Human Gene NAA38 (ENST00000575771.6_7) from GENCODE V47lift37
  Description: N-alpha-acetyltransferase 38, NatC auxiliary subunit, transcript variant 3 (from RefSeq NM_001320925.4)
Gencode Transcript: ENST00000575771.6_7
Gencode Gene: ENSG00000183011.14_14
Transcript (Including UTRs)
   Position: hg19 chr17:7,760,003-7,760,877 Size: 875 Total Exon Count: 3 Strand: -
Coding Region
   Position: hg19 chr17:7,760,049-7,760,781 Size: 733 Coding Exon Count: 3 

Page IndexSequence and LinksUniProtKB CommentsPrimersCTDGene Alleles
RNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther SpeciesGO Annotations
mRNA DescriptionsPathwaysOther NamesModel InformationMethods
Data last updated at UCSC: 2024-08-22 23:36:26

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr17:7,760,003-7,760,877)mRNA (may differ from genome)Protein (125 aa)
Gene SorterGenome BrowserOther Species FASTAGene interactionsTable SchemaAlphaFold
BioGPSEnsemblEntrez GeneExonPrimerGeneCardsHGNC
MGIOMIMPubMedReactomeUniProtKBBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: LSMD1_HUMAN
DESCRIPTION: RecName: Full=LSM domain-containing protein 1; AltName: Full=Phosphonoformate immuno-associated protein 2;
FUNCTION: Component of the N-terminal acetyltransferase C (NatC) complex which may catalyze acetylation of N-terminal methionine residues.
SUBUNIT: Component of the N-terminal acetyltransferase C (NatC) complex, which is composed of NAA35, LSMD1 and NAA30.
SUBCELLULAR LOCATION: Cytoplasm. Nucleus.
SIMILARITY: Belongs to the snRNP Sm proteins 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


-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene           more ... click here to view the complete list

+  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: 40.12 RPKM in Testis
Total median expression: 848.88 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 -28.3096-0.295 Picture PostScript Text
3' UTR -1.6046-0.035 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
IPR010920 - LSM_dom
IPR001163 - Ribonucl_LSM
IPR006649 - Ribonucl_LSM_euk/arc

Pfam Domains:
PF01423 - LSM domain

SCOP Domains:
50182 - Sm-like ribonucleoproteins

ModBase Predicted Comparative 3D Structure on Q9BRA0
FrontTopSide
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 orthologNo ortholog
Gene DetailsGene Details    
Gene SorterGene Sorter    
 RGD    
      
      

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0005515 protein binding

Biological Process:
GO:0043066 negative regulation of apoptotic process

Cellular Component:
GO:0005634 nucleus
GO:0005737 cytoplasm
GO:0031417 NatC complex
GO:0005844 polysome


-  Descriptions from all associated GenBank mRNAs
  LF209129 - JP 2014500723-A/16632: Polycomb-Associated Non-Coding RNAs.
LF209127 - JP 2014500723-A/16630: Polycomb-Associated Non-Coding RNAs.
LF326329 - JP 2014500723-A/133832: Polycomb-Associated Non-Coding RNAs.
BC059944 - Homo sapiens LSM domain containing 1, mRNA (cDNA clone MGC:74837 IMAGE:5223785), complete cds.
BC006407 - Homo sapiens LSM domain containing 1, mRNA (cDNA clone MGC:14151 IMAGE:3690202), complete cds.
BC033861 - Homo sapiens LSM domain containing 1, mRNA (cDNA clone MGC:44900 IMAGE:5171094), complete cds.
BC051846 - Homo sapiens LSM domain containing 1, mRNA (cDNA clone MGC:60160 IMAGE:4476019), complete cds.
JD429235 - Sequence 410259 from Patent EP1572962.
KJ894981 - Synthetic construct Homo sapiens clone ccsbBroadEn_04375 LSMD1 gene, encodes complete protein.
KJ903414 - Synthetic construct Homo sapiens clone ccsbBroadEn_12808 LSMD1 gene, encodes complete protein.
KJ904915 - Synthetic construct Homo sapiens clone ccsbBroadEn_14309 LSMD1 gene, encodes complete protein.
AF530060 - Homo sapiens phosphonoformate immuno-associated protein 2 (PFAAP2) mRNA, complete cds.
DQ893290 - Synthetic construct Homo sapiens clone IMAGE:100005920; FLH263586.01X; RZPDo839B10154D LSM domain containing 1 (LSMD1) gene, encodes complete protein.
DQ893319 - Synthetic construct clone IMAGE:100005949; FLH196132.01X; RZPDo839D12154D LSM domain containing 1 (LSMD1) gene, encodes complete protein.
DQ896634 - Synthetic construct Homo sapiens clone IMAGE:100011094; FLH196128.01L; RZPDo839D12153D LSM domain containing 1 (LSMD1) gene, encodes complete protein.
CU687386 - Synthetic construct Homo sapiens gateway clone IMAGE:100021564 5' read LSMD1 mRNA.
LF326328 - JP 2014500723-A/133831: Polycomb-Associated Non-Coding RNAs.
LF326327 - JP 2014500723-A/133830: Polycomb-Associated Non-Coding RNAs.
MA561906 - JP 2018138019-A/133832: Polycomb-Associated Non-Coding RNAs.
MA561905 - JP 2018138019-A/133831: Polycomb-Associated Non-Coding RNAs.
MA561904 - JP 2018138019-A/133830: Polycomb-Associated Non-Coding RNAs.
MA444706 - JP 2018138019-A/16632: Polycomb-Associated Non-Coding RNAs.
MA444704 - JP 2018138019-A/16630: Polycomb-Associated Non-Coding RNAs.

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

Protein Q9BRA0 (Reactome details) participates in the following event(s):

R-HSA-6814090 NatC acetylates ARFFRP1
R-HSA-6811440 Retrograde transport at the Trans-Golgi-Network
R-HSA-6811442 Intra-Golgi and retrograde Golgi-to-ER traffic
R-HSA-199991 Membrane Trafficking
R-HSA-5653656 Vesicle-mediated transport

-  Other Names for This Gene
  Alternate Gene Symbols: ENST00000575771.1, ENST00000575771.2, ENST00000575771.3, ENST00000575771.4, ENST00000575771.5, LSMD1, LSMD1_HUMAN, MAK31, NM_001320925, PFAAP2, Q8N4M0, Q9BRA0, uc326eat.1, uc326eat.2
UCSC ID: ENST00000575771.6_7
RefSeq Accession: NM_001320925.4
Protein: Q9BRA0 (aka LSMD1_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.