Details

SpeciesHuman_TCR
Species subgroup
Subgroup typenone
Sequence NameTRBV7-7*i01
IUIS Name
Alternative namesTRBV7-7*01 C315T, TRBV7-7*01_S0326
Affirmation Level1
Full Sequence
Coding Sequence
FunctionalityF
Inference TypeUnrearranged and Rearranged
Mapped
Paralogs
Paralog Rep

Evidence

The table below lists submissions to IARC , and the inferences within them, on which this IARC-affirmed sequence is based.

'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 OW165666C9P4_I9_S1_ogrdb_reportTRBV7-7*01_C315T

Observations in VDJbase

Inferred sequences in VDJbase that match this sequence:

VDJbase Allele NameSubjectsSequence Match
TRBV7-7*01_c315t 28

Un-rearranged Observations

Un-rearranged sequence observations that support this sequence:

AccessionTypeRepositoryStartEnd
AC229888LocationalGenBank5003250321
MZ339373NonlocationalGenBank335624

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 IDA02570
CuratorMats Ohlin
Curator addressDept. of Immunotechnology, Lund University, Medicon Village building 406, S-22381 Lund, Sweden
Version1
Release Date2023-06-01
Release Notes

IARC affirms the sequence at Meeting 121 on May 8th, 2023

LocusTRB
Sequence TypeV
Gene Subgroup7
Gene Designation7
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 assessed at multiple meetings and a decision was taken during meeting 121 on May 8th, 2023.

TRBV7-7*01_C315T has been inferred in seventeen genotypes in the VDJbase P4 data set, including in VDJbase P4_I9_S1, a haplotypable data set (based on heterozygocity in TRBJ1-6). The genotype is also implied to carry TRBV7-7*01. No other gene apart from IGHV7-6 (alleles of which also carry C315) in the IMGT database is highly similar to these alleles of TRBV7-7. The novel allele is the most expressed allele in the repertoire (58% allelic frequency; 0.16% of the total error-free population). It is represented by 37 error-free sequences and 33 unique CDR3s in the error-free set. Haplotyping based on allelic diversity in TRBJ1-6 demonstrates association of TRBV7-7*01_C315T with only one of the haplotypes (only few recorded cases; TRBV7-7*01 was not associated with any allele of TRBJ1-6).

IARC affirms the sequence based on inference of expression data alone at Level 1 up to and including base 325. It is acknowledged that the allele most likely carries 1 additional base, typically C, at base position 326. Trailing ā€œ.ā€ indicates IARCā€™s opinion that the sequence is likely to contain additional 3ā€™-nucleotides for which there is insufficient evidence to make an affirmation.

>TRBV7-7*i01 (TRBV7-7*01_C315T)
GGTGCTGGAGTCTCCCAGTCTCCCAGGTACAAAGTCACAAAGAGGGGACAGGATGTAACTCTCAGGTGTGATCCAATTTCGAGTCATGCAACCCTTTATTGGTATCAACAGGCCCTGGGGCAGGGCCCAGAGTTTCTGACTTACTTCAATTATGAAGCTCAACCAGACAAATCAGGGCTGCCCAGTGATCGGTTCTCTGCAGAGAGGCCTGAGGGATCCATCTCCACTCTGACGATTCAGCGCACAGAGCAGCGGGACTCAGCCATGTATCGCTGTGCTAGCAGCTTAG.

The allele has also been identified in a separate study as TRBV7-7*01_S0326 and Sanger validated (GenBank MZ339373) (Corcoran et al. (2023) Immunity 56, 635-652.E6 (DOI: 10.1016/j.immuni.2023.01.026)). It has been seen in a total of six Sanger sequenced genomic clones derived from two subjects.

>MZ339373
TTGAGAGAGGAAGTGATGTCACTGTGGGAACTGCCCTGTGGAGACAAGGACATCCCTCATCCTCCGCTCCTGCTCACAGTGACACTGATCTGGTAAAGCCCCCATCCTGGTCTGACACTGTCATGGGTACCAGTCTCCTATGCTGGGTGGTCCTGGGTTTCCTAGGGACAGGTGAGTCCTCAAAACACAAAGTAGTTTCATATTTTTTCTGTATGTAGGTGTGTGTGTGTATGCATGTGTGTCTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGAGATGACTACAAATGTTTTCCTTATTCTGTTGCCAGATTCTGTTTCCACAGATCACACAGGTGCTGGAGTCTCCCAGTCTCCCAGGTACAAAGTCACAAAGAGGGGACAGGATGTAACTCTCAGGTGTGATCCAATTTCGAGTCATGCAACCCTTTATTGGTATCAACAGGCCCTGGGGCAGGGCCCAGAGTTTCTGACTTACTTCAATTATGAAGCTCAACCAGACAAATCAGGGCTGCCCAGTGATCGGTTCTCTGCAGAGAGGCCTGAGGGATCCATCTCCACTCTGACGATTCAGCGCACAGAGCAGCGGGACTCAGCCATGTATCGCTGTGCTAGCAGCTTAGCCACAGCATGGCACAGTCGCCTCCTTCCTGTTCACAAACCTCATCCTTCT

It has also been identified in a BAC clone with accession number AC229888.

IARC affirms the sequence based on combined inference and genomic evidence at Level 1 up to and including base 326.

>TRBV7-7*i01 (TRBV7-7*01_C315T)
GGTGCTGGAGTCTCCCAGTCTCCCAGGTACAAAGTCACAAAGAGGGGACAGGATGTAACTCTCAGGTGTGATCCAATTTCGAGTCATGCAACCCTTTATTGGTATCAACAGGCCCTGGGGCAGGGCCCAGAGTTTCTGACTTACTTCAATTATGAAGCTCAACCAGACAAATCAGGGCTGCCCAGTGATCGGTTCTCTGCAGAGAGGCCTGAGGGATCCATCTCCACTCTGACGATTCAGCGCACAGAGCAGCGGGACTCAGCCATGTATCGCTGTGCTAGCAGCTTAGC

Attachments

Supplementary Files
 Assessment of inference TRBV7-7*i01.pdf

History

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

Mats Ohlin
2023-06-01 22:13:07
Version 1 published

IARC affirms the sequence at Meeting 121 on May 8th, 2023

Versions

All published versions of this sequence.

Sequence NameIMGT NameAlternative namesInference TypeAffirmation LevelSpecies subgroupSubgroup typeVersionDate
TRBV7-7*i01TRBV7-7*01 C315T, TRBV7-7*01_S0326Unrearranged and Rearranged1none12023-06-01