Subject: Re: Helping FlyBase: 'snRNP70K'
Rachel
Sorry to be slow late in replying. I have had a chance to check the Kim
and Baker reference. My specific answers follow.
> We have these two snRNP records which I think must represent the same
> gene. Could you confirm this for me please (you know us, we need
> everything in writing!)?
Yes, these are, without question, the same gene.
The Kim and Baker reference (FBgn0016978) cites Mancebo et al.
(FBgn0003458); it doesn't even report any new information. Yannoni and
White reported results obtained using our antibody, so this is also a
reference back to Mancebo et al. I believe that Paterson et al. describe
the protein itself, and the connection to the gene is, once again,
immunological. There is no evidence of any other gene for a U1 70K
protein. In summary, the snRNP70K = snRNP27D = U1-70K
The name we have used, and use informally, is 70K. The name snRNP70K is
acceptable, and is far preferable to snRNP27D. It also allows us to use
70K informally without confusion. So, I'd like to recommend that when you
fuse them you chose snRNP70K.
Finally, YES l(2)0210702107 is the same thing as 70K1. Exactly. We
stopped calling it 2107 and started calling it 70K1 after we showed that
it could be rescued by 70K produced from a transgene.
I hope this helps. It was a pleasure meeting you.
Steve Mount
\################################################
>
> \*a snRNP70K
> \*z FBgn0016978
> \*x FBrf0059040 == Kim and Baker, 1993, Molec. Cell. Biol. 13(1): 174--183
> \*x FBrf0054858 == Paterson et al., 1991, Nucleic Acids Res. 19: 5877--5882
> \*x FBrf0093796 == Yannoni and White, 1997, Chromosoma 105(6): 332--341
> \*p A sequence comparison and numerical analysis of the RRM-containing
> \*p (RNA recognition motif) proteins suggests that functionally related
> \*p RRM-containing proteins have significant sequence similarities in their
> \*p RRMs.
> \*i snRNP
> \#
> \*a snRNP27D
> \*e small nuclear ribonucleoprotein at 27D
> \*z FBgn0003458
> \*b 2-21
> \*c 27D1--2
> \*c Left limit from in situ hybridisation (FBrf0052549)
> \*c Right limit from in situ hybridisation (FBrf0052549)
> \*g AA201872;  BFD:LD03939 ;  dbEST:840982 
> \*g M31162; AAA28859
> \*g Z50206;  dbSTS:24170 
> \*m  PIR:A36311 
> \*m  SWP:P17133 
> \*J PS00030 == Eukaryotic putative RNA-binding region RNP-1 signature.
> \*d RNA-binding-protein
> \*d sn-ribonucleoprotein
> \*x FBrf0064457 == Fukami-Kobayashi et al., 1993, FEBS Lett. 335(2): 289--293
> \*x FBrf0100572 == Henriksson and Pettersson, 1997, J. Autoimmun. 10(6): 559--568
> \*x FBrf0052549 == Mancebo et al., 1990, Molec. Cell. Biol. 10: 2492--2502
> \*x FBrf0054858 == Paterson et al., 1991, Nucleic Acids Res. 19: 5877--5882
> \*x FBrf0101502 == Tseng et al., 1998, A. Conf. Dros. Res. 39: 465C
> \*x FBrf0054695 == Voelker et al., 1991, Molec. Cell. Biol. 11: 894--905
> \*x FBrf0093796 == Yannoni and White, 1997, Chromosoma 105(6): 332--341
> \*i U1 70K
> \*c 27D1--27D2 (determined by in situ hybridisation)
> \*p snRNP27D has been cloned and sequenced.
> \*u Isolated from a genomic library using a human U1 70K snRNP cDNA clone as
> \*u a probe.
> \*i U1snRNP-70K
> \*i U1-70K
> \*i snRNP
> \*i 70K
> \*i U1 70K snRNP
> \*A snRNP27D1
> \*z FBal0086333
> \*x FBrf0101502 == Tseng et al., 1998, A. Conf. Dros. Res. 39: 465C
> \*i 70K1
> \*o P-element activity
> \*G P{}snRNP27D1
> \*k Phenotypic class: lethal | recessive
> \*s P-element insertion in the 5' untranslated region.
> \*u Excision of the P-element restores viability, as do transgenes
> \*u carrying either a wildtype genomic fragment or cDNA under the control of
> \*u the Hsp70 promoter. Some partial revertants show partial female-specific
> \*u lethality and defects in oogenesis. A transgene construct lacking the
> \*u arginine-rich domain also rescues the lethality.
> \#
>
> You told me in Bellevue that l(2)02107 corresponds to snRNP27D (by hit
> of flanking sequence for P{PZ} insert in l(2)0210702107 to snRNP27D
> sequence). I will merge the record for l(2)02107 with that of
> snRNP27D. Is '70K1' of FBrf0101502 the same allele as
> l(2)0210702107 from the BDGP? Looks to be a distinct possibility.
>
> Many thanks for your help. I will curate your answer as a personal
> communication from you to FlyBase.
>
> Best wishes,
>
> Rachel.