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Ldhb lactate dehydrogenase B [ Rattus norvegicus (Norway rat) ]

Gene ID: 24534, updated on 4-Jun-2020

Summary

Official Symbol
Ldhbprovided by RGD
Official Full Name
lactate dehydrogenase Bprovided by RGD
Primary source
RGD:2997
See related
Ensembl:ENSRNOG00000013000
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Rattus norvegicus
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
Also known as
Ldh2
Summary
This gene encodes the B subunit of lactate dehydrogenase enzyme, which catalyzes the interconversion of pyruvate and lactate with concomitant interconversion of NADH and NAD+ in a post-glycolysis process. Alternatively spliced transcript variants have also been found for this gene. Recent studies have shown that a C-terminally extended isoform is produced by use of an alternative in-frame translation termination codon via a stop codon readthrough mechanism, and that this isoform is localized in the peroxisomes. Pseudogenes have been identified on chromosomes X and 9. [provided by RefSeq, Feb 2016]
Expression
Biased expression in Heart (RPKM 12336.6), Kidney (RPKM 2578.0) and 3 other tissues See more
Orthologs

Genomic context

See Ldhb in Genome Data Viewer
Location:
4q44
Exon count:
9
Annotation release Status Assembly Chr Location
106 current Rnor_6.0 (GCF_000001895.5) 4 NC_005103.4 (176701980..176719999, complement)
106 current Rn_Celera (GCF_000002265.2) 4 AC_000072.1 (163963498..163981517, complement)
104 previous assembly Rnor_5.0 (GCF_000001895.4) 4 NC_005103.3 (240918027..240936014, complement)

Chromosome 4 - NC_005103.4Genomic Context describing neighboring genes Neighboring gene spexin hormone Neighboring gene glycogen synthase 2 Neighboring gene potassium inwardly-rectifying channel, subfamily J, member 8 Neighboring gene ATP binding cassette subfamily C member 9

Genomic regions, transcripts, and products

Expression

  • Project title: A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages
  • Description: 320 RNA samples isolated from 11 organs (adrenal gland, brain, heart, kidney, liver, lung, muscle, spleen, thymus, and testes or uterus) from both sexes of Fischer 344 rats across four developmental stages (2-, 6-, 21-, and 104-weeks-old)
  • BioProject: PRJNA238328
  • Publication: PMID 24510058
  • Analysis date: Mon Jun 6 17:44:12 2016

Bibliography

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Pathways from PubChem

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Gene Ontology Provided by RGD

Function Evidence Code Pubs
L-lactate dehydrogenase activity IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
L-lactate dehydrogenase activity IDA
Inferred from Direct Assay
more info
PubMed 
L-lactate dehydrogenase activity ISO
Inferred from Sequence Orthology
more info
 
NAD binding IDA
Inferred from Direct Assay
more info
PubMed 
identical protein binding IDA
Inferred from Direct Assay
more info
PubMed 
identical protein binding ISO
Inferred from Sequence Orthology
more info
 
kinase binding IPI
Inferred from Physical Interaction
more info
PubMed 
lactate dehydrogenase activity IDA
Inferred from Direct Assay
more info
PubMed 
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
Process Evidence Code Pubs
NAD metabolic process IDA
Inferred from Direct Assay
more info
PubMed 
carbohydrate metabolic process IEA
Inferred from Electronic Annotation
more info
 
lactate metabolic process IDA
Inferred from Direct Assay
more info
PubMed 
oxidation-reduction process IEA
Inferred from Electronic Annotation
more info
 
Component Evidence Code Pubs
cytoplasm IEA
Inferred from Electronic Annotation
more info
 
cytosol ISO
Inferred from Sequence Orthology
more info
 
membrane raft ISO
Inferred from Sequence Orthology
more info
 

General protein information

Preferred Names
L-lactate dehydrogenase B chain
Names
LDH heart subunit
LDH-B
LDH-H
Lactate dehydrogenease B
NP_001303262.1
NP_001303263.1
NP_036727.1

NCBI Reference Sequences (RefSeq)

RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

mRNA and Protein(s)

  1. NM_001316333.1NP_001303262.1  L-lactate dehydrogenase B chain isoform Ldhbx

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) encodes two isoforms, which result from the use of alternative in-frame translation termination codons. The shorter isoform (Ldhb) results from translation termination at the upstream UGA stop codon, while the longer isoform (Ldhbx) results from UGA stop codon readthrough to the downstream UAG termination codon. This RefSeq represents the longer, C-terminally extended isoform (Ldhbx), which is localized in the peroxisomes. As the UGA stop codon has been reported to specify several alternative amino acids (tryptophan, cysteine, arginine and serine), its location in the longer isoform is denoted by an 'X'.
    Source sequence(s)
    BU759234, FM054345, U07181
    UniProtKB/Swiss-Prot
    P42123
    Conserved Domains (2) summary
    cd05293
    Location:20330
    LDH_1; A subgroup of L-lactate dehydrogenases
    PLN02602
    Location:4332
    PLN02602; lactate dehydrogenase
  2. NM_001316334.1NP_001303263.1  L-lactate dehydrogenase B chain isoform Ldhb

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) differs in the 5' UTR compared to variant 1. Variants 1 and 2 encode the same isoform (Ldhb).
    Source sequence(s)
    BU759234, CK355620, FM054345, U07181
    UniProtKB/Swiss-Prot
    P42123
    Conserved Domains (2) summary
    cd05293
    Location:20330
    LDH_1; A subgroup of L-lactate dehydrogenases
    PLN02602
    Location:4332
    PLN02602; lactate dehydrogenase
  3. NM_012595.2NP_036727.1  L-lactate dehydrogenase B chain isoform Ldhb

    See identical proteins and their annotated locations for NP_036727.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) encodes two isoforms, which result from the use of alternative in-frame translation termination codons. The shorter isoform (Ldhb) results from translation termination at the upstream UGA stop codon, while the longer isoform (Ldhbx) results from UGA stop codon readthrough to the downstream UAG termination codon. This RefSeq represents the shorter isoform (Ldhb), which is localized in the cytosol. Variants 1 and 2 encode the same isoform.
    Source sequence(s)
    BU759234, FM054345, U07181
    UniProtKB/Swiss-Prot
    P42123
    Related
    ENSRNOP00000017965.4, ENSRNOT00000017965.7
    Conserved Domains (2) summary
    cd05293
    Location:20330
    LDH_1; A subgroup of L-lactate dehydrogenases
    PLN02602
    Location:4332
    PLN02602; lactate dehydrogenase

RefSeqs of Annotated Genomes: Rattus norvegicus Annotation Release 106 details...Open this link in a new tab

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference Rnor_6.0 Primary Assembly

Genomic

  1. NC_005103.4 Reference Rnor_6.0 Primary Assembly

    Range
    176701980..176719999 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate Rn_Celera

Genomic

  1. AC_000072.1 Alternate Rn_Celera

    Range
    163963498..163981517 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
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