Details

OrganismHuman
Sequence NameIGLV2-14*i01
IMGT Name
Affirmation Level1
Full Sequence
Coding Sequence
FunctionalTrue
Inference TypeRearranged Only
Alternative names
Paralogs

Evidence

The table below lists the submissions, and the inferences within them, on which this published sequence is based. The list may be short when the sequence is first published, containing, for example, reference to just a single submission, but is expected to grow over time as additional inferences are submitted.

'Sequence Match' indicates whether the inference exactly matches the sequence, and clicking on the tick or cross will provide an alignment. Mismatches may be caused, for example, by the inclusion of leader sequences, or nucleotides in the inference which do not in IARC's opinion have sufficient evidence for inclusion in the sequence.

Submission IDAccession NoSubject IDGenotype NameSequence NameSequence Match
S00028 MK308863A007A007 VLIGLV2-14*03x

Supporting Observations

Sequences in other published genotypes which have been identified by IARC and support the inference:

No Items

Observations in VDJbase

Inferred sequences in VDJbase that match this sequence:

No Items

Extension

This affirmed sequence extends a partial sequence already affirmed and/or in IMGT GENE-DB.

5' ExtensionCAGTCTGCCCTGACTCAGCCTGC
5' start1
5' end23

Additional Information

Sequence IDA00053
CuratorMats Ohlin
Curator addressDept. of Immunotechnology, Lund University, Medicon Village building 406, S-22381 Lund, Sweden
Version1
Release Date2020-07-30 00:00:00
Release Notes

Submission published by IARC on July 30th 2020.

LocusIGL
Sequence TypeV
Gene Subgroup2
Gene Designation14
Allele Designationi01

Acknowledgements

Individuals acknowledged as contributing to this sequence:

NameInstitutionORCID ID
Néstor Vázquez BernatKarolinska Institutet SE-171 77 Stockholm

Notes

Notes are added by IARC reviewers.

Assessed by IARC on July 7, 2020 during meeting 57.

The committee considered IGLV2-14*03x (a 5’ extension of IGLV2-14*03) of submission S00028.

The sequence was seen in 6.08% of all unmutated rearrangements, with 71826 sequences including 7262 perfect matches to the inferred allele. The library had been generated from PBMC that had not been sorted for naïve B cells, resulting in the presence of reads of somatically hypermutated sequences in the data set, a fact that complicates the analysis. There was abundant variation in the CDR3 regions of the aligned sequences to an extent similar to that of other lambda germline alleles of this donor. One other alleles was present in the genotype. Haplotyping could not be performed. The inferred sequence includes 23 bases added to the 5’-end of incomplete reference allele IGLV2-14*03. There was support for the sequence being affirmed up to and including nucleotide 337, in line with IARC policy not to infer bases substantially affected by trimming during the rearrangement process, as a Level 1 sequence, with two additional 3’ nucleotide being likely present in the sequence. This is indicated in IARC and OGRDB publications by two dots at the end of the sequence. A genomic sequence (MK587524) has following the inference been cloned from the genotype of the donor that confirms the inference. It also confirms that bases 338-339 that cannot be inferred with confidence of the gene are T and C, respectively.

Attachments

Attachment File Name
 

History

History records log the times and reasons for the publication of each version of this sequence record.

Andrew Collins
2020-07-30 12:57:22
Version 1 published

Submission published by IARC on July 30th 2020.