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LIN54 lin-54 DREAM MuvB core complex component [ Homo sapiens (human) ]

Gene ID: 132660, updated on 23-Nov-2021

Summary

Official Symbol
LIN54provided by HGNC
Official Full Name
lin-54 DREAM MuvB core complex componentprovided by HGNC
Primary source
HGNC:HGNC:25397
See related
Ensembl:ENSG00000189308 MIM:613367
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
TCX1; JC8.6; CXCDC1; MIP120
Summary
LIN54 is a component of the LIN, or DREAM, complex, an essential regulator of cell cycle genes (Schmit et al., 2009 [PubMed 19725879]).[supplied by OMIM, Dec 2010]
Expression
Ubiquitous expression in thyroid (RPKM 5.1), esophagus (RPKM 4.0) and 25 other tissues See more
Orthologs
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Genomic context

See LIN54 in Genome Data Viewer
Location:
4q21.22
Exon count:
14
Annotation release Status Assembly Chr Location
109.20211119 current GRCh38.p13 (GCF_000001405.39) 4 NC_000004.12 (82924603..83012951, complement)
105.20201022 previous assembly GRCh37.p13 (GCF_000001405.25) 4 NC_000004.11 (83845756..83934094, complement)

Chromosome 4 - NC_000004.12Genomic Context describing neighboring genes Neighboring gene SEC31 homolog A, COPII coat complex component Neighboring gene THAP9 antisense RNA 1 Neighboring gene small nucleolar RNA, C/D box 144 Neighboring gene THAP domain containing 9 Neighboring gene RNA, U6 small nuclear 615, pseudogene Neighboring gene Sharpr-MPRA regulatory region 7954 Neighboring gene COP9 signalosome subunit 4 Neighboring gene placenta associated 8

Genomic regions, transcripts, and products

Expression

  • 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

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Pathways from PubChem

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Clone Names

  • MGC129905, DKFZp686L1814

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables metal ion binding IEA
Inferred from Electronic Annotation
more info
 
enables minor groove of adenine-thymine-rich DNA binding IDA
Inferred from Direct Assay
more info
PubMed 
enables protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
enables transcription regulatory region nucleic acid binding IDA
Inferred from Direct Assay
more info
PubMed 
Process Evidence Code Pubs
involved_in cell cycle IEA
Inferred from Electronic Annotation
more info
 
involved_in nucleosome positioning NAS
Non-traceable Author Statement
more info
PubMed 
involved_in regulation of transcription, DNA-templated IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
Component Evidence Code Pubs
located_in nucleoplasm TAS
Traceable Author Statement
more info
 
is_active_in nucleus IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 

General protein information

Preferred Names
protein lin-54 homolog
Names
CXC domain-containing protein 1
lin-54 homolog

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_001115007.3NP_001108479.1  protein lin-54 homolog isoform b

    See identical proteins and their annotated locations for NP_001108479.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (2) differs in the 5' UTR and uses an alternate in-frame splice site in the 5' coding region, compared to variant 1. Variants 2, 3 and 7 encode the same isoform (b) which is shorter than isoform a.
    Source sequence(s)
    AC021105
    Consensus CDS
    CCDS47089.1
    UniProtKB/Swiss-Prot
    Q6MZP7
    UniProtKB/TrEMBL
    Q7Z3G2
    Related
    ENSP00000421045.1, ENST00000510557.5
    Conserved Domains (2) summary
    pfam03154
    Location:5240
    Atrophin-1; Atrophin-1 family
    pfam03638
    Location:375410
    TCR; Tesmin/TSO1-like CXC domain, cysteine-rich domain
  2. NM_001115008.3NP_001108480.1  protein lin-54 homolog isoform b

    See identical proteins and their annotated locations for NP_001108480.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (3) uses an alternate in-frame splice site in the 5' coding region, compared to variant 1. Variants 2, 3 and 7 encode the same isoform (b) which is shorter than isoform a.
    Source sequence(s)
    AC021105
    Consensus CDS
    CCDS47089.1
    UniProtKB/Swiss-Prot
    Q6MZP7
    UniProtKB/TrEMBL
    Q7Z3G2
    Related
    ENSP00000398265.2, ENST00000442461.6
    Conserved Domains (2) summary
    pfam03154
    Location:5240
    Atrophin-1; Atrophin-1 family
    pfam03638
    Location:375410
    TCR; Tesmin/TSO1-like CXC domain, cysteine-rich domain
  3. NM_001288996.2NP_001275925.1  protein lin-54 homolog isoform c

    See identical proteins and their annotated locations for NP_001275925.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (4) lacks two consecutive alternate exons in the 5' coding region, compared to variant 1. It encodes isoform c, which lacks an internal in-frame segment and is shorter, compared to isoform a.
    Source sequence(s)
    AB111889, AC021105, AI208524, BC109278, BX108765, BX537919, BX640657, BX640966, CK819664, DC335927
    Consensus CDS
    CCDS75157.1
    UniProtKB/Swiss-Prot
    Q6MZP7
    UniProtKB/TrEMBL
    Q7Z3G2
    Related
    ENSP00000423475.1, ENST00000506560.5
    Conserved Domains (2) summary
    pfam03154
    Location:160432
    Atrophin-1; Atrophin-1 family
    pfam03638
    Location:507542
    TCR; Tesmin/TSO1-like CXC domain, cysteine-rich domain
  4. NM_001288997.1NP_001275926.1  protein lin-54 homolog isoform b

    See identical proteins and their annotated locations for NP_001275926.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (7) uses an alternate in-frame splice site in the 5' coding region, compared to variant 1. Variants 2, 3 and 7 encode the same isoform (b) which is shorter than isoform a.
    Source sequence(s)
    AB111889, AC021105, AI208524, BX108765, BX537919, BX640657, BX640966, CK819664, DC335927
    Consensus CDS
    CCDS47089.1
    UniProtKB/Swiss-Prot
    Q6MZP7
    UniProtKB/TrEMBL
    Q7Z3G2
    Related
    ENSP00000407139.2, ENST00000446851.6
    Conserved Domains (2) summary
    pfam03154
    Location:5240
    Atrophin-1; Atrophin-1 family
    pfam03638
    Location:375410
    TCR; Tesmin/TSO1-like CXC domain, cysteine-rich domain
  5. NM_194282.4NP_919258.2  protein lin-54 homolog isoform a

    See identical proteins and their annotated locations for NP_919258.2

    Status: VALIDATED

    Description
    Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (a).
    Source sequence(s)
    AC021105
    Consensus CDS
    CCDS3599.1
    UniProtKB/Swiss-Prot
    Q6MZP7
    UniProtKB/TrEMBL
    A0A024RDD8, Q7Z3G2
    Related
    ENSP00000341947.3, ENST00000340417.8
    Conserved Domains (2) summary
    pfam03154
    Location:211461
    Atrophin-1; Atrophin-1 family
    pfam03638
    Location:596631
    TCR; Tesmin/TSO1-like CXC domain, cysteine-rich domain

RNA

  1. NR_110253.2 RNA Sequence

    Status: VALIDATED

    Description
    Transcript Variant: This variant (5) lacks two internal exons compared to variant 1. This variant is represented as non-coding because the use of the 5'-most expected translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
    Source sequence(s)
    AB111889, AC021105, AI208524, BC109277, BX108765, BX537919, BX640657, BX640966, CK819664, DC335927
  2. NR_110254.2 RNA Sequence

    Status: VALIDATED

    Description
    Transcript Variant: This variant (6) uses an alternate splice site in the 5' region, compared to variant 1. This variant is represented as non-coding because the use of the 5'-most expected translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
    Source sequence(s)
    AC021105
    Related
    ENST00000510877.5

RefSeqs of Annotated Genomes: Homo sapiens Updated Annotation Release 109.20211119

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

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000004.12 Reference GRCh38.p13 Primary Assembly

    Range
    82924603..83012951 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_017007728.1XP_016863217.1  protein lin-54 homolog isoform X2

    UniProtKB/Swiss-Prot
    Q6MZP7
    Conserved Domains (2) summary
    pfam03154
    Location:160432
    Atrophin-1; Atrophin-1 family
    pfam03638
    Location:507542
    TCR; Tesmin/TSO1-like CXC domain, cysteine-rich domain
  2. XM_005262750.4XP_005262807.1  protein lin-54 homolog isoform X1

    See identical proteins and their annotated locations for XP_005262807.1

    UniProtKB/Swiss-Prot
    Q6MZP7
    UniProtKB/TrEMBL
    A0A024RDD8
    Related
    ENSP00000425844.1, ENST00000505397.1
    Conserved Domains (2) summary
    pfam03154
    Location:211461
    Atrophin-1; Atrophin-1 family
    pfam03638
    Location:596631
    TCR; Tesmin/TSO1-like CXC domain, cysteine-rich domain
  3. XM_006714081.3XP_006714144.1  protein lin-54 homolog isoform X1

    See identical proteins and their annotated locations for XP_006714144.1

    UniProtKB/Swiss-Prot
    Q6MZP7
    UniProtKB/TrEMBL
    A0A024RDD8
    Conserved Domains (2) summary
    pfam03154
    Location:211461
    Atrophin-1; Atrophin-1 family
    pfam03638
    Location:596631
    TCR; Tesmin/TSO1-like CXC domain, cysteine-rich domain
  4. XM_017007730.1XP_016863219.1  protein lin-54 homolog isoform X3

    UniProtKB/Swiss-Prot
    Q6MZP7
  5. XM_017007729.1XP_016863218.1  protein lin-54 homolog isoform X3

    UniProtKB/Swiss-Prot
    Q6MZP7
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