About RIKEN Mouse Encyclopedia

RIKEN Mouse Encyclopedia Index (Riken-MEI)

cDNA Library

- with high content of full-length cDNAs
- important information

Clustering algorithm

(1) Trim polyT and C-stretch from single pass sequencings
(2) Homology search in comparisons with BLASTN 2.0.9 E =1.0e-25, pvalue < E ) using 100bp out of all trimmed sequences
(3) Clustering
(4) 100bp =(2) of the new sequences is used for homology search in public databa ses with BLASTN 2.0.9
Reference: Altschul, Stephen F., Thomas L. Madden, Alejandro A. Sc haffer, Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), "Ga pped BLAST and PSI-BLAST: a new generation of protein database search programs", Nucleic Acids Res. 25:3389-3402)

(1) Trim polyT and C-stretch from single pass sequencings
(2) Homology search in comparisons with BLASTN 1.4.10 (E =1.0e-25, pvalue < E ) using 100bp out of all trimmed sequences
(3) Clustering
(4) 100bp =(2) of the new sequences is used for homology search in public databases with BLASTN 2.0.8
Reference: Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaffer, Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), "Gapped BLAST and PSI-BLAST: a new generation of protein database search programs", Nucleic Acids Res. 25:3389-3402)
The first release of Riken data (Riken-MEI 1.0) was roughly categorized as we did not categorize according to common standards. We posted single pass sequencing data using BLASTN 1.4.10. Later, we confirmed the Riken-MEI 1.0 data using the corresponding putative full-length sequence data. The results of the confirmation are now posted. Click here.

Release data

I. 3'-end sequences, 5'-end sequences

All sequences were submitted through DNA Data Bank of Japan (DDBJ)

Accession Number

3'-end sequences AV048147 AV133688 AV133799 AV149966 BB561685-BB624303 BB624305-BB624306 BB624308-BB667065 BB838020-BB840697 BB840699-BB873800 BY000001-BY275499 BY275501-BY353464 BY702772-BY748774 BY748776-BY751261 BY751263-BY754635 BY766244-BY794941 CJ039836-CJ188528 5'-end sequences AV000001-AV048146 AV048148-AV133687 AV133689-AV133798 AV133800-AV149965 AV149967-AV175734 AV204013-AV382295 BB000001-BB067308 BB067310-BB067348 BB067350-BB561684 BB667066-BB707419 BB709066-BB713813 BB715481 BB716494-BB725245 BB725313-BB733535 BB733537-BB733917 BB733919-BB735045 BB735047-BB746576 BB746578-BB746703 BB746705-BB746732 BB746734-BB746756 BB746758-BB746761 BB746763-BB746888 BB746890-BB747060 BB747062-BB838019 BY353465-BY489610 BY489612-BY529951 BY529953-BY531164 BY531166-BY531942 BY531944-BY533645 BY533647-BY534550 BY534552-BY537269 BY537271-BY546328 BY546330-BY702771 BY754636-BY764028 BY764030-BY765542 BY765544-BY765730 BY765732-BY766243 CJ188529-CJ273136 CJ273138-CJ273352 CJ273354-CJ326805

All sequence data will be regularly updated once a certain amount of sequence data has been pooled and reviewed.
Accession number-clone id list : 5'end , 3'end

Release 1	Riken-MEI 1.0	12-Jan-1999	107,088 redundant 3'-end sequences
Release 2	Riken-MEI 2.0	28-Mar-1999	27,892 non-redundant 3'-end sequences (176,678 redundant 3'-end sequences) including Release 1 (Riken-MEI 1.0)
Release 3	Riken-MEI 3.0	8-Oct-1999	66,626* non-redundant 3'-end sequences (438,004 redundant 3'-end sequences)
Release 4	Riken-MEI 4.0	10-Apr-2000	126,611* non-redundant 3'-end sequences (914,717 redundant 3'-end sequences)
	Riken-MEI 4.02	15-May-2000	126,693* non-redundant 3'-end sequences (914,452 redundant 3'-end sequences) Removed error data and refined.
Release 5	Riken-MEI 5.0	27-Nov-2000	32,697 non-redundant 5'-end sequences (50,206 redundant 5'-end sequences)
			127,385* non-redundant 3'-end sequences (939,725 redundant 3'-end sequences)
Release 6	Riken-MEI 6.0	20-Nov-2001	141,162 redundant 5'-end sequences
			1,086,655* redundant 3'-end sequences
Release 7	Riken-MEI 6.0	5-Dec-2002	405,328 redundant 5'-end sequences
			360,915 redundant 3'-end sequences
Release 8	Riken-MEI 7.0	27-Nov-2003	28,698 redundant 5'-end sequences
Release 9	Riken-MEI 8.0	2-Sep-2005	148,693 redundant 5'-end sequences
			138,275 redundant 3'-end sequences

*:including previous release.

II. Full sequences

All sequences were submitted through DNA Data Bank of Japan (DDBJ)

Accession Number

Full sequences AK002213-AK021412 AK027261-AK027262 AK027903-AK033202 AK033204-AK054560 AK075567-AK089867 AK089869-AK090394 AK117103-AK117104 AK131576-AK136323 AK136325-AK143556 AK143558-AK143568 AK143570-AK143598 AK143600-AK144005 AK144007-AK144011 AK144013-AK144014 AK144016-AK144017 AK144019-AK144021 AK144023-AK144028 AK144030-AK150533 AK150535-AK154401 AK154403-AK154439 AK154441-AK155166 AK155168-AK155260 AK155262-AK155282 AK155284-AK155303 AK155305-AK155417 AK155419-AK155475 AK155477-AK155541 AK155543-AK155655 AK155657-AK156523 AK156525-AK158794 AK158796-AK160363 AK160387-AK165484 AK165486-AK172723

All sequence data will be regularly updated once a certain amount of sequence data has been pooled and reviewed.
Accession number-clone id list : full sequence

Release 1	Riken-ME 1.0	6-Feb-2001	19,168 full sequences
Release 2	none	26-Mar-2002	1 full sequence
Release 3	Riken-ME 2.0	5-Dec-2002	59,971* full sequence
Release 4	Riken-ME 3.0	2-Sep-2005	101,789* full sequence

*:including previous release.