Details


Species	Human
Species subgroup
Subgroup type
Sequence Name	IGHV4-59*i03
IUIS Name
Alternative names
Affirmation Level	1
Full Sequence
Coding Sequence
Functionality	ORF
Inference Type	Rearranged Only
Mapped	False
Paralogs
Paralog Rep	False

Observations in VDJbase

Inferred sequences in VDJbase that match this sequence:

VDJbase Allele Name	Subjects	Sequence Match
IGHV4-59*01_g267a	1

Un-rearranged Observations

Un-rearranged sequence observations that support this sequence:

Accession	Type	Repository	Start	End
OW151138	Inferred	GenBank	1	292

CDR delineation


CDR1 Start	76
CDR1 End	99
CDR2 Start	151
CDR2 End	171
CDR3 Start	286

Extension


3' Extension	A
3' start
3' end

Additional Information


Sequence ID	A02564
Curator	William Lees
Curator address	Birkbeck College, University of London, Malet Street, London
Version	2
Release Date	2023-07-10
Release Notes	Bulk upload of sequences for the AIRR-C Human IG germline sets
Locus	IGH
Sequence Type	V
Gene Subgroup	4
Gene Designation	59
Allele Designation	i03

Acknowledgements

Individuals acknowledged as contributing to this sequence:

No Items

Notes

Notes are added by IARC reviewers.


This inference was assessed at IARC meeting 100 (June 8th, 2022) and meeting 101 (July 21st, 2022). IGHV4-5901_G267A was inferred in subject S36 (VDJ-base: P1_I39_S1). The genotype carried one other allele of IGHV4-59. This sample carries few IGHV reads. The inference was consequently supported by a relative small number of sequences (60) and unmutated sequences (43), a relatively low overall frequency in the unmutated population (0.58%) and a small but diverse set of unique CDR3s (43) in the unmutated sequence set. Its allelic ratio was 31%. Haplotyping based on allelic diversity in IGHJ6 was possible with excellent separation from reads associated to IGHV4-5901 (IGHV4-5901_G267A: 0:100; IGHV4-5901: 100:0). 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 IGHV4-59*i03. Additional information for this sequence was imported into OGRDB via bulk update with the following notes: Sequence annotation is based on Genbank sample OW151138

This inference was assessed at IARC meeting 100 (June 8th, 2022) and meeting 101 (July 21st, 2022).

IGHV4-59*01_G267A was inferred in subject S36 (VDJ-base: P1_I39_S1). The genotype carried one other allele of IGHV4-59. This sample carries few IGHV reads. The inference was consequently supported by a relative small number of sequences (60) and unmutated sequences (43), a relatively low overall frequency in the unmutated population (0.58%) and a small but diverse set of unique CDR3s (43) in the unmutated sequence set. Its allelic ratio was 31%. Haplotyping based on allelic diversity in IGHJ6 was possible with excellent separation from reads associated to IGHV4-59*01 (IGHV4-59*01_G267A: 0:100; IGHV4-59*01: 100:0). 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 IGHV4-59*i03.

Additional information for this sequence was imported into OGRDB via bulk update with the following notes:
Sequence annotation is based on Genbank sample OW151138

Attachments

No Items

History

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


Mats Ohlin 2022-09-28 10:41:40	Version 1 published The allele was published by IARC on Sept 28, 2022.


William Lees 2023-07-10 11:24:41	Version 2 published Bulk upload of sequences for the AIRR-C Human IG germline sets

Changes from previous version

	v1	v2
Curator	Mats Ohlin	William Lees
Curator address	Dept. of Immunotechnology, Lund University, Medicon Village building 406, S-22381 Lund, Sweden	Birkbeck College, University of London, Malet Street, London
Alternative names	IGHV4-59*01 G267A
Chromosome		14
Mapped		False
Functionality	F	ORF
Inference Type	Rearranged	Rearranged Only
Subgroup type	none
Full Sequence
Codon Frame	1
Paralog Rep		False
Extension?	False	True
3' Extension		A
5' Extension
curational_tags	likely_truncated	likely_full-length
Notes		changed

Versions

All published versions of this sequence.

Sequence Name	IMGT Name	Alternative names	Inference Type	Affirmation Level	Species subgroup	Subgroup type	Gene start	Gene end	UTR 5' Start	UTR 5' End	L-PART1 Start	L-PART1 End	L-PART2 Start	L-PART2 End	CDR1 Start	CDR1 End	CDR2 Start	CDR2 End	CDR3 Start	v_rs_start	v_rs_end	d_rs_3_prime_start	d_rs_3_prime_end	d_rs_5_prime_start	d_rs_5_prime_end	j_rs_start	j_rs_end	Codon Frame	Version	Date
IGHV4-59*i03		IGHV4-59*01 G267A	Rearranged	1		none	1	292							76	99	151	171	286									1	1	2022-09-28
IGHV4-59*i03			Rearranged Only	1			1	292							76	99	151	171	286										2	2023-07-10