Unable to find gene in UNIPORT

[oalavijeh]

Firstly, many thanks for taking the time to develop this really useful tool!

I am trying to run the following:

./lollipops IFT140 [some variants]

And getting:

GNC Symbol:  IFT140
Uniprot returned 8 hits for your gene symbol 'IFT140':
Entry   Entry name  Status  Gene names  Organism
Q9HBG6  IF122_HUMAN reviewed    IFT122 SPG WDR10 WDR140 Homo sapiens (Human)
Q8NDW8  TT21A_HUMAN reviewed    TTC21A STI2 Homo sapiens (Human)
Q7Z4L5  TT21B_HUMAN reviewed    TTC21B IFT139 KIAA1992 Nbla10696    Homo sapiens (Human)
Q96FT9  IFT43_HUMAN reviewed    IFT43 C14orf179 Homo sapiens (Human)
Q9P2L0  WDR35_HUMAN reviewed    WDR35 IFT121 KIAA1336   Homo sapiens (Human)
Q8NEZ3  WDR19_HUMAN reviewed    WDR19 IFT144 KIAA1638   Homo sapiens (Human)
Q96NG3  ODAD4_HUMAN reviewed    ODAD4 TTC25 Homo sapiens (Human)

However, on the UNIPORT website: https://www.uniprot.org/uniprot/Q96RY7#sequences the gene seems to exist.

I have tried importing my own json version of this gene and running locally: https://pfam.xfam.org/protein/Q96RY7/graphic

With this code: ./lollipops -l="./ift140.json" -o="json.svg" [some variants]

As per a previous issue but I keep getting this:

HGNC Symbol:  Q383X
Uniprot returned 0 hits for your gene symbol 'Q383X':
Unable to find protein ID for 'Q383X' (use -U XX to select one of the above)

Q383X is the first variant I am hoping to plot....

Your advice would be much appreciated thanks

All the best

[pbnjay]

I believe the command you want (to search using Uniprot ID instead of Symbol) would be:

./lollipops -U Q96RY7 Q383X

Although even this may not help much, I don't see any annotated domains in pfam where the graphic data comes from. If you wanted to show everything you can try this:

./lollipops -show-disordered -show-motifs -labels -U Q96RY7 Q383X

[oalavijeh]

Many thanks for taking the time to answer!