U.S. flag

An official website of the United States government

Format

Send to:

Choose Destination

LOC106804612 hemoglobin subunit alpha 2 recombination region [ Homo sapiens (human) ]

Gene ID: 106804612, updated on 17-Sep-2024

Summary

Go to the top of the page Help
Gene symbol
LOC106804612
Gene description
hemoglobin subunit alpha 2 recombination region
Gene type
biological region
Feature type(s)
misc_recomb: non_allelic_homologous
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Summary
This region is known to undergo non-allelic homologous recombination (NAHR) with a similar low-copy repeat region, the hemoglobin subunit alpha 1 (HBA1) recombination region, located about 900 bp centromere-proximal to this region, in direct orientation on the reference genome. Genomic rearrangements including duplications and deletions of the intervening sequence as a result of NAHR between these recombination regions have been observed. Unequal crossing-over between repeats sharing high sequence similarity can produce 3.7 kb and 4.2 kb deletions, resulting in alpha-thalassemia caused by a hemoglobin subunit alpha gene deletion. Regions of shared similarity with the HBA1 recombination region are subdivided into regions known as the X box, Y box and Z box (X2, Y2 and Z2 boxes for the HBA2 recombination region). Recombination between X box regions results in the 4.2 kb deletion, while recombination between Z box regions results in the 3.7 kb deletion. Recombination events between Y box regions has also been observed. Other deletions causing alpha-thalassemias have also been reported, but many of these deletions are not the result of homologous recombination between regions sharing high sequence similarity, and are not represented here. [provided by RefSeq, Oct 2016]
NEW
Try the new Gene table
Try the new Transcript table

Genomic context

Go to the top of the page Help
See LOC106804612 in Genome Data Viewer
Location:
16p13.3
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 16 NC_000016.10 (170362..173729)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 16 NC_060940.1 (164396..167770)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 16 NC_000016.9 (220361..223728)

Chromosome 16 - NC_000016.10Genomic Context describing neighboring genes Neighboring gene hemoglobin subunit mu Neighboring gene OCT4-H3K4me1 hESC enhancer GRCh37_chr16:220059-220561 Neighboring gene hemoglobin subunit alpha pseudogene 1 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:221864-222604 Neighboring gene OCT4-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:223344-224083 Neighboring gene OCT4-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:224084-224822 Neighboring gene hemoglobin subunit alpha 2 Neighboring gene hemoglobin subunit alpha 1 recombination region Neighboring gene hemoglobin subunit alpha 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10202 Neighboring gene hemoglobin subunit theta 1

Genomic regions, transcripts, and products

Go to the top of the page Help

Go to nucleotide: Graphics FASTA GenBank

Bibliography

Go to the top of the pageHelp

GeneRIFs: Gene References Into Functions

Phenotypes

Go to the top of the page Help

Review eQTL and phenotype association data in this region using PheGenI

Variation

Go to the top of the page Help

See variants in ClinVar

See Variation Viewer (GRCh37.p13)

General gene information

Go to the top of the page Help

Other Names

  • HBA2 recombination region

NCBI Reference Sequences (RefSeq)

Go to the top of the page Help

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.

Genomic

  1. NG_046165.1 

    Range
    101..3468
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

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_000016.10 Reference GRCh38.p14 Primary Assembly

    Range
    170362..173729
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060940.1 Alternate T2T-CHM13v2.0

    Range
    164396..167770
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

Gene LinkOut

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

Molecular Biology Databases
Research Materials