ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq

Sequence

atgc intronic sequence ATGC exonic sequence

GGTTGCTAAAGCCCAAAAGGTTCCTGAGGAAGGATGGACAATGCAGGATGGAACTCCATGGCCCGGAAATAATGTCCGTGATCATCCTGGAATGATTCAGgtatgctttgacagttactaattaacagtgcatgtggtgggatgttttttttcttcactgtgccacaagaaaatatttatttattttccaccaatag

Basic information

species	Zea mays
transcript	GRMZM2G113137_T01
intron #	8
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G113137_T01 (Zea mays), 5'ss of exon 8
lower sequence: LOC_Os03g62090.1 (Oryza sativa), 5'ss of exon 8

GGTTGCTAAAGCCCAAAAGGTTCCTGAGGAAGGATGGACAATGCAGGATGGAACTCCATGGCCCGGAAATAATGTCCGTGATCATCCTGGAATGATTCAGgtatgctttgacagtta----------ctaattaacagtgcatgtggtgggatg----ttttttttcttcactgtgccacaagaaaatatttatttattttccaccaatag
||||||||||||||| || |||||||||||||||||||||||||||||||||||||| ||||| ||||| || || ||||||||||||||||||||||||||||||||| ||||||            |||||| | |   |  || || ||||     |||     |    ||    || |  | | || |     |||| || | ||||
GGTTGCTAAAGCCCAGAAAGTTCCTGAGGAAGGATGGACAATGCAGGATGGAACTCCCTGGCCTGGAAACAACGTTCGTGATCATCCTGGAATGATTCAGgtatgcttttacagttcatggtgctgtttaattatctgctgacatgatgtgatggctactttccccttctcttgctttaccatgacaaatctcaaacttttgcaaccatag

upper sequence: GRMZM2G113137_T01 (Zea mays), 5'ss of exon 8
lower sequence: GLYMA06G47420.1 (Glycine max), 5'ss of exon 10

GGTTGCTAAAGCCCAAAAGGTTCCTGAGGAAGGATGGACAATGCAGGATGGAACTCCATGGCCCGGAAATAATGTCCGTGATCATCCTGGAATGATTCAGgt-----atgctttgacagttactaat-taacagtgcatgtggtgggatgttttttttcttcactgtgccacaagaaaatatttatttattttccaccaatag
 ||||||||  |    ||||| || || ||||| ||||||||||| |||||||| |||||||| ||||||||||| |||||||| || |||||||| |||||     ||  ||  | ||| | || | ||  | |  |    ||   || |  | |  ||  | | | |||  | |      | || |||||       ||  
AGTTGCTAAGTCTAGGAAGGTCCCAGAAGAAGGGTGGACAATGCAAGATGGAACACCATGGCCTGGAAATAATGTTCGTGATCACCCAGGAATGATACAGgttggtaatagttaaaaagtaaatagtatatgaatctaaagtgtaaaatatcatgtgactcta-tattccattatactgagatcatatatttatacaagat--

upper sequence: GRMZM2G113137_T01 (Zea mays), 5'ss of exon 8
lower sequence: Vv03s0038g04250.t01 (Vitis vinifera), 5'ss of exon 8

GGTTGCTAAAGCCCAAAAGGTTCCTGAGGAAGGATGGACAATGCAGGATGGAACTCCATGGCCCGGAAATAATGTCCGTGATCATCCTGGAATGATTCAGgtatgc---tttgacagttactaattaacagtgcatgtggtgggatgttttttttcttcactgtgccacaagaaaatatttatttattttccaccaatag
|||||| ||||| |||||||| || || ||||| ||||||||||||||||| || || ||||| |||||||||||||||||||| |||||||||||||||||||     | ||| ||||| | || |   || |   || |  |||  || || |  | |   | |     | |    ||| | ||              
GGTTGCCAAAGCTCAAAAGGTCCCAGAAGAAGGGTGGACAATGCAGGATGGGACGCCTTGGCCAGGAAATAATGTCCGTGATCACCCTGGAATGATTCAGgtatatatttctgagagttatttatgagatgtcc---tgatctgatcattcttgttctaagcattcttttgggat---tttctctag-------------

upper sequence: GRMZM2G113137_T01 (Zea mays), 5'ss of exon 8
lower sequence: Vv18s0122g00120.t01 (Vitis vinifera), 5'ss of exon 8

GGTTGCTAAAGCCCAAAAGGTTCCTGAGGAAGGATGGACAATGCAGGATGGAACTCCATGGCCCGGAAATAATGTCCGTGATCATCCTGGAATGATTCAGgtatgctttgacagttactaattaacagtgcatgtggtgggatgttttttttcttcactgtgccacaagaaaatatttatttattttccaccaatag
|||||| || || |||||||| || || ||||| ||||||||||||||||| ||||||||||| || |||||  |||| ||||||||||||||||||||||||       ||  ||   ||||  ||||  || | ||    ||||      | |  | ||    |   || || | |  ||   || |   |    
GGTTGCCAAGGCACAAAAGGTCCCAGAAGAAGGGTGGACAATGCAGGATGGGACTCCATGGCCTGGGAATAACATCCGAGATCATCCTGGAATGATTCAGgtac------acgatttgaaatt--cagtatatttagtttt-tgttgagacccattgcagttgggccttaacatgtgttcttggatttctatag---

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|26559388|gb|CA831623.1|CA831623

EST:     GAACTCCATGGCCCGGAAATAATGTCCGTGATCATCCTGGAATGATTCAG                         GTTTTCCTTGGTCAAAGTGGTGGCCATGATGTGGAAGGAAATGAGCTGCCT
genomic: GAACTCCATGGCCCGGAAATAATGTCCGTGATCATCCTGGAATGATTCAGgtatgctttg ... ccaccaatagGTTTTCCTTGGTCAAAGTGGTGGCCATGATGTGGAAGGAAATGAGCTGCCT

EST: gi|87156952|gb|DY401741.1|DY401741

EST:     GAACTCCATGGCCCGGAAATAATGTCCGTGATCATCCTGGAATGATTCAG                         GTTTTCCTTGGTCAAAGTGGTGGCCATGATGTGGAAGGAAATGAGCTGCCT
genomic: GAACTCCATGGCCCGGAAATAATGTCCGTGATCATCCTGGAATGATTCAGgtatgctttg ... ccaccaatagGTTTTCCTTGGTCAAAGTGGTGGCCATGATGTGGAAGGAAATGAGCTGCCT

EST: gi|22715464|gb|BU197778.1|BU197778

EST:     GAACTCCATGGCCCGGAAATAATGTCCGTGATCATCCTGGAATGATTCAG                         GTTTTCCTTGGTCAAAGTGGTGGCCATGATGTGGAAGGAAATGAGCTGCCT
genomic: GAACTCCATGGCCCGGAAATAATGTCCGTGATCATCCTGGAATGATTCAGgtatgctttg ... ccaccaatagGTTTTCCTTGGTCAAAGTGGTGGCCATGATGTGGAAGGAAATGAGCTGCCT

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: 294

GGTTGCTAAAGCCCAAAAGGTTCCTGAGGAAGGATGGACAATGCAGGATGGAACTCCATGGCCCGGAAATAATGTCCGTGATCATCCTGGAATGATTCAGgtatgctttg ... ccaccaatagGTTTTCCTTGGTCAAAGTGGTGGCCATGATGTGGAAGGAAATGAGCTGCCTCGATTGGTTTATGTTTCAAGAGAAAAACGGCCAGGCTACAACCATCACA

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 586

Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 389