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NIF3L1 NGG1 interacting factor 3 like 1 [ Homo sapiens (human) ]

Gene ID: 60491, updated on 7-Apr-2024

Summary

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Official Symbol
NIF3L1provided by HGNC
Official Full Name
NGG1 interacting factor 3 like 1provided by HGNC
Primary source
HGNC:HGNC:13390
See related
Ensembl:ENSG00000196290 MIM:605778; AllianceGenome:HGNC:13390
Gene type
protein coding
RefSeq status
VALIDATED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
CALS-7; MDS015; ALS2CR1
Summary
Enables identical protein binding activity. Involved in positive regulation of transcription, DNA-templated. Located in cytoplasm. [provided by Alliance of Genome Resources, Apr 2022]
Expression
Ubiquitous expression in lymph node (RPKM 6.5), testis (RPKM 6.0) and 25 other tissues See more
Orthologs
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Genomic context

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Location:
2q33.1
Exon count:
8
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 2 NC_000002.12 (200889327..200903932)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 2 NC_060926.1 (201372777..201387382)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 2 NC_000002.11 (201754050..201768655)

Chromosome 2 - NC_000002.12Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16963 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16964 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16965 Neighboring gene CDC like kinase 1 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr2:201753436-201754635 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16968 Neighboring gene RNA, U6 small nuclear 312, pseudogene Neighboring gene peptidylprolyl isomerase like 3 Neighboring gene RNA, U6 small nuclear 762, pseudogene Neighboring gene origin recognition complex subunit 2 Neighboring gene OCT4 hESC enhancer GRCh37_chr2:201799831-201800332 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16969 Neighboring gene uncharacterized LOC105373835 Neighboring gene ReSE screen-validated silencer GRCh37_chr2:201828394-201828792 Neighboring gene hyccin PI4KA lipid kinase complex subunit 2 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16970 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr2:201907391-201907902 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr2:201907903-201908415 Neighboring gene heterogeneous nuclear ribonucleoprotein A1 pseudogene 35

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • Project title: HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

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Related articles in PubMed

  1. The role of transcriptional corepressor Nif3l1 in early stage of neural differentiation via cooperation with Trip15/CSN2. Akiyama H, et al. J Biol Chem, 2003 Mar 21. PMID 12522100
  2. Identification and characterization of NIF3L1 BP1, a novel cytoplasmic interaction partner of the NIF3L1 protein. Tascou S, et al. Biochem Biophys Res Commun, 2003 Sep 19. PMID 12951069
  3. Cloning and characterization of three novel genes, ALS2CR1, ALS2CR2, and ALS2CR3, in the juvenile amyotrophic lateral sclerosis (ALS2) critical region at chromosome 2q33-q34: candidate genes for ALS2. Hadano S, et al. Genomics, 2001 Jan 15. PMID 11161814
  4. The subcellular localization of the ChoRE-binding protein, encoded by the Williams-Beuren syndrome critical region gene 14, is regulated by 14-3-3. Merla G, et al. Hum Mol Genet, 2004 Jul 15. PMID 15163635
  5. Host-pathogen interactome mapping for HTLV-1 and -2 retroviruses. Simonis N, et al. Retrovirology, 2012 Mar 29. PMID 22458338, Free PMC Article

See all (36) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Observational study of gene-disease association. (HuGE Navigator)
    Title: Genetic variants in nuclear-encoded mitochondrial genes influence AIDS progression.
Submit: New GeneRIF Correction

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Genotypes

Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables RNA polymerase II-specific DNA-binding transcription factor binding IPI
Inferred from Physical Interaction
more info
 PubMed 
enables identical protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
Process Evidence Code Pubs
involved_in negative regulation of transcription by RNA polymerase II ISS
Inferred from Sequence or Structural Similarity
more info
  
involved_in neuron differentiation ISS
Inferred from Sequence or Structural Similarity
more info
  
involved_in positive regulation of DNA-templated transcription IDA
Inferred from Direct Assay
more info
 PubMed 
Component Evidence Code Pubs
is_active_in cytoplasm IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in cytoplasm IDA
Inferred from Direct Assay
more info
 PubMed 
is_active_in mitochondrion IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in nucleus ISS
Inferred from Sequence or Structural Similarity
more info
  

General protein information

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Preferred Names
NIF3-like protein 1
Names
GTP cyclohydrolase I
NIF3 (Ngg1 interacting factor 3, S.pombe homolog)-like 1
NIF3 NGG1 interacting factor 3-like 1
amyotrophic lateral sclerosis 2 (juvenile) chromosome region, candidate 1
amyotrophic lateral sclerosis 2 chromosomal region candidate gene 1 protein
putative GTP cyclohydrolase 1 type 2 NIF3L1
NP_001129511.1
NP_001135827.1
NP_001135828.1
NP_001356370.1
NP_001356371.1
NP_001356372.1
NP_001356373.1
NP_001356374.1
NP_068596.2
XP_047301327.1
XP_047301328.1
XP_054199248.1
XP_054199249.1

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

mRNA and Protein(s)

  1. NM_001136039.2 → NP_001129511.1  NIF3-like protein 1 isoform 1

    See identical proteins and their annotated locations for NP_001129511.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (1) encodes the longest isoform (1).
    Source sequence(s)
    AF283538, BM974977, BP194872
    Consensus CDS
    CCDS46485.1
    UniProtKB/Swiss-Prot
    Q53TX4, Q6X735, Q9GZT8, Q9H2D2, Q9HC18
    UniProtKB/TrEMBL
    Q658J0
    Conserved Domains (1) summary
    pfam01784
    Location:33 → 354
    NIF3; NIF3 (NGG1p interacting factor 3)

  2. NM_001142355.1 → NP_001135827.1  NIF3-like protein 1 isoform 2

    See identical proteins and their annotated locations for NP_001135827.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (3) differs in the 5' UTR and uses a downstream in-frame translation initiation codon, compared to variant 1. The resulting isoform (2) is shorter at the N-terminus, compared to isoform 1. Both variants 2 and 3 encode the same isoform.
    Source sequence(s)
    AF060513, BM974977, BP194872
    Consensus CDS
    CCDS42797.1
    UniProtKB/TrEMBL
    Q658J0
    Conserved Domains (1) summary
    pfam01784
    Location:6 → 327
    NIF3; NIF3 (NGG1p interacting factor 3)

  3. NM_001142356.1 → NP_001135828.1  NIF3-like protein 1 isoform 3

    See identical proteins and their annotated locations for NP_001135828.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (4) differs in the 5' UTR and lacks an alternate exon in the 3' coding region, compared to variant 1, resulting in a frameshift. The encoded isoform (3) has a distinct C-terminus and is shorter than isoform 1.
    Source sequence(s)
    AY251943, BM974977
    Consensus CDS
    CCDS46486.1
    UniProtKB/TrEMBL
    Q6X734
    Related
    ENSP00000387021.1, ENST00000409588.1
    Conserved Domains (1) summary
    pfam01784
    Location:33 → 196
    NIF3; NIF3 (NGG1p interacting factor 3)

  4. NM_001369441.2 → NP_001356370.1  NIF3-like protein 1 isoform 1

    Status: VALIDATED

    Source sequence(s)
    AC005037
    Consensus CDS
    CCDS46485.1
    UniProtKB/Swiss-Prot
    Q53TX4, Q6X735, Q9GZT8, Q9H2D2, Q9HC18
    UniProtKB/TrEMBL
    Q658J0
    Related
    ENSP00000386394.1, ENST00000409020.6
    Conserved Domains (1) summary
    pfam01784
    Location:33 → 354
    NIF3; NIF3 (NGG1p interacting factor 3)

  5. NM_001369442.1 → NP_001356371.1  NIF3-like protein 1 isoform 1

    Status: VALIDATED

    Source sequence(s)
    AC005037
    Consensus CDS
    CCDS46485.1
    UniProtKB/Swiss-Prot
    Q53TX4, Q6X735, Q9GZT8, Q9H2D2, Q9HC18
    UniProtKB/TrEMBL
    Q658J0
    Conserved Domains (1) summary
    pfam01784
    Location:33 → 354
    NIF3; NIF3 (NGG1p interacting factor 3)

  6. NM_001369443.1 → NP_001356372.1  NIF3-like protein 1 isoform 2

    Status: VALIDATED

    Source sequence(s)
    AC005037
    Consensus CDS
    CCDS42797.1
    UniProtKB/TrEMBL
    Q658J0
    Conserved Domains (1) summary
    pfam01784
    Location:6 → 327
    NIF3; NIF3 (NGG1p interacting factor 3)

  7. NM_001369444.1 → NP_001356373.1  NIF3-like protein 1 isoform 1

    Status: VALIDATED

    Source sequence(s)
    AC005037
    Consensus CDS
    CCDS46485.1
    UniProtKB/Swiss-Prot
    Q53TX4, Q6X735, Q9GZT8, Q9H2D2, Q9HC18
    UniProtKB/TrEMBL
    Q658J0
    Conserved Domains (1) summary
    pfam01784
    Location:33 → 354
    NIF3; NIF3 (NGG1p interacting factor 3)

  8. NM_001369445.2 → NP_001356374.1  NIF3-like protein 1 isoform 1

    Status: VALIDATED

    Source sequence(s)
    AC005037
    Consensus CDS
    CCDS46485.1
    UniProtKB/Swiss-Prot
    Q53TX4, Q6X735, Q9GZT8, Q9H2D2, Q9HC18
    UniProtKB/TrEMBL
    Q658J0
    Conserved Domains (1) summary
    pfam01784
    Location:33 → 354
    NIF3; NIF3 (NGG1p interacting factor 3)

  9. NM_021824.3 → NP_068596.2  NIF3-like protein 1 isoform 2

    See identical proteins and their annotated locations for NP_068596.2

    Status: VALIDATED

    Description
    Transcript Variant: This variant (2) differs in the 5' UTR and uses a downstream in-frame translation initiation codon, compared to variant 1. The resulting isoform (2) is shorter at the N-terminus, compared to isoform 1. Both variants 2 and 3 encode the same isoform.
    Source sequence(s)
    AB038949, BG724012, BM974977
    Consensus CDS
    CCDS42797.1
    UniProtKB/TrEMBL
    Q658J0
    Related
    ENSP00000352711.4, ENST00000359683.8
    Conserved Domains (1) summary
    pfam01784
    Location:6 → 327
    NIF3; NIF3 (NGG1p interacting factor 3)

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000002.12 Reference GRCh38.p14 Primary Assembly

    Range
    200889327..200903932
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_047445371.1 → XP_047301327.1  NIF3-like protein 1 isoform X1

    UniProtKB/Swiss-Prot
    Q53TX4, Q6X735, Q9GZT8, Q9H2D2, Q9HC18

  2. XM_047445372.1 → XP_047301328.1  NIF3-like protein 1 isoform X1

    UniProtKB/Swiss-Prot
    Q53TX4, Q6X735, Q9GZT8, Q9H2D2, Q9HC18

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060926.1 Alternate T2T-CHM13v2.0

    Range
    201372777..201387382
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054343274.1 → XP_054199249.1  NIF3-like protein 1 isoform X1

    UniProtKB/Swiss-Prot
    Q53TX4, Q6X735, Q9GZT8, Q9H2D2, Q9HC18

  2. XM_054343273.1 → XP_054199248.1  NIF3-like protein 1 isoform X1

    UniProtKB/Swiss-Prot
    Q53TX4, Q6X735, Q9GZT8, Q9H2D2, Q9HC18
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q9GZT8.2 GenPept UniProtKB/Swiss-Prot:Q9GZT8

Gene LinkOut

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