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IFT56 intraflagellar transport 56 [ Homo sapiens (human) ]

Gene ID: 79989, updated on 1-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
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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)

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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_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)