Shmt2 (serine hydroxymethyltransferase 2) - Rat Genome Database

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Gene: Shmt2 (serine hydroxymethyltransferase 2) Chinchilla lanigera
Analyze
Symbol: Shmt2
Name: serine hydroxymethyltransferase 2
RGD ID: 8997578
Description: ENCODES a protein that exhibits amino acid binding (ortholog); chromatin binding (ortholog); glycine hydroxymethyltransferase activity (ortholog); INVOLVED IN glycine biosynthetic process (ortholog); glycine biosynthetic process from serine (ortholog); glycine metabolic process (ortholog); PARTICIPATES IN dihydropyrimidine dehydrogenase deficiency pathway; dimethylglycine dehydrogenase deficiency pathway; folate cycle metabolic pathway; ASSOCIATED WITH cataract 15 multiple types (ortholog); Charcot-Marie-Tooth disease axonal type 2U (ortholog); familial melanoma (ortholog); FOUND IN BRISC complex (ortholog); cytoplasm (ortholog); microtubule cytoskeleton (ortholog)
Type: protein-coding
RefSeq Status: MODEL
Previously known as: serine hydroxymethyltransferase 2 (mitochondrial); serine hydroxymethyltransferase, mitochondrial
RGD Orthologs
Human
Mouse
Rat
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Orthologs
More Info more info ...
Latest Assembly: ChiLan1.0 - Chinchilla ChiLan1.0 Assembly
Position:
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554584,957,602 - 4,962,691 (+)EnsemblChiLan1.0
ChiLan1.0NW_0049554584,957,614 - 4,962,691 (+)NCBIChiLan1.0ChiLan1.0
JBrowse: View Region in Genome Browser (JBrowse)
Model


References

References - curated
# Reference Title Reference Citation
1. Transitive Annotation Pipeline Automated assignment of GO, PW and RDO ISO annotations across species
Additional References at PubMed
PMID:22301074   PMID:30032202  


Genomics

Comparative Map Data
Shmt2
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554584,957,602 - 4,962,691 (+)EnsemblChiLan1.0
ChiLan1.0NW_0049554584,957,614 - 4,962,691 (+)NCBIChiLan1.0ChiLan1.0
SHMT2
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh381257,229,711 - 57,234,935 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl1257,229,573 - 57,234,935 (+)EnsemblGRCh38hg38GRCh38
GRCh371257,623,494 - 57,628,718 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 361255,909,819 - 55,914,981 (+)NCBINCBI36Build 36hg18NCBI36
Build 341255,909,818 - 55,914,981NCBI
Celera1257,277,587 - 57,282,945 (+)NCBICelera
Cytogenetic Map12q13.3NCBI
HuRef1254,662,237 - 54,667,595 (+)NCBIHuRef
CHM1_11257,591,454 - 57,596,816 (+)NCBICHM1_1
T2T-CHM13v2.01257,197,949 - 57,203,173 (+)NCBIT2T-CHM13v2.0
Shmt2
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm3910127,352,992 - 127,358,313 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl10127,352,992 - 127,358,313 (-)EnsemblGRCm39 Ensembl
GRCm3810127,517,123 - 127,522,444 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl10127,517,123 - 127,522,444 (-)EnsemblGRCm38mm10GRCm38
MGSCv3710126,954,195 - 126,959,491 (-)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv3610126,920,088 - 126,925,384 (-)NCBIMGSCv36mm8
Celera10129,908,893 - 129,914,189 (-)NCBICelera
Cytogenetic Map10D3NCBI
cM Map1074.51NCBI
Shmt2
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8765,244,247 - 65,249,580 (-)NCBIGRCr8
mRatBN7.2763,358,961 - 63,364,293 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl763,358,961 - 63,364,236 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx765,248,234 - 65,253,554 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0767,450,661 - 67,455,981 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0767,251,885 - 67,257,207 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.0770,824,718 - 70,829,822 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl770,824,715 - 70,829,815 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0770,998,103 - 71,003,197 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4767,494,470 - 67,499,540 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.1767,515,199 - 67,520,270 (-)NCBI
Celera760,498,180 - 60,503,250 (-)NCBICelera
Cytogenetic Map7q22NCBI
SHMT2
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v21037,106,967 - 37,112,419 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan11237,103,737 - 37,108,804 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v01231,692,451 - 31,697,727 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.11231,944,787 - 31,950,138 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1231,944,785 - 31,950,138 (-)Ensemblpanpan1.1panPan2
SHMT2
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1101,357,347 - 1,362,511 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl101,356,706 - 1,362,305 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha101,421,107 - 1,426,256 (+)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.0101,367,808 - 1,372,957 (+)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl101,367,831 - 1,372,939 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1101,344,398 - 1,349,547 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0101,586,394 - 1,591,543 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0101,711,303 - 1,716,453 (+)NCBIUU_Cfam_GSD_1.0
Shmt2
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440494557,442,306 - 57,447,426 (-)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049366461,422,817 - 1,429,037 (+)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_0049366461,422,844 - 1,427,929 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
SHMT2
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl522,532,894 - 22,540,319 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1522,535,780 - 22,540,322 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2524,368,828 - 24,374,450 (+)NCBISscrofa10.2Sscrofa10.2susScr3
SHMT2
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11153,141,435 - 53,146,625 (+)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl1153,141,462 - 53,147,795 (+)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_023666037192,825,670 - 192,831,284 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Shmt2
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_00462480210,713,276 - 10,719,253 (-)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_00462480210,713,276 - 10,718,391 (-)NCBIHetGla_female_1.0HetGla 1.0hetGla2


Expression

RNA-SEQ Expression


Sequence


Ensembl Acc Id: ENSCLAT00000021191   ⟹   ENSCLAP00000020990
Type: CODING
Position:
Chinchilla AssemblyChrPosition (strand)Source
ChiLan1.0 EnsemblNW_0049554584,957,602 - 4,962,691 (+)Ensembl
RefSeq Acc Id: XM_005397350   ⟹   XP_005397407
Type: CODING
Position:
Chinchilla AssemblyChrPosition (strand)Source
ChiLan1.0NW_0049554584,957,614 - 4,962,691 (+)NCBI
Sequence:
Protein Sequences
Protein RefSeqs XP_005397407 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSCLAP00000020990
  ENSCLAP00000020990.1
RefSeq Acc Id: XP_005397407   ⟸   XM_005397350
- UniProtKB: A0A8C2VUU4 (UniProtKB/TrEMBL)
- Sequence:
Ensembl Acc Id: ENSCLAP00000020990   ⟸   ENSCLAT00000021191

Additional Information

Database Acc Id Source(s)
Ensembl Genes ENSCLAG00000014378 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSCLAT00000021191 ENTREZGENE
  ENSCLAT00000021191.1 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
NCBI Gene Shmt2 ENTREZGENE
PANTHER PTHR11680 UniProtKB/TrEMBL
  SERINE HYDROXYMETHYLTRANSFERASE, MITOCHONDRIAL UniProtKB/TrEMBL
Pfam SHMT UniProtKB/TrEMBL
PIRSF SHMT UniProtKB/TrEMBL
PROSITE SHMT UniProtKB/TrEMBL
Superfamily-SCOP SSF53383 UniProtKB/TrEMBL
UniProt A0A8C2VUU4 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2016-08-03 Shmt2  serine hydroxymethyltransferase 2    serine hydroxymethyltransferase 2 (mitochondrial)  Symbol and/or name change 5135510 APPROVED