Table 1.

Summary of Previously Identified ncRNAs or Their Possible Homologs Found in FANTOM2 Clone Set

FANTOM2 clone ID	Homologous noncoding RNA	GenBank/EMBL/DDBJ accession no.	Status of identity	Organism	References
C130002M05	KvLQT-as	AF119385	97.8% in 2467 nt	Mm	Smilinich et al. 1999
3830421G02	U17 snoRNA host gene	AJ006836	99.7% in 383 nt	Mm	Pelczar and Filipowicz 1998
A730062M15	U22 snoRNA host gene	U40654	100% in 476 nt	Mm	Tycowski et al. 1996
E130201N16	G90	AJ132433	98.4% in 833 nt	Mm	Krause et al. 1999
A430022B11	XIST	L04961	99.3% in 1497 nt	Mm	Hong et al. 1999
B230105C16	IPW	U69888	97.9% in 617 nt	Mm	Wevrick and Francke 1997
1100001A04	H19	NM_023123	99.2% in 870 nt	Mm	Hurst and Smith 1999
9630004F23	CIOR	AF140607	99.9% in 2118 nt	Mm	Inoue et al. 2002
6430597C21	Rian	AB063319	100% in 1496 nt	Mm	Hatada et al. 2001
2900019G14	NTAB	AY035551	89.7% in 955 nt	Rn	French et al. 2001
5930439P04	Synapse-specific 7H4	L33722	79.1% in 3668 nt	Rn	Velleca et al. 1994
A530032L19	NTT	U54776	61.0% in 2635 nt	Hs	Liu et al. 1997
D630034O16	DGCR5	X91348	73.7% in 243 nt	Hs	Sutherland et al. 1996
D930049J19	NCRMS	XR_000104	72.6% in 446 nt	Hs	Chan et al. 2002
E430001E02	U19 snoRNA host gene	AJ224166	80.7% in 451 nt	Hs	Bortolin and Kiss 1998
5430416N02	adapt33	U29660	63.6% in 676 nt	Cg	Wang et al. 1996

Homology search was initially performed by BLASTN. Then the best hit sequence having its e value <1.0e - 10 in same orientation were picked up. For this sequence, Ssearch (Pearson 1991) was carried out for stricter alignment. Hs indicates Homo sapiens; Mm, Mus musculus; Rn, Rattus norvegicus; and Cg, Cricetulus griseus

Identification of Putative Noncoding RNAs Among the RIKEN Mouse Full-Length cDNA Collection