ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq

Sequence

atgc intronic sequence ATGC exonic sequence

ACCATACGCGGAAGTTGAGGTTATGAAGATGTGCATGCCTCTCTTGTCACCTGCTTCTGGTGTCATTCATTGTATGATGTCTGAGGGCCAGGCATTGCAGgttatattcgcacatgtccattccttgcattgtgctttcatcacataatatttcatgtaacatttatcaacttatattttgttttag

Basic information

species	Zea mays
transcript	GRMZM5G858094_T02
intron #	19
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM5G858094_T01 (Zea mays), 5'ss of exon 19
lower sequence: LOC_Os05g22940.1 (Oryza sativa), 5'ss of exon 21

ACCATACGCGGAAGTTGAGGTTATGAAGATGTGCATGCCTCTCTTGTCACCTGCTTCTGGTGTCATTCATTGTATGATGTCTGAGGGCCAGGCATTGCAGgttatattcgcacatgtccattccttgcattgtgctttcatcacataatatttcatgtaacatttatcaacttatattttgttttag
|||||| |||||||||||||||||||||||||||||||| ||||| ||||| |||||||||||||| |||  | | |||||||||||||| ||| ||||||| | ||||  |||| ||||||| |||   ||||||  ||| |    | |||||| ||||        ||||| | | || || |||
ACCATATGCGGAAGTTGAGGTTATGAAGATGTGCATGCCCCTCTTATCACCCGCTTCTGGTGTCATACATGTTGTAATGTCTGAGGGCCAAGCAATGCAGgt-acattcctacat-tccattcattgtgctgtgctgacatga----acatttcaagtaaatacctgtaacttgtttattattctag

upper sequence: GRMZM5G858094_T01 (Zea mays), 5'ss of exon 19
lower sequence: GLYMA06G11120.1 (Glycine max), 5'ss of exon 18

ACCATACGCGGAAGTTGAGGTTATGAAGATGTGCATGCCTCTCTTGTCACCTGCTTCTGGTGTCATTCATTGTATGATGTCTGAGGGCCAGGCATTGCAGgttatattcgcacatgtccattccttgcattgtgctttcatcacataatatttcatgtaacatttatcaacttatattttgttttag
|||||| || ||||||||||| ||||| ||||||||||||||  | || |||||||||||  | |||||||  |  |||||||| || || ||| ||||||| ||||     ||| || |||||   |||||    | ||     | |||||  | |  | | | |   | |   | | | ||  ||
ACCATATGCTGAAGTTGAGGTCATGAAAATGTGCATGCCTCTTCTTTCGCCTGCTTCTGGGATTATTCATTTCAAAATGTCTGAAGGTCAAGCAATGCAGgt-atat---agcat-tctattcc--acattggaagtacaggtgttcatattgaaagagataataaaatagtatcactgt-ttgcag

upper sequence: GRMZM5G858094_T01 (Zea mays), 5'ss of exon 19
lower sequence: GLYMA04G11550.1 (Glycine max), 5'ss of exon 18

ACCATACGCGGAAGTTGAGGTTATGAAGATGTGCATGCCTCTCTTGTCACCTGCTTCTGGTGTCATTCATTGTATGATGTCTGAGGGCCAGGCATTGCAGgttatattcgcacatgtccattccttgcattgtgctttcatcacataatatttcatgtaacatttatcaacttatattttgttttag--
||| || || ||||||||||| ||||| ||||||||||||||  | || |||||||||||  | |||||||  |  |||||||| || || ||| ||||||| ||||     ||| || |||||   ||| |    | ||     | | |||  |   ||   | || || || |||    ||||    
ACCGTATGCTGAAGTTGAGGTCATGAAAATGTGCATGCCTCTTCTTTCGCCTGCTTCTGGGATTATTCATTTCAAAATGTCTGAAGGTCAAGCAATGCAGgt-atat---agcat-tctattcc--acataggaagtacaattgttgaaattgaa---aaagataataaaattgtatcaccttttgcag

upper sequence: GRMZM5G858094_T01 (Zea mays), 5'ss of exon 19
lower sequence: AT1G36160.1 (Arabidopsis thaliana), 5'ss of exon 18

ACCATACGCGGAAGTTGAGGTTATGAAGATGTGCATGCCTCTCTTGTCACCTGCTTCTGGTGTCATTCATTGTATGATGTCTGAGGGCCAGGCATTGCAGgttatattcgcacatgtccattccttgcattgtgctttcatcacataatatttcatgtaacatttatcaacttatattttgttttag
 || || || ||||||||||| ||||||||||||||||| ||  | ||||||||||| || || || |||| ||  |||||||| || || ||  ||||||||   |||     |   ||        |  || || |    |   | ||   |||  |  |||| |    | | |           
GCCTTATGCCGAAGTTGAGGTCATGAAGATGTGCATGCCACTTCTTTCACCTGCTTCAGGAGTTATCCATTTTAAAATGTCTGAAGGACAAGCCATGCAGgttcacttcattgctaaacaaaaagcctacagttctgtttaaattgattaacccatccattatttttt---tcacag----------

upper sequence: GRMZM5G858094_T01 (Zea mays), 5'ss of exon 19
lower sequence: Vv18s0001g04980.t01 (Vitis vinifera), 5'ss of exon 19

ACCATACGCGGAAGTTGAGGTTATGAAGATGTGCATGCCTCTCTTGTCACCTGCTTCTGGTGTCATTCATTGTATGATGTCTGAGGGCCAGGCATTGCAGgttatattcgcacatgtccattccttgcattgtgctttcatcacataatatttcatgtaacatttatcaacttatattttgttttag
||| || || || |||||||||||||||||||| ||||| ||  | || |||||||||||  | ||||| | || ||||||||| || || ||| ||||||| | ||      |||| |         ||||    ||  |   ||  |||     |||    |||  || | | ||||||| |   
ACCGTATGCAGAGGTTGAGGTTATGAAGATGTGTATGCCACTTCTTTCGCCTGCTTCTGGAATTATTCAATTTAAGATGTCTGAAGGTCAAGCAATGCAGgtaaaat------atgttc------catattggaagttt-tagtatcctatccttggtagagattaagaaatcacattttgtgtag-

upper sequence: GRMZM5G858094_T01 (Zea mays), 5'ss of exon 19
lower sequence: PP1S13_171V6.1 (Physcomitrella patens), 5'ss of exon 17

ACCATACGCGGAAGTTGAGGTTATGAAGATGTGCATGCCTCTCTTGTCACCTGCTTCTGGTGTCATTCATTGTATGATGTCTGAGGGCCAGGC----ATTGCAGgttatattcgcacatgtccattccttgcattgtgctttcatcacataatatttcatgtaacatttatcaacttatattttgttttag--------------------------------------
 ||||||||||| || |||||||||||||||||||||||||| |||   || || |||||   ||||||||  |   |||||||||||  |||    || | | ||| | ||   | || | | ||  |  || | |  | ||||    | |||    | |||| ||||   || | | || | | | |                                        
TCCATACGCGGAGGTGGAGGTTATGAAGATGTGCATGCCTCTTTTGAGCCCAGCATCTGGAACCATTCATTTCAGATTGTCTGAGGGCTCGGCCATGATGgtatgttgtctttttagattttc-tttgtgacactattgtctcattt--tcataaacaaagtaaaattt-cgaagtgaaatatgggtgtgatgtgttgagttaagatgtgccttccccttgtattccag

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|32803950|gb|CD956186.1|CD956186

EST:     CTGCTTCTGGTGTCATTCATTGTATGATGTCTGAGGGCCAGGCATTGCAG                         GCTGGTGATCTTATAGCAAGGTTGGATC
genomic: CTGCTTCTGGTGTCATTCATTGTATGATGTCTGAGGGCCAGGCATTGCAGgttatattcg ... tttgttttagGCTGGTGATCTTATAGCAAGGTTGGATC

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), 48 (downstream exon)
Score: 107

ACCATACGCGGAAGTTGAGGTTATGAAGATGTGCATGCCTCTCTTGTCACCTGCTTCTGGTGTCATTCATTGTATGATGTCTGAGGGCCAGGCATTGCAGgttatattcg ... tttgttttagGCTGGTGATCTTATAGCAAGGTTGGATCTTGATGACCCTTCTGCTGTGAAAAGAGCTGAGCCATTTGATGGAATATTTCCACAAATGGAGCTCCCTGTTG

Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 104

Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 55