XB-FEAT-947684: Difference between revisions
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=slc45a2= | |||
This is the community wiki page for the gene ''slc45a2'' please feel free to add any information that is relevant to this gene that is not already captured elsewhere in Xenbase | This is the community wiki page for the gene ''slc45a2'' please feel free to add any information that is relevant to this gene that is not already captured elsewhere in Xenbase | ||
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'''<u>Analysis of Pseudogene</u>''' | '''<u>Analysis of Pseudogene</u>''' | ||
Entrez gene 108705441 was identified as slc45a2.S via BLAST and synteny analyses. The mRNA of slc45a2.S was extracted from JBrowse and multi-sequence aligned against the RefSeq mRNAs of slc45a2 (X. tropicalis: NM_001011335.1) and slc45a2.L (X. laevis: NM_001095910). The alignment | Entrez gene 108705441 was identified as slc45a2.S via BLAST and synteny analyses. The mRNA of slc45a2.S was extracted from JBrowse and multi-sequence aligned against the RefSeq mRNAs of slc45a2 (X. tropicalis: NM_001011335.1) and slc45a2.L (X. laevis: NM_001095910). The alignment shows erroneous stop codons, frameshifts, and the mutation of the ATG start site. Each of these mutations would cause a misformed or untranslated protein. | ||
The frame shift and stop codon mutations were confirmed by performing a tBLASTn between the slc45a2.L protein (NP_001089379.1) and the pseudogene mRNA. This analysis | [[File:Slc45a2_-_Multi-sequence_alignment.pdf|Multi-sequence alignment]] | ||
The frame shift and stop codon mutations were confirmed by performing a tBLASTn between the slc45a2.L protein (NP_001089379.1) and the pseudogene mRNA. This analysis shows multiple stop codons (red) and the multiple frameshifts, designated by switching from frame 1 to frame 2 in order for the mRNA to stay in-frame with the protein. | |||
[[File:Slc45a2_-_tBLASTn.pdf|tBLASTn]] | |||
To confirm the start codon, orthologs were collected from the Ensembl slc25a2 gene tree and multi-sequence aligned. Before alignment, low quality proteins were removed. This left the following alignment sets: | To confirm the start codon, orthologs were collected from the Ensembl slc25a2 gene tree and multi-sequence aligned. Before alignment, low quality proteins were removed. This left the following alignment sets: | ||
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* Coelacanth | * Coelacanth | ||
Because the Mammalia and Amniota+ sequences have different beginning CDSs, these groups were multi-sequence aligned separately, and consensus sequences were established. These consensus sequences were then multi-sequence aligned with the NCBI slc45a2 and slc45a2.L proteins to determine a consensus start codon. The result | |||
]] | Because the Mammalia and Amniota+ sequences have different beginning CDSs, these groups were multi-sequence aligned separately, and consensus sequences were established. These consensus sequences were then multi-sequence aligned with the NCBI slc45a2 and slc45a2.L proteins to determine a consensus start codon. The result shows that the Xenopus slc45a2 start codons show consensus with fish and amniotes. This provides strong evidence that the mutation in the aligned region of the slc45a2.s mRNA was the canonical start codon. | ||
[[File:Slc45a2_-_Start_Codon_-_Consensus.pdf|Consensus Start Codon]] | |||
Latest revision as of 06:29, 17 February 2020
slc45a2
This is the community wiki page for the gene slc45a2 please feel free to add any information that is relevant to this gene that is not already captured elsewhere in Xenbase
slc45a2.S is a pseudogene. There are several mutations that disrupt protein translation when compared to mRNA of the L homeolog (NM_001095910.1) and the X. tropicalis ortholog (NM_001011335.1). The first four of these mutations are:
| Mutation | Result | Note |
| c.110T>G | Removed Start Codon | Changed ATG to AGG |
| c.235C>T | Added Stop Codon | Changed CAG to TAG |
| c.445C>T | Added Stop Codon | Changed CGA to TGA |
| c.574-578delATTTT | Frameshift | NM_001095910.1 (L homeolog) used a nucleotide reference |
Note: Because LOC108705441 is a pseudogene, all numbers are relative to the beginning of the cDNA, not the A of the ATG start codon
Analysis of Pseudogene
Entrez gene 108705441 was identified as slc45a2.S via BLAST and synteny analyses. The mRNA of slc45a2.S was extracted from JBrowse and multi-sequence aligned against the RefSeq mRNAs of slc45a2 (X. tropicalis: NM_001011335.1) and slc45a2.L (X. laevis: NM_001095910). The alignment shows erroneous stop codons, frameshifts, and the mutation of the ATG start site. Each of these mutations would cause a misformed or untranslated protein.
File:Slc45a2 - Multi-sequence alignment.pdf
The frame shift and stop codon mutations were confirmed by performing a tBLASTn between the slc45a2.L protein (NP_001089379.1) and the pseudogene mRNA. This analysis shows multiple stop codons (red) and the multiple frameshifts, designated by switching from frame 1 to frame 2 in order for the mRNA to stay in-frame with the protein.
To confirm the start codon, orthologs were collected from the Ensembl slc25a2 gene tree and multi-sequence aligned. Before alignment, low quality proteins were removed. This left the following alignment sets:
Mammals (Mammalia)
- Chimpanzee
- Rabbit
- Rat
- Macaque
- Squirrel
- Human
- Mouse
- Gorilla
- Elephant
Amniota, Frog, Fish (Amniota+)
- Painted turtle
- Zebrafish
- Duck
- Australian saltwater crocodile
- Zebra finch
- Chicken
- Coelacanth
Because the Mammalia and Amniota+ sequences have different beginning CDSs, these groups were multi-sequence aligned separately, and consensus sequences were established. These consensus sequences were then multi-sequence aligned with the NCBI slc45a2 and slc45a2.L proteins to determine a consensus start codon. The result shows that the Xenopus slc45a2 start codons show consensus with fish and amniotes. This provides strong evidence that the mutation in the aligned region of the slc45a2.s mRNA was the canonical start codon.