How can a gene exist on three different chromosomes!?!?

Question

[sviatoslav.kendall]

I recently downloaded a list of genes from the UCSC Genome browser from the "Table Browser" section. I used the following setting from the dropdown menu:

clade: Mammal

genome: Human

assembly: Feb.2009(GRCh37/hg19)

group: Genes and Gene Predictions

track: RefSeq Genes

table: refGene

region: genome

After unzipping the file, I had a table with the following columns:

1. #bin
2. name
3. chrom
4. strand
5. txStart
6. txEnd
7. cdsStart
8. cdsEnd
9. exonCount
10. exonStarts
11. exonEnds
12. score
13. name2
14. cdsStartStat
15. cdsEndStat
16. exonFrames

At some point, I noticed something weird and ran the following command:

grep "SNORD141B" All_Genes.tsv | cut -f3,7,8,13 | less

which returned:

chr5    14652491        14652491        SNORD141B
chr6    74228161        74228161        SNORD141B
chr9    135895921       135895921       SNORD141B

How could this gene exist on three different chromosomes? I've looked up "snord141b" on Gene Cards and found nothing. This is not an urgent or important question for me but I am perplexed nonetheless. Any clue how/why this gene shows up in these three different genomic regions?

[GenoMax]

Like rDNA repeat which has ~400 copies on 5 chromosomes: entire human rDNA

Answer 1

[Ram]

It is a small nuclueolar RNA (snoRNA). These are known to be present in multiple copies in the genome, I think.

Answer 2

[Chris Miller]

The annotations are right.

To prove it to yourself, grab the sequence here: https://www.ncbi.nlm.nih.gov/nuccore/NR_132981

Blat it here: https://genome.ucsc.edu/cgi-bin/hgBlat

and look at the results:

   ACTIONS      QUERY           SCORE START  END QSIZE IDENTITY CHRO STRAND  START    END      SPAN
---------------------------------------------------------------------------------------------------
browser details YourSeq          105     1   105   105 100.0%     5   -   14652278  14652382    105
browser details YourSeq          105     1   105   105 100.0%     9   +  133020430 133020534    105
browser details YourSeq          104     1   105   105 100.0%     6   -   73518245  73518438    194

Sure enough - this RNA species is present several times in the genome. :)

[Ram]

Isn't that redundant? Seeing how the data is from UCSC, Blat to hg19 is just self-affirmation, no? I'm curious on why this is seen - why snoRNAs are found in multiple copies.

[Chris Miller]

a) Why wouldn't there be multiple copies? Evolution isn't designed for non-redundancy - Gene duplications happen all the time. Either this is a recent event in the human lineage, or there is a high level of constraint on the sequence that keeps them all around.

b) blat tells us that it's not just an annotation error, or different sequences with a namespace collision. This sequence really does appear three times.

[GenoMax]

In general RNA genes are in multiple copies because a lot of RNA may be needed in a short amount of time. See: http://www.ncbi.nlm.nih.gov/books/NBK26887/

In contrast, the RNA components of the ribosome are final gene products, and a growing mammalian cell must synthesize approximately 10 million copies of each type of ribosomal RNA in each cell generation to construct its 10 million ribosomes. Adequate quantities of ribosomal RNAs can be produced only because the cell contains multiple copies of the rRNA genes that code for ribosomal RNAs (rRNAs). Even E. coli needs seven copies of its rRNA genes to meet the cell's need for ribosomes. Human cells contain about 200 rRNA gene copies per haploid genome, spread out in small clusters on five different chromosomes (see Figure 4-11), while cells of the frog Xenopus contain about 600 rRNA gene copies per haploid genome in a single cluster on one chromosome