ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq

Sequence

atgc intronic sequence ATGC exonic sequence

TTGTCCGCTCTTGGAGACGTCATATTTTCTCTACCGCAGAAGAATGCTCATGTACCCTACCGGAACAGCAAACTTACACAAGTCCTACAGAGTTCTTTGGgtgcttaccattgctgattgttctatatactatttacatgttatcagttatctaatatttttcatctgcag

Basic information

species	Zea mays
transcript	GRMZM2G093391_T01
intron #	2
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G093391_T01 (Zea mays), 5'ss of exon 2
lower sequence: AT1G63640.1 (Arabidopsis thaliana), 5'ss of exon 17

TTGTCCGCTCTTGGAGACGTCATATTTTCTCTACCGCAGAAGAATGCTCATGTACCCTACCGGAACAGCAAACTTACACAAGTCCTACAGAGTTCTTTGGgtgcttaccattg-ctgattgttctatatactatttacatgttat-cagttatctaatatttttcatctgcag----------------------------------
||||| || ||||| || ||||||||| || || |||| |||||  ||||||| || ||| | ||||||||| | || |||||||| || ||||||||||||   || || |  ||||      || ||  | |||| ||||  | ||   |  | || |||    | ||  |                                  
TTGTCAGCACTTGGGGATGTCATATTTGCTTTAGCGCACAAGAACCCTCATGTTCCTTACAGAAACAGCAAATTGACTCAAGTCCTTCAAAGTTCTTTGGgtaagtatcactctctgaagaaaatagat-ttgtttatatgtattgcataaaattgatgtttgctttatgttgttgattcccttagctattctctcttttttcttag

upper sequence: GRMZM2G093391_T01 (Zea mays), 5'ss of exon 2
lower sequence: AT5G41310.1 (Arabidopsis thaliana), 5'ss of exon 15

TTGTCCGCTCTTGGAGACGTCATATTTTCTCTACCGCAGAAGAATGCTCATGTACCCTACCGGAACAGCAAACTTACACAAGTCCTACAGAGTTCTTTGGgtgct-taccattg--ctgattgttctatatactatttacatgttatcagttatctaatatttttcatctgcag--------
||||| ||||| ||||| || |||||  ||||| | || |||||| |||||||||| ||  | |||||||| || ||||||||||| |||| |||||| ||| || ||  || |   | | |     | ||| || ||  || || |   ||   |  |   |    | |  |         
TTGTCTGCTCTCGGAGATGTTATATTCGCTCTAGCACATAAGAATCCTCATGTACCTTATAGAAACAGCAAGCTAACACAAGTCCTCCAGAATTCTTTAGgtactataagatagacttcaataaaaaaaatattacttg-atattgttgcttgcttctttactcctctttttaattttttag

upper sequence: GRMZM2G093391_T01 (Zea mays), 5'ss of exon 2
lower sequence: PP1S101_161V6.1 (Physcomitrella patens), 5'ss of exon 15

TTGTCCGCTCTTGGAGACGTCATATTTTCTCTACCGCAGAAGAATGCTCATGTACCCTACCGGAACAGCAAACTTACACAAGTCCTACAGAGTTCTTTGGgtgctt-----accattgc-tgattgttctatatactatttacatgttat---cagttatctaatat-ttttcatctgcag-------------------
 | || || || || || || || | | || |  | ||||| |||| |||||| |||||||||||||||||||| || ||  |||| |||  |||| | ||||  |     ||  || | ||    || | |    | | | | ||||||   || | || |  ||| |||| ||  |||                    
CTTTCAGCCCTGGGTGATGTTATCTCTGCTTTGGCACAGAAAAATGGTCATGTGCCCTACCGGAACAGCAAACTCACTCAGCTCCTCCAGGATTCTATAGgtgtgttatgaacacttacgtggccatttttttctttgtctccttgttattttcaatgatttcttatgttttgataagcattactttctcagaagaatta

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|32908957|gb|CF013770.1|CF013770

EST:     TGTACCCTACCGGAACAGCAAACTTACACAAGTCCTACAGAGTTCTTTGG                         GCGGCCATGCAAAAACCTTGATGTTTGTGCAGATCAACCCAGATGTCTCAT
genomic: TGTACCCTACCGGAACAGCAAACTTACACAAGTCCTACAGAGTTCTTTGGgtgcttacca ... tcatctgcagGCGGCCATGCAAAAACCTTGATGTTTGTGCAGATCAACCCAGATGTCTCAT

EST: gi|71441862|gb|DR822912.1|DR822912

EST:     TGTACCCTACCGGAACAGCAAACTTACACAAGTCCTACAGAGTTCTTTGG                         GCGGCCATGCAAAAACCTTGATGTTTGTGCAGATCAACCCAGATGTCTCAT
genomic: TGTACCCTACCGGAACAGCAAACTTACACAAGTCCTACAGAGTTCTTTGGgtgcttacca ... tcatctgcagGCGGCCATGCAAAAACCTTGATGTTTGTGCAGATCAACCCAGATGTCTCAT

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: 45 (upstream exon), 23 (downstream exon)
Score: 2

TTGTCCGCTCTTGGAGACGTCATATTTTCTCTACCGCAGAAGAATGCTCATGTACCCTACCGGAACAGCAAACTTACACAAGTCCTACAGAGTTCTTTGGgtgcttacca ... tcatctgcagGCGGCCATGCAAAAACCTTGATGTTTGTGCAGATCAACCCAGATGTCTCATCTTATTCGGAGACTTTAAGTACTTTGAAGTTTGCTGAAAGGGTTTCTGG

Block sizes: 48 (upstream exon), 45 (downstream exon)
Score: 41

Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 88