1

Many to 1 Gene Associations

The following slides show a few examples of gene predictions by one annotation group that overlap one or more genes from another group.

Some of the examples that follow also illustrate issues related to - differences in annotation type (e.g., pseudogene versus

gene),and -in confusing nomenclature (e.g., different genes assigned the same official gene name).

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2:110788585..110968584One gene or two?

Orientation issue for OTT15152?

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8:4238129..4254528 One gene or two?

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3:105659594..105759593One gene or two?

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11:69491920..69516919 One gene or two or three?

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5:106920574..107155573 One gene or two or three?

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6:145313224..145563223One gene or two?

The VEGA gene model seems to unite two separate gene models in NCBI

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One gene or two?9:15109186..15189185

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7:127057560..127247315 One gene or two?

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7:52670474..52680473 One gene or two?

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4:146600055..146731054 One gene or two?

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2:37243166..37343165n:mENSMUSG00000050714 and ENSMUSG00000066798 overlap OTTMUSG00000012648 and OTTMUSG00000012652

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2:155895575..155939706n:mENSMUSG00000074643 overlaps ENSMUSG00000038171 OTTMUSG00000016087, OTTMUSG00000016088, and OTTMUSG00000019746

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6:113326848..113366847 n:mOTTMUSG00000017554 overlaps OTTMUSG00000016376 and EG68089 and EG101100.

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8:47538900..47638899 Are EG667337 and EG14081 different genes?

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7:126992968..127042967 Are EG233805 and EG1000043396 different genes?

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6:122655579..122665578 Are EG71950 and EG100038891 different genes?

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16:84828048..84836547 Are EG11957 and EG100039950 different genes?

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7:87385985..87410984 Are EG61000042379 and EG269954 different genes?

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9:43622106..43900000Are EG61000042548 and EG21838 different genes?

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13:22073239..22080498 Are OTT00466 and OTT13227 different genes?

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4:122937497..122988738 Are OTT08975 and OTT08978 different genes?

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3:94933437..94938148 Are OTT22306 and OTT19657 different genes?

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3:107728458..107736457 Are OTT25890 and OTT07101 the same gene?

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1:172123537..172148536 Are OTT21542 and OTT21543 different genes?

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1:173164903..173177002Are OTT21571 and OTT21573 different genes?

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2:90744183..90753182 Are OTT14319 and OTT14315 different genes?

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4:42236997..42261996 Are ENS78738 and ENS78736 different genes?

Are the genes predicted new members of the chemokine (C-C motif) ligand family?

In Ensembl multiple gene predictions are assigned to the same gene symbol/MGI id.

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15:79611961..79691960 One gene or two or three?

Are Nptxr and Cbx6 Overlapping?

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2:120535197..120698446 One gene or two?

Are Cdan1 and Ttbk2 Overlapping?

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X:9598695..9848694Srpx and Rpgr Overlapping?

One gene or two?

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2:181092767..181132366 Zgpat and Lime1 Overlapping?

One gene or two?

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5:31435474..31485473One gene or two?

Mpv17 and Gtf3c2 overlapping?

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16:96582252..96792251 One gene or two?

Are Pcp4 and Igsf5 two different genes?

Next slide

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In Ensembl currently it looks as though Pcp4 and Igsf5 are considered synonyms for the same gene?

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6:87895874..87954921 One gene or two?

NCBI gene is a pseudogene, Ensembl gene is a protein coding gene.

Pseudogene

Protein coding gene

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13:75781991..75782990

Pseudogene

Protein coding gene

Protein coding gene

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14:3046445..3080444

Pseudogene

Protein coding gene

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Retrotransposed vs pseudogene6:128882645..128993644

Pseudogene

Pseudogene

Retrotransposed

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Gene Family Challenges

killer cell lectin-like receptor (Klra) family

UDP glucuronosyltransferase 1 family

Gene families present many challenges to determining equivalency among gene predictions and for nomenclature. Examples from two gene families are shown in the following slides….

cysteine-rich perinuclear theca

C-type lectin domain family 2

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6:129837719..130337718 killer cell lectin-like receptor (Klra) family

Next slide

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6:130198815..130298814 killer cell lectin-like receptor (Klra) family

Gene identity crisis!

Pseudogene

Protein coding gene

Protein coding gene

Next slide

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6:130275414..130375413 1. Overlapping NCBI annotation2. Overlapping features of different types

1.

2.

Pseudogene

Protein coding gene

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1:89943192..90125441

Next slide

UDP glucuronosyltransferase 1 family

Ensembl maintains a single gene id for all of the members of the family.

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9:24428665..24431164cysteine-rich perinuclear theca

Gene identity crisis!

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C-type lectin domain family 2 6:128882645..128993644

Ensembl and VEGA predict only a single gene with multiple transcripts rather than two genes Clec2g and Clec2f.

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Unique to MGI

MGI does not have a high-throughput computational genome annotation pipeline. However, we integrated the results of high throughput cDNA sequencing projects into the database prior to the availability of the mouse genome. Many of these genes have remained unique to MGI.

The following slides illustrate several cases where MGI has a gene that has not been predicted by one of the three major annotation groups.

Many (most) of these MGI-unique genes are from the RIKEN cDNA sequencing initiative. Many of them likely represent non-protein coding genes.

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11:79796866..79857365

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9:106742778..106752777 Unique to MGI

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11:69491920..69516919