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    IFT56 intraflagellar transport 56 [ Homo sapiens (human) ]

    Gene ID: 79989, updated on 5-Mar-2024

    Summary

    Official Symbol
    IFT56provided by HGNC
    Official Full Name
    intraflagellar transport 56provided by HGNC
    Primary source
    HGNC:HGNC:21882
    See related
    Ensembl:ENSG00000105948 MIM:617453; AllianceGenome:HGNC:21882
    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
    BRENS; DYF13; TTC26; dyf-13
    Summary
    Predicted to enable intraciliary transport particle B binding activity. Predicted to be involved in cilium organization; protein localization to cilium; and smoothened signaling pathway. Predicted to act upstream of or within manchette assembly. Predicted to be located in cilium. Predicted to be part of intraciliary transport particle B. Predicted to be active in ciliary basal body and ciliary base. [provided by Alliance of Genome Resources, Apr 2022]
    Expression
    Broad expression in testis (RPKM 5.7), thyroid (RPKM 2.6) and 23 other tissues See more
    Orthologs
    NEW
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    Try the new Transcript table

    Genomic context

    See IFT56 in Genome Data Viewer
    Location:
    7q34
    Exon count:
    19
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 7 NC_000007.14 (139133778..139191986)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 7 NC_060931.1 (140447060..140505276)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 7 NC_000007.13 (138818524..138876732)

    Chromosome 7 - NC_000007.14Genomic Context describing neighboring genes Neighboring gene microRNA 10399 Neighboring gene zinc finger CCCH-type containing, antiviral 1 Neighboring gene ribosomal protein L17 pseudogene 28 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr7:138786521-138787092 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26746 Neighboring gene H3K27ac hESC enhancer GRCh37_chr7:138794119-138794622 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26749 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26750 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26751 Neighboring gene Sharpr-MPRA regulatory region 4033 Neighboring gene Sharpr-MPRA regulatory region 8039 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:138859395-138860231 Neighboring gene NANOG hESC enhancer GRCh37_chr7:138867531-138868130 Neighboring gene Sharpr-MPRA regulatory region 12471 Neighboring gene MSL3 pseudogene 2 Neighboring gene uncharacterized LOC124901756 Neighboring gene FCF1 pseudogene 11

    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

    Clone Names

    • FLJ12571, MGC163211

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables intraciliary transport particle B binding IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    Process Evidence Code Pubs
    involved_in axoneme assembly ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in cilium assembly IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in cilium assembly ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in cilium assembly NAS
    Non-traceable Author Statement
    more info
    PubMed 
    involved_in intraciliary anterograde transport IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in intraciliary anterograde transport NAS
    Non-traceable Author Statement
    more info
    PubMed 
    involved_in intraciliary transport ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in intraciliary transport involved in cilium assembly IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in manchette assembly IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in protein localization to cilium ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in protein transport IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in smoothened signaling pathway ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    Component Evidence Code Pubs
    located_in centrosome IEA
    Inferred from Electronic Annotation
    more info
     
    is_active_in ciliary basal body IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    is_active_in ciliary base IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    located_in ciliary tip TAS
    Traceable Author Statement
    more info
     
    located_in cilium IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    located_in cilium ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    located_in cilium NAS
    Non-traceable Author Statement
    more info
    PubMed 
    located_in cilium TAS
    Traceable Author Statement
    more info
     
    part_of intraciliary transport particle B IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    part_of intraciliary transport particle B IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    part_of intraciliary transport particle B ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    located_in neuron projection IEA
    Inferred from Electronic Annotation
    more info
     

    General protein information

    Preferred Names
    intraflagellar transport protein 56
    Names
    TPR repeat protein 26
    tetratricopeptide repeat domain 26
    tetratricopeptide repeat protein 26

    NCBI Reference Sequences (RefSeq)

    NEW Try the new Transcript table

    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_001144920.3NP_001138392.1  intraflagellar transport protein 56 isoform 2

      See identical proteins and their annotated locations for NP_001138392.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) lacks lacks an alternate exon that results in a frameshift in the 3' coding region, compared to variant 1. The encoded isoform (2) has a distinct C-terminus and is shorter than isoform 1.
      Source sequence(s)
      AC009220, BC144151, BP315162, CA450032
      Consensus CDS
      CCDS55172.1
      UniProtKB/Swiss-Prot
      A0AVF1
      Related
      ENSP00000410655.1, ENST00000430935.5
      Conserved Domains (2) summary
      sd00006
      Location:5886
      TPR; TPR repeat [structural motif]
      cl26002
      Location:33323
      TPR_11; TPR repeat
    2. NM_001144923.3NP_001138395.1  intraflagellar transport protein 56 isoform 3

      Status: VALIDATED

      Description
      Transcript Variant: This variant (3) lacks an alternate in-frame exon in the 5' coding region, compared to variant 1, resulting in an isoform (3) that is shorter than isoform 1.
      Source sequence(s)
      AC009220, AK299132, BP315162, CA450032
      Consensus CDS
      CCDS55173.1
      UniProtKB/Swiss-Prot
      A0AVF1
      Related
      ENSP00000339135.4, ENST00000343187.8
      Conserved Domains (2) summary
      TIGR02917
      Location:33286
      PEP_TPR_lipo; putative PEP-CTERM system TPR-repeat lipoprotein
      sd00006
      Location:124148
      TPR; TPR repeat [structural motif]
    3. NM_001287512.2NP_001274441.1  intraflagellar transport protein 56 isoform 4

      See identical proteins and their annotated locations for NP_001274441.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (4) lacks three alternate exons that result in the loss of an in-frame segment in the 5' coding region, compared to variant 1. The encoded isoform (4) is shorter than isoform 1.
      Source sequence(s)
      AC009220, AK295092, CA450032
      Consensus CDS
      CCDS75665.1
      UniProtKB/TrEMBL
      B7Z2T3, B7Z6R6
      Related
      ENSP00000418788.1, ENST00000495038.5
      Conserved Domains (3) summary
      sd00006
      Location:5886
      TPR; TPR repeat [structural motif]
      pfam10345
      Location:14190
      Cohesin_load; Cohesin loading factor
      pfam12895
      Location:35113
      ANAPC3; Anaphase-promoting complex, cyclosome, subunit 3
    4. NM_001287513.2NP_001274442.1  intraflagellar transport protein 56 isoform 5

      See identical proteins and their annotated locations for NP_001274442.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (5) differs in its 5' UTR and initiates translation at a downstream in-frame start codon, compared to variant 1. The encoded isoform (5) is shorter at the N-terminus, compared to isoform 1.
      Source sequence(s)
      AC009220, AK293444, BP315162, CA450032
      UniProtKB/TrEMBL
      B7Z1H0
      Conserved Domains (2) summary
      TIGR02917
      Location:53218
      PEP_TPR_lipo; putative PEP-CTERM system TPR-repeat lipoprotein
      sd00006
      Location:5074
      TPR; TPR repeat [structural motif]
    5. NM_001318333.2NP_001305262.1  intraflagellar transport protein 56 isoform 6

      Status: VALIDATED

      Description
      Transcript Variant: This variant (6) uses an alternate splice site in its 5' UTR and a downstream in-frame start codon, compared to variant 1. The encoded isoform (6) has a shorter N-terminus, compared to isoform 1.
      Source sequence(s)
      AC009220, BC013912, BC034466, BP315162, CA450032
      UniProtKB/TrEMBL
      Q96CU4
      Conserved Domains (2) summary
      TIGR02917
      Location:18206
      PEP_TPR_lipo; putative PEP-CTERM system TPR-repeat lipoprotein
      sd00006
      Location:1539
      TPR; TPR repeat [structural motif]
    6. NM_001321740.2NP_001308669.1  intraflagellar transport protein 56 isoform 7

      Status: VALIDATED

      Source sequence(s)
      AC009220, BC013912, BC034466, CA450032
      UniProtKB/TrEMBL
      Q96CU4
      Conserved Domains (2) summary
      sd00006
      Location:5886
      TPR; TPR repeat [structural motif]
      pfam13414
      Location:64113
      TPR_11; TPR repeat
    7. NM_001321741.2NP_001308670.1  intraflagellar transport protein 56 isoform 8

      Status: VALIDATED

      Source sequence(s)
      AC009220, BC013912, BC034466, BP315162, CA450032
      UniProtKB/TrEMBL
      B7Z6R6
      Related
      ENSP00000419178.2, ENST00000478836.6
      Conserved Domains (2) summary
      sd00006
      Location:5886
      TPR; TPR repeat [structural motif]
      pfam12895
      Location:35113
      ANAPC3; Anaphase-promoting complex, cyclosome, subunit 3
    8. NM_001321742.2NP_001308671.1  intraflagellar transport protein 56 isoform 9

      Status: VALIDATED

      Source sequence(s)
      AC009220, BC013912
      Consensus CDS
      CCDS83230.1
      UniProtKB/TrEMBL
      Q96CU4
      Related
      ENSP00000443253.1, ENST00000474035.6
      Conserved Domains (2) summary
      sd00006
      Location:5686
      TPR; TPR repeat [structural motif]
      cl26002
      Location:33252
      TPR_11; TPR repeat
    9. NM_024926.4NP_079202.2  intraflagellar transport protein 56 isoform 1

      See identical proteins and their annotated locations for NP_079202.2

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) encodes the longest isoform (1).
      Source sequence(s)
      AC009220, BC126331, BP315162, CA450032
      Consensus CDS
      CCDS5852.1
      UniProtKB/Swiss-Prot
      A0AVF1, A4D1S3, B7Z5M0, C9J2N7, F8W724, Q9H9S8, Q9NTC0
      UniProtKB/TrEMBL
      B7Z6R6
      Related
      ENSP00000419279.1, ENST00000464848.5
      Conserved Domains (2) summary
      sd00006
      Location:5886
      TPR; TPR repeat [structural motif]
      pfam13414
      Location:64113
      TPR_11; TPR repeat

    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_000007.14 Reference GRCh38.p14 Primary Assembly

      Range
      139133778..139191986
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060931.1 Alternate T2T-CHM13v2.0

      Range
      140447060..140505276
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)