ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq

Sequence

atgc intronic sequence ATGC exonic sequence

GCCATATGCGGAAGTTGAGGTTATGAAGATGTGCATGCCTCTCTTGTCACCTGCTTCTGGTGTCATTCATTGTATGATGTCTGAGGGCCAGGCGTTGCAGgttatattcatacatgtccattccttgcattgttgctttcatcacatagtatttcatgtaaaatttaccaacttatattttgttttag

Basic information

species	Zea mays
transcript	AC197672.3_FGT002
intron #	19
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: AC197672.3_FGT002 (Zea mays), 5'ss of exon 19
lower sequence: LOC_Os05g22940.1 (Oryza sativa), 5'ss of exon 21

GCCATATGCGGAAGTTGAGGTTATGAAGATGTGCATGCCTCTCTTGTCACCTGCTTCTGGTGTCATTCATTGTATGATGTCTGAGGGCCAGGCGTTGCAGgttatattcatacatgtccattccttgcattgttgctttcatcacatagtatttcatgtaaaatttaccaacttatattttgttttag
 |||||||||||||||||||||||||||||||||||||| ||||| ||||| |||||||||||||| |||  | | |||||||||||||| ||  ||||||| | |||| ||||| ||||||| |||   ||| |||  ||| |      |||||| |||||       ||||| | | || || |||
ACCATATGCGGAAGTTGAGGTTATGAAGATGTGCATGCCCCTCTTATCACCCGCTTCTGGTGTCATACATGTTGTAATGTCTGAGGGCCAAGCAATGCAGgt-acattcctacat-tccattcattgtgctgt-gctgacatga----acatttcaagtaaatacctgtaacttgtttattattctag

upper sequence: AC197672.3_FGT002 (Zea mays), 5'ss of exon 19
lower sequence: GLYMA06G11120.1 (Glycine max), 5'ss of exon 18

GCCATATGCGGAAGTTGAGGTTATGAAGATGTGCATGCCTCTCTTGTCACCTGCTTCTGGTGTCATTCATTGTATGATGTCTGAGGGCCAGGCGTTGCAGgt-tatattcatacatgtc-cattccttgcattgttgctttcatcacatagtatttcatgtaaaatttaccaacttatattttgttttag
 |||||||| ||||||||||| ||||| ||||||||||||||  | || |||||||||||  | |||||||  |  |||||||| || || ||  ||||||| ||||    |  ||  | ||||    | |  | || |   ||   |    ||   |   | | | |  |   ||  |           
ACCATATGCTGAAGTTGAGGTCATGAAAATGTGCATGCCTCTTCTTTCGCCTGCTTCTGGGATTATTCATTTCAAAATGTCTGAAGGTCAAGCAATGCAGgtatatagcattctattccacattggaagtacaggtgttcatattgaaagagataataaa-atagtatcactgtttgcag----------

upper sequence: AC197672.3_FGT002 (Zea mays), 5'ss of exon 19
lower sequence: GLYMA04G11550.1 (Glycine max), 5'ss of exon 18

GCCATATGCGGAAGTTGAGGTTATGAAGATGTGCATGCCTCTCTTGTCACCTGCTTCTGGTGTCATTCATTGTATGATGTCTGAGGGCCAGGCGTTGCAGgttatattcatacatgtccattccttgcattgttgctttcatcacatagtatttcatgtaaaatttaccaacttatattttgttttag--
 || ||||| ||||||||||| ||||| ||||||||||||||  | || |||||||||||  | |||||||  |  |||||||| || || ||  ||||||| ||||     ||| || |||||   ||| |    |   ||    |   |||  |   |||  | |  || || |||    ||||    
ACCGTATGCTGAAGTTGAGGTCATGAAAATGTGCATGCCTCTTCTTTCGCCTGCTTCTGGGATTATTCATTTCAAAATGTCTGAAGGTCAAGCAATGCAGgt-atata---gcat-tctattcc--acataggaagtacaattgt-tgaaattgaa---aaagataataaaattgtatcaccttttgcag

upper sequence: AC197672.3_FGT002 (Zea mays), 5'ss of exon 19
lower sequence: AT1G36160.1 (Arabidopsis thaliana), 5'ss of exon 18

GCCATATGCGGAAGTTGAGGTTATGAAGATGTGCATGCCTCTCTTGTCACCTGCTTCTGGTGTCATTCATTGTATGATGTCTGAGGGCCAGGCGTTGCAGgttatattcatacatgtccattc--cttgcattgttgctttcatcacatagtatttcatgtaaaatttaccaacttatattttgttttag
||| ||||| ||||||||||| ||||||||||||||||| ||  | ||||||||||| || || || |||| ||  |||||||| || || ||  ||||||||   |||||   |   ||     | | || |  || ||  ||    ||     ||   ||   ||| |  |                 
GCCTTATGCCGAAGTTGAGGTCATGAAGATGTGCATGCCACTTCTTTCACCTGCTTCAGGAGTTATCCATTTTAAAATGTCTGAAGGACAAGCCATGCAGgttcacttcattgctaaacaaaaagcctacagttctgtttaaattgattaacccatccattatttttttcacag----------------

upper sequence: AC197672.3_FGT002 (Zea mays), 5'ss of exon 19
lower sequence: PP1S13_171V6.1 (Physcomitrella patens), 5'ss of exon 17

GCCATATGCGGAAGTTGAGGTTATGAAGATGTGCATGCCTCTCTTGTCACCTGCTTCTGGTGTCATTCATTGTATGATGTCTGAGGGCCAGGC----GTTGCAGgttatattcatacatgtccattccttgcattgttgctttcatcacatagtatttcatgtaaaatttaccaacttatattttgttttag--------------------------------------
 ||||| ||||| || |||||||||||||||||||||||||| |||   || || |||||   ||||||||  |   |||||||||||  |||     | | | ||| | ||  || || | | ||  |  || | |||  |   |  ||||       | ||||||||| | || | | || | | | |                                        
TCCATACGCGGAGGTGGAGGTTATGAAGATGTGCATGCCTCTTTTGAGCCCAGCATCTGGAACCATTCATTTCAGATTGTCTGAGGGCTCGGCCATGATGgtatgttgtctttttagattttc-tttgtgacactattgtctcattttcataa---acaaagtaaaattt-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|32801855|gb|CD954091.1|CD954091

EST:     CTGCTTCTGGTGTCATTCATTGTATGATGTCTGAGGGCCAGGCGTTGCAG                         GCTGGTGATCTTATAGCAAGGCCGGATC
genomic: CTGCTTCTGGTGTCATTCATTGTATGATGTCTGAGGGCCAGGCGTTGCAGgttatattca ... tttgttttagGCTGGTGATCTTATAGCAAGGCTGGATC

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), 47 (downstream exon)
Score: 89

GCCATATGCGGAAGTTGAGGTTATGAAGATGTGCATGCCTCTCTTGTCACCTGCTTCTGGTGTCATTCATTGTATGATGTCTGAGGGCCAGGCGTTGCAGgttatattca ... tttgttttagGCTGGTGATCTTATAGCAAGGCTGGATCTTGATGACCCTTCTGCTGTGAAAAGAGCTGAACCATTTGATGGAATGTTTCCACTAATGGACCTCCCTGTTG

Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 43

Block sizes: 44 (upstream exon), 47 (downstream exon)
Score: 14