Human Gene ACSM2B (uc002dhk.4)
  Description: Homo sapiens acyl-CoA synthetase medium-chain family member 2B (ACSM2B), transcript variant 2, mRNA.
Transcript (Including UTRs)
   Position: hg19 chr16:20,548,083-20,587,695 Size: 39,613 Total Exon Count: 14 Strand: -
Coding Region
   Position: hg19 chr16:20,548,580-20,576,167 Size: 27,588 Coding Exon Count: 13 

Page IndexSequence and LinksUniProtKB CommentsPrimersGenetic AssociationsCTD
Gene AllelesRNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther Species
GO AnnotationsmRNA DescriptionsPathwaysOther NamesModel InformationMethods
Data last updated at UCSC: 2013-06-14

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr16:20,548,083-20,587,695)mRNA (may differ from genome)Protein (577 aa)
Gene SorterGenome BrowserOther Species FASTAGene interactionsTable SchemaAlphaFold
BioGPSEnsemblEntrez GeneExonPrimerGeneCardsH-INV
HGNCHPRDLynxMGIneXtProtOMIM
PubMedReactomeUniProtKBWikipediaBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: ACS2B_HUMAN
DESCRIPTION: RecName: Full=Acyl-coenzyme A synthetase ACSM2B, mitochondrial; EC=6.2.1.2; AltName: Full=Acyl-CoA synthetase medium-chain family member 2B; AltName: Full=Butyrate--CoA ligase 2B; AltName: Full=Butyryl-coenzyme A synthetase 2B; AltName: Full=Middle-chain acyl-CoA synthetase 2B; AltName: Full=Xenobiotic/medium-chain fatty acid-CoA ligase HXM-A; Flags: Precursor;
FUNCTION: Has medium-chain fatty acid:CoA ligase activity with broad substrate specificity (in vitro). Acts on acids from C(4) to C(11) and on the corresponding 3-hydroxy- and 2,3- or 3,4- unsaturated acids (in vitro).
CATALYTIC ACTIVITY: ATP + a carboxylate + CoA = AMP + diphosphate + an acyl-CoA.
COFACTOR: Magnesium or manganese.
ENZYME REGULATION: Activated by monovalent cations, such as potassium, rubidium or ammonium.
SUBUNIT: Monomer.
SUBCELLULAR LOCATION: Mitochondrion matrix.
TISSUE SPECIFICITY: Detected in liver.
SIMILARITY: Belongs to the ATP-dependent AMP-binding enzyme family.

-  Primer design for this transcript
 

Primer3Plus can design qPCR Primers that straddle exon-exon-junctions, which amplify only cDNA, not genomic DNA.
Click here to load the transcript sequence and exon structure into Primer3Plus

Exonprimer can design one pair of Sanger sequencing primers around every exon, located in non-genic sequence.
Click here to open Exonprimer with this transcript

To design primers for a non-coding sequence, zoom to a region of interest and select from the drop-down menu: View > In External Tools > Primer3


-  Genetic Association Studies of Complex Diseases and Disorders
  Genetic Association Database (archive): ACSM2B
CDC HuGE Published Literature: ACSM2B

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene

+  Common Gene Haplotype Alleles
  Press "+" in the title bar above to open this section.

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 93.73 RPKM in Liver
Total median expression: 126.09 RPKM



View in GTEx track of Genome Browser    View at GTEx portal     View GTEx Body Map

+  Microarray Expression Data
  Press "+" in the title bar above to open this section.

-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -61.50175-0.351 Picture PostScript Text
3' UTR -88.50497-0.178 Picture PostScript Text

The RNAfold program from the Vienna RNA Package is used to perform the secondary structure predictions and folding calculations. The estimated folding energy is in kcal/mol. The more negative the energy, the more secondary structure the RNA is likely to have.

-  Protein Domain and Structure Information
  InterPro Domains: Graphical view of domain structure
IPR020845 - AMP-binding_CS
IPR000873 - AMP-dep_Synth/Lig
IPR025110 - DUF4009

Pfam Domains:
PF00501 - AMP-binding enzyme
PF13193 - AMP-binding enzyme C-terminal domain

SCOP Domains:
56801 - Acetyl-CoA synthetase-like

ModBase Predicted Comparative 3D Structure on Q68CK6
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The pictures above may be empty if there is no ModBase structure for the protein. The ModBase structure frequently covers just a fragment of the protein. You may be asked to log onto ModBase the first time you click on the pictures. It is simplest after logging in to just click on the picture again to get to the specific info on that model.

-  Orthologous Genes in Other Species
  Orthologies between human, mouse, and rat are computed by taking the best BLASTP hit, and filtering out non-syntenic hits. For more distant species reciprocal-best BLASTP hits are used. Note that the absence of an ortholog in the table below may reflect incomplete annotations in the other species rather than a true absence of the orthologous gene.
MouseRatZebrafishD. melanogasterC. elegansS. cerevisiae
No orthologGenome BrowserNo orthologNo orthologNo orthologNo ortholog
Gene DetailsGene Details    
Gene SorterGene Sorter    
 RGD    
 Protein Sequence    
 Alignment    

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0000166 nucleotide binding
GO:0003674 molecular_function
GO:0003824 catalytic activity
GO:0003996 acyl-CoA ligase activity
GO:0004321 fatty-acyl-CoA synthase activity
GO:0005524 ATP binding
GO:0015645 fatty acid ligase activity
GO:0016405 CoA-ligase activity
GO:0016874 ligase activity
GO:0046872 metal ion binding
GO:0047760 butyrate-CoA ligase activity

Biological Process:
GO:0006629 lipid metabolic process
GO:0006631 fatty acid metabolic process
GO:0006633 fatty acid biosynthetic process
GO:0006637 acyl-CoA metabolic process
GO:0006805 xenobiotic metabolic process
GO:0008152 metabolic process

Cellular Component:
GO:0005739 mitochondrion
GO:0005759 mitochondrial matrix


-  Descriptions from all associated GenBank mRNAs
  AK129944 - Homo sapiens cDNA FLJ26434 fis, clone KDN01892.
AB073604 - Homo sapiens primary hepatoblastoma cDNA, clone:HYST1046, full insert sequence.
AK289416 - Homo sapiens cDNA FLJ76695 complete cds, highly similar to Homo sapiens acyl-CoA synthetase medium-chain family member 2 (ACSM2), nuclear gene encoding mitochondrial protein, mRNA.
AK309601 - Homo sapiens cDNA, FLJ99642.
BC026010 - Homo sapiens, clone IMAGE:4715175, mRNA.
JD215498 - Sequence 196522 from Patent EP1572962.
JD043558 - Sequence 24582 from Patent EP1572962.
JD037696 - Sequence 18720 from Patent EP1572962.
JD067310 - Sequence 48334 from Patent EP1572962.
JD073773 - Sequence 54797 from Patent EP1572962.
JD045016 - Sequence 26040 from Patent EP1572962.
JD082385 - Sequence 63409 from Patent EP1572962.
JD492687 - Sequence 473711 from Patent EP1572962.
JD302311 - Sequence 283335 from Patent EP1572962.
JD494793 - Sequence 475817 from Patent EP1572962.
JD266274 - Sequence 247298 from Patent EP1572962.
JD437324 - Sequence 418348 from Patent EP1572962.
JD214612 - Sequence 195636 from Patent EP1572962.
JD314171 - Sequence 295195 from Patent EP1572962.
JD166557 - Sequence 147581 from Patent EP1572962.
JD392354 - Sequence 373378 from Patent EP1572962.
AY160217 - Homo sapiens xenobiotic/medium-chain fatty acid:CoA ligase mRNA, complete cds; nuclear gene for mitochondrial product.
BC172335 - Synthetic construct Homo sapiens clone IMAGE:100069029, MGC:199040 acyl-CoA synthetase medium-chain family member 2B (ACSM2B) mRNA, encodes complete protein.
JD283929 - Sequence 264953 from Patent EP1572962.
JD075315 - Sequence 56339 from Patent EP1572962.
JD438497 - Sequence 419521 from Patent EP1572962.
JD537106 - Sequence 518130 from Patent EP1572962.
JD230647 - Sequence 211671 from Patent EP1572962.
JD482208 - Sequence 463232 from Patent EP1572962.
JD254304 - Sequence 235328 from Patent EP1572962.
JD530961 - Sequence 511985 from Patent EP1572962.
JD120940 - Sequence 101964 from Patent EP1572962.
JD536222 - Sequence 517246 from Patent EP1572962.
JD517167 - Sequence 498191 from Patent EP1572962.
JD486371 - Sequence 467395 from Patent EP1572962.
JD525155 - Sequence 506179 from Patent EP1572962.
JD288790 - Sequence 269814 from Patent EP1572962.

-  Biochemical and Signaling Pathways
  KEGG - Kyoto Encyclopedia of Genes and Genomes
hsa00650 - Butanoate metabolism
hsa01100 - Metabolic pathways

Reactome (by CSHL, EBI, and GO)

Protein Q68CK6 (Reactome details) participates in the following event(s):

R-HSA-159443 benzoate + Coenzyme A + ATP => benzoyl-CoA + AMP + pyrophosphate
R-HSA-177157 phenylacetate + Coenzyme A + ATP => phenylacetyl-CoA + AMP + pyrophosphate
R-HSA-159567 salicylic acid + Coenzyme A + ATP => salicylate-CoA + AMP + pyrophosphate
R-HSA-177135 Conjugation of benzoate with glycine
R-HSA-177162 Conjugation of phenylacetate with glutamine
R-HSA-177128 Conjugation of salicylate with glycine
R-HSA-159424 Conjugation of carboxylic acids
R-HSA-156587 Amino Acid conjugation
R-HSA-156580 Phase II - Conjugation of compounds
R-HSA-211859 Biological oxidations
R-HSA-1430728 Metabolism

-  Other Names for This Gene
  Alternate Gene Symbols: ACS2B_HUMAN, ACSM2, HYST1046, NM_001105069, NP_872423, Q68CK6, Q86YT1
UCSC ID: uc002dhk.4
RefSeq Accession: NM_001105069
Protein: Q68CK6 (aka ACS2B_HUMAN)
CCDS: CCDS10586.1

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_001105069.1
exon count: 14CDS single in 3' UTR: no RNA size: 2409
ORF size: 1734CDS single in intron: no Alignment % ID: 99.92
txCdsPredict score: 3394.00frame shift in genome: no % Coverage: 99.88
has start codon: yes stop codon in genome: no # of Alignments: 1
has end codon: yes retained intron: no # AT/AC introns 0
selenocysteine: no end bleed into intron: 0# strange splices: 0
Click here for a detailed description of the fields of the table above.

-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.