ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq
cis-regulatory elements

Sequence

atgc intronic sequence ATGC exonic sequence

GGGAAATGGGGCCTGTGGATTCTCCACAAACTTGTGCTTACTGGAGTCTATGGGCTGATTGTTTTCATGCATCATTCAAGATGGAGAGACAGGCTGCCTGgtaatcggttactgtctttgtatgtttcaaaattctgttgtttgatgtttcatgaccataatctccttgttgctttattgcag

Basic information

species	Zea mays
transcript	GRMZM2G086497_T02
intron #	1
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G086497_T01 (Zea mays), 5'ss of exon 4
lower sequence: LOC_Os03g54920.1 (Oryza sativa), 5'ss of exon 3

GGGAAATGGGGCCTGTGGATTCTCCACAAACTTGTGCTTACTGGAGTCTATGGGCTGATTGTTTTCATGCATCATTCAAGATGGAGAGACAGGCTGCCTGgtaatcggttactgtct---------ttgtatgtttcaaaattctgttgtttgatgtttcatgaccataatctccttgttgctttattgcag
||||| |||||||| ||| |||| |||||| | ||||||||||| |||||||| |||||||| |||||| |||| ||||| |||||||||||| | ||||||||| ||||||  | |         || | | | |  |  || ||| ||||| |||| ||| | ||  || |  || ||  ||| ||||||
GGGAAGTGGGGCCTATGGTTTCTACACAAATTGGTGCTTACTGGTGTCTATGGCCTGATTGTGTTCATGTATCACTCAAGGTGGAGAGACAGGTTACCTGgtaattggttacaatttacagcacagttatgtttgtttaggttgtgt-gtttgctgttccataatcagcatttt-ttattattttgttgcag

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|20507678|gb|BQ279726.1|BQ279726

EST:     TGGGCTGATTGTTTTCATGCATCATTCAAGATGGAGAGACAGGCTGCCTG                         CAAAACCAGCATACTACAACTATGTATGTGTGATGTTGCTACTGAATGGCA
genomic: TGGGCTGATTGTTTTCATGCATCATTCAAGATGGAGAGACAGGCTGCCTGgtaatcggtt ... tttattgcagCAAAACCAGCATACTACAACTATGTATGTGTGATGTTGCTACTGAATGGCA

EST: gi|149101731|gb|EE187868.2|EE187868

EST:     TGGGCTGATTGTTTTCATGCATCATTCAAGATGGAGAGACAGGCTGCCTG                         CAAAACCAGCATACTACAACTATGTATGTGTGATGTTGCTACTGAATGGCA
genomic: TGGGCTGATTGTTTTCATGCATCATTCAAGATGGAGAGACAGGCTGCCTGgtaatcggtt ... tttattgcagCAAAACCAGCATACTACAACTATGTATGTGTGATGTTGCTACTGAATGGCA

EST: gi|211021098|gb|FL442866.1|FL442866

EST:     TGGGCTGATTGTTTTCATGCATCATTCAAGATGGAGAGACAGGCTGCCTG                         CAAAACCAGCATACTACAACTATGTATGTGTGATGTTGCTACTGAATGGCA
genomic: TGGGCTGATTGTTTTCATGCATCATTCAAGATGGAGAGACAGGCTGCCTGgtaatcggtt ... tttattgcagCAAAACCAGCATACTACAACTATGTATGTGTGATGTTGCTACTGAATGGCA

EST: gi|211314374|gb|FL453743.1|FL453743

EST:     TGGGCTGATTGTTTTCATGCATCATTCAAGATGGAGAGACAGGCTGCCTG                         CAAAACCAGCATACTACAACTATGTATGTGTGATGTTGCTACTGAATGGCA
genomic: TGGGCTGATTGTTTTCATGCATCATTCAAGATGGAGAGACAGGCTGCCTGgtaatcggtt ... tttattgcagCAAAACCAGCATACTACAACTATGTATGTGTGATGTTGCTACTGAATGGCA

EST: gi|28982919|gb|BQ538440.2|BQ538440

EST:     TGGGCTGATTGTTTTCATGCATCATTCAAGATGGAGAGACAGGCTGCCTG                         CAAAACCAGCATACTACAACTATGTATGTGTGATGTTGCTACTGAATGGCA
genomic: TGGGCTGATTGTTTTCATGCATCATTCAAGATGGAGAGACAGGCTGCCTGgtaatcggtt ... tttattgcagCAAAACCAGCATACTACAACTATGTATGTGTGATGTTGCTACTGAATGGCA

EST: gi|149004863|gb|EE039371.2|EE039371

EST:     TGGGCTGATTGTTTTCATGCATCATTCAAGATGGAGAGACAGGCTGCCTG                         CAAAACCAGCATACTACAACTATGTATGTGTGATGTTGCTACTGAATGGCA
genomic: TGGGCTGATTGTTTTCATGCATCATTCAAGATGGAGAGACAGGCTGCCTGgtaatcggtt ... tttattgcagCAAAACCAGCATACTACAACTATGTATGTGTGATGTTGCTACTGAATGGCA

EST: gi|78123014|gb|DV541398.1|DV541398

EST:     TGGGCTGATTGTTTTCATGCATCATTCAAGATGGAGAGACAGGCTGCCTG                         CAAAACCAGCATACTACAACTATGTATGTGTGATGTTGCTACTGAATGGCA
genomic: TGGGCTGATTGTTTTCATGCATCATTCAAGATGGAGAGACAGGCTGCCTGgtaatcggtt ... tttattgcagCAAAACCAGCATACTACAACTATGTATGTGTGATGTTGCTACTGAATGGCA

EST: gi|6865283|gb|AW360633.1|AW360633

EST:     TGGGCTGATTGTTTTCATGCATCATTCAAGATGGAGAGACAGGCTGCCTG                         CAAAACCAGCATACTACAACTATGTATGTGTGATGTTGCTACTGAATGGCA
genomic: TGGGCTGATTGTTTTCATGCATCATTCAAGATGGAGAGACAGGCTGCCTGgtaatcggtt ... tttattgcagCAAAACCAGCATACTACAACTATGTATGTGTGATGTTGCTACTGAATGGCA

EST: gi|116814069|gb|EC856569.1|EC856569

EST:     GAGA-AGGCTG-CTG                         CAAAA-CAGCATACTACAACTATGTATGTGTGAT-TTGCTACTGAATGGCA
genomic: GAGACAGGCTGCCTGgtaatcggtt ... tttattgcagCAAAACCAGCATACTACAACTATGTATGTGTGATGTTGCTACTGAATGGCA

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), 49 (downstream exon)
Score: 160

GGGAAATGGGGCCTGTGGATTCTCCACAAACTTGTGCTTACTGGAGTCTATGGGCTGATTGTTTTCATGCATCATTCAAGATGGAGAGACAGGCTGCCTGgtaatcggtt ... tttattgcagCAAAACCAGCATACTACAACTATGTATGTGTGATGTTGCTACTGAATGGCATATCACTGTTTGGATGTTTCCTTATTGCAAGTGGAGCTGGATTTGGTTT

Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 139

Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 258

Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 156

Putative cis-regulatory sequences

atgc	intron	ATGC	exonic elements by Pertea et al.
ATGC	exon	atgc	putative intronic elements
		ATGC	putative exonic elements identified for retained introns

        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGGAAATGGGGCCTGTGGATTCTCCACAAACTTGTGCTTACTGGAGTCTATGGGCTGATTGTTTTCATGCATCATTCAAGATGGAGAGACAGGCTGCCTGgtaatcggttactgtctttgtatgtttcaaaattctgttgtttgatgtttcatgaccataatctccttgttgctttattgcag

- - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGA