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. 2020 Apr 27;16(4):e1007837. doi: 10.1371/journal.pcbi.1007837

Table 4. Novel variations of D genes validated using genomic data from human, camel, rhesus macaque, mouse, rat, and rabbit datasets.

“Original” refers to the sequence in the IMGT database. In three of the inferred sequences, there is an extra nucleotide at the end that was not found in the genomic reads, e.g., the novel variation inferred from mice datasets TTTATTACTACGATGGTAGCTACg is only present as TTTATTACTACGATGGTAGCTAC in the genomic reads. Other polymorphisms that were found using genomic validation of the inferred genes are underlined. For example, GATACAGCGGGTACAGT was inferred by MINING-D as a variant of the macaque gene IGHD5S3*01, but the whole sequence GGGGATACAGCGGGTACAGTTAC was found in the genomic reads.

Human
IGHD3-10*01
Original        GTATTACTATGGTTCGGGGAGTTATTATAAC
N_Var-3        GTATTACTATGGTTCAGGGAGTTATTATAAC 		IGHD3-16*02
Original        GTATTATGATTACGTTTGGGGGAGTTATCGTTATACC
N_Var-0        ---TTATGATTACATTTGGGGGAGTTATCGTTAT---
Camel
IGHD3*01 (Alpaca)
Original        GTATTACTACTGCTCAGGCTATGGGTGTTATGAC
N_Var-1        ----GACTGCTATTCAGGCTCTTGGTGTTATG--
N_Var-0        ---TGACTACTGTTCAGGCTCTTGGTGT------ 		IGHD2*01 (Alpaca)
Original        ACATACTATAGTGGTAGTTACTACTACACC
N_Var-1        --ATATTGTAGTGGTGGTTACTGCTAC---
N_Var-0        GCATACTATAGTGGTGGTTACTAC------
IGHD4*01 (Alpaca)
Original        TTACTATAGCGACTATGAC
N_Var-1        CTACTATAGCGACTATG--
N_Var-0        CTACTATAACGAATATG-- 		IGHD6*01 (Alpaca)
Original        GTACGGTAGTAGCTGGTAC
N_Var-2        GTACGGTGGTAGCTGGTAC
IGHD5*01 (Alpaca)
Original        AGACTACGGGTTGGGGTAC
N_Var-0        ----TATGGGTT-GGGTAC
Rhesus Macaque
IGHD1S39*01
Original        GGTATAGTGGGAACTACAAC
N_Var-0        -----AGTGGGAGCTAC--- 		IGHD3S18*01
Original        GTACTGGGGTGATTATTATGAC
N_Var-0        --ACTGGAGTGATTATTA----
IGHD5S3*01
Original        GTGGATACAGTGGGTACAGTTAC
N_Var-0        -G-GATACAGCGGGTACAGT--- 		IGHD2S11*01
Original        AGAATATTGTAGTAGTACTTACTGCTCCTCC
N_Var-0        --C--ATTGTAGTGGTACTTACTGCTATG--
IGHD2S17*01
Original        AGAATACTGTACTGGTAGTGGTTGCTATGCC
N_Var-0        ----TACTGTACTGGTAGTGGTTGCTAC--- 		IGHD3S23*01
Original        GTATTACTATGATAGTGGTTATTACACCCACAGCGT
N_Var-0        ---TTACTATGGTAGTGGTTATTAC-----------
Mouse
IGHD1-1*01
Original        TTTATTACTACGGTAGTAGCTAC-
N_Var-0        TTTATTACTACGATGGTAGCTACg
Rat
IGHD1-3*01
Original        TTTTTAACTATGGTAGCTAC
N_Var-0        -TTTTAACTACGGTAGCTAC 		IGHD1-9*01
Original        TACATACTATGGGTATAACTAC-
N_Var-1        --CATACTACGGGTATACCTACg
IGHD1-12*02
Original        TTTATTACTATGATGGTAGTTATTACTAC-
N_Var-0        -TTATTACTATGATGGTACTTATTACTACg
Rabbit
IGHD6-1*01
Original        --------------GTTACTATAGTTATGGTTATGCTTATGCTACC
N_Var-4        GTTACTATACTTATGGTTATGCTGGTTATGCTTATGCTACC
N_Var-3        GTTA------TGCTGGTTATGCTGGTTATGGTTATGCTACC 		IGHD1-1*01
Original        GCATATACTAGTAGTAGTGGTTATTATATAC
N_Var-2        GCATATGCTAGTAGTAGTGGTTATTAT----