Is there a reference database where I can find the expected copy number of a given gene in the human germline genome?
It is my understanding that most human genes have 1 copy on each chromosome. However, there are genes that are commonly deleted or duplicated.
In other organisms I know elephants have many copies of TP53.
1 answer
Based on the current gene annotation found in https://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_48/gencode.v48.annotation.gtf.gz one can count the gene name entries that are labeled "protein_coding" using a small script
$ more gene.sh
#!/bin/bash
awk '$3 == "gene" && $0 ~ /gene_type "protein_coding"/ {
match($0, /gene_name "([^"]+)"/, arr)
print arr[1]
}' "$1" | sort | uniq -c | sort -nr
If you run the script using the file above, you can count gene entries (Note: these are protein coding genes).
./gene.sh gencode.v48.annotation.gtf > human_genes
There are only a few two copy genes (where are rest appear to be single copy).
2 ZBED1
2 WASH6P
2 VAMP7
2 SLC25A6
2 SHOX
2 PPP2R3B
2 POLR2J3
2 PLCXD1
2 PINX1
2 PDE8B
2 PDE4C
2 P2RY8
2 MATR3
2 KYAT1
2 IL9R
2 IL3RA
2 HERC3
2 GTPBP6
2 FAM174C
2 DUSP13B
2 DHRSX
2 CSF2RA
2 CRLF2
2 CD99
2 C4orf36
2 ASMTL
2 ASMT
2 AKAP17A
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