ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq

Sequence

atgc intronic sequence ATGC exonic sequence

GTCCTCGGTACGCCAACAAGGGAAGAAATTAAATGCATGAACCCAAATTACACAGAGTTTAAGTTCCCACAAATCAAAGCACACCCATGGCACAAGgtgctcaaatctttctacattttgttacaatactctaagaaaactgttactgttgtgttactaatttactttttgtacattttatctttcag

Basic information

species	Zea mays
transcript	GRMZM2G024151_T01
intron #	9
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G024151_T01 (Zea mays), 5'ss of exon 9
lower sequence: LOC_Os01g14860.3 (Oryza sativa), 5'ss of exon 9

GTCCTCGGTACGCCAACAAGGGAAGAAATTAAATGCATGAACCCAAATTACACAGAGTTTAAGTTCCCACAAATCAAAGCACACCCATGGCACAAGgtgctcaaatctttctacattttgttacaatactctaagaaaactgttactgttgtgttactaatt-tactttttgtacattttatctttcag
||||| || || || |||||||| ||||||||||||||||| ||||| || || ||||| ||||| ||||| || |||||||||||||||||||||||||  || ||| ||||  || ||||   ||||| | || || |    | | |   || | |||   ||  | |   | ||||          
GTCCTTGGAACACCTACAAGGGAGGAAATTAAATGCATGAATCCAAACTATACCGAGTTCAAGTTTCCACAGATTAAAGCACACCCATGGCACAAGgtgca-aagtctatctat-ttctgttgttatactttcagcaatcgtccagtatcaggtgattaaccatatatgtaaaatatttag--------

upper sequence: GRMZM2G024151_T01 (Zea mays), 5'ss of exon 9
lower sequence: PP1S60_100V6.1 (Physcomitrella patens), 5'ss of exon 9

GTCCTCGGTACGCCAACAAGGGAAGAAATTAAATGCATGAACCCAAATTACACAGAGTTTAAGTTCCCACAAATCAAAGCACACCCATGGCACAAGgtgctcaaatctt-tctacattttgttacaatact----ctaagaaaactgttactgttgtgttactaatttac--tttttgtacattttatctttcag-
||  | || || || ||  | || || || || |||||||| || || ||||| ||||| ||||| || |||||||| || |||||||||||||| ||          | |  |     ||||   ||  |     |  | |   |  | | |  |||    |     ||  | |||     | | | |  |  | 
GTGTTGGGGACACCGACTCGTGAGGAGATCAAGTGCATGAATCCGAACTACACGGAGTTCAAGTTTCCGCAAATCAAGGCTCACCCATGGCACAAAgtatgtggtctgtgtgaatgcactgttttcatcttgggctttggtagtgtagtccagaagtggagatgtacgaccgtgttttcgtgtgtgagcggtgggt

upper sequence: GRMZM2G024151_T01 (Zea mays), 5'ss of exon 9
lower sequence: PP1S306_62V6.1 (Physcomitrella patens), 5'ss of exon 8

GTCCTCGGTACGCCAACAAGGGAAGAAATTAAATGCATGAACCCAAATTACACAGAGTTTAAGTTCCCACAAATCAAAGCACACCCATGGCACAAGgtgctcaaatctttctacattttgttacaatactctaagaaaactgttactgttgtgttactaatttactttttgtacattttatctttcag-----------------------------------------------------------------------------------------
||  | || || || ||  | || || || || |||||||| || || ||||||||||| ||||| ||||||||||| || ||||| |||||||| ||       | | |    ||  | | |    |  ||  |      | |  |  || | || |   |     |  |    | |  | |  | |                                                                                         
GTTTTGGGGACACCGACTCGTGAGGAGATCAAGTGCATGAATCCGAACTACACAGAGTTCAAGTTTCCACAAATCAAGGCGCACCCGTGGCACAAAgtatgttt-tttgtgcgaatgctatgatgtcatcctgggtgttgcggttgtagtgcggtagtggatgtgggtcagcctttctcgtgtagcggcattgttagttgcgtgcgtcgtggtttgttggatgttgggttttgacgacggtaaccggcgtttggtatggccgatgtgggaattgcag

upper sequence: GRMZM2G024151_T01 (Zea mays), 5'ss of exon 9
lower sequence: EFJ07923 (Selaginella moellendorffii), 5'ss of exon 10

GTCCTCGGTACGCCAACAAGGGAAGAAATTAAATGCATGAACCCAAATTACACAGAGTTTAAGTTCCCACAAATCAAAGCACACCCATGGCACAAGgtgctcaaatctttctacattttgttacaatactctaagaaaactgttactgttg-tgttactaatttactttttgtacattttatctttcag
||| | ||||| || ||  |||| ||||| ||||||||||| ||||| ||||| |||||||||||||| || || ||||| || || |||||||||||    | | |  ||     |  | || |   ||||       ||||  || ||| |||  ||  || ||                       
GTCTTAGGTACTCCTACTCGGGAGGAAATCAAATGCATGAATCCAAACTACACGGAGTTTAAGTTCCCTCAGATTAAAGCGCATCCCTGGCACAAGgta---agagcaatca----tccggtatatctctctct-----ctgtctctcttgatgtggctcgttgacag---------------------

upper sequence: GRMZM2G024151_T01 (Zea mays), 5'ss of exon 9
lower sequence: EFJ07216 (Selaginella moellendorffii), 5'ss of exon 10

GTCCTCGGTACGCCAACAAGGGAAGAAATTAAATGCATGAACCCAAATTACACAGAGTTTAAGTTCCCACAAATCAAAGCACACCCATGGCACAAGgtgctcaaatctttctacattttgttacaatactctaagaaaactgttactgttg-tgttactaatttactttttgtacattttatctttcag
||| | ||||| || ||  | || ||||| ||||||||||| ||||| ||||| |||||||||||||| || || ||||| || || |||||||||||    | | |  ||     |  | || |   ||||       ||||  || ||| |||  ||  || ||                       
GTCTTAGGTACTCCTACTCGCGAGGAAATCAAATGCATGAATCCAAACTACACGGAGTTTAAGTTCCCTCAGATTAAAGCGCATCCCTGGCACAAGgta---agagcaatca----tccggtatatctctctct-----ctgtctctcttgatgtggctcgttgacag---------------------

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|211161694|gb|FL418712.1|FL418712

EST:     ATTACACAGAGTTTAAGTTCCCACAAATCAAAGCACACCCATGGCACAAG                         GTATTCCACAAAAGGATGCCGCCAGAAGCTGTTGATCTGGTCTCTCGGCTA
genomic: ATTACACAGAGTTTAAGTTCCCACAAATCAAAGCACACCCATGGCACAAGgtgctcaaat ... tatctttcagGTATTCCACAAAAGGATGCCGCCAGAAGCTGTTGATCTGGTCTCTCGGCTA

EST: gi|61117965|gb|DN558926.1|DN558926

EST:     ATTACACAGAGTTTAAGTTCCCACAAATCAAAGCACACCCATGGCACAAG                         GTATTCCACAAAAGGATGCCGCCAGAAGCTGTTGATCTGGTCTCTCGGCTA
genomic: ATTACACAGAGTTTAAGTTCCCACAAATCAAAGCACACCCATGGCACAAGgtgctcaaat ... tatctttcagGTATTCCACAAAAGGATGCCGCCAGAAGCTGTTGATCTGGTCTCTCGGCTA

EST: gi|61117966|gb|DN558927.1|DN558927

EST:     ATTACACAGAGTTTAAGTTCCCACAAATCAAAGCACACCCATGGCACAAG                         GTATTCCACAAAAGGATGCCGCCAGAAGCTGTTGATCTGGTCTCTCGGCTA
genomic: ATTACACAGAGTTTAAGTTCCCACAAATCAAAGCACACCCATGGCACAAGgtgctcaaat ... tatctttcagGTATTCCACAAAAGGATGCCGCCAGAAGCTGTTGATCTGGTCTCTCGGCTA

EST: gi|33097248|gb|CF057208.1|CF057208

EST:     ATTACACAGAGTTTAAGTTCCCACAAATCAAAGCACACCCATGGCACAAG                         GTATTCCACAAAAGGATGCCGCCAGAAGCTGTTGATCTGGTCTCTCGGCTA
genomic: ATTACACAGAGTTTAAGTTCCCACAAATCAAAGCACACCCATGGCACAAGgtgctcaaat ... tatctttcagGTATTCCACAAAAGGATGCCGCCAGAAGCTGTTGATCTGGTCTCTCGGCTA

EST: gi|33104403|gb|CF064363.1|CF064363

EST:     TAAGTTCCCACAAATCAAAGCACACCCATGGCACAAG                         GTATTCCACAAAAGGATGCCGCCAGAAGCTGTTGATCTGGTCTCTCGGCTA
genomic: TAAGTTCCCACAAATCAAAGCACACCCATGGCACAAGgtgctcaaat ... tatctttcagGTATTCCACAAAAGGATGCCGCCAGAAGCTGTTGATCTGGTCTCTCGGCTA

EST: gi|32827595|gb|CD967273.1|CD967273

EST:     TAAGTTCCCACAAATCGAAGCACACCCATGGCACAAG                         GTATTCCACAAAAGGATGCCGCCAGAAGCTGTTGATCTGGTCTCTCGGCTA
genomic: TAAGTTCCCACAAATCAAAGCACACCCATGGCACAAGgtgctcaaat ... tatctttcagGTATTCCACAAAAGGATGCCGCCAGAAGCTGTTGATCTGGTCTCTCGGCTA

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: 6676

GTCCTCGGTACGCCAACAAGGGAAGAAATTAAATGCATGAACCCAAATTACACAGAGTTTAAGTTCCCACAAATCAAAGCACACCCATGGCACAAGgtgctcaaat ... tatctttcagGTATTCCACAAAAGGATGCCGCCAGAAGCTGTTGATCTGGTCTCTCGGCTACTCCAGTACTCCCCAAATCTGAGATGCACTGCT

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 1859

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 1264