Many articles on RNA-seq have shown that expression levels of certain mouse genes (such as GM22641, GM23935 and GM24703) change under various conditions. However, I couldn’t find their sequences in MGI or NCBI. Can anyone help find out this information?
None of these genes are in the current genome assembly. However, for Gm23935,
Gm23935 MGI Mouse Gene Detail - MGI:5453712 - predicted gene, 23935,
MGI includes a link to the Expression Atlas.
Hi David,
Thanks for the info!
How can we get the sequence of this gene?
These genes were created based on ENSEMBL release 73 (build 38) but they are no longer valid. You can probably use the coordinates to pull the sequence from a version of build 38, but they have been dropped from the current assembly, so I wouldn’t trust them.
Gene Gm22641 predicted gene, 22641 7 In Progress J:91388 ENSMUSG00000093098 is on chr7:130834437-130834523, + strand. ENSEMBL annotation of mouse reference assembly GRCm38, Gene type: miRNA; Gene Name: Mir5102.
http://uswest.ensembl.org/Mus_musculus/Gene/Idhistory?g=ENSMUSG00000093098
Based on the coordinates of the original ENSEMBL gene, chr7:130834437-130834523, it is likely a rRNA according to UCSC Browser.
“ENSMUSG00000093098 is on chr7:130834437-130834523, + strand. ENSEMBL annotation of mouse reference assembly GRCm38, Gene type: miRNA; Gene Name: Mir5102.
Gene Gm23935 predicted gene, 23935 16
ENSMUSG00000076258 is on chr16:11144125-11144181, + strand.
ENSEMBL annotation of mouse reference assembly GRCm38, Gene type: miRNA; Gene Name: mmu-mir-689-2.
Gene Gm24703 predicted gene, 24703 5
ENSMUSG00000095995 is on chr5:12155104-12155174, + strand. ENSEMBL annotation of mouse reference assembly GRCm38, Gene type: miRNA; Gene Name: AC134325.1.
Lucky to have found a true expert. Thank you so much, David!
Hi David,
I have been trying to access Ensembl 73, but it is not available (see list below). How did you access Ensembl 73? I wish I could show you a picture or provide a link but I was not allowed to because I am a new user.
See or search Ensembl Archives (linked not allowed)
Ensembl 93: Jul 2018
Ensembl 92: Apr 2018
Ensembl 91: Dec 2017
Ensembl 80: May 2015
Ensembl 77: Oct 2014
Ensembl 75: Feb 2014
Ensembl 54: May 2009
IN search of Gm24703 sequence, we found the following info provided by Alliance of Genome Resources.
Gm24703
Species: Mus musculus
Symbol: Gm24703
Name: predicted gene, 24703
Synonyms: None
Biotype: miRNA gene
Automated Description: Not Available
MGI Description: Not Available
Cross References: Not Available
No sequence is available.