I do not get what I expected from Biomart
0
0
Entering edit mode
3.6 years ago
ManuelDB ▴ 110

I am using Biomart to get transcripts start and end from a list of 87 NM_transcripts I have like this

NM_000090.3

NM_000138.4

NM_000169.2

The steps I am following are: CHOOSE DATABASE ---> Ensemble Genes 105

CHOOSE DATASET ---> Human genes

Go to Filters, go to GENE, click on Input external references ID list [Max 500 advised.

Select RefSeq mRNA id(s) [e.g. NM_000014]

Copy and paste my transcripts

Click on count (to see if input was accepted)

Click on Attributes

Click on GENE

Select Gene start (bp) and Gene end (bp) and also Gene name (to check if they match because I also have this info.

Click Results

And then I got this

Gene start (bp) Gene end (bp)   Gene name

577 647 MT-TF

648 1601    MT-RNR1

1602    1670    MT-TV

1671    3229    MT-RNR2

3230    3304    MT-TL1

3307    4262    MT-ND1

4263    4331    MT-TI

4329    4400    MT-TQ

4402    4469    MT-TM

4470    5511    MT-ND2

What is significantly less genes that the ones I introduce

What I am doing wrong?

Biomart Ensemble Bed • 794 views
ADD COMMENT
0
Entering edit mode

Looks like these are genes in Mitochondria? There are only 37 of those in Ensembl.

Gene stable ID  Transcript stable ID    Gene name   RefSeq match transcript (MANE Plus Clinical)
ENSG00000210049     ENST00000387314     MT-TF   
ENSG00000211459     ENST00000389680     MT-RNR1     
ENSG00000210077     ENST00000387342     MT-TV   
ENSG00000210082     ENST00000387347     MT-RNR2     
ENSG00000209082     ENST00000386347     MT-TL1  
ENSG00000198888     ENST00000361390     MT-ND1  
ENSG00000210100     ENST00000387365     MT-TI   
ENSG00000210107     ENST00000387372     MT-TQ   
ENSG00000210112     ENST00000387377     MT-TM   
ENSG00000198763     ENST00000361453     MT-ND2  
ENSG00000210117     ENST00000387382     MT-TW   
ENSG00000210127     ENST00000387392     MT-TA   
ENSG00000210135     ENST00000387400     MT-TN   
ENSG00000210140     ENST00000387405     MT-TC   
ENSG00000210144     ENST00000387409     MT-TY   
ENSG00000198804     ENST00000361624     MT-CO1  
ENSG00000210151     ENST00000387416     MT-TS1  
ENSG00000210154     ENST00000387419     MT-TD   
ENSG00000198712     ENST00000361739     MT-CO2  
ENSG00000210156     ENST00000387421     MT-TK   
ENSG00000228253     ENST00000361851     MT-ATP8     
ENSG00000198899     ENST00000361899     MT-ATP6     
ENSG00000198938     ENST00000362079     MT-CO3  
ENSG00000210164     ENST00000387429     MT-TG   
ENSG00000198840     ENST00000361227     MT-ND3  
ENSG00000210174     ENST00000387439     MT-TR   
ENSG00000212907     ENST00000361335     MT-ND4L     
ENSG00000198886     ENST00000361381     MT-ND4  
ENSG00000210176     ENST00000387441     MT-TH   
ENSG00000210184     ENST00000387449     MT-TS2  
ENSG00000210191     ENST00000387456     MT-TL2  
ENSG00000198786     ENST00000361567     MT-ND5  
ENSG00000198695     ENST00000361681     MT-ND6  
ENSG00000210194     ENST00000387459     MT-TE   
ENSG00000198727     ENST00000361789     MT-CYB  
ENSG00000210195     ENST00000387460     MT-TT   
ENSG00000210196     ENST00000387461     MT-TP   
ADD REPLY

Login before adding your answer.

Traffic: 3004 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6