Details

SpeciesHomo sapiens
Species subgroup
Subgroup type
Sequence NameIGHV4-39*i03
IUIS Name
Alternative names
Affirmation Level1
Full Sequence
Coding Sequence
FunctionalityORF
Inference TypeRearranged Only
MappedFalse
Paralogs
Paralog RepFalse

Observations in VDJbase

Inferred sequences in VDJbase that match this sequence:

VDJbase Allele NameSubjectsSequence Match
IGHV4-39*01_g315a 3

Un-rearranged Observations

Un-rearranged sequence observations that support this sequence:

AccessionTypeRepositoryStartEnd
OW151140InferredGenBank1297

CDR delineation

CDR1 Start76
CDR1 End105
CDR2 Start157
CDR2 End177
CDR3 Start292

Extension

3' ExtensionA
3' start
3' end

Additional Information

Sequence IDA02561
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 Subgroup4
Gene Designation39
Allele Designationi03
Gene start1
Gene end298

Acknowledgements

Individuals acknowledged as contributing to this sequence:

No Items

Notes

Notes are added by IARC reviewers.

This inferred allele was assessed at IARC meeting 100 on June 8th, 2022. IGHV4-39*01_G315A was inferred in subject S57 (VDJ-base: P1_I60_S1). The genotype carried one other allele of IGHV4-39 (IGHV4-39*01, and a variant allele with a low number of associated reads that likely represents 3’-trimmed reads of IGHV4-39*01). The inference was supported by a large number of sequences (1424) and unmutated sequences (1151), a high overall frequency in the unmutated population (2.47%) and a large set of unique diverse CDR3s (1048) in the unmutated sequence set. It represented 48% of sequences associated with the gene. Haplotyping based on allelic diversity in IGHJ6 was not possible. IARC affirms the sequence at level 1 up to and including base 319 in agreement with past practice. It is acknowledged that the allele most likely carries one additional base, typically A at base position 320. A trailing “.” indicates IARC’s opinion that the sequence is likely to contain one additional 3’-nucleotides for which there is insufficient evidence to make an affirmation. The allele is given the name IGHV4-39*i03.

Additional information for this sequence was imported into OGRDB via bulk update with the following notes:
Sequence annotation is based on Genbank sample OW151140
VDJbase example haplotype: P1_I60

Attachments

No Items

History

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

Mats Ohlin
2022-07-25 10:54:25
Version 1 published

The allele was published by IARC on July 25th, 2022.

Mats Ohlin
2023-06-02 14:44:22
Version 2 published

A typographical error in the Notes section was corrected: “The genotype carried one other allele of IGHV4-39 (IGHV4-31*01, and a variant allele with a low number of associated reads that likely represents 3’-trimmed reads of IGHV4-39*01).” was corrected to “The genotype carried one other allele of IGHV4-39 (IGHV4-39*01, and a variant allele with a low number of associated reads that likely represents 3’-trimmed reads of IGHV4-39*01).”.

William Lees
2023-07-10 11:24:41
Version 3 published

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

Changes from previous version

v2v3
CuratorMats OhlinWilliam Lees
Curator addressDept. of Immunotechnology, Lund University, Medicon Village building 406, S-22381 Lund, SwedenBirkbeck College, University of London, Malet Street, London
Alternative namesIGHV4-39*01 G315A
Chromosome14
MappedFalse
FunctionalityFORF
Inference TypeRearrangedRearranged Only
Subgroup typenone
Full Sequence
Codon Frame1
Paralog RepFalse
Extension?FalseTrue
3' ExtensionA
5' Extension
Noteschanged

Versions

All published versions of this sequence.

Sequence NameIMGT NameVersionDate
IGHV4-39*i0312022-07-25
IGHV4-39*i0322023-06-02
IGHV4-39*i0332023-07-10