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CYB561A3 cytochrome b561 family member A3 [ Homo sapiens (human) ]

Gene ID: 220002, updated on 10-Dec-2024

Summary

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Official Symbol
CYB561A3provided by HGNC
Official Full Name
cytochrome b561 family member A3provided by HGNC
Primary source
HGNC:HGNC:23014
See related
Ensembl:ENSG00000162144 MIM:618757; AllianceGenome:HGNC:23014
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
LCYTB; CYBASC3
Summary
Predicted to enable transmembrane ascorbate ferrireductase activity. Predicted to be involved in intracellular iron ion homeostasis. Located in nucleolus. [provided by Alliance of Genome Resources, Dec 2024]
Expression
Broad expression in adrenal (RPKM 44.3), lymph node (RPKM 18.0) and 23 other tissues See more
Orthologs
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Genomic context

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See CYB561A3 in Genome Data Viewer
Location:
11q12.2
Exon count:
10
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 11 NC_000011.10 (61348745..61362283, complement)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 11 NC_060935.1 (61337352..61350891, complement)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 11 NC_000011.9 (61116217..61129755, complement)

Chromosome 11 - NC_000011.10Genomic Context describing neighboring genes Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr11:61033788-61034987 Neighboring gene von Willebrand factor C and EGF domains Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:61048939-61049860 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3387 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:61061839-61062541 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3389 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr11:61067594-61068793 Neighboring gene damage specific DNA binding protein 1 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:61100139-61100661 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:61100662-61101184 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:61112523-61113449 Neighboring gene triokinase and FMN cyclase Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4795 Neighboring gene H3K27ac hESC enhancer GRCh37_chr11:61129243-61129964 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4797 Neighboring gene transmembrane protein 138 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3391 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:61159824-61160785 Neighboring gene transmembrane protein 216

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • Project title: Tissue-specific circular RNA induction during human fetal development
  • Description: 35 human fetal samples from 6 tissues (3 - 7 replicates per tissue) collected between 10 and 20 weeks gestational time were sequenced using Illumina TruSeq Stranded Total RNA
  • BioProject: PRJNA270632
  • Publication: PMID 26076956
  • Analysis date: Mon Apr 2 22:54:59 2018

Bibliography

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Related articles in PubMed

  1. CYB561A3 is the key lysosomal iron reductase required for Burkitt B-cell growth and survival. Wang Z, et al. Blood, 2021 Dec 2. PMID 34232987, Free PMC Article
  2. Cytochromes b561: ascorbate-mediated trans-membrane electron transport. Asard H, et al. Antioxid Redox Signal, 2013 Sep 20. PMID 23249217, Free PMC Article
  3. Integral and associated lysosomal membrane proteins. Schröder B, et al. Traffic, 2007 Dec. PMID 17897319
  4. Generation and analysis of 280,000 human expressed sequence tags. Hillier LD, et al. Genome Res, 1996 Sep. PMID 8889549
  5. Signal sequence and keyword trap in silico for selection of full-length human cDNAs encoding secretion or membrane proteins from oligo-capped cDNA libraries. Otsuki T, et al. DNA Res, 2005. PMID 16303743

See all (16) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. CYB561A3 is the key lysosomal iron reductase required for Burkitt B-cell growth and survival.
    Title: CYB561A3 is the key lysosomal iron reductase required for Burkitt B-cell growth and survival.
Submit: New GeneRIF Correction

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Clone Names

  • FLJ39724, MGC20446

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables metal ion binding IEA
Inferred from Electronic Annotation
more info
  
enables oxidoreductase activity IBA
Inferred from Biological aspect of Ancestor
more info
  
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
enables transmembrane ascorbate ferrireductase activity ISS
Inferred from Sequence or Structural Similarity
more info
  
Process Evidence Code Pubs
involved_in intracellular iron ion homeostasis ISS
Inferred from Sequence or Structural Similarity
more info
  
involved_in transmembrane transport IEA
Inferred from Electronic Annotation
more info
  
Component Evidence Code Pubs
located_in intracellular membrane-bounded organelle IDA
Inferred from Direct Assay
more info
  
located_in late endosome membrane ISS
Inferred from Sequence or Structural Similarity
more info
  
located_in lysosomal membrane HDA PubMed 
is_active_in lysosomal membrane IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in lysosomal membrane ISS
Inferred from Sequence or Structural Similarity
more info
  
located_in nucleolus IDA
Inferred from Direct Assay
more info
  

General protein information

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Preferred Names
lysosomal membrane ascorbate-dependent ferrireductase CYB561A3
Names
cytochrome b ascorbate-dependent protein 3
cytochrome b, ascorbate dependent 3
lysosomal cytochrome b
lysosomal cytochrome b561
NP_001154924.1
NP_001154926.1
NP_001287692.1
NP_705839.3
XP_011543123.1
XP_024304166.2
XP_047282511.1
XP_054223987.1
XP_054223988.1
XP_054223989.1
XP_054223990.1

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_001161452.2 → NP_001154924.1  lysosomal membrane ascorbate-dependent ferrireductase CYB561A3 isoform 2

    See identical proteins and their annotated locations for NP_001154924.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (3) differs in the 5' UTR and uses an alternate splice junction at the 5' end of the last exon compared to variant 4. The encoded isoform (2) has a shorter and distinct C-terminus compared to isoform 3. Variants 2 and 3 both encode the same isoform (2).
    Source sequence(s)
    AK025870, AK225754, AP003108, BM692535, BP296553, BP396674, CF541093, DA948287
    Consensus CDS
    CCDS8004.1
    UniProtKB/Swiss-Prot
    B3KPU2, B4DLN9, J3KQH4, Q6PK96, Q8NBI2
    UniProtKB/TrEMBL
    F5H5L0
    Related
    ENSP00000437390.1, ENST00000536915.5
    Conserved Domains (1) summary
    cd08762
    Location:19 → 188
    Cyt_b561_CYBASC3; Vertebrate cytochrome b(561), CYBASC3 gene product

  2. NM_001161454.1 → NP_001154926.1  lysosomal membrane ascorbate-dependent ferrireductase CYB561A3 isoform 1

    See identical proteins and their annotated locations for NP_001154926.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (1) contains an alternate exon and uses an alternate splice junction at the 5' end of the last exon compared to variant 4. The resulting isoform (1) is longer at the N-terminus and has a shorter and distinct C-terminus compared to isoform 3.
    Source sequence(s)
    AA085565, AK025870, AK297084, BP366144, BP396674, CF125719, DC378209, DC389589
    Consensus CDS
    CCDS53639.1
    UniProtKB/Swiss-Prot
    Q8NBI2
    Related
    ENSP00000398979.2, ENST00000426130.6
    Conserved Domains (1) summary
    cd08762
    Location:36 → 205
    Cyt_b561_CYBASC3; Vertebrate cytochrome b(561), CYBASC3 gene product

  3. NM_001300763.2 → NP_001287692.1  lysosomal membrane ascorbate-dependent ferrireductase CYB561A3 isoform 3

    See identical proteins and their annotated locations for NP_001287692.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (4) encodes the longest isoform (3).
    Source sequence(s)
    AI813810, AK056751, AP003108, CF125719
    Consensus CDS
    CCDS73296.1
    UniProtKB/TrEMBL
    F5H1Q2
    Related
    ENSP00000389745.2, ENST00000447532.6
    Conserved Domains (1) summary
    cd08762
    Location:19 → 188
    Cyt_b561_CYBASC3; Vertebrate cytochrome b(561), CYBASC3 gene product

  4. NM_153611.6 → NP_705839.3  lysosomal membrane ascorbate-dependent ferrireductase CYB561A3 isoform 2

    See identical proteins and their annotated locations for NP_705839.3

    Status: VALIDATED

    Description
    Transcript Variant: This variant (2) uses an alternate splice junction at the 5' end of the last exon compared to variant 4. The resulting isoform (2) has a shorter and distinct C-terminus compared to isoform 3. Variants 2 and 3 both encode the same isoform (2).
    Source sequence(s)
    AP003108
    Consensus CDS
    CCDS8004.1
    UniProtKB/Swiss-Prot
    B3KPU2, B4DLN9, J3KQH4, Q6PK96, Q8NBI2
    UniProtKB/TrEMBL
    F5H5L0
    Related
    ENSP00000294072.4, ENST00000294072.9
    Conserved Domains (1) summary
    cd08762
    Location:19 → 188
    Cyt_b561_CYBASC3; Vertebrate cytochrome b(561), CYBASC3 gene product

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

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

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000011.10 Reference GRCh38.p14 Primary Assembly

    Range
    61348745..61362283 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_011544821.3 → XP_011543123.1  lysosomal membrane ascorbate-dependent ferrireductase CYB561A3 isoform X1

    See identical proteins and their annotated locations for XP_011543123.1

    Conserved Domains (1) summary
    cd08762
    Location:36 → 205
    Cyt_b561_CYBASC3; Vertebrate cytochrome b(561), CYBASC3 gene product

  2. XM_047426555.1 → XP_047282511.1  lysosomal membrane ascorbate-dependent ferrireductase CYB561A3 isoform X1

  3. XM_024448398.2 → XP_024304166.2  lysosomal membrane ascorbate-dependent ferrireductase CYB561A3 isoform X2

RNA

  1. XR_007062461.1 RNA Sequence

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060935.1 Alternate T2T-CHM13v2.0

    Range
    61337352..61350891 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054368012.1 → XP_054223987.1  lysosomal membrane ascorbate-dependent ferrireductase CYB561A3 isoform X1

  2. XM_054368014.1 → XP_054223989.1  lysosomal membrane ascorbate-dependent ferrireductase CYB561A3 isoform X1

  3. XM_054368013.1 → XP_054223988.1  lysosomal membrane ascorbate-dependent ferrireductase CYB561A3 isoform X1

  4. XM_054368015.1 → XP_054223990.1  lysosomal membrane ascorbate-dependent ferrireductase CYB561A3 isoform X2

RNA

  1. XR_008488363.1 RNA Sequence

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q8NBI2.1 GenPept UniProtKB/Swiss-Prot:Q8NBI2

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