LDHAL6B (lactate dehydrogenase A like 6B) - Rat Genome Database

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Gene: LDHAL6B (lactate dehydrogenase A like 6B) Homo sapiens
Analyze
Symbol: LDHAL6B
Name: lactate dehydrogenase A like 6B
RGD ID: 1342929
HGNC Page HGNC
Description: Predicted to have L-lactate dehydrogenase activity. Predicted to be involved in pyruvate metabolic process. Localizes to nucleus; PARTICIPATES IN malonic aciduria pathway; methylmalonic aciduria, cobalamin-related pathway; propanoate metabolic pathway; INTERACTS WITH copper(II) sulfate; sunitinib; 2,3,7,8-tetrachlorodibenzodioxine (ortholog).
Type: protein-coding
RefSeq Status: VALIDATED
Also known as: L-lactate dehydrogenase A-like 6B; lactate dehydrogenase A -like; lactate dehydrogenase A-like 6; lactate dehydrogenase A-like 6B; LDH6B; LDHAL6; LDHL; testicular tissue protein Li 105
RGD Orthologs
Mouse
Rat
Chinchilla
Bonobo
Dog
Squirrel
Green Monkey
Alliance Genes
More Info more info ...
Related Pseudogenes: LDHAL6CP   LDHAL6DP   LDHAL6EP   LDHAL6FP  
Allele / Splice: See ClinVar data
Latest Assembly: GRCh38 - Human Genome Assembly GRCh38
Position:
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl1559,206,843 - 59,208,588 (+)EnsemblGRCh38hg38GRCh38
GRCh381559,206,843 - 59,208,588 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh371559,499,042 - 59,500,787 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 361557,286,334 - 57,288,006 (+)NCBINCBI36hg18NCBI36
Build 341557,286,333 - 57,287,999NCBI
Celera1536,386,997 - 36,388,669 (+)NCBI
Cytogenetic Map15q22.2NCBI
HuRef1536,321,043 - 36,322,815 (+)NCBIHuRef
CHM1_11559,616,979 - 59,618,751 (+)NCBICHM1_1
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View

Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Cellular Component

Molecular Function

Phenotype Annotations     Click to see Annotation Detail View

Human Phenotype
Colon cancer  (IAGP)
References

Additional References at PubMed
PMID:12107167   PMID:12477932   PMID:14702039   PMID:15489334   PMID:15870898   PMID:20800603   PMID:20877624   PMID:21630459   PMID:21873635   PMID:22863883   PMID:22939629   PMID:23455924  
PMID:25814554   PMID:26186194   PMID:26344197   PMID:28514442   PMID:30404004   PMID:32814053  


Genomics

Comparative Map Data
LDHAL6B
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl1559,206,843 - 59,208,588 (+)EnsemblGRCh38hg38GRCh38
GRCh381559,206,843 - 59,208,588 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh371559,499,042 - 59,500,787 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 361557,286,334 - 57,288,006 (+)NCBINCBI36hg18NCBI36
Build 341557,286,333 - 57,287,999NCBI
Celera1536,386,997 - 36,388,669 (+)NCBI
Cytogenetic Map15q22.2NCBI
HuRef1536,321,043 - 36,322,815 (+)NCBIHuRef
CHM1_11559,616,979 - 59,618,751 (+)NCBICHM1_1
Ldhal6b
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39175,467,598 - 5,469,042 (-)NCBIGRCm39mm39
GRCm39 Ensembl175,467,598 - 5,469,042 (-)Ensembl
GRCm38175,417,323 - 5,418,767 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl175,417,323 - 5,418,767 (-)EnsemblGRCm38mm10GRCm38
MGSCv37175,417,323 - 5,418,767 (-)NCBIGRCm37mm9NCBIm37
MGSCv36175,373,805 - 5,375,249 (-)NCBImm8
Celera175,959,766 - 5,961,210 (-)NCBICelera
Cytogenetic Map17A1NCBI
Ldhal6b
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2145,997,845 - 45,999,268 (-)NCBI
Rnor_6.0146,307,853 - 46,309,276 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.0147,622,971 - 47,624,394 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4140,399,144 - 40,400,567 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1140,402,089 - 40,403,512 (-)NCBI
Celera141,691,980 - 41,693,403 (-)NCBICelera
Cytogenetic Map1q11NCBI
Ldhal6b
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0NW_0049554394,954,208 - 4,956,660 (+)NCBIChiLan1.0ChiLan1.0
LDHAL6B
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.11556,484,213 - 56,485,921 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1556,484,343 - 56,485,488 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v01538,176,451 - 38,179,189 (+)NCBIMhudiblu_PPA_v0panPan3
LDHAL6B
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1146,878,452 - 46,880,160 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha147,723,470 - 47,725,173 (-)NCBI
ROS_Cfam_1.0147,065,791 - 47,067,494 (-)NCBI
UMICH_Zoey_3.1146,944,607 - 46,946,309 (-)NCBI
UNSW_CanFamBas_1.0146,807,518 - 46,809,220 (-)NCBI
UU_Cfam_GSD_1.0147,365,968 - 47,367,670 (-)NCBI
Ldhal6b
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024404946142,029,441 - 142,034,003 (-)NCBI
SpeTri2.0NW_0049364899,281,228 - 9,283,132 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
LDHAL6B
(Chlorocebus sabaeus - African green monkey)
Vervet AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.12624,304,857 - 24,307,906 (-)NCBI
ChlSab1.1 Ensembl2624,305,289 - 24,306,434 (-)Ensembl

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:109
Count of miRNA genes:103
Interacting mature miRNAs:106
Transcripts:ENST00000307144
Prediction methods:Miranda, Rnahybrid
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.


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 renal system reproductive system respiratory system sensory system adipose tissue appendage entire extraembryonic component
High
Medium 366
Low 367 951 181 71 431 66 2002 70 394 35 258 296 7 563 1324 2
Below cutoff 1875 1349 1294 459 778 305 2118 1818 2154 274 686 1135 160 621 1353

Sequence


Reference Sequences
RefSeq Acc Id: ENST00000307144   ⟹   ENSP00000302393
RefSeq Status:
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p13 Ensembl1559,206,843 - 59,208,588 (+)Ensembl
RefSeq Acc Id: NM_033195   ⟹   NP_149972
RefSeq Status: VALIDATED
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh381559,206,843 - 59,208,588 (+)NCBI
GRCh371559,499,015 - 59,500,787 (+)NCBI
Build 361557,286,334 - 57,288,006 (+)NCBI Archive
Celera1536,386,997 - 36,388,669 (+)RGD
HuRef1536,321,043 - 36,322,815 (+)NCBI
CHM1_11559,616,979 - 59,618,751 (+)NCBI
Sequence:
Reference Sequences
RefSeq Acc Id: NP_149972   ⟸   NM_033195
- UniProtKB: Q9BYZ2 (UniProtKB/Swiss-Prot),   A0A140VJM9 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSP00000302393   ⟸   ENST00000307144
Protein Domains
Ldh_1_C   Ldh_1_N

Promoters
RGD ID:6792413
Promoter ID:HG_KWN:21539
Type:Non-CpG
SO ACC ID:SO:0000170
Source:MPROMDB
Tissues & Cell Lines:Lymphoblastoid
Transcripts:OTTHUMT00000256015
Position:
Human AssemblyChrPosition (strand)Source
Build 361557,285,151 - 57,285,651 (+)MPROMDB

Clinical Variants
Name Type Condition(s) Position(s) Clinical significance
GRCh38/hg38 15q21.3-22.2(chr15:57456076-61907285)x1 copy number loss See cases [RCV000050884] Chr15:57456076..61907285 [GRCh38]
Chr15:57748274..62199484 [GRCh37]
Chr15:55535566..59986776 [NCBI36]
Chr15:15q21.3-22.2
pathogenic
GRCh38/hg38 15q21.2-22.2(chr15:50864913-59646577)x1 copy number loss See cases [RCV000051621] Chr15:50864913..59646577 [GRCh38]
Chr15:51157110..59938776 [GRCh37]
Chr15:48944402..57726068 [NCBI36]
Chr15:15q21.2-22.2
pathogenic
GRCh38/hg38 15q21.3-22.2(chr15:57567950-63019415)x1 copy number loss See cases [RCV000051622] Chr15:57567950..63019415 [GRCh38]
Chr15:57860148..63311614 [GRCh37]
Chr15:55647440..61098667 [NCBI36]
Chr15:15q21.3-22.2
pathogenic
NM_004998.3(MYO1E):c.1536C>T (p.Ser512=) single nucleotide variant Malignant melanoma [RCV000070842] Chr15:59205480 [GRCh38]
Chr15:59497679 [GRCh37]
Chr15:57284971 [NCBI36]
Chr15:15q22.2
not provided
GRCh37/hg19 15q22.1-26.3(chr15:59297293-102480888)x3 copy number gain not provided [RCV000415836] Chr15:59297293..102480888 [GRCh37]
Chr15:15q22.1-26.3
likely pathogenic
GRCh37/hg19 15q21.3-22.2(chr15:54713558-62769295)x1 copy number loss See cases [RCV000446622] Chr15:54713558..62769295 [GRCh37]
Chr15:15q21.3-22.2
pathogenic
GRCh37/hg19 15q15.1-26.3(chr15:41745084-102354798)x4 copy number gain See cases [RCV000447123] Chr15:41745084..102354798 [GRCh37]
Chr15:15q15.1-26.3
pathogenic
GRCh37/hg19 15q11.2-26.3(chr15:20733395-102511616)x4 copy number gain See cases [RCV000447765] Chr15:20733395..102511616 [GRCh37]
Chr15:15q11.2-26.3
pathogenic
GRCh37/hg19 15q11.2-26.3(chr15:22770422-102429112)x3 copy number gain See cases [RCV000510717] Chr15:22770422..102429112 [GRCh37]
Chr15:15q11.2-26.3
pathogenic
GRCh37/hg19 15q11.2-26.3(chr15:22770422-102429112) copy number gain See cases [RCV000512019] Chr15:22770422..102429112 [GRCh37]
Chr15:15q11.2-26.3
pathogenic
GRCh37/hg19 15q21.3-22.2(chr15:58088503-62221756)x1 copy number loss See cases [RCV000510898] Chr15:58088503..62221756 [GRCh37]
Chr15:15q21.3-22.2
pathogenic
Single allele duplication not provided [RCV000677926] Chr15:31115047..102354857 [GRCh37]
Chr15:15q13.2-26.3
pathogenic
GRCh37/hg19 15q21.3-22.2(chr15:58441151-60270526)x3 copy number gain not provided [RCV000683699] Chr15:58441151..60270526 [GRCh37]
Chr15:15q21.3-22.2
uncertain significance
GRCh37/hg19 15q11.1-26.3(chr15:20016811-102493540)x3 copy number gain not provided [RCV000751155] Chr15:20016811..102493540 [GRCh37]
Chr15:15q11.1-26.3
pathogenic
GRCh37/hg19 15q11.1-26.3(chr15:20071673-102461162)x3 copy number gain not provided [RCV000751156] Chr15:20071673..102461162 [GRCh37]
Chr15:15q11.1-26.3
pathogenic
GRCh37/hg19 15q21.1-22.2(chr15:48000433-60747551)x3 copy number gain not provided [RCV000845891] Chr15:48000433..60747551 [GRCh37]
Chr15:15q21.1-22.2
pathogenic
NC_000015.9:g.(?_32964879)_(91358519_?)dup duplication Bloom syndrome [RCV001343104]|Familial colorectal cancer [RCV001325176] Chr15:32964879..91358519 [GRCh37]
Chr15:15q13.3-26.1
uncertain significance
NM_004998.4(MYO1E):c.1530+1127dup duplication Focal segmental glomerulosclerosis 6 [RCV001334355] Chr15:59207549..59207550 [GRCh38]
Chr15:59499748..59499749 [GRCh37]
Chr15:15q22.2
pathogenic

Additional Information

Database Acc Id Source(s)
AGR Gene HGNC:21481 AgrOrtholog
COSMIC LDHAL6B COSMIC
Ensembl Genes ENSG00000171989 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Protein ENSP00000302393 ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Transcript ENST00000307144 ENTREZGENE, UniProtKB/Swiss-Prot
Gene3D-CATH 3.90.110.10 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
GTEx ENSG00000171989 GTEx
HGNC ID HGNC:21481 ENTREZGENE
Human Proteome Map LDHAL6B Human Proteome Map
InterPro L-lactate/malate_DH UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  L-lactate_DH UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  L-lactate_DH_AS UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Lactate/malate_DH_C UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Lactate/malate_DH_N UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Lactate_DH/Glyco_Ohase_4_C UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  NAD(P)-bd_dom_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report hsa:92483 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
NCBI Gene 92483 ENTREZGENE
Pfam Ldh_1_C UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Ldh_1_N UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PharmGKB PA134943157 PharmGKB
PIRSF Lac_mal_DH UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PRINTS LLDHDRGNASE UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PROSITE L_LDH UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Superfamily-SCOP SSF51735 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SSF56327 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
TIGRFAMs L-LDH-NAD UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniProt A0A140VJM9 ENTREZGENE, UniProtKB/TrEMBL
  LDH6B_HUMAN UniProtKB/Swiss-Prot, ENTREZGENE
UniProt Secondary Q6DUY4 UniProtKB/Swiss-Prot
  Q96LI2 UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2016-05-03 LDHAL6B  lactate dehydrogenase A like 6B    lactate dehydrogenase A-like 6B  Symbol and/or name change 5135510 APPROVED