Details

SpeciesHomo sapiens
Species subgroup
Subgroup type
Sequence NameIGHV3-21*05
IUIS NameIGHV3-21*05
Alternative namesIGHV3-21*i01
Affirmation Level1
Full Sequence
Coding Sequence
FunctionalityORF
Inference TypeRearranged Only
MappedTrue
Paralogs
Paralog RepFalse

Un-rearranged Observations

Un-rearranged sequence observations that support this sequence:

AccessionTypeRepositoryStartEnd
MK308859InferredGenBank1295

Observations in AIRR-seq Repertoires

Click here to review supporting data in VDJbase.

Clicking the link will take you to VDJbase. Open in a new tab if you want to keep this page open. In VDJbase, click on the count in the Apperances column to see a list of samples in which the sequence was found.

CDR delineation

CDR1 Start76
CDR1 End99
CDR2 Start151
CDR2 End174
CDR3 Start289

Extension

3' ExtensionA
3' start
3' end

Additional Information

Sequence IDA00037
CuratorWilliam Lees
Curator addressBirkbeck College, University of London, Malet Street, London
Version3
Release Date2023-07-10
Release Notes

Bulk upload of sequences for the AIRR-C Human IG germline sets

LocusIGH
Sequence TypeV
Gene Subgroup3
Gene Designation21
Allele Designation05
Gene start1
Gene end295

Acknowledgements

Individuals acknowledged as contributing to this sequence:

No Items

Notes

Notes are added by IARC reviewers.

The 40th meeting of the IARC on August 7th 2019 considered the sequence IGHV3-21*01_S5868. The sequence represents IGHV3-21*01 C159T C164A in the IMGT numbering system. The committee noted a rearrangement frequency of 1.5%, with 9064 alignments including 5167 perfect matches to the inferred allele. Alignments were also seen to four other IGHV3-21 sequences, though only one of these sequences was abundant (IGHV3-21*01: 12914 alignments, 8386 unmutated alignments). Haplotyping based on IGHJ6 alleles confirmed the segregation of reads associated with these two alleles to the different haplotypes Alignments to the three other alleles shown in the genotype were at trivial levels (<0.01% of ‘unmutated’ alignments, in each case). There were 1394 different CDR3s associated with the inference, including 614 different CDR3s associated with unmutated alignments. The committee agreed that the sequence should be accepted as a Level 1 sequence as IGHV3-21*i01. In line with previous policy, the submitted sequence is recognized up to and including nucleotide 319. A trailing “.” in the affirmed sequence indicates IARC’s opinion that the sequence is likely to contain an additional 3’ nucleotide for which there is insufficient evidence to make an affirmation.

Reanalysis of the original submission at Meeting 43 of the IARC on October 7, 2019 again identified the same novel allele IGHV3-21*01_S5868 (IGHV3-21*01 C159T C164A) with 9370 sequences and 5226 perfect matches and 628 Unique CDR3s with unmutated Seqs. In this analysis only one other allele of IGHV3-21 was seen (as very rare inferences had been removed by IgDiscover filtering), IGHV3-21*01 with 13799 sequences and 8576 perfect matches giving a 40:60 allelic ratio. These alleles were very well separated by IGHJ6-based haplotype analysis (1:99 and 99:1, respectively). The re-analysis thus confirmed the inference of IGHV3-21*i01 as a Level 1 sequence. In line with previous policy, the submitted sequence is recognized up to and including nucleotide 319. A trailing “.” in the affirmed sequence indicates IARC’s opinion that the sequence is likely to contain an additional 3’ nucleotide for which there is insufficient evidence to make an affirmation.

Additional information for this sequence was imported into OGRDB via bulk update with the following notes:
Sequence annotation is based on Genbank sample MK308859
Mapped by IARC haplotype

Attachments

No Items

History

History logs the times and reasons for the publication of each version of this sequence.

Andrew Collins
2019-10-31 05:31:42
Version 1 published

This sequence was considered and affirmed at IARC Meetings 40 and 43.

Mats Ohlin
2019-11-26 21:07:26
Version 2 published

Updated with IMGT name.

William Lees
2023-07-10 11:24:37
Version 3 published

Bulk upload of sequences for the AIRR-C Human IG germline sets

Changes from previous version

v2v3
CuratorWilliam Lees
Curator addressSchool of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney AustraliaBirkbeck College, University of London, Malet Street, London
Sequence NameIGHV3-21*i01IGHV3-21*05
Alternative namesIGHV3-21*i01
MappedTrue
FunctionalityFORF
Species subgroup
Subgroup type
Allele Designationi0105
Full Sequence
Paralog RepFalse
Extension?FalseTrue
3' ExtensionA
5' Extension
curational_tagslikely_full-length
Noteschanged

Versions

All published versions of this sequence.

Sequence NameIMGT NameVersionDate
IGHV3-21*i0112019-10-31
IGHV3-21*i01IGHV3-21*0522019-11-26
IGHV3-21*05IGHV3-21*0532023-07-10