ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq

Sequence

atgc intronic sequence ATGC exonic sequence

GATTTGCTGGTTATTTTGACTCTGTACTTTATAAAGATGTTCATCTTGGAATCGAGCCAAACACAGCTACACCAAACATGTTTAGCTGgtaacctgcaacctgatctttacaaaagctggaaatagaatctctcaaacctcgacatcaataactgtatcttcatgccgtaacactgtcag

Basic information

species	Zea mays
transcript	GRMZM2G169927_T03
intron #	20
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G169927_T03 (Zea mays), 5'ss of exon 20
lower sequence: LOC_Os02g04660.1 (Oryza sativa), 5'ss of exon 20

GATTTGCTGGTTATTTTGACTCTGTACTTTATAAAGATGTTCATCTTGGAATCGAGCCAAACACAGCTACACCAAACATGTTTAGCTGgtaacctgca-------acctgatctttacaaaagctggaaatagaatctctcaaacctcgacatcaataactgtatcttcatgccgtaacactgtcag
|||||||||| ||||||||  | ||| | ||||||||||||||||||||||| || |||||||| ||||||||||||||||||||||||||  ||  |       ||||||| ||||     ||||| ||||     |||  ||    | | ||||||      | |   |  |  | ||       
GATTTGCTGGATATTTTGATGCCGTATTGTATAAAGATGTTCATCTTGGAATTGAACCAAACACGGCTACACCAAACATGTTTAGCTGgtacactaaatggcaaaacctgatttttatgt--gctggcaataactgttcttgaatagtgccttcaatattatcttttatgtatctcatcag------

upper sequence: GRMZM2G169927_T03 (Zea mays), 5'ss of exon 20
lower sequence: AT4G31120.1 (Arabidopsis thaliana), 5'ss of exon 21

GATTTGCTGGTTATTTTGACTCTGTACTTTATAAAGATGTTCATCTTGGAATCGAGCCAAACACAGCTACACCAAACATGTTTAGCTGgtaacctgcaacctgatctttacaaaagctg-gaaatagaa------tctctcaaacctcg-acatcaataactgtatcttcatgccgtaacactgtcag
|||| ||||| |||||||| || || ||||||||||||||||||||||| |||||||| |  ||||| |||||||||||||| |||||||||         | || | || ||| | |   ||| |||       ||| || ||||||  || ||||       |   || ||   |     || |||
GATTCGCTGGCTATTTTGATTCCGTCCTTTATAAAGATGTTCATCTTGGGATCGAGCCTACAACAGCAACACCAAACATGTTCAGCTGgtaat----ggattaatgtctataaatgttttaaaacagagctttcttctatcgaacctcttacttcaaccgagagaaaatcgtgt--tccttttggcag

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|211483572|gb|FL225317.1|FL225317

EST:     GTTCATCTTGGAATCGAGCCAAACACAGCTACACCAAACATGTTTAGCTG                         GTTCCCCATCTTCTTCCCATTGAGAAAACCCATCTATGTGCCGGAAGGGTC
genomic: GTTCATCTTGGAATCGAGCCAAACACAGCTACACCAAACATGTTTAGCTGgtaacctgca ... acactgtcagGTTCCCCATCTTCTTCCCATTGAGAAAACCCATCTATGTGCCGGAAGGGTC

EST: gi|211483570|gb|FL225315.1|FL225315

EST:     GTTCATCTTGGAATCGAGCCAAACACAGCTACACCAAACATGTTTAGCTG                         GTTCCCCATCTTCTTCCCATTGAGAAAACCCATCTATGTGCCGGAAGGGTC
genomic: GTTCATCTTGGAATCGAGCCAAACACAGCTACACCAAACATGTTTAGCTGgtaacctgca ... acactgtcagGTTCCCCATCTTCTTCCCATTGAGAAAACCCATCTATGTGCCGGAAGGGTC

EST: gi|5816272|gb|AI987188.1|AI987188

EST:     GTTCATCTTGGAATCGAGCCAAACACAGCTACACCAAACATGTTTAGCTG                         GTTCCCCATCTTCTTCCCATTGAGAAAACCCATCTACGTGCCGGAAGGGTC
genomic: GTTCATCTTGGAATCGAGCCAAACACAGCTACACCAAACATGTTTAGCTGgtaacctgca ... acactgtcagGTTCCCCATCTTCTTCCCATTGAGAAAACCCATCTATGTGCCGGAAGGGTC

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: 47 (upstream exon), 47 (downstream exon)
Score: 54

GATTTGCTGGTTATTTTGACTCTGTACTTTATAAAGATGTTCATCTTGGAATCGAGCCAAACACAGCTACACCAAACATGTTTAGCTGgtaacctgca ... acactgtcagGTTCCCCATCTTCTTCCCATTGAGAAAACCCATCTATGTGCCGGAAGGGTCTCCTATAGAAGTGCACTTCTGGCGGTGCTGTGCCCCCACAAAG

Block sizes: 42 (upstream exon), 44 (downstream exon)
Score: 22

Block sizes: 49 (upstream exon), 44 (downstream exon)
Score: 40