Human Gene NSL1 (uc001hjn.3)
  Description: Homo sapiens NSL1, MIND kinetochore complex component, homolog (S. cerevisiae) (NSL1), transcript variant 1, mRNA.
RefSeq Summary (NM_015471): This gene encodes a protein with two coiled-coil domains that localizes to kinetochores, which are chromosome-associated structures that attach to microtubules and mediate chromosome movements during cell division. The encoded protein is part of a conserved protein complex that includes two chromodomain-containing proteins and a component of the outer plate of the kinetochore. This protein complex is proposed to bridge centromeric heterochromatin with the outer kinetochore structure. Multiple transcript variants encoding different isoforms have been found for this gene. There is a pseudogene of the 3' UTR region of this gene on chromosome X. [provided by RefSeq, Jul 2014].
Transcript (Including UTRs)
   Position: hg19 chr1:212,899,495-212,965,139 Size: 65,645 Total Exon Count: 6 Strand: -
Coding Region
   Position: hg19 chr1:212,911,750-212,965,105 Size: 53,356 Coding Exon Count: 6 

Page IndexSequence and LinksUniProtKB CommentsPrimersGenetic AssociationsMalaCards
CTDGene AllelesRNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein Structure
Other SpeciesGO AnnotationsmRNA DescriptionsPathwaysOther NamesModel Information
Methods
Data last updated at UCSC: 2013-06-14

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr1:212,899,495-212,965,139)mRNA (may differ from genome)Protein (281 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
AlphaFoldBioGPSEnsemblEntrez GeneExonPrimerGeneCards
GeneNetworkH-INVHGNCHPRDLynxMalacards
MGIneXtProtOMIMPubMedReactomeTreefam
UniProtKBWikipediaBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: NSL1_HUMAN
DESCRIPTION: RecName: Full=Kinetochore-associated protein NSL1 homolog;
FUNCTION: Part of the MIS12 complex which is required for normal chromosome alignment and segregation and kinetochore formation during mitosis.
SUBUNIT: Component of the MIS12 complex composed of MIS12, DSN1, NSL1/DC8 and PMF1. Interacts with CASC5.
SUBCELLULAR LOCATION: Nucleus. Chromosome, centromere, kinetochore. Note=Associated with the kinetochore.
PTM: Phosphorylated upon DNA damage, probably by ATM or ATR.
SEQUENCE CAUTION: Sequence=AAF86877.1; Type=Frameshift; Positions=41;

-  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): NSL1
CDC HuGE Published Literature: NSL1

-  MalaCards Disease Associations
  MalaCards Gene Search: NSL1
Diseases sorted by gene-association score: malaria (1)

-  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: 7.80 RPKM in Brain - Spinal cord (cervical c-1)
Total median expression: 208.75 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 -1.0034-0.029 Picture PostScript Text
3' UTR -3935.0512255-0.321 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
IPR013950 - Kinetochore_Mis14

Pfam Domains:
PF08641 - Kinetochore protein Mis14 like

ModBase Predicted Comparative 3D Structure on Q96IY1
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 orthologGenome BrowserNo orthologNo orthologNo ortholog
Gene Details     
Gene Sorter     
  Ensembl   
  Protein Sequence   
  Alignment   

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

Biological Process:
GO:0000070 mitotic sister chromatid segregation
GO:0007049 cell cycle
GO:0007059 chromosome segregation
GO:0051301 cell division

Cellular Component:
GO:0000444 MIS12/MIND type complex
GO:0000775 chromosome, centromeric region
GO:0000776 kinetochore
GO:0000777 condensed chromosome kinetochore
GO:0005634 nucleus
GO:0005654 nucleoplasm
GO:0005694 chromosome
GO:0005829 cytosol
GO:0016607 nuclear speck


-  Descriptions from all associated GenBank mRNAs
  LF383673 - JP 2014500723-A/191176: Polycomb-Associated Non-Coding RNAs.
AK092359 - Homo sapiens cDNA FLJ35040 fis, clone OCBBF2017055.
AK124596 - Homo sapiens cDNA FLJ42605 fis, clone BRACE3012043.
DQ591768 - Homo sapiens piRNA piR-58880, complete sequence.
JD560738 - Sequence 541762 from Patent EP1572962.
JD352345 - Sequence 333369 from Patent EP1572962.
JD346372 - Sequence 327396 from Patent EP1572962.
JD311889 - Sequence 292913 from Patent EP1572962.
JD554462 - Sequence 535486 from Patent EP1572962.
JD425902 - Sequence 406926 from Patent EP1572962.
JD255762 - Sequence 236786 from Patent EP1572962.
JD135012 - Sequence 116036 from Patent EP1572962.
JD164384 - Sequence 145408 from Patent EP1572962.
JD481345 - Sequence 462369 from Patent EP1572962.
JD512688 - Sequence 493712 from Patent EP1572962.
JD412734 - Sequence 393758 from Patent EP1572962.
JD197778 - Sequence 178802 from Patent EP1572962.
JD311787 - Sequence 292811 from Patent EP1572962.
JD304116 - Sequence 285140 from Patent EP1572962.
JD304114 - Sequence 285138 from Patent EP1572962.
JD304115 - Sequence 285139 from Patent EP1572962.
JD339100 - Sequence 320124 from Patent EP1572962.
JD397047 - Sequence 378071 from Patent EP1572962.
JD311784 - Sequence 292808 from Patent EP1572962.
JD261009 - Sequence 242033 from Patent EP1572962.
JD105090 - Sequence 86114 from Patent EP1572962.
JD142460 - Sequence 123484 from Patent EP1572962.
JD256540 - Sequence 237564 from Patent EP1572962.
JD513918 - Sequence 494942 from Patent EP1572962.
JD379668 - Sequence 360692 from Patent EP1572962.
JD094116 - Sequence 75140 from Patent EP1572962.
JD379667 - Sequence 360691 from Patent EP1572962.
JD120558 - Sequence 101582 from Patent EP1572962.
JD120559 - Sequence 101583 from Patent EP1572962.
JD148683 - Sequence 129707 from Patent EP1572962.
JD414809 - Sequence 395833 from Patent EP1572962.
JD495785 - Sequence 476809 from Patent EP1572962.
AF255793 - Homo sapiens DC31 mRNA, complete cds.
AK223260 - Homo sapiens mRNA for chromosome 1 open reading frame 48 variant, clone: SYN01568.
AL050084 - Homo sapiens mRNA; cDNA DKFZp566O1646 (from clone DKFZp566O1646).
AF201941 - Homo sapiens DC8 (DC8) mRNA, complete cds.
BC007067 - Homo sapiens NSL1, MIND kinetochore complex component, homolog (S. cerevisiae), mRNA (cDNA clone MGC:12522 IMAGE:3997280), complete cds.
BC036048 - Homo sapiens, similar to DKFZP566O1646 protein, clone IMAGE:5273529, mRNA.
AK222996 - Homo sapiens mRNA for chromosome 1 open reading frame 48 variant, clone: HSI10556.
JD268544 - Sequence 249568 from Patent EP1572962.
AK303250 - Homo sapiens cDNA FLJ54215 complete cds.
JD130192 - Sequence 111216 from Patent EP1572962.
JD154472 - Sequence 135496 from Patent EP1572962.
AK313730 - Homo sapiens cDNA, FLJ94330.
KJ898572 - Synthetic construct Homo sapiens clone ccsbBroadEn_07966 NSL1 gene, encodes complete protein.
CU675531 - Synthetic construct Homo sapiens gateway clone IMAGE:100018713 5' read NSL1 mRNA.
DQ892899 - Synthetic construct clone IMAGE:100005529; FLH193414.01X; RZPDo839F1278D chromosome 1 open reading frame 48 (C1orf48) gene, encodes complete protein.
DQ896149 - Synthetic construct Homo sapiens clone IMAGE:100010609; FLH193410.01L; RZPDo839F1268D chromosome 1 open reading frame 48 (C1orf48) gene, encodes complete protein.
AB528354 - Synthetic construct DNA, clone: pF1KB6318, Homo sapiens NSL1 gene for NSL1, MIND kinetochore complex component, homolog, without stop codon, in Flexi system.
MA619250 - JP 2018138019-A/191176: Polycomb-Associated Non-Coding RNAs.

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

Protein Q96IY1 (Reactome details) participates in the following event(s):

R-HSA-141409 Mad1 binds kinetochore
R-HSA-375302 Kinetochore capture of astral microtubules
R-HSA-5666129 CDC42:GTP recruits DIAPH2-2 to kinetochores
R-HSA-5666169 Kinetochore capture of astral microtubules is positively regulated by CDC42:GTP:p-S196-DIAPH2-2
R-HSA-141431 MAD2 associates with the Mad1 kinetochore complex
R-HSA-141439 Release of activated MAD2 from kinetochores
R-HSA-2467811 Separation of sister chromatids
R-HSA-2467809 ESPL1 (Separase) cleaves centromeric cohesin
R-HSA-5666160 AURKB phosphorylates DIAPH2-2 at kinetochores
R-HSA-141422 MAD2 converted to an inhibitory state via interaction with Mad1
R-HSA-1638821 PP2A-B56 dephosphorylates centromeric cohesin
R-HSA-1638803 Phosphorylation of cohesin by PLK1 at centromeres
R-HSA-2468287 CDK1 phosphorylates CDCA5 (Sororin) at centromeres
R-HSA-141444 Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal
R-HSA-68877 Mitotic Prometaphase
R-HSA-5663220 RHO GTPases Activate Formins
R-HSA-2500257 Resolution of Sister Chromatid Cohesion
R-HSA-2467813 Separation of Sister Chromatids
R-HSA-141424 Amplification of signal from the kinetochores
R-HSA-68886 M Phase
R-HSA-195258 RHO GTPase Effectors
R-HSA-68882 Mitotic Anaphase
R-HSA-69618 Mitotic Spindle Checkpoint
R-HSA-69278 Cell Cycle (Mitotic)
R-HSA-194315 Signaling by Rho GTPases
R-HSA-2555396 Mitotic Metaphase and Anaphase
R-HSA-69620 Cell Cycle Checkpoints
R-HSA-1640170 Cell Cycle
R-HSA-162582 Signal Transduction

-  Other Names for This Gene
  Alternate Gene Symbols: C1orf48, DC31, DC8, MIS14, NM_015471, NP_056286, NSL1_HUMAN, Q5SY75, Q96IY1, Q9H2M5, Q9NRN8, Q9Y415
UCSC ID: uc001hjn.3
RefSeq Accession: NM_015471
Protein: Q96IY1 (aka NSL1_HUMAN)
CCDS: CCDS1509.1

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_015471.3
exon count: 6CDS single in 3' UTR: no RNA size: 13148
ORF size: 846CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 1892.00frame shift in genome: no % Coverage: 99.90
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.