ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq
PPT, BS, UA-tract

Sequence

atgc intronic sequence ATGC exonic sequence

gtacatttggtagctatcaaatagtagtaccttctagatttgtctgttttgccaaaattttccacggtaagggtttcttgtaatggctattaactgtatgcagGATACTTGCAATAGGAAAAGTAACCAGCAGAATCTGGGCACAATTAAATCGTCAAACCTGTGCACTGAAATAATTGAGTTTACAAGCCCTACTGAGACCG

Basic information

species	Zea mays
transcript	GRMZM2G304362_T01
intron #	8
splice site	3'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G304362_T01 (Zea mays), 3'ss of exon 8
lower sequence: LOC_Os06g07210.1 (Oryza sativa), 3'ss of exon 8

gtacatttggtagc--------tatcaaatagtagtaccttctagatttgtctgttttgccaaaatttt-----ccacggtaagg--------gtttcttgtaatggctattaactgtatgcagGATACTTGCAATAGGAAAAGTAACCAGCAGAATCTGGGCACAATTAAATCGTCAAACCTGTGCACTGAAATAATTGAGTTTACAAGCCCTACTGAGACCG
||| ||||||||||        || |||  |||| |   || | ||        |  | | || ||  |     | |  || |||         ||  ||   |  ||| ||         |||||||| ||||||||||||||||||||||||||| |||||||||||||||| |||||| | |||||||| ||||||||||  |||||||||||||| || |
gtaaatttggtagcaaaattagtagcaaggagtacttgattttggacccaagattcctccaaatatgctgctggctatagtcaggttccaagtattcattccgaatgctcttgttgtcccacagGATACATGCAATAGGAAAAGTAACCAGCAGAATTTGGGCACAATTAAATCTTCAAACTTATGCACTGAGATAATTGAGTACACAAGCCCTACTGAAACTG

upper sequence: GRMZM2G304362_T01 (Zea mays), 3'ss of exon 8
lower sequence: GLYMA06G15350.1 (Glycine max), 3'ss of exon 8

gtacatttggtagctatcaaatagtagt-accttctagatttgtctgttttgccaaaattttc-cacggtaagggtttcttgtaatggctattaactgtatgcagGATACTTGCAATAGGAAAAGTAACCAGCAGAATCTGGGCACAATTAAATCGTCAAACCTGTGCACTGAAATAATTGAGTTTACAAGCCCTACTGAGACCG
       |||| | | | | ||     | || |||   ||  |  | | |    |   ||||| | || | ||   |||  | | |   | || ||  ||   |||||||||||||||||||||| || || |||||| |||| |||||||||||||||||| |||| ||||| |||||||| | | |||| || ||||| || |
------gtggt-gttcttagatgtctttgactttcctcatgagattttgtatttattgttttcacccgttgagtaattccagcattt-ttgtttacactac-tagGATACTTGCAATAGGAAAAGCAATCAACAGAATTTGGGTACAATTAAATCGTCAAACTTGTGTACTGAGATAATTGAATATTCAAGTCCAACTGAAACTG

upper sequence: GRMZM2G304362_T01 (Zea mays), 3'ss of exon 8
lower sequence: GLYMA08G15360.1 (Glycine max), 3'ss of exon 8

gtacatttggtagctatcaaatagtagtaccttctagatttgtctgttttgccaaaattttccacggtaagggtttcttgtaatggcta---ttaactgtatgc-agGATACTTGCAATAGGAAAAGTAACCAGCAGAATCTGGGCACAATTAAATCGTCAAACCTGTGCACTGAAATAATTGAGTTTACAAGCCCTACTGAGACCG
         || | |  |||||  | ||      |    |      || || ||     ||      | |   ||  ||| ||   ||    ||  || ||| | |||| ||||||||||||||||| ||||| |||||| |||||||||| ||                                                     
---------gtggtttacaaatgcttgtttgacttttgctaagt--ttctgtcagtgcattttgtatttatt-ttcattgaaacctcttcatttttctatatcctagGACACTTGCAATAGGAAAAGCAACCAACAGAATTTGGGCACAATCAA-----------------------------------------------------

upper sequence: GRMZM2G304362_T01 (Zea mays), 3'ss of exon 8
lower sequence: GLYMA04G39500.1 (Glycine max), 3'ss of exon 8

gtacatttggtagctatcaaatagtagtaccttctagatttgtctgttttgccaaaattttccacggtaagggtttcttgtaatggctattaactgtatgcagGATACTTGCAATAGGAAAAGTAACCAGCAGAATCTGGGCACAATTAAATCGTCAAACCTGTGCACTGAAATAATTGAGTTTACAAGCCCTACTGAGACCG
||  |     ||| | ||   || |    || |     ||||| | | |||      |||  |  | | |     ||    | |   |||| ||  ||   |||||||||||||||||||||| ||||| |||||| |||| ||||||||||| |||||| |||| ||||| |||||||||| | |||| || ||||| || |
gtggaacacttagatgtcttttactttccccatgagattttgtatttattgt-----tttcacctgttgaataaatccaacattt-ttatttacactac-tagGATACTTGCAATAGGAAAAGCAACCAACAGAATTTGGGTACAATTAAATCATCAAACTTGTGTACTGAGATAATTGAGTATTCAAGTCCAACTGAAACTG

Mapped EST sequences

Showing partial alignments of ESTs and genomic sequences. See full alignments

ATGC    EST sequence
ATGC    genomic sequence (exon)
ATGC    genomic sequence (truncated intron)

EST: gi|32933128|gb|CF037940.1|CF037940

EST:     ACACCATATATGCTTTACAAG                         GATACTTGCAATAGGAAAAGTAACCAGCAGAATCTGGGCACAATTAAATCG
genomic: ACACCATATATGCTTTATAAGgtacatttgg ... ctgtatgcagGATACTTGCAATAGGAAAAGTAACCAGCAGAATCTGGGCACAATTAAATCG

EST: gi|33098100|gb|CF058060.1|CF058060

EST:     TACACCATATATGCTTTACAAG                         GATACTTGCAATAGGAAAAGTAACCAGCAGAATCTGGGCACAATTAAATCG
genomic: TACACCATATATGCTTTATAAGgtacatttgg ... ctgtatgcagGATACTTGCAATAGGAAAAGTAACCAGCAGAATCTGGGCACAATTAAATCG

EST: gi|32931387|gb|CF036199.1|CF036199

EST:     ACACCATATATGCTTTACAAG                         GATACTTGCAATAGGAAAAGTAACCAGCAGAATCTGGGCACAATTAAATCG
genomic: ACACCATATATGCTTTATAAGgtacatttgg ... ctgtatgcagGATACTTGCAATAGGAAAAGTAACCAGCAGAATCTGGGCACAATTAAATCG

EST: gi|211102667|gb|FK948701.1|FK948701

EST:     ACATTTTGAAGGCACAGATAGAGACTGGTACACCATATATGCTTTACAAG                         GATACTTGCAATAGGAAAAGTAACCAGCAGAATCTGGGCACAATTAAATCG
genomic: ACATTTTGAAGGCACAGATAGAGACTGGTACACCATATATGCTTTATAAGgtacatttgg ... ctgtatgcagGATACTTGCAATAGGAAAAGTAACCAGCAGAATCTGGGCACAATTAAATCG

EST: gi|32930756|gb|CF035568.1|CF035568

EST:     TACACCATATATGCTTTACAAG                         GATACTTGCGATAGGAAAAGTAACCAGCAGAATCTGGGCACAATTAAATCG
genomic: TACACCATATATGCTTTATAAGgtacatttgg ... ctgtatgcagGATACTTGCAATAGGAAAAGTAACCAGCAGAATCTGGGCACAATTAAATCG

RNA-Seq data

ATGC Supported by RNA-Seq exonic block that spans over the splice site

atgs Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.

Found data for 4 RNA-Seq libraries.

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 245

GGCAAGGCAAAGAAAGTTGTTCCGGCACAGACCCTTTGGTTTGACATTTTGAAGGCACAGATAGAGACTGGTACACCATATATGCTTTATAAGgtacatttgg ... ctgtatgcagGATACTTGCAATAGGAAAAGTAACCAGCAGAATCTGGGCACAATTAAATCGTCAAACCTGTGCACTGAAATAATTGAGTTTACAAGCCCTACTGAGACCG

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 72

Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 32

Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 51

atgc intronic sequence ATGC exonic sequence

Intronic sequence truncated to 55 bases.

ttgccaaaattttccacggtaagggtttcttgtaatggctattaactgtatgcagGATACTTGCAATAGGAAAAGTAACCAGCAGAATCTGGGCACAATTAAATCGTCAAACCTGTGCACTGAAATAATTGAGTTTACAAGCCCTACTGAGACCG