It is the case of V and J genes of IGK, IGL, TRA and TRG loci.
Example: the rearranged sequence with accession number AB006843
When we read the IMGT annotations (in IMGT/LIGM-DB), we note that this rearranged sequence of a kappa light chain comes from the genes and the alleles rearrangement: IGKV2-28*01 [or IGKV2D-28*01 (identical score)] and IGKJ2*01.
If, in IMGT Repertoire > Alignments of alleles, we look at the V and J germline genes from which the sequence derives, we observe:
It is the case of the V, D and J genes of IGH, TRB and TRD loci.
Example: the rearranged sequence with accession number AF052379.
When we read IMGT annotations (in IMGT/LIGM-DB), we note that this rearranged sequence of an heavy ../_FRchain comes from the genes and alleles rearrangement: IGHV5-51*03, IGHD1-7*01 and IGHJ4*02.
If, in IMGT Repertoire > Alignments of alleles, we look at the V, D and J germline genes from which the sequence derives, we observe:
No, it is not easy to identify and locate a D gene in a V-D-J junction. Indeed, it is a short gene (only a few tens nucleotides) which may have somatic mutations, deletions and nucleotide insertions (N-diversity) at the 5' and 3' ends.
268 sequences (01/07/2003)
22 sequences (01/07/2003)
ACcession number line
Feature Table lines
RN: Reference Number, RC: Reference Comment, RP: Reference Positions, RX: Reference Cross-reference, RA: Reference Author(s), RT: Reference Title, RL: Reference Location
Example: sequence with accession number M11954
In IMGT/LIGM-DB, the option "9 IMGT/V-QUEST analysis" allows to obtain the translation of JUNCTION as follows:
Translation of the JUNCTION 104 118 C S A K L V G T D T Q Y F G P G M11954 TGC AGT GCT AAA CTA GTA GGT ACA GAT ACG CAG TAT TTT GGC CCA GGC
TGC AGT GCT AAA CTA GTA GGT ACA GAT ACG CAG TAT TTT
Ngc=2/6, it means that among the 6 added nucleotides during the N-diversity, 2 are C or G
Yes, it is an adenine (A) downstream of the V-REGION
The CDR3-IMGT is 11 amino acids long.
Indeed, Cys 104 (2nd-CYS) and Trp/Phe 118 (J-TRP/J-PHE) are not included into the CDR3-IMGT.
In contrast, they are part of the junction and mark the junction ends.