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    Etl4 enhancer trap locus 4 [ Mus musculus (house mouse) ]

    Gene ID: 208618, updated on 27-Nov-2024

    Summary

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    Official Symbol
    Etl4provided by MGI
    Official Full Name
    enhancer trap locus 4provided by MGI
    Primary source
    MGI:MGI:95454
    See related
    Ensembl:ENSMUSG00000036617 AllianceGenome:MGI:95454
    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
    Also known as
    Skt; Etl-4; 6620402G01Rik; 9430077C05Rik; E330027G05Rik
    Summary
    Involved in embryonic skeletal system development. Located in cytoplasm. Is expressed in several structures, including alimentary system; branchial arch; genitourinary system; sensory organ; and surface ectoderm. Orthologous to human KIAA1217 (KIAA1217). [provided by Alliance of Genome Resources, Nov 2024]
    Expression
    Ubiquitous expression in cortex adult (RPKM 4.1), frontal lobe adult (RPKM 3.9) and 28 other tissues See more
    Orthologs
    human all
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    Genomic context

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    See Etl4 in Genome Data Viewer
    Location:
    2 A3; 2 14.27 cM
    Exon count:
    32
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCm39 (GCF_000001635.27) 2 NC_000068.8 (19915018..20815346)
    108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) 2 NC_000068.7 (19910207..20810535)

    Chromosome 2 - NC_000068.8Genomic Context describing neighboring genes Neighboring gene CapStarr-seq enhancer MGSCv37_chr2:19656187-19656410 Neighboring gene STARR-seq mESC enhancer starr_03834 Neighboring gene GTPase activating protein (SH3 domain) binding protein 2 pseudogene Neighboring gene predicted gene, 24670 Neighboring gene STARR-seq mESC enhancer starr_03835 Neighboring gene STARR-seq mESC enhancer starr_03836 Neighboring gene Ngfi-A binding protein 1 pseudogene Neighboring gene predicted gene 13363 Neighboring gene STARR-seq mESC enhancer starr_03837 Neighboring gene voltage-dependent anion channel 1 pseudogene Neighboring gene STARR-seq mESC enhancer starr_03838 Neighboring gene STARR-seq mESC enhancer starr_03839 Neighboring gene STARR-seq mESC enhancer starr_03840 Neighboring gene mitochondrial ribosomal protein S5 pseudogene Neighboring gene predicted gene, 23970 Neighboring gene STARR-seq mESC enhancer starr_03841 Neighboring gene STARR-seq mESC enhancer starr_03842 Neighboring gene predicted gene 17171 Neighboring gene predicted gene, 54104 Neighboring gene STARR-seq mESC enhancer starr_03843 Neighboring gene STARR-seq mESC enhancer starr_03846 Neighboring gene CRISPRi-validated Etl4 enhancer cluster Neighboring gene STARR-seq mESC enhancer starr_03863 Neighboring gene STARR-seq mESC enhancer starr_03867 Neighboring gene STARR-seq mESC enhancer starr_03870 Neighboring gene Rho GTPase activating protein 21 Neighboring gene STARR-positive B cell enhancer mm9_chr2:20885831-20886131 Neighboring gene STARR-positive B cell enhancer ABC_E5897 Neighboring gene STARR-seq mESC enhancer starr_03884 Neighboring gene STARR-seq mESC enhancer starr_03887 Neighboring gene VISTA enhancer mm1447 Neighboring gene predicted gene 13375 Neighboring gene STARR-seq mESC enhancer starr_03890 Neighboring gene phosphoribosyltransferase domain containing 1 pseudogene

    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. A Genetic Screen Identifies Etl4-Deficiency Capable of Stabilizing the Haploidy in Embryonic Stem Cells. Zhang G, et al. Stem Cell Reports, 2021 Jan 12. PMID 33440180, Free PMC Article
    2. A Cre knock-in mouse line on the Sickle tail locus induces recombination in the notochord and intervertebral disks. Abe K, et al. Genesis, 2012 Oct. PMID 22522943
    3. Enhancer trap integrations in mouse embryonic stem cells give rise to staining patterns in chimaeric embryos with a high frequency and detect endogenous genes. Korn R, et al. Mech Dev, 1992 Nov. PMID 1283314
    4. A novel murine gene, Sickle tail, linked to the Danforth's short tail locus, is required for normal development of the intervertebral disc. Semba K, et al. Genetics, 2006 Jan. PMID 16204209, Free PMC Article
    5. The Skt gene, required for anorectal development, is a candidate for a molecular marker of the cloacal plate. Suda H, et al. Pediatr Surg Int, 2011 Mar. PMID 21069351

    See all (52) 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)

    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 MGI

    Function Evidence Code Pubs
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in embryonic skeletal system development IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    Component Evidence Code Pubs
    located_in centrosome ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in centrosome ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    is_active_in cytoplasm IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in cytoplasm IDA
    Inferred from Direct Assay
    more info
    		 PubMed 

    General protein information

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    Preferred Names
    sickle tail protein

    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_001081006.1 → NP_001074475.1  sickle tail protein isoform c

      See identical proteins and their annotated locations for NP_001074475.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (c) encodes the longest protein (isoform c).
      Source sequence(s)
      AB125594, AK147510, AL929100, BC158051, CF744489
      Consensus CDS
      CCDS38053.1
      UniProtKB/TrEMBL
      E9QAU4
      Related
      ENSMUSP00000110274.2, ENSMUST00000114627.8
      Conserved Domains (1) summary
      pfam03915
      Location:239 → 317
      AIP3; Actin interacting protein 3

    2. NM_001177630.2 → NP_001171101.2  sickle tail protein isoform d

      Status: VALIDATED

      Description
      Transcript Variant: This variant (d) has multiple differences, compared to variant c. These differences result in a distinct 5' UTR and cause translation initiation at a downstream start codon, compared to variant c. The encoded protein (isoform d) is shorter when it is compared to isoform c.
      Source sequence(s)
      AB125594, AL929100, BB040164, BC158051
      Consensus CDS
      CCDS50509.1
      UniProtKB/TrEMBL
      B2RY09, D3Z781
      Related
      ENSMUSP00000110251.3, ENSMUST00000114604.9
      Conserved Domains (1) summary
      pfam03915
      Location:188 → 259
      AIP3; Actin interacting protein 3

    3. NM_001177631.1 → NP_001171102.1  sickle tail protein isoform e

      Status: VALIDATED

      Description
      Transcript Variant: This variant (e) has multiple differences, compared to variant c. These differences result in a distinct 5' UTR and cause translation initiation at a downstream start codon, compared to variant c. The encoded protein (isoform e) is shorter when it is compared to isoform c.
      Source sequence(s)
      AK147510, AL844538, AL929100, BC158051, BC172143
      UniProtKB/TrEMBL
      B2RY09
      Conserved Domains (1) summary
      pfam03915
      Location:188 → 259
      AIP3; Actin interacting protein 3

    4. NM_001369134.1 → NP_001356063.1  sickle tail protein isoform f

      Status: VALIDATED

      Source sequence(s)
      AL844538, AL929100
      Consensus CDS
      CCDS89430.1
      UniProtKB/Swiss-Prot
      A2AQ25, A2AUE9, A2AUF0, A2AUF1, Q75UV8, Q75UV9, Q80VK2, Q8BHX8, Q8BHY1, Q8CHA8, Q8R0K6
      Related
      ENSMUSP00000066170.4, ENSMUST00000066509.10
      Conserved Domains (1) summary
      pfam03915
      Location:188 → 266
      AIP3; Actin interacting protein 3

    5. NM_029895.4 → NP_084171.2  sickle tail protein isoform b

      See identical proteins and their annotated locations for NP_084171.2

      Status: VALIDATED

      Description
      Transcript Variant: This variant (b) has multiple differences, compared to variant c. These differences result in a distinct 5' UTR and cause translation initiation at a downstream start codon, compared to variant c. The encoded protein (isoform b) is shorter when it is compared to isoform c.
      Source sequence(s)
      AB125595, AL929100
      Consensus CDS
      CCDS50510.1
      UniProtKB/TrEMBL
      B2RY09
      Related
      ENSMUSP00000110261.2, ENSMUST00000114614.8
      Conserved Domains (1) summary
      pfam03915
      Location:188 → 259
      AIP3; Actin interacting protein 3

    6. NM_178059.5 → NP_835160.2  sickle tail protein isoform a

      See identical proteins and their annotated locations for NP_835160.2

      Status: VALIDATED

      Description
      Transcript Variant: This variant (a) has multiple differences, compared to variant c. These differences result in a distinct 5' UTR and cause translation initiation at a downstream start codon, compared to variant c. The encoded protein (isoform a) is shorter when it is compared to isoform c.
      Source sequence(s)
      AB125594, AL929100
      Consensus CDS
      CCDS50511.1
      UniProtKB/TrEMBL
      B2RY09
      Related
      ENSMUSP00000041431.5, ENSMUST00000045555.11
      Conserved Domains (2) summary
      pfam03915
      Location:188 → 266
      AIP3; Actin interacting protein 3
      NF033930
      Location:644 → 909
      pneumo_PspA; pneumococcal surface protein A

    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_000068.8 Reference GRCm39 C57BL/6J

      Range
      19915018..20815346
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_036160115.1 → XP_036016008.1  sickle tail protein isoform X1

      Conserved Domains (2) summary
      pfam03915
      Location:266 → 344
      AIP3; Actin interacting protein 3
      NF033930
      Location:757 → 1022
      pneumo_PspA; pneumococcal surface protein A

    2. XM_006497408.4 → XP_006497471.1  sickle tail protein isoform X2

      See identical proteins and their annotated locations for XP_006497471.1

      UniProtKB/TrEMBL
      E9QAU4
      Conserved Domains (1) summary
      pfam03915
      Location:239 → 317
      AIP3; Actin interacting protein 3

    3. XM_006497428.3 → XP_006497491.1  sickle tail protein isoform X12

      UniProtKB/TrEMBL
      B2RY09
      Conserved Domains (1) summary
      pfam03915
      Location:239 → 317
      AIP3; Actin interacting protein 3

    4. XM_006497427.3 → XP_006497490.1  sickle tail protein isoform X11

      UniProtKB/TrEMBL
      B2RY09
      Conserved Domains (1) summary
      pfam03915
      Location:239 → 317
      AIP3; Actin interacting protein 3

    5. XM_036160127.1 → XP_036016020.1  sickle tail protein isoform X5

      Conserved Domains (2) summary
      pfam03915
      Location:108 → 186
      AIP3; Actin interacting protein 3
      NF033930
      Location:599 → 864
      pneumo_PspA; pneumococcal surface protein A

    6. XM_036160128.1 → XP_036016021.1  sickle tail protein isoform X5

      Conserved Domains (2) summary
      pfam03915
      Location:108 → 186
      AIP3; Actin interacting protein 3
      NF033930
      Location:599 → 864
      pneumo_PspA; pneumococcal surface protein A

    7. XM_036160138.1 → XP_036016031.1  sickle tail protein isoform X13

      UniProtKB/TrEMBL
      B2RY09
      Conserved Domains (2) summary
      pfam03915
      Location:188 → 266
      AIP3; Actin interacting protein 3
      NF033930
      Location:679 → 944
      pneumo_PspA; pneumococcal surface protein A

    8. XM_036160141.1 → XP_036016034.1  sickle tail protein isoform X15

      UniProtKB/TrEMBL
      B2RY09
      Conserved Domains (2) summary
      pfam03915
      Location:188 → 266
      AIP3; Actin interacting protein 3
      NF033930
      Location:644 → 909
      pneumo_PspA; pneumococcal surface protein A

    9. XM_036160144.1 → XP_036016037.1  sickle tail protein isoform X17

      UniProtKB/TrEMBL
      B2RY09
      Conserved Domains (2) summary
      pfam03915
      Location:188 → 266
      AIP3; Actin interacting protein 3
      NF033930
      Location:644 → 909
      pneumo_PspA; pneumococcal surface protein A

    10. XM_036160139.1 → XP_036016032.1  sickle tail protein isoform X14

      UniProtKB/TrEMBL
      B2RY09
      Conserved Domains (2) summary
      pfam03915
      Location:188 → 266
      AIP3; Actin interacting protein 3
      NF033930
      Location:679 → 944
      pneumo_PspA; pneumococcal surface protein A

    11. XM_036160142.1 → XP_036016035.1  sickle tail protein isoform X16

      UniProtKB/TrEMBL
      B2RY09
      Conserved Domains (2) summary
      pfam03915
      Location:188 → 266
      AIP3; Actin interacting protein 3
      NF033930
      Location:679 → 944
      pneumo_PspA; pneumococcal surface protein A

    12. XM_036160147.1 → XP_036016040.1  sickle tail protein isoform X18

      UniProtKB/TrEMBL
      B2RY09
      Conserved Domains (2) summary
      pfam03915
      Location:188 → 266
      AIP3; Actin interacting protein 3
      NF033930
      Location:644 → 909
      pneumo_PspA; pneumococcal surface protein A

    13. XM_036160119.1 → XP_036016012.1  sickle tail protein isoform X3

      Conserved Domains (2) summary
      pfam03915
      Location:215 → 293
      AIP3; Actin interacting protein 3
      NF033930
      Location:706 → 971
      pneumo_PspA; pneumococcal surface protein A

    14. XM_036160124.1 → XP_036016017.1  sickle tail protein isoform X4

      Conserved Domains (2) summary
      pfam03915
      Location:215 → 293
      AIP3; Actin interacting protein 3
      NF033930
      Location:671 → 936
      pneumo_PspA; pneumococcal surface protein A

    15. XM_006497419.4 → XP_006497482.1  sickle tail protein isoform X7

      Conserved Domains (1) summary
      pfam03915
      Location:38 → 116
      AIP3; Actin interacting protein 3

    16. XM_036160150.1 → XP_036016043.1  sickle tail protein isoform X19

      UniProtKB/TrEMBL
      B2RY09
      Conserved Domains (2) summary
      pfam03915
      Location:38 → 116
      AIP3; Actin interacting protein 3
      NF033930
      Location:529 → 794
      pneumo_PspA; pneumococcal surface protein A

    17. XM_006497417.5 → XP_006497480.1  sickle tail protein isoform X6

      Conserved Domains (1) summary
      pfam03915
      Location:104 → 182
      AIP3; Actin interacting protein 3

    18. XM_017316832.3 → XP_017172321.1  sickle tail protein isoform X20

      Conserved Domains (1) summary
      NF033930
      Location:397 → 662
      pneumo_PspA; pneumococcal surface protein A

    19. XM_006497422.5 → XP_006497485.1  sickle tail protein isoform X8

      See identical proteins and their annotated locations for XP_006497485.1

    20. XM_006497424.5 → XP_006497487.1  sickle tail protein isoform X9

      UniProtKB/Swiss-Prot
      A2AQ25

    21. XM_036160131.1 → XP_036016024.1  sickle tail protein isoform X10

      Conserved Domains (1) summary
      NF033930
      Location:362 → 627
      pneumo_PspA; pneumococcal surface protein A

    22. XM_036160151.1 → XP_036016044.1  sickle tail protein isoform X22

      Related
      ENSMUSP00000110253.2, ENSMUST00000114606.8
      Conserved Domains (1) summary
      NF033930
      Location:362 → 627
      pneumo_PspA; pneumococcal surface protein A

    23. XM_017316833.3 → XP_017172322.1  sickle tail protein isoform X21

    24. XM_006497423.5 → XP_006497486.1  sickle tail protein isoform X8

      See identical proteins and their annotated locations for XP_006497486.1

      Conserved Domains (2) summary
      PHA02682
      Location:16 → 103
      PHA02682; ORF080 virion core protein; Provisional
      pfam09606
      Location:549 → 666
      Med15; ARC105 or Med15 subunit of Mediator complex non-fungal

    25. XM_030249074.2 → XP_030104934.1  sickle tail protein isoform X9

      Related
      ENSMUSP00000110255.2, ENSMUST00000114608.3

    26. XM_036160152.1 → XP_036016045.1  sickle tail protein isoform X20

      Conserved Domains (1) summary
      NF033930
      Location:397 → 662
      pneumo_PspA; pneumococcal surface protein A
    Nucleotide Protein Strain
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    A2AQ25.1 GenPept UniProtKB/Swiss-Prot:A2AQ25

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