ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq

Sequence

atgc intronic sequence ATGC exonic sequence

AGAGCTCGAAACTGCAATACAAGATACTGAATCAGAGGCAAATTCTATGCTATTTCTTAACCAAAATGTTTTGCAGGAGTATCAAAACCGGCAACATGAGgtatcaaaatatgtctggttcatatgtgctggccagttagcaatggttatgttttactgtcttggtattattgctggcagaattatccattgagaacata...

Basic information

species	Zea mays
transcript	GRMZM2G440916_T01
intron #	21
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G440916_T01 (Zea mays), 5'ss of exon 21
lower sequence: LOC_Os05g51790.2 (Oryza sativa), 5'ss of exon 21

AGAGCTCGAAACTGCAATACAAGATACTGAATCAGAGGCAAATTCTATGCTATTTCTTAACCAAAATGTTTTGCAGGAGTATCAAAACCGGCAACATGAGgtatcaaaatatgtctggttcatatgtgctggccagttagcaatggttatg-ttttactgtcttggtat-tattgctggcagaattatccattgagaacata-
||| || ||   |||||| |||||||||||||| || |||||||||||||| |||||||| ||||||||||||  ||||||||||| |||||| | |||||||  |     |     ||  |  | |  |    | ||   | |   | |  ||  | |||     |||  ||   | |   |   |||  ||     |||  
AGAACTGGATTGTGCAATTCAAGATACTGAATCCGAAGCAAATTCTATGCTTTTTCTTAATCAAAATGTTTTGTTGGAGTATCAAAGCCGGCAGCGTGAGgtacaatggattaataagtgtacctctttt--ttatttcatactttctttacttccagtgttgcaatatgcataagttgttcagc-atcagtttgtctcatca

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|78075394|gb|DV503828.1|DV503828

EST:     TATTTCTTAACCAAAATGTTTTGCAGGAGTATCAAAACCGGCAACATGAG                         ATAGAATCAATCTCAAATAAACTTAAGGATGATAAGGGTGAACATGAGATC
genomic: TATTTCTTAACCAAAATGTTTTGCAGGAGTATCAAAACCGGCAACATGAGgtatcaaaat ... gattttacagATAGAATCAATCTCAAATAAACTTAAGGATGATAAGGGTGAACATGAGATC

EST: gi|33092036|gb|CF052030.1|CF052030

EST:     CGGCAACATGAG                         ATAGAATCAATCTCAAATAAACTTAAGGATGATAAGGGTGAACATGAGATC
genomic: CGGCAACATGAGgtatcaaaat ... gattttacagATAGAATCAATCTCAAATAAACTTAAGGATGATAAGGGTGAACATGAGATC

EST: gi|211323884|gb|FK953780.1|FK953780

EST:     CAAAACCGGCAACATGAG                         ATAGAATCAATCTCAAATAAACTTAAGGATGATAAGGGTGAACATGAGATC
genomic: CAAAACCGGCAACATGAGgtatcaaaat ... gattttacagATAGAATCAATCTCAAATAAACTTAAGGATGATAAGGGTGAACATGAGATC

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: 48 (upstream exon), 49 (downstream exon)
Score: 184

AGAGCTCGAAACTGCAATACAAGATACTGAATCAGAGGCAAATTCTATGCTATTTCTTAACCAAAATGTTTTGCAGGAGTATCAAAACCGGCAACATGAGgtatcaaaat ... gattttacagATAGAATCAATCTCAAATAAACTTAAGGATGATAAGGGTGAACATGAGATCTGCTGTTCTGAAATCGAAACAGTAAAG

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 53

Block sizes: 48 (upstream exon), 47 (downstream exon)
Score: 48