Human Gene NIF3L1 (uc002uwm.2) Description and Page Index
  Description: Homo sapiens NIF3 NGG1 interacting factor 3-like 1 (S. cerevisiae) (NIF3L1), transcript variant 1, mRNA.
Transcript (Including UTRs)
   Position: hg19 chr2:201,754,050-201,768,655 Size: 14,606 Total Exon Count: 7 Strand: +
Coding Region
   Position: hg19 chr2:201,756,667-201,768,401 Size: 11,735 Coding Exon Count: 6 

Page IndexSequence and LinksUniProtKB CommentsGenetic AssociationsMalaCardsCTD
Gene AllelesRNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther Species
GO AnnotationsmRNA DescriptionsOther NamesModel InformationMethods
Data last updated: 2013-06-14

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr2:201,754,050-201,768,655)mRNA (may differ from genome)Protein (377 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
BioGPSCGAPEnsemblEntrez GeneExonPrimerGeneCards
GeneNetworkH-INVHGNCLynxMGIneXtProt
OMIMPubMedStanford SOURCEUniProtKBWikipedia

-  Comments and Description Text from UniProtKB
  ID: NIF3L_HUMAN
DESCRIPTION: RecName: Full=NIF3-like protein 1; AltName: Full=Amyotrophic lateral sclerosis 2 chromosomal region candidate gene 1 protein;
SUBUNIT: Homodimer. Interacts with COPS2 (By similarity). Interacts with THOC7.
INTERACTION: Q8N7W2:BEND7; NbExp=3; IntAct=EBI-740897, EBI-743382; P49366:DHPS; NbExp=3; IntAct=EBI-740897, EBI-741925; Q9UI14:RABAC1; NbExp=3; IntAct=EBI-740897, EBI-712367; Q15645:TRIP13; NbExp=3; IntAct=EBI-740897, EBI-358993;
SUBCELLULAR LOCATION: Cytoplasm.
SIMILARITY: Belongs to the UPF0135 (NIF3) family.
SEQUENCE CAUTION: Sequence=AAG14952.1; Type=Frameshift; Positions=104, 109;

-  Genetic Association Studies of Complex Diseases and Disorders
  Genetic Association Database (archive): NIF3L1
CDC HuGE Published Literature: NIF3L1

-  MalaCards Disease Associations
  MalaCards Gene Search: NIF3L1
Diseases sorted by gene-association score: juvenile amyotrophic lateral sclerosis (2)

-  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: 13.47 RPKM in Cells - EBV-transformed lymphocytes
Total median expression: 399.59 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 -22.1091-0.243 Picture PostScript Text
3' UTR -45.10254-0.178 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
IPR002678 - Interacting_NIF3
IPR017222 - UCP037490_NIF3_euk

Pfam Domains:
PF01784 - NIF3 (NGG1p interacting factor 3)

SCOP Domains:
102705 - NIF3 (NGG1p interacting factor 3)-like

ModBase Predicted Comparative 3D Structure on Q9GZT8
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 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:0005515 protein binding
GO:0008134 transcription factor binding
GO:0042802 identical protein binding

Biological Process:
GO:0030182 neuron differentiation
GO:0045893 positive regulation of transcription, DNA-templated
GO:1903507 negative regulation of nucleic acid-templated transcription

Cellular Component:
GO:0005634 nucleus
GO:0005737 cytoplasm
GO:0005739 mitochondrion


-  Descriptions from all associated GenBank mRNAs
  AF060513 - Homo sapiens clone 016d06 My018 protein mRNA, complete cds.
AF283538 - Homo sapiens NIF3L1 protein mRNA, complete cds.
AK314709 - Homo sapiens cDNA, FLJ95566.
AK225905 - Homo sapiens mRNA for NIF3 NGG1 interacting factor 3-like 1 variant, clone: FCC119H02.
AB038949 - Homo sapiens ALS2CR1 mRNA for amyotrophic lateral sclerosis 2, candidate 1, complete cds.
AK023378 - Homo sapiens cDNA FLJ13316 fis, clone OVARC1001555, weakly similar to NGG1-INTERACTING FACTOR 3.
AF182416 - Homo sapiens MDS015 (MDS015) mRNA, complete cds.
AY251943 - Homo sapiens NIF3L1 isoform beta (NIF3L1) mRNA, complete cds.
AY251944 - Homo sapiens NIF3L1 isoform gamma (NIF3L1) mRNA, complete cds.
BC007654 - Homo sapiens NIF3 NGG1 interacting factor 3-like 1 (S. pombe), mRNA (cDNA clone MGC:2595 IMAGE:3346099), complete cds.
CU675739 - Synthetic construct Homo sapiens gateway clone IMAGE:100019149 5' read NIF3L1 mRNA.
DQ896612 - Synthetic construct Homo sapiens clone IMAGE:100011072; FLH195910.01L; RZPDo839H08151D NIF3 NGG1 interacting factor 3-like 1 (S. pombe) (NIF3L1) gene, encodes complete protein.
KJ894496 - Synthetic construct Homo sapiens clone ccsbBroadEn_03890 NIF3L1 gene, encodes complete protein.
AB463931 - Synthetic construct DNA, clone: pF1KB6454, Homo sapiens NIF3L1 gene for NIF3 NGG1 interacting factor 3-like 1, without stop codon, in Flexi system.
AL834430 - Homo sapiens mRNA; cDNA DKFZp762L015 (from clone DKFZp762L015).
AK125652 - Homo sapiens cDNA FLJ43664 fis, clone SYNOV4006256.
JD052286 - Sequence 33310 from Patent EP1572962.
JD382447 - Sequence 363471 from Patent EP1572962.

-  Other Names for This Gene
  Alternate Gene Symbols: ALS2CR1, MDS015, My018, NIF3L_HUMAN, NM_001136039, NP_001129511, Q53TX4, Q6X735, Q9GZT8, Q9H2D2, Q9HC18
UCSC ID: uc002uwm.2
RefSeq Accession: NM_001136039
Protein: Q9GZT8 (aka NIF3L_HUMAN or NF3L_HUMAN)
CCDS: CCDS46485.1

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_001136039.2
exon count: 7CDS single in 3' UTR: no RNA size: 1497
ORF size: 1134CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 2368.00frame shift in genome: no % Coverage: 98.80
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.