Details


Species	Human
Species subgroup
Subgroup type
Sequence Name	IGLV6-57*04
IUIS Name	IGLV6-57*04
Alternative names	IGLV6-57*i01
Affirmation Level	1
Full Sequence
Coding Sequence
Functionality	ORF
Inference Type	Genomic and rearranged
Mapped	False
Paralogs
Paralog Rep	False

Observations in VDJbase

Inferred sequences in VDJbase that match this sequence:

VDJbase Allele Name	Subjects	Sequence Match
IGLV6-57*03_c21g	47

Un-rearranged Observations

Un-rearranged sequence observations that support this sequence:

Accession	Type	Repository	Start	End
MK308866	Inferred	GenBank	1	294

CDR delineation


CDR1 Start	138
CDR1 End	161
CDR2 Start	213
CDR2 End	221
CDR3 Start	336

Non-Core Regions


UTR 5' Start
UTR 5' End
L-PART1 Start
L-PART1 End
L_PART1
L-PART2 Start	52
L-PART2 End	62
L_PART2	GTTCTTGGGCC
v_rs_start	359
v_rs_end	397
V_HEPTAMER	CACAGTG
V_NONAMER	ACAGAAACT

Extension


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

Additional Information


Sequence ID	A00059
Curator	William Lees
Curator address	Birkbeck College, University of London, Malet Street, London
Version	3
Release Date	2023-07-10
Release Notes	Bulk upload of sequences for the AIRR-C Human IG germline sets
Locus	IGL
Sequence Type	V
Gene Subgroup	6
Gene Designation	57
Allele Designation	04

Acknowledgements

Individuals acknowledged as contributing to this sequence:

No Items

Notes

Notes are added by IARC reviewers.


At the IARC meeting on July 20th 2020, the following features of the inference in the S000028 submission were noted: The sequence was seen in 1.49% of all unmutated rearrangements, with 14,472 sequences including 1776 perfect alignments to the inferred allele. There was abundant variation in the CDR3 regions of the aligned sequences. The IGLV6-5701 allele was also present in the genotype, at a somewhat lower frequency. Haplotype data is unavailable. Plots of the final 3’ nucleotides were considered, but the variability seen made it impossible to be certain of the final two nucleotides of the germline sequence. The sequence, up to and including nucleotide 333, was affirmed as the Level 1 sequence, IGLV6-57i01. Uncertainty regarding nucleotides 334-335 will be indicated in IARC and OGRDB publications by two dots at the end of the affirmed sequence. Additional information for this sequence was imported into OGRDB via bulk update with the following notes: Sequence annotation is based on Genbank sample MW316677

At the IARC meeting on July 20th 2020, the following features of the inference in the S000028 submission were noted:

The sequence was seen in 1.49% of all unmutated rearrangements, with 14,472 sequences including 1776 perfect alignments to the inferred allele. There was abundant variation in the CDR3 regions of the aligned sequences. The IGLV6-57*01 allele was also present in the genotype, at a somewhat lower frequency. Haplotype data is unavailable. Plots of the final 3’ nucleotides were considered, but the variability seen made it impossible to be certain of the final two nucleotides of the germline sequence. The sequence, up to and including nucleotide 333, was affirmed as the Level 1 sequence, IGLV6-57*i01. Uncertainty regarding nucleotides 334-335 will be indicated in IARC and OGRDB publications by two dots at the end of the affirmed sequence.

Additional information for this sequence was imported into OGRDB via bulk update with the following notes:
Sequence annotation is based on Genbank sample MW316677

Attachments

No Items

History

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


Andrew Collins 2020-08-01 13:19:38	Version 1 published Published by the IARC on 1/8/2020.


William Lees 2020-08-10 15:55:56	Version 2 published Correct sequence name from IGLV-6-57*i01


Mats Ohlin 2021-04-29 22:32:20	*IMGT Name updated to IGLV6-5704** IMGT Name updated.


William Lees 2023-07-10 11:24:48	Version 3 published Bulk upload of sequences for the AIRR-C Human IG germline sets

Changes from previous version

	v2	v3
Curator		William Lees
Curator address	School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney Australia	Birkbeck College, University of London, Malet Street, London
Sequence Name	IGLV6-57*i01	IGLV6-57*04
Alternative names		IGLV6-57*i01
Mapped		False
Functionality	F	ORF
Inference Type	Rearranged Only	Genomic and rearranged
Species subgroup
Subgroup type
Gene Subgroup	-6	6
Allele Designation	i01	04
Full Sequence
Gene start	1	63
Gene end	294	356
L-PART2 Start		52
L-PART2 End		62
CDR1 Start	76	138
CDR1 End	99	161
CDR2 Start	151	213
CDR2 End	159	221
CDR3 Start	274	336
v_rs_start		359
v_rs_end		397
Paralog Rep		False
Extension?	False	True
3' Extension		CA
5' Extension
curational_tags		likely_full-length
Notes		changed

Versions

All published versions of this sequence.

Sequence Name	IMGT Name	Alternative names	Inference Type	Affirmation Level	Subgroup type	Gene start	Gene 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	Codon Frame	Version	Date
IGLV-6-57*i01			Rearranged Only	1		1	294					76	99	151	159	274				1	2020-08-01
IGLV6-57*i01	IGLV6-57*04		Rearranged Only	1		1	294					76	99	151	159	274				2	2020-08-10
IGLV6-57*04	IGLV6-57*04	IGLV6-57*i01	Genomic and rearranged	1		63	356			52	62	138	161	213	221	336	359	397		3	2023-07-10
IGLV6-57*04	IGLV6-57*04	IGLV6-57*i01	Genomic and rearranged	1	none	183	476	1	46	172	182	258	281	333	341	456	479	517	1	4	2024-02-22