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6030458C11Rik RIKEN cDNA 6030458C11 gene [ Mus musculus (house mouse) ]

Gene ID: 77877, updated on 5-Mar-2024

Summary

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Official Symbol
6030458C11Rikprovided by MGI
Official Full Name
RIKEN cDNA 6030458C11 geneprovided by MGI
Primary source
MGI:MGI:1925127
See related
Ensembl:ENSMUSG00000022195 AllianceGenome:MGI:1925127
Gene type
protein coding
RefSeq status
VALIDATED
Organism
Mus musculus
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Mus; Mus
Summary
Orthologous to human C5orf22 (chromosome 5 open reading frame 22). [provided by Alliance of Genome Resources, Apr 2022]
Expression
Ubiquitous expression in liver E14 (RPKM 7.9), liver E14.5 (RPKM 7.7) and 28 other tissues See more
Orthologs
human all
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Genomic context

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Location:
15 A1; 15 5.98 cM
Exon count:
11
Annotation release Status Assembly Chr Location
RS_2024_02 current GRCm39 (GCF_000001635.27) 15 NC_000081.7 (12806012..12824767, complement)
108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) 15 NC_000081.6 (12808177..12824679, complement)

Chromosome 15 - NC_000081.7Genomic Context describing neighboring genes Neighboring gene predicted gene, 17756 Neighboring gene STARR-positive B cell enhancer ABC_E4128 Neighboring gene CapStarr-seq enhancer MGSCv37_chr15:12754551-12754660 Neighboring gene CapStarr-seq enhancer MGSCv37_chr15:12754713-12754896 Neighboring gene predicted gene, 41274 Neighboring gene STARR-seq mESC enhancer starr_38037 Neighboring gene drosha, ribonuclease type III Neighboring gene STARR-seq mESC enhancer starr_38041 Neighboring gene STARR-seq mESC enhancer starr_38042 Neighboring gene cadherin 6 Neighboring gene STARR-seq mESC enhancer starr_38043 Neighboring gene predicted gene, 35018

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • Project title: Mouse ENCODE transcriptome data
  • Description: RNA profiling data sets generated by the Mouse ENCODE project.
  • BioProject: PRJNA66167
  • Publication: PMID 25409824
  • Analysis date: n/a

Bibliography

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Related articles in PubMed

  1. Targeting a complex transcriptome: the construction of the mouse full-length cDNA encyclopedia. Carninci P, et al. Genome Res, 2003 Jun. PMID 12819125, Free PMC Article
  2. Database resources of the National Center for Biotechnology Information. Wheeler DL, et al. Nucleic Acids Res, 2001 Jan 1. PMID 11125038, Free PMC Article
  3. EUCOMM--the European conditional mouse mutagenesis program. Friedel RH, et al. Brief Funct Genomic Proteomic, 2007 Sep. PMID 17967808
  4. Libraries enriched for alternatively spliced exons reveal splicing patterns in melanocytes and melanomas. Watahiki A, et al. Nat Methods, 2004 Dec. PMID 15782199
  5. Large-scale gene trapping in C57BL/6N mouse embryonic stem cells. Hansen GM, et al. Genome Res, 2008 Oct. PMID 18799693, Free PMC Article

See all (16) citations in PubMed

GeneRIFs: Gene References Into Functions

Variation

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Alleles

Alleles of this type are documented at Mouse Genome Informatics  (MGI)
  • Endonuclease-mediated (1) 

General gene information

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Markers

Homology

Clone Names

  • MGC118638

Gene Ontology Provided by MGI

Function Evidence Code Pubs
enables molecular_function ND
No biological Data available
more info
  
Process Evidence Code Pubs
involved_in biological_process ND
No biological Data available
more info
  
Component Evidence Code Pubs
is_active_in cellular_component ND
No biological Data available
more info
  

General protein information

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Preferred Names
UPF0489 protein C5orf22 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_001166360.2 → NP_001159832.1  UPF0489 protein C5orf22 homolog isoform a

    See identical proteins and their annotated locations for NP_001159832.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (1) contains a distinct 3' UTR and lacks most of the 3' coding region, compared to variant 1. These differences result in a protein (isoform a) with a shorter C-terminus, compared to isoform b.
    Source sequence(s)
    AC133189
    UniProtKB/Swiss-Prot
    Q8BGC1
    Related
    ENSMUST00000228888.2
    Conserved Domains (1) summary
    pfam12640
    Location:19 → 104
    UPF0489; UPF0489 domain

  2. NM_001357761.2 → NP_001344690.1  UPF0489 protein C5orf22 homolog isoform c

    Status: VALIDATED

    Description
    Transcript Variant: This variant (3) lacks an alternate in-frame exon in the 5' coding region and uses a downstream start codon compared to variant 2. It encodes isoform c which has a shorter N-terminus compared to isoform b.
    Source sequence(s)
    AC133189
    Consensus CDS
    CCDS88737.1
    UniProtKB/TrEMBL
    A0A2I3BRJ4
    Related
    ENSMUSP00000154605.2, ENSMUST00000227299.2
    Conserved Domains (1) summary
    pfam12640
    Location:1 → 95
    UPF0489; UPF0489 domain

  3. NM_029998.4 → NP_084274.1  UPF0489 protein C5orf22 homolog isoform b

    See identical proteins and their annotated locations for NP_084274.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (2) represents the longest transcript and encodes the longest isoform (b).
    Source sequence(s)
    AC133189
    Consensus CDS
    CCDS27392.1
    UniProtKB/Swiss-Prot
    B2RQ49, Q8BGC1, Q8BYV3, Q8BZ46, Q9CX64
    Related
    ENSMUSP00000055656.4, ENSMUST00000057256.5
    Conserved Domains (1) summary
    pfam12640
    Location:19 → 169
    UPF0489; UPF0489 domain

RefSeqs of Annotated Genomes: GCF_000001635.27-RS_2024_02

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

Reference GRCm39 C57BL/6J

Genomic

  1. NC_000081.7 Reference GRCm39 C57BL/6J

    Range
    12806012..12824767 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_036159632.1 → XP_036015525.1  UPF0489 protein C5orf22 homolog isoform X1

    Conserved Domains (1) summary
    pfam12640
    Location:19 → 169
    UPF0489; UPF0489 domain

  2. XM_036159633.1 → XP_036015526.1  UPF0489 protein C5orf22 homolog isoform X2

    Conserved Domains (1) summary
    pfam12640
    Location:19 → 169
    UPF0489; UPF0489 domain

RNA

  1. XR_004938878.1 RNA Sequence

Nucleotide Protein Strain
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q8BGC1.1 GenPept UniProtKB/Swiss-Prot:Q8BGC1

Gene LinkOut

The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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