ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq

Sequence

atgc intronic sequence ATGC exonic sequence

ACAATGGAAACCTAGAACAATGGCTTCATGGAGCTATGAGTCAACATGGCTCTCTTACATGGGAGGCCCGCATAAAGATTCTTCTTGGGACTGCTAAAGCgtcagtgcaaaatacactttaactttttattaccattgtctgcattattttccagctcaccttaggatatgaatgctataaaaattctaaagctaattat...

Basic information

species	Zea mays
transcript	GRMZM2G034855_T01
intron #	4
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G034855_T02 (Zea mays), 5'ss of exon 4
lower sequence: LOC_Os01g21960.1 (Oryza sativa), 5'ss of exon 4

ACAATGGAAACCTAGAACAATGGCTTCATGGAGCTATGAGTCAACATGGCTCTCTTACATGGGAGGCCCGCATAAAGATTCTTCTTGGGACTGCTAAAGCgtcagtgc----aaaatacactttaactttttattaccatt-------gtctgcattatttt-ccagctcaccttaggatatgaatgctataaaaattctaaagctaattat
|||||||||||||||| |||||||||||||||||||||||||| | ||| || |||||||||||||||||  ||||||||||||||||||| |||||||||| ||| |       | |     |  ||||||  ||  | |        | |   |||| ||  |||  | |||||||  |    |  | | |   | |||           
ACAATGGAAACCTAGAGCAATGGCTTCATGGAGCTATGAGTCACCGTGGTTCCCTTACATGGGAGGCCCGTGTAAAGATTCTTCTTGGGACAGCTAAAGCgtaagttcttcctggagatgtcatttctttttgctagtacttcaccatatttttgttatattgtcagtccgccttagggca-atgtaatcttatgttccta-----------

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|211042367|gb|FL052105.1|FL052105

EST:     TCTCTTACATGGGAGGCCCGCATAAAGATTCTTCTTGGGACTGCTAAAGC                         GCTTGCTTACTTGCATGAGGCGATTGAACCCAAAGTTGTGCACCGTGACAT
genomic: TCTCTTACATGGGAGGCCCGCATAAAGATTCTTCTTGGGACTGCTAAAGCgtcagtgcaa ... ttgtccacagGCTTGCTTACTTGCATGAGGCGATTGAACCCAAAGTTGTGCACCGTGACAT

EST: gi|60397397|gb|DN230213.1|DN230213

EST:     TCTCTTACATGGGAGGCCCGCATAAAGATTCTTCTTGGGACTGCTAAAGC                         GCTTGCTTACTTGCATGAGGCGATTGAACCCAAAGTTGTGCACCGTGACAT
genomic: TCTCTTACATGGGAGGCCCGCATAAAGATTCTTCTTGGGACTGCTAAAGCgtcagtgcaa ... ttgtccacagGCTTGCTTACTTGCATGAGGCGATTGAACCCAAAGTTGTGCACCGTGACAT

EST: gi|211042366|gb|FL052104.1|FL052104

EST:     TCTCTTACATGGGAGGCCCGCATAAAGATTCTTCTTGGGACTGCTAAAGC                         GCTTGCTTACTTGCATGAGGCGATTGAACCCAAAGTTGTGCACCGTGACAT
genomic: TCTCTTACATGGGAGGCCCGCATAAAGATTCTTCTTGGGACTGCTAAAGCgtcagtgcaa ... ttgtccacagGCTTGCTTACTTGCATGAGGCGATTGAACCCAAAGTTGTGCACCGTGACAT

EST: gi|40334583|gb|CK368653.1|CK368653

EST:     TCTCTTACATGGGAGGCCCGCATAAAGATTCTTCTTGGGACTGCTAAAGC                         GCTTGCTTACTTGCATGAGGCGATTGAACCCAAAGTTGTGCACCGTGACAT
genomic: TCTCTTACATGGGAGGCCCGCATAAAGATTCTTCTTGGGACTGCTAAAGCgtcagtgcaa ... ttgtccacagGCTTGCTTACTTGCATGAGGCGATTGAACCCAAAGTTGTGCACCGTGACAT

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), 49 (downstream exon)
Score: 188

ACAATGGAAACCTAGAACAATGGCTTCATGGAGCTATGAGTCAACATGGCTCTCTTACATGGGAGGCCCGCATAAAGATTCTTCTTGGGACTGCTAAAGCgtcagtgcaa ... ttgtccacagGCTTGCTTACTTGCATGAGGCGATTGAACCCAAAGTTGTGCACCGTGACATCAAATCCAGCAATATTTTGATTGATGATGAGTTCGAGTCCAAAGTATCA

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 178

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 134