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Lin54 lin-54 DREAM MuvB core complex component [ Rattus norvegicus (Norway rat) ]

Gene ID: 305171, updated on 2-Nov-2024

Summary

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Official Symbol
Lin54provided by RGD
Official Full Name
lin-54 DREAM MuvB core complex componentprovided by RGD
Primary source
RGD:1311361
See related
EnsemblRapid:ENSRNOG00000002203 AllianceGenome:RGD:1311361
Gene type
protein coding
RefSeq status
VALIDATED
Organism
Rattus norvegicus
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
Also known as
RGD1311361
Summary
Predicted to enable minor groove of adenine-thymine-rich DNA binding activity and transcription regulatory region nucleic acid binding activity. Predicted to be involved in regulation of DNA-templated transcription. Predicted to act upstream of or within nucleosome organization. Predicted to be part of RNA polymerase II transcription repressor complex. Predicted to be active in nucleus. Orthologous to human LIN54 (lin-54 DREAM MuvB core complex component). [provided by Alliance of Genome Resources, Nov 2024]
Expression
Biased expression in Thymus (RPKM 88.5), Spleen (RPKM 65.8) and 9 other tissues See more
Orthologs
human mouse all
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Genomic context

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See Lin54 in Genome Data Viewer
Location:
14p22
Exon count:
20
Annotation release Status Assembly Chr Location
RS_2024_02 current GRCr8 (GCF_036323735.1) 14 NC_086032.1 (9434093..9514091)
RS_2023_06 previous assembly mRatBN7.2 (GCF_015227675.2) 14 NC_051349.1 (9129775..9188244)
106 previous assembly Rnor_6.0 (GCF_000001895.5) 14 NC_005113.4 (10770072..10828115)

Chromosome 14 - NC_086032.1Genomic Context describing neighboring genes Neighboring gene COP9 signalosome subunit 4 Neighboring gene uncharacterized LOC102550950 Neighboring gene SEC31 homolog A, COPII coat complex component Neighboring gene transfer RNA serine (anticodon AGA) 37

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • Project title: A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages
  • Description: 320 RNA samples isolated from 11 organs (adrenal gland, brain, heart, kidney, liver, lung, muscle, spleen, thymus, and testes or uterus) from both sexes of Fischer 344 rats across four developmental stages (2-, 6-, 21-, and 104-weeks-old)
  • BioProject: PRJNA238328
  • Publication: PMID 24510058
  • Analysis date: Mon Jun 6 17:44:12 2016

Bibliography

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Related articles in PubMed

  1. Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. Strausberg RL, et al. Proc Natl Acad Sci U S A, 2002 Dec 24. PMID 12477932, Free PMC Article
  2. Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium. Gaudet P, et al. Brief Bioinform, 2011 Sep. PMID 21873635, Free PMC Article

GeneRIFs: Gene References Into Functions

Pathways from PubChem

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General gene information

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Markers

Homology

Gene Ontology Provided by RGD

Function Evidence Code Pubs
enables DNA binding IEA
Inferred from Electronic Annotation
more info
  
enables metal ion binding IEA
Inferred from Electronic Annotation
more info
  
enables minor groove of adenine-thymine-rich DNA binding IEA
Inferred from Electronic Annotation
more info
  
enables minor groove of adenine-thymine-rich DNA binding ISO
Inferred from Sequence Orthology
more info
  
enables transcription regulatory region nucleic acid binding IEA
Inferred from Electronic Annotation
more info
  
enables transcription regulatory region nucleic acid binding ISO
Inferred from Sequence Orthology
more info
  
Process Evidence Code Pubs
involved_in nucleosome organization IEA
Inferred from Electronic Annotation
more info
  
acts_upstream_of_or_within nucleosome organization ISO
Inferred from Sequence Orthology
more info
  
involved_in regulation of DNA-templated transcription IBA
Inferred from Biological aspect of Ancestor
more info
  
Component Evidence Code Pubs
part_of RNA polymerase II transcription repressor complex IEA
Inferred from Electronic Annotation
more info
  
part_of RNA polymerase II transcription repressor complex ISO
Inferred from Sequence Orthology
more info
  
is_active_in nucleus IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in nucleus IEA
Inferred from Electronic Annotation
more info
  

General protein information

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Preferred Names
protein 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_001100564.2 → NP_001094034.1  protein lin-54 homolog isoform 1

    See identical proteins and their annotated locations for NP_001094034.1

    Status: VALIDATED

    Source sequence(s)
    JAXUCZ010000014
    UniProtKB/Swiss-Prot
    Q4FZV6, Q641Z1
    UniProtKB/TrEMBL
    A0A8L2Q0T4, A6K5Z8
    Related
    ENSRNOP00000096414.2, ENSRNOT00000102075.2
    Conserved Domains (1) summary
    pfam03638
    Location:596 → 631
    TCR; Tesmin/TSO1-like CXC domain, cysteine-rich domain

  2. NM_001428575.1 → NP_001415504.1  protein lin-54 homolog isoform 2

    Status: VALIDATED

    Source sequence(s)
    JAXUCZ010000014
    UniProtKB/TrEMBL
    A0A8I6G8M1

  3. NM_001428576.1 → NP_001415505.1  protein lin-54 homolog isoform 3

    Status: VALIDATED

    Source sequence(s)
    JAXUCZ010000014
    UniProtKB/TrEMBL
    A6K600

  4. NM_001428577.1 → NP_001415506.1  protein lin-54 homolog isoform 4

    Status: VALIDATED

    Source sequence(s)
    JAXUCZ010000014
    UniProtKB/TrEMBL
    A0A8I5ZJ81

  5. NM_001428578.1 → NP_001415507.1  protein lin-54 homolog isoform 1

    Status: VALIDATED

    Source sequence(s)
    JAXUCZ010000014
    UniProtKB/Swiss-Prot
    Q4FZV6, Q641Z1
    UniProtKB/TrEMBL
    A6K5Z8

  6. NM_001428579.1 → NP_001415508.1  protein lin-54 homolog isoform 2

    Status: VALIDATED

    Source sequence(s)
    JAXUCZ010000014
    UniProtKB/TrEMBL
    A0A8I6G8M1

RefSeqs of Annotated Genomes: GCF_036323735.1-RS_2024_02

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

Reference GRCr8

Genomic

  1. NC_086032.1 Reference GRCr8

    Range
    9434093..9514091
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_006250658.5 → XP_006250720.1  protein lin-54 homolog isoform X2

    See identical proteins and their annotated locations for XP_006250720.1

    UniProtKB/Swiss-Prot
    Q4FZV6, Q641Z1
    UniProtKB/TrEMBL
    A0A8L2Q0T4, A6K5Z8
    Conserved Domains (1) summary
    pfam03638
    Location:596 → 631
    TCR; Tesmin/TSO1-like CXC domain, cysteine-rich domain

  2. XM_006250661.5 → XP_006250723.1  protein lin-54 homolog isoform X4

    UniProtKB/TrEMBL
    A0A8I6G8M1
    Conserved Domains (1) summary
    pfam03638
    Location:375 → 410
    TCR; Tesmin/TSO1-like CXC domain, cysteine-rich domain

  3. XM_006250657.5 → XP_006250719.1  protein lin-54 homolog isoform X1

    UniProtKB/TrEMBL
    A0A8I5ZJ81, A0A8L2Q0T4
    Related
    ENSRNOP00000083208.2, ENSRNOT00000119980.2
    Conserved Domains (1) summary
    pfam03638
    Location:614 → 649
    TCR; Tesmin/TSO1-like CXC domain, cysteine-rich domain

  4. XM_008770022.4 → XP_008768244.1  protein lin-54 homolog isoform X3

    Conserved Domains (1) summary
    pfam03638
    Location:393 → 428
    TCR; Tesmin/TSO1-like CXC domain, cysteine-rich domain

  5. XM_006250659.5 → XP_006250721.1  protein lin-54 homolog isoform X2

    See identical proteins and their annotated locations for XP_006250721.1

    UniProtKB/Swiss-Prot
    Q4FZV6, Q641Z1
    UniProtKB/TrEMBL
    A0A8L2Q0T4, A6K5Z8
    Conserved Domains (1) summary
    pfam03638
    Location:596 → 631
    TCR; Tesmin/TSO1-like CXC domain, cysteine-rich domain

  6. XM_017599168.3 → XP_017454657.1  protein lin-54 homolog isoform X4

    UniProtKB/TrEMBL
    A0A8I6G8M1
    Conserved Domains (1) summary
    pfam03638
    Location:375 → 410
    TCR; Tesmin/TSO1-like CXC domain, cysteine-rich domain

  7. XM_039091835.2 → XP_038947763.1  protein lin-54 homolog isoform X5

    UniProtKB/TrEMBL
    A6K600
    Conserved Domains (2) summary
    pfam03638
    Location:266 → 301
    TCR; Tesmin/TSO1-like CXC domain, cysteine-rich domain
    NF033645
    Location:4 → 172
    pilus_FilE; putative pilus assembly protein FilE
Nucleotide Protein Strain
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q641Z1.2 GenPept UniProtKB/Swiss-Prot:Q641Z1

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