Genome and gene alterations by insertions and deletions in the evolution of human and chimpanzee chromosome 22

BMC Genomics

Table 2 Laboratory results of the insertions/deletions that are predicted to have an effect on coding regions of genes

Gene	Size (bp)	Impact	Confirmation	Ancestral state
NEFH	24	truncation from 1020 to 753 aas	yes	unknown
CELSR1	21	7 aa insert	unknown	-
FLJ44385	68	truncation from 125 to 113 aas	yes	Del
UNC84B	65	truncated from 717 to 68 aas	yes	Del
TCF20	515	truncation from 1960 to 1893 aas	unknown	-
SMC1L2	74	truncates from 1235 to 1220 aas	yes	Ins
FLJ41993	36	undetermined	yes	unknown
RUTBC3	250	truncates from 849 to 734 aas	different ins	unknown
NEFH	18	truncated from 1020 to 252 aas	unknown	-
RUTBC3	13	substitution in protein	unknown	-
Various*	10–148	splice site mismatch with no impact

With the use of GENSCAN, the 23 indels found in coding exons or in splice site regions of the human REFseq genes were analyzed for their impact to these genes. Out of the 23, 10 of these indels impact genes through truncation/insertion of amino acids or substitution within a protein. The other 13 indels had no affect on the proteins generated from genes DGCR8, ZDHHC8, BRD1, SELO, SBF1, CHKB, PCQAP, BCR, PRODH, RUTBC3, CYP2D7P1, &ACSIN2. In order to confirm the presence of an insertion or a deletion, the loci and its harboring regions were sequenced in each of the species. Assembly confirmation is dependent on whether the indel product is completely present (all of the bases) in the corresponding species predicted. For gene FLJ44385, the indel was present in its entirety. The assembly was also confirmed for genes SMC1L2 and FLJ41993 with all of the bases of the indel present, however additional sequence was also detected. The inferred ancestral state of each indel is based on whether a species has the insertion or deletion of that locus and the species' position on the phylogenetic tree.
* DGCR8, ACSIN2, BCR, BRD1, CHKB, CYP2D7P1, DGCR8, PCQAP, PRODH, RUTBC3, SBF1, SELO, &ZDHHC8
**Indel verified and additional sequence is present

ISSN: 1471-2164