Human Gene HACD2 (ENST00000383657.10_7) from GENCODE V47lift37
  Description: 3-hydroxyacyl-CoA dehydratase 2, transcript variant 2 (from RefSeq NM_198402.5)
Gencode Transcript: ENST00000383657.10_7
Gencode Gene: ENSG00000206527.10_13
Transcript (Including UTRs)
   Position: hg19 chr3:123,210,401-123,303,900 Size: 93,500 Total Exon Count: 7 Strand: -
Coding Region
   Position: hg19 chr3:123,213,735-123,303,874 Size: 90,140 Coding Exon Count: 7 

Page IndexSequence and LinksUniProtKB CommentsPrimersGene AllelesRNA-Seq Expression
Microarray ExpressionRNA StructureProtein StructureOther SpeciesGO AnnotationsmRNA Descriptions
PathwaysOther NamesModel InformationMethods
Data last updated at UCSC: 2024-08-22 23:36:26

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr3:123,210,401-123,303,900)mRNA (may differ from genome)Protein (254 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneTable SchemaAlphaFold
BioGPSEnsemblEntrez GeneExonPrimerGeneCardsMGI
OMIMPubMedReactomeUniProtKBWikipediaBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: HACD2_HUMAN
DESCRIPTION: RecName: Full=Very-long-chain (3R)-3-hydroxyacyl-[acyl-carrier protein] dehydratase 2; EC=4.2.1.134; AltName: Full=3-hydroxyacyl-CoA dehydratase 2; Short=HACD2; AltName: Full=Protein-tyrosine phosphatase-like member B;
FUNCTION: Responsible for the dehydration step in very long-chain fatty acids (VLCFAs) synthesis.
CATALYTIC ACTIVITY: A very-long-chain (3R)-3-hydroxyacyl-[acyl- carrier protein] = a very-long-chain trans-2,3-dehydroacyl-[acyl- carrier protein] + H(2)O.
SUBUNIT: Interacts with the condensation enzymes of the ELOVL family. Interacts with BCAP31.
INTERACTION: P51572:BCAP31; NbExp=4; IntAct=EBI-530257, EBI-77683;
SUBCELLULAR LOCATION: Endoplasmic reticulum membrane; Multi-pass membrane protein.
TISSUE SPECIFICITY: Highly expressed in testis, spleen, prostate, colon and heart, followed by moderate expression in thymus, ovary, small intestine, peripheral blood leukocytes, liver, skeletal muscle and pancreas. Weakly detected in kidney, placenta, brain and lung.
MISCELLANEOUS: Turns over rapidly through degradation by the proteasome system.
SIMILARITY: Belongs to the very long-chain fatty acids dehydratase HACD family.
CAUTION: Shares some similarity with tyrosine phosphatase proteins but it has probably no phosphatase activity.

-  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


+  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: 14.57 RPKM in Brain - Caudate (basal ganglia)
Total median expression: 401.81 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 -2.3026-0.088 Picture PostScript Text
3' UTR -842.493334-0.253 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
IPR007482 - Tyr_Pase-like_PTPLA

Pfam Domains:
PF04387 - Protein tyrosine phosphatase-like protein, PTPLA

ModBase Predicted Comparative 3D Structure on Q6Y1H2
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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 orthologNo orthologNo orthologNo orthologNo orthologGenome Browser
Gene DetailsGene Details Gene Details Gene Details
Gene SorterGene Sorter Gene Sorter Gene Sorter
 RGDEnsembl  SGD
     Protein Sequence
     Alignment

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0005515 protein binding
GO:0016829 lyase activity
GO:0018812 3-hydroxyacyl-CoA dehydratase activity
GO:0019899 enzyme binding
GO:0080023 3R-hydroxyacyl-CoA dehydratase activity
GO:0102344 3-hydroxy-behenoyl-CoA dehydratase activity
GO:0102345 3-hydroxy-lignoceroyl-CoA dehydratase activity
GO:0004725 protein tyrosine phosphatase activity

Biological Process:
GO:0006629 lipid metabolic process
GO:0006631 fatty acid metabolic process
GO:0006633 fatty acid biosynthetic process
GO:0030148 sphingolipid biosynthetic process
GO:0030497 fatty acid elongation
GO:0035338 long-chain fatty-acyl-CoA biosynthetic process
GO:0042761 very long-chain fatty acid biosynthetic process

Cellular Component:
GO:0005783 endoplasmic reticulum
GO:0005789 endoplasmic reticulum membrane
GO:0016020 membrane
GO:0016021 integral component of membrane
GO:0030176 integral component of endoplasmic reticulum membrane


-  Descriptions from all associated GenBank mRNAs
  BC060839 - Homo sapiens protein tyrosine phosphatase-like (proline instead of catalytic arginine), member b, mRNA (cDNA clone MGC:71739 IMAGE:5273705), complete cds.
BC049369 - Homo sapiens protein tyrosine phosphatase-like (proline instead of catalytic arginine), member b, mRNA (cDNA clone MGC:57203 IMAGE:5286864), complete cds.
AF052159 - Homo sapiens clone 24416 mRNA sequence.
AY191814 - Homo sapiens protein tyrosine phosphatase-like member b (PTPLB) mRNA, complete cds.
AL832532 - Homo sapiens mRNA; cDNA DKFZp547H0216 (from clone DKFZp547H0216).
JD082234 - Sequence 63258 from Patent EP1572962.
JD450985 - Sequence 432009 from Patent EP1572962.
JD265687 - Sequence 246711 from Patent EP1572962.
JD048878 - Sequence 29902 from Patent EP1572962.
JD305288 - Sequence 286312 from Patent EP1572962.
JD301426 - Sequence 282450 from Patent EP1572962.
JD088190 - Sequence 69214 from Patent EP1572962.
JD377497 - Sequence 358521 from Patent EP1572962.
JD454922 - Sequence 435946 from Patent EP1572962.
JD475700 - Sequence 456724 from Patent EP1572962.
JD075187 - Sequence 56211 from Patent EP1572962.
JD535761 - Sequence 516785 from Patent EP1572962.
JD300311 - Sequence 281335 from Patent EP1572962.
JD544319 - Sequence 525343 from Patent EP1572962.
AK074605 - Homo sapiens cDNA FLJ90124 fis, clone HEMBA1007241, moderately similar to Protein tyrosine phosphatase-like protein PTPLB.
AK125375 - Homo sapiens cDNA FLJ43385 fis, clone OCBBF2006151, highly similar to Mus musculus protein tyrosine phosphatase-like protein PTPLB (Ptplb) mRNA.
JD337394 - Sequence 318418 from Patent EP1572962.
JD337808 - Sequence 318832 from Patent EP1572962.
JD219352 - Sequence 200376 from Patent EP1572962.
JD466293 - Sequence 447317 from Patent EP1572962.
JD394318 - Sequence 375342 from Patent EP1572962.
AK289983 - Homo sapiens cDNA FLJ77861 complete cds.
JD474079 - Sequence 455103 from Patent EP1572962.
JD455802 - Sequence 436826 from Patent EP1572962.
JD455801 - Sequence 436825 from Patent EP1572962.
JD052890 - Sequence 33914 from Patent EP1572962.
JD304889 - Sequence 285913 from Patent EP1572962.
CU687458 - Synthetic construct Homo sapiens gateway clone IMAGE:100021127 5' read PTPLB mRNA.
KJ895804 - Synthetic construct Homo sapiens clone ccsbBroadEn_05198 PTPLB gene, encodes complete protein.
LF339082 - JP 2014500723-A/146585: Polycomb-Associated Non-Coding RNAs.
MA574659 - JP 2018138019-A/146585: Polycomb-Associated Non-Coding RNAs.
BC016990 - Homo sapiens protein tyrosine phosphatase-like (proline instead of catalytic arginine), member b, mRNA (cDNA clone IMAGE:4398482), partial cds.

-  Biochemical and Signaling Pathways
  Reactome (by CSHL, EBI, and GO)

Protein Q6Y1H2 (Reactome details) participates in the following event(s):

R-HSA-5676637 PTPLs dehydrate VLC3HA-CoA to VLCTDA-CoA
R-HSA-75876 Synthesis of very long-chain fatty acyl-CoAs
R-HSA-75105 Fatty acyl-CoA biosynthesis
R-HSA-8978868 Fatty acid metabolism
R-HSA-556833 Metabolism of lipids
R-HSA-1430728 Metabolism

-  Other Names for This Gene
  Alternate Gene Symbols: ENST00000383657.1, ENST00000383657.2, ENST00000383657.3, ENST00000383657.4, ENST00000383657.5, ENST00000383657.6, ENST00000383657.7, ENST00000383657.8, ENST00000383657.9, HACD2 , HACD2_HUMAN, NM_198402, PTPLB , Q6Y1H2, uc318rej.1, uc318rej.2
UCSC ID: ENST00000383657.10_7
RefSeq Accession: NM_198402.5
Protein: Q6Y1H2 (aka HACD2_HUMAN)

-  Gene Model Information
  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.