Bhmt2 (betaine-homocysteine S-methyltransferase 2) - Rat Genome Database

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Gene: Bhmt2 (betaine-homocysteine S-methyltransferase 2) Rattus norvegicus
Analyze
Symbol: Bhmt2
Name: betaine-homocysteine S-methyltransferase 2
RGD ID: 1359418
Description: Predicted to enable S-methylmethionine-homocysteine S-methyltransferase activity and zinc ion binding activity. Predicted to be involved in L-methionine salvage; S-adenosylmethionine metabolic process; and S-methylmethionine metabolic process. Predicted to be active in cytosol. Human ortholog(s) of this gene implicated in congenital heart disease. Orthologous to human BHMT2 (betaine--homocysteine S-methyltransferase 2); INTERACTS WITH (+)-schisandrin B; 1-benzylpiperazine; 17beta-estradiol.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: betaine--homocysteine S-methyltransferase 2; betaine-homocysteine methyltransferase 2; LOC365972; S-methylmethionine--homocysteine S-methyltransferase BHMT2; similar to betaine-homocysteine methyltransferase 2; SMM-hcy methyltransferase
RGD Orthologs
Human
Mouse
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Orthologs
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8226,630,502 - 26,647,450 (-)NCBIGRCr8
mRatBN7.2224,895,525 - 24,912,475 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl224,895,533 - 24,912,475 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx231,922,826 - 31,939,776 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0230,023,092 - 30,040,035 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0224,848,839 - 24,865,761 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.0223,272,320 - 23,289,266 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl223,272,328 - 23,289,266 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0242,452,894 - 42,469,840 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4223,958,062 - 23,976,438 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.1223,878,437 - 23,896,807 (-)NCBI
Celera220,969,823 - 20,986,770 (-)NCBICelera
Cytogenetic Map2q12NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View

Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Cellular Component
cytosol  (IBA)

References

References - curated
# Reference Title Reference Citation
1. Significant Down-Regulation of Urea Cycle Generates Clinically Relevant Proteomic Signature in Hepatocellular Carcinoma Patients with Macrovascular Invasion. Cao Y, etal., J Proteome Res. 2019 May 3;18(5):2032-2044. doi: 10.1021/acs.jproteome.8b00921. Epub 2019 Mar 29.
2. Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
3. A Three-Way Interaction among Maternal and Fetal Variants Contributing to Congenital Heart Defects. Li M, etal., Ann Hum Genet. 2016 Jan;80(1):20-31. doi: 10.1111/ahg.12139. Epub 2015 Nov 27.
4. GOA pipeline RGD automated data pipeline
5. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
6. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
7. Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. Strausberg RL, etal., Proc Natl Acad Sci U S A. 2002 Dec 24;99(26):16899-903. Epub 2002 Dec 11.
Additional References at PubMed
PMID:10329001   PMID:15489334   PMID:18230605   PMID:19056867   PMID:23533145   PMID:29804940  


Genomics

Comparative Map Data
Bhmt2
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8226,630,502 - 26,647,450 (-)NCBIGRCr8
mRatBN7.2224,895,525 - 24,912,475 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl224,895,533 - 24,912,475 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx231,922,826 - 31,939,776 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0230,023,092 - 30,040,035 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0224,848,839 - 24,865,761 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.0223,272,320 - 23,289,266 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl223,272,328 - 23,289,266 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0242,452,894 - 42,469,840 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4223,958,062 - 23,976,438 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.1223,878,437 - 23,896,807 (-)NCBI
Celera220,969,823 - 20,986,770 (-)NCBICelera
Cytogenetic Map2q12NCBI
BHMT2
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38579,069,767 - 79,090,069 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl579,069,767 - 79,090,069 (+)EnsemblGRCh38hg38GRCh38
GRCh37578,365,590 - 78,385,892 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 36578,401,339 - 78,421,045 (+)NCBINCBI36Build 36hg18NCBI36
Build 34578,401,338 - 78,421,029NCBI
Celera574,258,430 - 74,278,792 (+)NCBICelera
Cytogenetic Map5q14.1NCBI
HuRef573,571,483 - 73,591,845 (+)NCBIHuRef
CHM1_1577,798,019 - 77,818,372 (+)NCBICHM1_1
T2T-CHM13v2.0579,550,871 - 79,571,174 (+)NCBIT2T-CHM13v2.0
Bhmt2
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391393,792,605 - 93,810,810 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1393,792,228 - 93,810,810 (-)EnsemblGRCm39 Ensembl
GRCm381393,656,097 - 93,674,302 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1393,655,720 - 93,674,302 (-)EnsemblGRCm38mm10GRCm38
MGSCv371394,426,052 - 94,444,257 (-)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv361394,757,008 - 94,775,032 (-)NCBIMGSCv36mm8
Celera1397,262,133 - 97,280,354 (-)NCBICelera
Cytogenetic Map13C3NCBI
cM Map1347.88NCBI
BHMT2
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v2436,217,192 - 36,235,946 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan1534,370,819 - 34,389,555 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v0536,223,429 - 36,242,187 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.1536,713,179 - 36,725,144 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl536,670,854 - 36,728,993 (-)Ensemblpanpan1.1panPan2
BHMT2
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1327,775,779 - 27,804,603 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl327,776,084 - 27,789,960 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha329,015,000 - 29,030,182 (-)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.0327,694,621 - 27,709,761 (-)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl327,694,625 - 27,708,820 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1327,633,714 - 27,648,761 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0327,612,238 - 27,627,369 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0327,892,957 - 27,908,103 (-)NCBIUU_Cfam_GSD_1.0
LOC101971919
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024407213183,945,559 - 183,959,144 (-)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049365496,899,948 - 6,914,263 (+)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_0049365496,900,075 - 6,914,217 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
BHMT2
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl287,866,621 - 87,882,716 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1287,866,631 - 87,882,623 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2289,459,626 - 89,475,622 (-)NCBISscrofa10.2Sscrofa10.2susScr3
BHMT2
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1473,289,836 - 73,310,312 (+)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl473,289,652 - 73,312,358 (+)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_02366604922,136,327 - 22,156,786 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Bhmt2
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_0046248693,576,369 - 3,599,275 (+)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_0046248693,571,154 - 3,596,389 (+)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Bhmt2
83 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:494
Count of miRNA genes:248
Interacting mature miRNAs:298
Transcripts:ENSRNOT00000061708
Prediction methods:Microtar, Miranda, Targetscan
Result types:miRGate_prediction

The detailed report is available here: Full Report CSV TAB Printer

miRNA Target Status data imported from miRGate (http://mirgate.bioinfo.cnio.es/).
For more information about miRGate, see PMID:25858286 or access the full paper here.


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
10755430Coatc6Coat color QTL 60.02576coat/hair pigmentation trait (VT:0010463)pigmented ventral coat/hair area to total ventral coat/hair area ratio (CMO:0001812)21159110056591100Rat
1600379Mcs18Mammary carcinoma susceptibility QTL 182.6mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)2788777242804738Rat
7387318Stl32Serum triglyceride level QTL 323.20.0003blood triglyceride amount (VT:0002644)plasma triglyceride level (CMO:0000548)22238462767384627Rat
631682Bp115Blood pressure QTL 1154.30.0001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)2137410502Rat
61355Bp36Blood pressure QTL 362.9blood pressure trait (VT:0000183)systolic blood pressure (CMO:0000004)25873687102844969Rat
2300168Bmd47Bone mineral density QTL 476.60.0001femur mineral mass (VT:0010011)bone mineral density (CMO:0001226)22066244865662448Rat
10755499Bp389Blood pressure QTL 3892.61arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)218960362228801039Rat
1578664Bmd9Bone mineral QTL density 95femur mineral mass (VT:0010011)total volumetric bone mineral density (CMO:0001728)21185206249003364Rat
738010Lnnr3Liver neoplastic nodule remodeling QTL 32.94liver integrity trait (VT:0010547)liver remodeling tumorous lesion number (CMO:0001461)2141244106Rat
1357990Ael1Aortic elastin QTL 13.10.00091aorta elastin amount (VT:0003905)aortic elastin21907682564076825Rat
731167Glom4Glomerulus QTL 42.40.0082kidney glomerulus morphology trait (VT:0005325)count of superficial glomeruli not directly contacting the kidney surface (CMO:0001002)22030467265304672Rat
738012Anxrr3Anxiety related response QTL 33.8exploratory behavior trait (VT:0010471)percentage of entries into a discrete space in an experimental apparatus (CMO:0000961)2902351954023519Rat
731184Mamtr4Mammary tumor resistance QTL 40.0003mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)21649174061491740Rat
10402051Gdil2Gastrointestinal dilation QTL 2enteric ganglion morphology trait (VT:0001045)length of intestine affected by colonic aganglionosis to total length of colon ratio (CMO:0001836)22490385374786777Rat

Markers in Region
D2Rat252  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2224,903,853 - 24,904,033 (+)MAPPERmRatBN7.2
Rnor_6.0223,280,647 - 23,280,826NCBIRnor6.0
Rnor_5.0242,461,221 - 42,461,400UniSTSRnor5.0
RGSC_v3.4223,966,484 - 23,966,663UniSTSRGSC3.4
RGSC_v3.1223,886,852 - 23,887,032RGD
Celera220,978,151 - 20,978,330UniSTS
FHH x ACI Map211.4598UniSTS
FHH x ACI Map211.4598RGD
Cytogenetic Map2q12UniSTS


Expression

RNA-SEQ Expression

alimentary part of gastrointestinal system
appendage
circulatory system
ectoderm
endocrine system
endoderm
exocrine system
hemolymphoid system
hepatobiliary system
integumental system
mesenchyme
mesoderm
nervous system
renal system
reproductive system
respiratory system
5 9 18 84 89 86 59 21 59 6 175 58 65 45 56 27

Sequence


Ensembl Acc Id: ENSRNOT00000061708   ⟹   ENSRNOP00000058419
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl224,895,533 - 24,912,475 (-)Ensembl
Rnor_6.0 Ensembl223,272,328 - 23,289,266 (-)Ensembl
Ensembl Acc Id: ENSRNOT00000106169   ⟹   ENSRNOP00000076807
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl224,895,533 - 24,909,227 (-)Ensembl
RefSeq Acc Id: NM_001014256   ⟹   NP_001014278
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8226,630,502 - 26,647,450 (-)NCBI
mRatBN7.2224,895,525 - 24,912,475 (-)NCBI
Rnor_6.0223,272,320 - 23,289,266 (-)NCBI
Rnor_5.0242,452,894 - 42,469,840 (-)NCBI
RGSC_v3.4223,958,062 - 23,976,438 (-)RGD
Celera220,969,823 - 20,986,770 (-)RGD
Sequence:
Protein Sequences
Protein RefSeqs NP_001014278 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein AAH79366 (Get FASTA)   NCBI Sequence Viewer  
  EDM10064 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000058419.5
  ENSRNOP00000076807.1
GenBank Protein Q68FT5 (Get FASTA)   NCBI Sequence Viewer  
RefSeq Acc Id: NP_001014278   ⟸   NM_001014256
- UniProtKB: Q68FT5 (UniProtKB/Swiss-Prot),   F1LMG2 (UniProtKB/TrEMBL),   A6I4V7 (UniProtKB/TrEMBL)
- Sequence:
Ensembl Acc Id: ENSRNOP00000058419   ⟸   ENSRNOT00000061708
Ensembl Acc Id: ENSRNOP00000076807   ⟸   ENSRNOT00000106169
Protein Domains
Hcy-binding

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-Q68FT5-F1-model_v2 AlphaFold Q68FT5 1-363 view protein structure

Transcriptome

eQTL   View at Phenogen
WGCNA   View at Phenogen
Tissue/Strain Expression   View at Phenogen

Promoters
RGD ID:13691071
Promoter ID:EPDNEW_R1594
Type:multiple initiation site
Name:Bhmt2_1
Description:betaine-homocysteine S-methyltransferase 2
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Experiment Methods:Single-end sequencing.
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0223,289,257 - 23,289,317EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1359418 AgrOrtholog
BioCyc Gene G2FUF-54843 BioCyc
BioCyc Pathway ADENOSYLHOMOCYSCAT-PWY [L-methionine salvage from L-homocysteine] BioCyc
BioCyc Pathway Image ADENOSYLHOMOCYSCAT-PWY BioCyc
Ensembl Genes ENSRNOG00000040120 Ensembl, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000061708.5 UniProtKB/TrEMBL
  ENSRNOT00000106169.1 UniProtKB/TrEMBL
Gene3D-CATH 3.20.20.330 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
IMAGE_CLONE IMAGE:7109516 IMAGE-MGC_LOAD
InterPro Betaine-hCys_S-MeTrfase_BHMT UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  BHMT UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  HCY_dom UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  HCY_dom_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report rno:365972 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
MGC_CLONE MGC:94849 IMAGE-MGC_LOAD
NCBI Gene 365972 ENTREZGENE
PANTHER BETAINE--HOMOCYSTEINE S-METHYLTRANSFERASE 1 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  S-METHYLMETHIONINE--HOMOCYSTEINE S-METHYLTRANSFERASE BHMT2 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Pfam S-methyl_trans UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Bhmt2 PhenoGen
PIRSF Betaine_HMT UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PROSITE HCY UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
RatGTEx ENSRNOG00000040120 RatGTEx
Superfamily-SCOP SSF82282 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniProt A0A8I5XVF4_RAT UniProtKB/TrEMBL
  A6I4V7 ENTREZGENE, UniProtKB/TrEMBL
  BHMT2_RAT UniProtKB/Swiss-Prot
  F1LMG2 ENTREZGENE, UniProtKB/TrEMBL
  Q68FT5 ENTREZGENE


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2011-07-28 Bhmt2  betaine-homocysteine S-methyltransferase 2  Bhmt2  betaine-homocysteine methyltransferase 2  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-03-05 Bhmt2  betaine-homocysteine methyltransferase 2  LOC365972  similar to betaine-homocysteine methyltransferase 2  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2005-07-29 LOC365972  similar to betaine-homocysteine methyltransferase 2      Symbol and Name status set to provisional 70820 PROVISIONAL