Details

SpeciesHuman_TCR
Species subgroup
Subgroup typenone
Sequence NameTRBV12-4*i01
IUIS Name
Alternative names
Affirmation Level1
Full Sequence
Coding Sequence
FunctionalityF
Inference TypeUnrearranged and Rearranged
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
S00036 OW166725S24P4_I24_S1_ogrdb_reportTRBV12-4*01_C87T

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:

VDJbase Allele NameSubjectsSequence Match
TRBV12-4*01_c87t 19

Un-rearranged Observations

Un-rearranged sequence observations that support this sequence:

AccessionTypeRepositoryStartEnd
DOI: 10.1016/j.xgen.2022.100228 (Supplementary Table S4)LocationalJournal supplementary information

Non-Core Regions

UTR 5' Start
UTR 5' End
L-PART1 Start
L-PART1 End
L-PART2 Start
L-PART2 End
v_rs_start
v_rs_end

Extension

3' Extension
3' start
3' end
5' start
5' end

Additional Information

Sequence IDA02565
Curator addressDept. of Immunotechnology, Lund University, Medicon Village building 406, S-22381 Lund, Sweden
Version1
Release Date2023-03-20
Release Notes

Published by IARC on March 20, 2023

LocusTRB
Sequence TypeV
Gene Subgroup12
Gene Designation4
Allele Designationi01

Acknowledgements

Individuals acknowledged as contributing to this sequence:

NameInstitutionORCID ID
William LeesBirkbeck College, University of London, Malet Street, London
Ayelet PeresBar-Ilan University, Ramat-Gan, Israel
Gur YaariBar-Ilan University, Ramat-Gan, Israel

Notes

Notes are added by IARC reviewers.

This inference was discussed during IARC Meeting 112 on Jan 9th, 2023.

TRBV12-4*01_C87T has been inferred in nine genotypes in the VDJbase P4 data set, including in VDJbase P4_I24_S1, a haplotypable data set (based on heterozygocity in TRBJ1-6). The genotype is also implied to carry TRBV12-4*01. No other gene apart from TRBV12-3 in the IMGT database is closely related to these alleles of TRBV12-4. The novel allele is the most expressed allele in the repertoire (72% allelic frequency; 1.47% of the total error-free population). It is represented by 499 error-free sequences and 467 unique CDR3s in the error-free set. Haplotyping based on allelic diversity in TRBJ1-6 demonstrates perfect separation from TRBV12-4*01. The data defining the 3ā€™-end of sequences is negatively affected by trimming during the rearrangement process. IARC affirms the sequence (as TRBV12-4*i01) at Level 1 up to and including base 323 based on inference alone. It is acknowledged that the allele most likely carries 3 additional bases, typically AGC, at base positions 324-326. Analysis of sequences that have not been trimmed upstream of each position strongly suggest that the 3ā€™-end of the sequence is indeed AGC. For many applications, IARC recommends the use of germline sequences representing their most likely full length base sequence. There is, however, insufficient evidence to make an affirmation of the full length sequence based on inference alone. In this case genomic data confirming the full length sequence is available from two other subjects (Rodrigues et al. Cell Genomics 2, 12, 100228 (https://doi.org/10.1016/j.xgen.2022.100228 (Supplementary Table S4)). Hence the full length sequence is approved based on inference in combination with genomic data. The locus that carries human TRBV genes is highly complex. Genes may be duplicated or deleted, and identical sequences may be found in more than one gene. The name (with an ā€œiā€ allele designation) of an inferred allele does not imply that its precise genetic location is known. It just relates to the most similar allele presently found in the IMGT database, or to the gene with the lowest alphanumeric value, should alleles of multiple genes be equally matched to the novel allele in question. The only other similar gene has been mentioned above (TRBV12-3).

Attachments

No Items

History

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

Mats Ohlin
2023-03-20 09:04:32
Version 1 published

Published by IARC on March 20, 2023

Versions

All published versions of this sequence.

Sequence NameIMGT NameAlternative namesInference TypeAffirmation LevelSpecies subgroupSubgroup typeVersionDate
TRBV12-4*i01Unrearranged and Rearranged1none12023-03-20