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ICE2 interactor of little elongation complex ELL subunit 2 [ Homo sapiens (human) ]

Gene ID: 79664, updated on 5-Mar-2024

Summary

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Official Symbol
ICE2provided by HGNC
Official Full Name
interactor of little elongation complex ELL subunit 2provided by HGNC
Primary source
HGNC:HGNC:29885
See related
Ensembl:ENSG00000128915 MIM:610835; AllianceGenome:HGNC:29885
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
BRCC1; NARG2
Summary
This gene encodes a protein component of the little elongation complex (LEC), which plays a role in small nuclear RNA (snRNA) transcription. The LEC regulates snRNA transcription by enhancing both RNA Polymerase II occupancy and transcriptional elongation. The encoded protein and other LEC components have been shown to localize to Cajal bodies, which are sites of ribonucleoprotein (RNP) complex assembly. Pseudogenes of this gene have been identified on chromosomes 3 and 4. [provided by RefSeq, May 2017]
Expression
Ubiquitous expression in thyroid (RPKM 5.8), ovary (RPKM 4.5) and 25 other tissues See more
Orthologs
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Genomic context

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Location:
15q22.2
Exon count:
20
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 15 NC_000015.10 (60419609..60479142, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 15 NC_060939.1 (58222800..58282631, complement)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 15 NC_000015.9 (60711808..60771341, complement)

Chromosome 15 - NC_000015.10Genomic Context describing neighboring genes Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr15:60683199-60683790 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr15:60684938-60686137 Neighboring gene H3K27ac hESC enhancer GRCh37_chr15:60688531-60689122 Neighboring gene H3K27ac hESC enhancer GRCh37_chr15:60689123-60689714 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6494 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6495 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6496 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr15:60699237-60700436 Neighboring gene ribosomal protein L36a pseudogene 44 Neighboring gene annexin A2 Neighboring gene ribosomal protein S10 pseudogene 22 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9508 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr15:60770615-60771142 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9509 Neighboring gene RORA antisense RNA 1 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6497 Neighboring gene NANOG hESC enhancer GRCh37_chr15:60848032-60848533 Neighboring gene Sharpr-MPRA regulatory region 281 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr15:60868357-60868906 Neighboring gene NANOG hESC enhancer GRCh37_chr15:60872753-60873579 Neighboring gene RAR related orphan receptor A Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9510 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6498 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6499 Neighboring gene CYCS pseudogene 38 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:60912500-60913000 Neighboring gene uncharacterized LOC105370846 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:60927049-60927862 Neighboring gene NANOG hESC enhancer GRCh37_chr15:60942340-60942841 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6500 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9512

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. Gene expression and pathway analysis of CTNNB1 in cancer and stem cells. Tanabe S, et al. World J Stem Cells, 2016 Nov 26. PMID 27928465, Free PMC Article
  2. NARG2 encodes a novel nuclear protein with (S/T)PXX motifs that is expressed during development. Sugiura N, et al. Eur J Biochem, 2004 Dec. PMID 15606750
  3. p53 represses the transcription of snRNA genes by preventing the formation of little elongation complex. Anwar D, et al. Biochim Biophys Acta, 2016 Aug. PMID 27268141
  4. MED26 regulates the transcription of snRNA genes through the recruitment of little elongation complex. Takahashi H, et al. Nat Commun, 2015 Jan 9. PMID 25575120, Free PMC Article
  5. N-methyl-D-aspartate receptors regulate a group of transiently expressed genes in the developing brain. Sugiura N, et al. J Biol Chem, 2001 Apr 27. PMID 11297529

See all (34) citations in PubMed

GeneRIFs: Gene References Into Functions

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

Pathways from PubChem

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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 protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
Process Evidence Code Pubs
involved_in positive regulation of transcription by RNA polymerase III IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in positive regulation of transcription by RNA polymerase III IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in snRNA transcription by RNA polymerase II IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in snRNA transcription by RNA polymerase II IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in snRNA transcription by RNA polymerase III IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in snRNA transcription by RNA polymerase III IMP
Inferred from Mutant Phenotype
more info
 PubMed 
Component Evidence Code Pubs
located_in Cajal body IDA
Inferred from Direct Assay
more info
 PubMed 
located_in cytosol IDA
Inferred from Direct Assay
more info
  
part_of euchromatin IDA
Inferred from Direct Assay
more info
 PubMed 
located_in histone locus body IDA
Inferred from Direct Assay
more info
 PubMed 
located_in nuclear body IDA
Inferred from Direct Assay
more info
  
located_in nucleoplasm IDA
Inferred from Direct Assay
more info
  
located_in nucleoplasm TAS
Traceable Author Statement
more info
  
part_of transcription elongation factor complex IDA
Inferred from Direct Assay
more info
 PubMed 
part_of transcription elongation factor complex IMP
Inferred from Mutant Phenotype
more info
 PubMed 

General protein information

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Preferred Names
little elongation complex subunit 2
Names
NMDA receptor regulated 2
NMDA receptor-regulated gene 2
NMDA receptor-regulated protein 2
breast cancer cell 1
interactor of little elongator complex ELL subunit 2

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.

Genomic

  1. NG_054881.1 RefSeqGene

    Range
    5019..64552
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001018089.3 → NP_001018099.1  little elongation complex subunit 2 isoform b

    See identical proteins and their annotated locations for NP_001018099.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) uses an alternate splice site in its 5' UTR and initiates translation at a downstream in-frame start codon, compared to variant 1. The encoded isoform (b) is shorter at the N-terminus, compared to isoform a.
    Source sequence(s)
    AC087385, BU738348, BX647873, CN342776
    UniProtKB/Swiss-Prot
    Q659A1
    Conserved Domains (1) summary
    pfam10505
    Location:585 → 793
    NARG2_C; NMDA receptor-regulated gene protein 2 C-terminus

  2. NM_001276385.2 → NP_001263314.1  little elongation complex subunit 2 isoform c

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) lacks several 3' exons but includes an alternate 3' terminal exon, and it thus differs in the 3' coding region and 3' UTR, compared to variant 1. The encoded isoform (c) is significantly shorter and has a distinct C-terminus, compared to isoform a.
    Source sequence(s)
    AC087385, BC151844, CN342776
    Consensus CDS
    CCDS61657.1
    UniProtKB/TrEMBL
    H0YK97, H0YNU9
    Related
    ENSP00000454162.1, ENST00000561114.5

  3. NM_024611.6 → NP_078887.2  little elongation complex subunit 2 isoform a

    See identical proteins and their annotated locations for NP_078887.2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (a).
    Source sequence(s)
    AC087385, BC140894, BU738348, CN342776
    Consensus CDS
    CCDS10176.1
    UniProtKB/Swiss-Prot
    B2RU08, Q05CT1, Q3B7W6, Q63HP4, Q658Q0, Q659A1, Q68CN8, Q6IPW7, Q6UX23, Q71H65, Q96CY5, Q9HAA2
    Related
    ENSP00000261520.4, ENST00000261520.9
    Conserved Domains (1) summary
    pfam10505
    Location:722 → 930
    NARG2_C; NMDA receptor-regulated gene protein 2 C-terminus

RNA

  1. NR_147171.2 RNA Sequence

    Status: REVIEWED

    Description
    Transcript Variant: This variant (4) uses an alternate splice site and contains an alternate exon compared to variant 1. This variant is represented as non-coding because the use of the 5'-most expected translational start codon renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
    Source sequence(s)
    AC087385, BU738348
    Related
    ENST00000558181.5

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_000015.10 Reference GRCh38.p14 Primary Assembly

    Range
    60419609..60479142 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_011522009.3 → XP_011520311.1  little elongation complex subunit 2 isoform X1

    See identical proteins and their annotated locations for XP_011520311.1

    UniProtKB/Swiss-Prot
    B2RU08, Q05CT1, Q3B7W6, Q63HP4, Q658Q0, Q659A1, Q68CN8, Q6IPW7, Q6UX23, Q71H65, Q96CY5, Q9HAA2
    Conserved Domains (1) summary
    pfam10505
    Location:722 → 930
    NARG2_C; NMDA receptor-regulated gene protein 2 C-terminus

  2. XM_017022569.3 → XP_016878058.1  little elongation complex subunit 2 isoform X1

    UniProtKB/Swiss-Prot
    B2RU08, Q05CT1, Q3B7W6, Q63HP4, Q658Q0, Q659A1, Q68CN8, Q6IPW7, Q6UX23, Q71H65, Q96CY5, Q9HAA2
    Conserved Domains (1) summary
    pfam10505
    Location:722 → 930
    NARG2_C; NMDA receptor-regulated gene protein 2 C-terminus

  3. XM_047433030.1 → XP_047288986.1  little elongation complex subunit 2 isoform X3

  4. XM_047433029.1 → XP_047288985.1  little elongation complex subunit 2 isoform X2

  5. XM_047433028.1 → XP_047288984.1  little elongation complex subunit 2 isoform X2

  6. XM_047433027.1 → XP_047288983.1  little elongation complex subunit 2 isoform X2

  7. XM_047433031.1 → XP_047288987.1  little elongation complex subunit 2 isoform X4

  8. XM_047433032.1 → XP_047288988.1  little elongation complex subunit 2 isoform X4

  9. XM_047433033.1 → XP_047288989.1  little elongation complex subunit 2 isoform X5

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060939.1 Alternate T2T-CHM13v2.0

    Range
    58222800..58282631 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054378774.1 → XP_054234749.1  little elongation complex subunit 2 isoform X1

    UniProtKB/Swiss-Prot
    B2RU08, Q05CT1, Q3B7W6, Q63HP4, Q658Q0, Q659A1, Q68CN8, Q6IPW7, Q6UX23, Q71H65, Q96CY5, Q9HAA2

  2. XM_054378775.1 → XP_054234750.1  little elongation complex subunit 2 isoform X1

    UniProtKB/Swiss-Prot
    B2RU08, Q05CT1, Q3B7W6, Q63HP4, Q658Q0, Q659A1, Q68CN8, Q6IPW7, Q6UX23, Q71H65, Q96CY5, Q9HAA2

  3. XM_054378773.1 → XP_054234748.1  little elongation complex subunit 2 isoform X1

    UniProtKB/Swiss-Prot
    B2RU08, Q05CT1, Q3B7W6, Q63HP4, Q658Q0, Q659A1, Q68CN8, Q6IPW7, Q6UX23, Q71H65, Q96CY5, Q9HAA2

  4. XM_054378779.1 → XP_054234754.1  little elongation complex subunit 2 isoform X3

  5. XM_054378778.1 → XP_054234753.1  little elongation complex subunit 2 isoform X2

  6. XM_054378777.1 → XP_054234752.1  little elongation complex subunit 2 isoform X2

  7. XM_054378776.1 → XP_054234751.1  little elongation complex subunit 2 isoform X2

  8. XM_054378780.1 → XP_054234755.1  little elongation complex subunit 2 isoform X4

  9. XM_054378781.1 → XP_054234756.1  little elongation complex subunit 2 isoform X4

  10. XM_054378782.1 → XP_054234757.1  little elongation complex subunit 2 isoform X5

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q659A1.2 GenPept UniProtKB/Swiss-Prot:Q659A1

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