help need！ - (Feb/17/2004 )

A cDNA with 621bp was cloned by SSH. When we blast it in nr database of Genebank，the result is（Mus musculus BAC clone RP24-126O19 from chromosome 9, complete sequence， Length = 181337
Score = 168 bits (85), Expect = 8e-39
Identities = 148/168 (88%),）;When we blast it in EST database of Genebank，the result is（B0286C08-5 NIA Mouse Embryonic Germ Cell cDNA Library (Long) Mus musculus cDNA clone NIA:B0286C08 IMAGE:30111679 5'.
Length = 576
Score = 161 bits (81), Expect = 2e-36
Identities = 99/105 (94%)）；When we blast it in HTGS database of Genebank，we found these was 99%(620/621) homology. However, these was a intron with 2331bp inserted in the middle of the cDNA sequenc. So, I would like to know if the cDNA is a novel sequence. Is it necessary for me to amplify the full length of the cDNA? Thank you very much in advance!

Please let us know from which organism you cloned your sequence, mouse?

Thanks a lot!

Yes, it is cloned from mouse, and it hits Mus musculus clone RP24-161145(working draft sequence, 5 unordered pieces, Length=175830)

Your sequence may be a novel gene. To make it meaningful, you have to find a ORF of reasonable length within it. The TIGR mouse gene index is a good source to check for putative genes and is compiled by align all mouse EST sequences. You can blast your sequence agaisnt the index. Certainly you need to clone the whole length of the cDNA.

TIGR mouse gene index:
http://www.tigr.org/tigr-scripts/tgi/T_ind...i?species=mouse

Good luck.

sage

Sage, Thank you so much!

Dingkui