Human Gene MSL3 (ENST00000312196.10_10) from GENCODE V47lift37
  Description: MSL complex subunit 3, transcript variant 1 (from RefSeq NM_078629.4)
Gencode Transcript: ENST00000312196.10_10
Gencode Gene: ENSG00000005302.19_20
Transcript (Including UTRs)
   Position: hg19 chrX:11,776,356-11,793,891 Size: 17,536 Total Exon Count: 13 Strand: +
Coding Region
   Position: hg19 chrX:11,776,383-11,793,198 Size: 16,816 Coding Exon Count: 13 

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 (chrX:11,776,356-11,793,891)mRNA (may differ from genome)Protein (521 aa)
Gene SorterGenome BrowserOther Species FASTAGene interactionsTable SchemaAlphaFold
BioGPSEnsemblEntrez GeneExonPrimerGeneCardsHGNC
MGIOMIMPubMedReactomeUniProtKBBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: MS3L1_HUMAN
DESCRIPTION: RecName: Full=Male-specific lethal 3 homolog; AltName: Full=Male-specific lethal-3 homolog 1; AltName: Full=Male-specific lethal-3 protein-like 1; Short=MSL3-like 1;
FUNCTION: May be involved in chromatin remodeling and transcriptional regulation. May have a role in X inactivation. Component of the MSL complex which is responsible for the majority of histone H4 acetylation at 'Lys-16' which is implicated in the formation of higher-order chromatin structure. Specifically recognizes histone H4 monomethylated at 'Lys-20' (H4K20Me1) in a DNA-dependent manner and is proposed to be involved in chromosomal targeting of the MSL complex.
SUBUNIT: Component the MSL histone acetyltransferase complex at least composed of the MOF/KAT8, MSL1/hampin, MSL2 and MSL3.
SUBCELLULAR LOCATION: Nucleus (Probable).
TISSUE SPECIFICITY: Expressed in many tissues including liver, pancreas, heart, lung, kidney, skeletal muscle, brain, and placenta, with highest expression in skeletal muscle and heart.
MISCELLANEOUS: MSL3L1 gene undergoes X inactivation.
SIMILARITY: Contains 1 chromo domain.
SIMILARITY: Contains 1 MRG domain.

-  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: 25.91 RPKM in Cells - EBV-transformed lymphocytes
Total median expression: 346.75 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 -2.1027-0.078 Picture PostScript Text
3' UTR -197.20693-0.285 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
IPR000953 - Chromo_domain/shadow
IPR016197 - Chromodomain-like
IPR008676 - MRG
IPR026541 - MRG_dom
IPR025995 - Tudor-knot

Pfam Domains:
PF05712 - MRG
PF11717 - RNA binding activity-knot of a chromodomain

SCOP Domains:
54160 - Chromo domain-like

Protein Data Bank (PDB) 3-D Structure
MuPIT help
2Y0N - X-ray MuPIT 3OA6 - X-ray MuPIT 3OB9 - X-ray MuPIT


ModBase Predicted Comparative 3D Structure on Q8N5Y2
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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 orthologNo ortholog
Gene DetailsGene Details    
Gene SorterGene Sorter    
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-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0003677 DNA binding
GO:0035064 methylated histone binding

Biological Process:
GO:0006325 chromatin organization
GO:0006338 chromatin remodeling
GO:0006342 chromatin silencing
GO:0006351 transcription, DNA-templated
GO:0006355 regulation of transcription, DNA-templated
GO:0016575 histone deacetylation
GO:0043968 histone H2A acetylation
GO:0043984 histone H4-K16 acetylation

Cellular Component:
GO:0005634 nucleus
GO:0005654 nucleoplasm
GO:0035267 NuA4 histone acetyltransferase complex
GO:0072487 MSL complex


-  Descriptions from all associated GenBank mRNAs
  AF117065 - Homo sapiens male-specific lethal-3 homolog 1 (MSL3L1) mRNA, complete cds.
LF211731 - JP 2014500723-A/19234: Polycomb-Associated Non-Coding RNAs.
BC031210 - Homo sapiens male-specific lethal 3 homolog (Drosophila), mRNA (cDNA clone MGC:39484 IMAGE:5313214), complete cds.
BC010925 - Homo sapiens male-specific lethal 3-like 1 (Drosophila), mRNA (cDNA clone IMAGE:4251360), with apparent retained intron.
AK289780 - Homo sapiens cDNA FLJ76747 complete cds, highly similar to Homo sapiens male-specific lethal 3-like 1 (MSL3L1), transcript variant 4, mRNA.
BC017267 - Homo sapiens cDNA clone IMAGE:4584653, containing frame-shift errors.
AB463853 - Synthetic construct DNA, clone: pF1KB5983, Homo sapiens MSL3L1 gene for male-specific lethal 3-like 1protein, without stop codon, in Flexi system.
KJ898317 - Synthetic construct Homo sapiens clone ccsbBroadEn_07711 MSL3 gene, encodes complete protein.
DQ894848 - Synthetic construct Homo sapiens clone IMAGE:100009308; FLH179059.01L; RZPDo839C05129D male-specific lethal 3-like 1 (Drosophila) (MSL3L1) gene, encodes complete protein.
DQ891661 - Synthetic construct clone IMAGE:100004291; FLH179063.01X; RZPDo839C05130D male-specific lethal 3-like 1 (Drosophila) (MSL3L1) gene, encodes complete protein.
AK294255 - Homo sapiens cDNA FLJ61627 complete cds, highly similar to Male-specific lethal 3-like 1.
AK300814 - Homo sapiens cDNA FLJ56156 complete cds, highly similar to Male-specific lethal 3-like 1.
AK025642 - Homo sapiens cDNA: FLJ21989 fis, clone HEP06349, highly similar to AF117065 Homo sapiens male-specific lethal-3 homolog 1 (MSL3L1) mRNA.
LF383202 - JP 2014500723-A/190705: Polycomb-Associated Non-Coding RNAs.
JD382110 - Sequence 363134 from Patent EP1572962.
JD559844 - Sequence 540868 from Patent EP1572962.
AK304419 - Homo sapiens cDNA FLJ58883 complete cds, highly similar to Male-specific lethal 3-like 1.
LF383201 - JP 2014500723-A/190704: Polycomb-Associated Non-Coding RNAs.
LF383200 - JP 2014500723-A/190703: Polycomb-Associated Non-Coding RNAs.
JD098455 - Sequence 79479 from Patent EP1572962.
JD460181 - Sequence 441205 from Patent EP1572962.
JD397520 - Sequence 378544 from Patent EP1572962.
LF383198 - JP 2014500723-A/190701: Polycomb-Associated Non-Coding RNAs.
JD082829 - Sequence 63853 from Patent EP1572962.
JD328597 - Sequence 309621 from Patent EP1572962.
JD328598 - Sequence 309622 from Patent EP1572962.
JD043352 - Sequence 24376 from Patent EP1572962.
LF383197 - JP 2014500723-A/190700: Polycomb-Associated Non-Coding RNAs.
AK000793 - Homo sapiens cDNA FLJ20786 fis, clone COL02309, highly similar to AF117065 Homo sapiens male-specific lethal-3 homolog 1.
AL050178 - Homo sapiens mRNA; cDNA DKFZp586J1822 (from clone DKFZp586J1822); partial cds.
AL713667 - Homo sapiens mRNA; cDNA DKFZp586J1822 (from clone DKFZp586J1822).
LF383196 - JP 2014500723-A/190699: Polycomb-Associated Non-Coding RNAs.
LF383195 - JP 2014500723-A/190698: Polycomb-Associated Non-Coding RNAs.
JD270340 - Sequence 251364 from Patent EP1572962.
JD564739 - Sequence 545763 from Patent EP1572962.
JD113979 - Sequence 95003 from Patent EP1572962.
JD530327 - Sequence 511351 from Patent EP1572962.
MA618779 - JP 2018138019-A/190705: Polycomb-Associated Non-Coding RNAs.
MA618778 - JP 2018138019-A/190704: Polycomb-Associated Non-Coding RNAs.
MA618777 - JP 2018138019-A/190703: Polycomb-Associated Non-Coding RNAs.
MA618775 - JP 2018138019-A/190701: Polycomb-Associated Non-Coding RNAs.
MA618774 - JP 2018138019-A/190700: Polycomb-Associated Non-Coding RNAs.
MA618773 - JP 2018138019-A/190699: Polycomb-Associated Non-Coding RNAs.
MA618772 - JP 2018138019-A/190698: Polycomb-Associated Non-Coding RNAs.
MA447308 - JP 2018138019-A/19234: Polycomb-Associated Non-Coding RNAs.

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

Protein Q8N5Y2 (Reactome details) participates in the following event(s):

R-HSA-3321883 MSL acetylates histone H4
R-HSA-3214847 HATs acetylate histones
R-HSA-3247509 Chromatin modifying enzymes
R-HSA-4839726 Chromatin organization

-  Other Names for This Gene
  Alternate Gene Symbols: A6NCU2, A6NHW8, A8K165, B4DUV8, B7Z227, ENST00000312196.1, ENST00000312196.2, ENST00000312196.3, ENST00000312196.4, ENST00000312196.5, ENST00000312196.6, ENST00000312196.7, ENST00000312196.8, ENST00000312196.9, MS3L1_HUMAN, MSL3L1, NM_078629, Q8N5Y2, Q9UG70, Q9Y5Z8, uc317pec.1, uc317pec.2
UCSC ID: ENST00000312196.10_10
RefSeq Accession: NM_078629.4
Protein: Q8N5Y2 (aka MS3L1_HUMAN or M3L1_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.