸   XM_005620143
- Peptide Label: isoform X5
- UniProtKB: A0A8C0LY66 (UniProtKB/TrEMBL),   A0A8I3PGW1 (UniProtKB/TrEMBL),   A0A8C0RW38 (UniProtKB/TrEMBL),   A0A8C0R542 (UniProtKB/TrEMBL),   A0A8I3S1J1 (UniProtKB/TrEMBL)
- Sequence:
Ensembl Acc Id: ENSCAFP00000044478   ⟸   ENSCAFT00000064633
Ensembl Acc Id: ENSCAFP00000026966   ⟸   ENSCAFT00000028996
Ensembl Acc Id: ENSCAFP00000060399   ⟸   ENSCAFT00000089953
Ensembl Acc Id: ENSCAFP00000047028   ⟸   ENSCAFT00000085743
RefSeq Acc Id: XP_038331831   ⟸   XM_038475903
- Peptide Label: isoform X2
RefSeq Acc Id: XP_038331832   ⟸   XM_038475904
- Peptide Label: isoform X2
RefSeq Acc Id: XP_038457152   ⟸   XM_038601224
- Peptide Label: isoform X3
RefSeq Acc Id: XP_038457153   ⟸   XM_038601225
- Peptide Label: isoform X3
RefSeq Acc Id: XP_038521714   ⟸   XM_038665786
- Peptide Label: isoform X1
- UniProtKB: A0A8C0LY66 (UniProtKB/TrEMBL),   A0A8I3PGW1 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_038393021   ⟸   XM_038537093
- Peptide Label: isoform X4
- UniProtKB: A0A8C0LY66 (UniProtKB/TrEMBL),   A0A8C0R542 (UniProtKB/TrEMBL),   A0A8C0RW38 (UniProtKB/TrEMBL),   A0A8I3PGW1 (UniProtKB/TrEMBL),   A0A8I3S1J1 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_038393022   ⟸   XM_038537094
- Peptide Label: isoform X4
- UniProtKB: A0A8C0LY66 (UniProtKB/TrEMBL),   A0A8C0R542 (UniProtKB/TrEMBL),   A0A8C0RW38 (UniProtKB/TrEMBL),   A0A8I3PGW1 (UniProtKB/TrEMBL),   A0A8I3S1J1 (UniProtKB/TrEMBL)
Ensembl Acc Id: ENSCAFP00845027835   ⟸   ENSCAFT00845035582
Ensembl Acc Id: ENSCAFP00845027772   ⟸   ENSCAFT00845035493
Promoters
RGD ID:13683279
Promoter ID:EPDNEW_C1346
Type:initiation region
Name:SHMT1_1
Description:serine hydroxymethyltransferase 1
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Experiment Methods:Single-end sequencing.
Position:
Dog AssemblyChrPosition (strand)Source
CanFam3.1541,221,626 - 41,221,686EPDNEW

Additional Information

Database Acc Id Source(s)
Ensembl Genes ENSCAFG00000018253 Ensembl, UniProtKB/TrEMBL
  ENSCAFG00030000427 UniProtKB/TrEMBL
  ENSCAFG00040002445 UniProtKB/TrEMBL
  ENSCAFG00845020125 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSCAFT00000028996.5 UniProtKB/TrEMBL
  ENSCAFT00000064633.2 UniProtKB/TrEMBL
  ENSCAFT00030000747.1 UniProtKB/TrEMBL
  ENSCAFT00030000781.1 UniProtKB/TrEMBL
  ENSCAFT00040004673.1 UniProtKB/TrEMBL
  ENSCAFT00040004714.1 UniProtKB/TrEMBL
  ENSCAFT00040004723.1 UniProtKB/TrEMBL
  ENSCAFT00845035493 ENTREZGENE
  ENSCAFT00845035493.1 UniProtKB/TrEMBL
  ENSCAFT00845035582.1 UniProtKB/TrEMBL
Gene3D-CATH 3.40.640.10 UniProtKB/TrEMBL
  3.90.1150.10 UniProtKB/TrEMBL
InterPro PyrdxlP-dep_Trfase UniProtKB/TrEMBL
  PyrdxlP-dep_Trfase_major UniProtKB/TrEMBL
  PyrdxlP-dep_Trfase_small UniProtKB/TrEMBL
  Ser_HO-MeTrfase UniProtKB/TrEMBL
  Ser_HO-MeTrfase-like UniProtKB/TrEMBL
  Ser_HO-MeTrfase_PLP_BS UniProtKB/TrEMBL
  SHMT-like_dom UniProtKB/TrEMBL
KEGG Report cfa:489536 UniProtKB/TrEMBL
NCBI Gene SHMT1 ENTREZGENE
PANTHER PTHR11680 UniProtKB/TrEMBL
  SERINE HYDROXYMETHYLTRANSFERASE, CYTOSOLIC UniProtKB/TrEMBL
Pfam SHMT UniProtKB/TrEMBL
PIRSF SHMT UniProtKB/TrEMBL
PROSITE SHMT UniProtKB/TrEMBL
Superfamily-SCOP SSF53383 UniProtKB/TrEMBL
UniProt A0A8C0LY66 ENTREZGENE, UniProtKB/TrEMBL
  A0A8C0PTW6_CANLF UniProtKB/TrEMBL
  A0A8C0R542 ENTREZGENE
  A0A8C0RW38 ENTREZGENE, UniProtKB/TrEMBL
  A0A8I3PGW1 ENTREZGENE, UniProtKB/TrEMBL
  A0A8I3S1J1 ENTREZGENE, UniProtKB/TrEMBL
  A0A8P0NUV5_CANLF UniProtKB/TrEMBL
VGNC ID VGNC:46150 ENTREZGENE