SHMT1 (serine hydroxymethyltransferase 1) - Rat Genome Database

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Gene: SHMT1 (serine hydroxymethyltransferase 1) Canis lupus familiaris
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Symbol: SHMT1
Name: serine hydroxymethyltransferase 1
RGD ID: 12290979
Description: ENCODES a protein that exhibits amino acid binding (ortholog); glycine hydroxymethyltransferase activity (ortholog); identical protein binding (ortholog); INVOLVED IN cellular response to leukemia inhibitory factor (ortholog); dTMP biosynthetic process (ortholog); glycine 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); 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 Genes
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 (+)NCBI
ROS_Cfam_1.0541,329,062 - 41,356,290 (+)NCBI
ROS_Cfam_1.0 Ensembl541,329,080 - 41,356,907 (+)Ensembl
UMICH_Zoey_3.1541,296,632 - 41,323,803 (+)NCBI
UNSW_CanFamBas_1.0541,244,262 - 41,272,073 (+)NCBI
UU_Cfam_GSD_1.0541,435,940 - 41,463,042 (+)NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


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

References

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 (+)NCBI
ROS_Cfam_1.0541,329,062 - 41,356,290 (+)NCBI
ROS_Cfam_1.0 Ensembl541,329,080 - 41,356,907 (+)Ensembl
UMICH_Zoey_3.1541,296,632 - 41,323,803 (+)NCBI
UNSW_CanFamBas_1.0541,244,262 - 41,272,073 (+)NCBI
UU_Cfam_GSD_1.0541,435,940 - 41,463,042 (+)NCBI
SHMT1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh381718,327,873 - 18,363,550 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p13 Ensembl1718,327,860 - 18,363,563 (-)EnsemblGRCh38hg38GRCh38
GRCh371718,231,187 - 18,266,864 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 361718,171,912 - 18,207,581 (-)NCBINCBI36hg18NCBI36
Build 341718,171,912 - 18,207,581NCBI
Celera1719,172,258 - 19,207,893 (-)NCBI
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 (-)NCBI
Shmt1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391160,678,933 - 60,702,091 (-)NCBIGRCm39mm39
GRCm39 Ensembl1160,678,930 - 60,702,544 (-)Ensembl
GRCm381160,788,897 - 60,811,265 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1160,788,104 - 60,811,718 (-)EnsemblGRCm38mm10GRCm38
MGSCv371160,602,399 - 60,624,767 (-)NCBIGRCm37mm9NCBIm37
MGSCv361161,219,982 - 61,242,350 (-)NCBImm8
MGSCv361160,605,092 - 60,627,460 (-)NCBImm8
Cytogenetic Map11B2NCBI
Shmt1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21045,468,698 - 45,497,820 (-)NCBImRatBN7.2
mRatBN7.2 Ensembl1045,468,700 - 45,497,820 (-)Ensembl
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 (-)NCBIRGSC3.4rn4RGSC3.4
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
PanPan1.11737,849,206 - 37,884,220 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1737,849,206 - 37,884,220 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v01732,870,949 - 32,905,690 (-)NCBIMhudiblu_PPA_v0panPan3
Shmt1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440560260,989,489 - 61,018,689 (+)NCBI
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 (-)NCBIChlSab1.1chlSab2
Vero_WHO_p1.0NW_0236660593,494,856 - 3,535,333 (+)NCBIVero_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_1.0hetGla2
HetGla 1.0NW_0046248493,108,875 - 3,146,669 (+)NCBIHetGla_female_1.0hetGla2


Expression


RNA-SEQ Expression
High: > 1000 TPM value   Medium: Between 11 and 1000 TPM
Low: Between 0.5 and 10 TPM   Below Cutoff: < 0.5 TPM

alimentary part of gastrointestinal system circulatory system endocrine system exocrine system hemolymphoid system hepatobiliary system integumental system musculoskeletal system nervous system reproductive system respiratory system adipose tissue
High
Medium 5 21 6 6 6 6 6 10 6
Low 5 1 6 6 8
Below cutoff

Sequence


Reference Sequences
RefSeq Acc Id: ENSCAFT00000028996   ⟹   ENSCAFP00000026966
RefSeq Status:
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
CanFam3.1 Ensembl541,221,562 - 41,249,073 (+)Ensembl
RefSeq Acc Id: ENSCAFT00000064633   ⟹   ENSCAFP00000044478
RefSeq Status:
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
CanFam3.1 Ensembl541,221,562 - 41,249,073 (+)Ensembl
RefSeq Acc Id: ENSCAFT00000085743   ⟹   ENSCAFP00000047028
RefSeq Status:
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
CanFam3.1 Ensembl541,221,562 - 41,249,073 (+)Ensembl
RefSeq Acc Id: ENSCAFT00000089953   ⟹   ENSCAFP00000060399
RefSeq Status:
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
CanFam3.1 Ensembl541,221,562 - 41,253,166 (+)Ensembl
RefSeq Acc Id: ENSCAFT00845035493   ⟹   ENSCAFP00845027772
RefSeq Status:
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
ROS_Cfam_1.0 Ensembl541,329,080 - 41,356,907 (+)Ensembl
RefSeq Acc Id: ENSCAFT00845035582   ⟹   ENSCAFP00845027835
RefSeq Status:
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
RefSeq Status:
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
RefSeq Status:
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
UMICH_Zoey_3.1541,296,632 - 41,323,803 (+)NCBI
RefSeq Acc Id: XM_038475904   ⟹   XP_038331832
RefSeq Status:
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
UMICH_Zoey_3.1541,297,651 - 41,323,803 (+)NCBI
RefSeq Acc Id: XM_038537093   ⟹   XP_038393021
RefSeq Status:
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
RefSeq Status:
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
RefSeq Status:
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
UNSW_CanFamBas_1.0541,244,262 - 41,272,073 (+)NCBI
RefSeq Acc Id: XM_038601225   ⟹   XP_038457153
RefSeq Status:
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
UNSW_CanFamBas_1.0541,245,289 - 41,272,073 (+)NCBI
RefSeq Acc Id: XM_038665786   ⟹   XP_038521714
RefSeq Status:
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
ROS_Cfam_1.0541,329,062 - 41,356,290 (+)NCBI
RefSeq Acc Id: XM_846726   ⟹   XP_851819
RefSeq Status:
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:
Reference Sequences
RefSeq Acc Id: XP_851819   ⟸   XM_846726
- Peptide Label: isoform X5
- UniProtKB: E2RIV3 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_005620200   ⟸   XM_005620143
- Peptide Label: isoform X5
- UniProtKB: E2RIV3 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSCAFP00000044478   ⟸   ENSCAFT00000064633
RefSeq Acc Id: ENSCAFP00000026966   ⟸   ENSCAFT00000028996
RefSeq Acc Id: ENSCAFP00000060399   ⟸   ENSCAFT00000089953
RefSeq 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
RefSeq Acc Id: XP_038393021   ⟸   XM_038537093
- Peptide Label: isoform X4
RefSeq Acc Id: XP_038393022   ⟸   XM_038537094
- Peptide Label: isoform X4
RefSeq Acc Id: ENSCAFP00845027835   ⟸   ENSCAFT00845035582
RefSeq Acc Id: ENSCAFP00845027772   ⟸   ENSCAFT00845035493
Protein Domains
SHMT

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
  ENSCAFG00030000427 UniProtKB/TrEMBL
  ENSCAFG00040002445 UniProtKB/TrEMBL
  ENSCAFG00845020125 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSCAFP00030000648.1 UniProtKB/TrEMBL
  ENSCAFP00030000673.1 UniProtKB/TrEMBL
  ENSCAFP00040004016 UniProtKB/TrEMBL
  ENSCAFP00040004051 UniProtKB/TrEMBL
  ENSCAFP00040004059 UniProtKB/TrEMBL
  ENSCAFP00845027772 ENTREZGENE
  ENSCAFP00845027772.1 UniProtKB/TrEMBL
  ENSCAFP00845027835.1 UniProtKB/TrEMBL
Ensembl Transcript ENSCAFT00030000747.1 UniProtKB/TrEMBL
  ENSCAFT00030000781.1 UniProtKB/TrEMBL
  ENSCAFT00040004673 UniProtKB/TrEMBL
  ENSCAFT00040004714 UniProtKB/TrEMBL
  ENSCAFT00040004723 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_PLP_BS UniProtKB/TrEMBL
  SHMT-like_dom UniProtKB/TrEMBL
NCBI Gene SHMT1 ENTREZGENE
PANTHER PTHR11680 UniProtKB/TrEMBL
Pfam SHMT UniProtKB/TrEMBL
PIRSF SHMT UniProtKB/TrEMBL
PROSITE SHMT UniProtKB/TrEMBL
Superfamily-SCOP SSF53383 UniProtKB/TrEMBL
UniProt A0A8C0LY66_CANLF UniProtKB/TrEMBL
  A0A8C0PTW6_CANLF UniProtKB/TrEMBL
  A0A8C0RW38_CANLF UniProtKB/TrEMBL
  A0A8I3PGW1_CANLF UniProtKB/TrEMBL
  A0A8I3S1J1_CANLF UniProtKB/TrEMBL
  E2RIV3 ENTREZGENE
VGNC ID VGNC:46150 ENTREZGENE