ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq
cis-regulatory elements

Sequence

atgc intronic sequence ATGC exonic sequence

TGCCATGATGAGTGTAGATGAGACATTGATGTGCTCCTTCCAAATACTGAAACCTGCGAGGAAGGTGTTGGGTGGTTCAACTAATAACAAATCAGGCTTCaaggtatacatcattaacatgaaaactgtttatatgtatcatgtagttagcacaatttgttgtcctataaaaatgtttggtcccttccctctagaaatga...

Basic information

species	Zea mays
transcript	GRMZM2G390076_T02
intron #	3
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G390076_T02 (Zea mays), 5'ss of exon 3
lower sequence: LOC_Os02g57450.2 (Oryza sativa), 5'ss of exon 3

TGCCATGATGAGTGTAGATGAGACATTGATGTGCTCCTTCCAAATACTGAAACCTGCGAGGAAGGTGTTGGGTGGTTCAACTAATAACAAATCAGGCTTCaaggtatacatcattaacatgaaaactgtttatatgtatcat-gtagttagcacaatttgttgtcctataaaaatgtttggtcccttccctctagaaatga------
   |||||||||||||||||| ||| |||||||||| || |||||||| ||||| ||||||||  ||||||||||||| || |||  |||||| ||||||||||||| ||| | ||  | | |  |   | | |  |||  |  |  ||   ||||| | | |   |        ||   |||||||||    | ||  ||      
---CATGATGAGTGTAGATGATACACTGATGTGCTCTTTTCAAATACTAAAACCAGCGAGGAAAATGTTGGGTGGTTCCACGAATTCCAAATCCGGCTTCAAGgtatgcataactagta-gtatgcaagtgacagatatttttattatttatacaatatatagcgattccctgcagt---gtcccttccaaaaaaaagggacatgct

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|6695722|gb|AW288800.1|AW288800

EST:     AACCTGCGAGGAAAGTGTTGGGTGGTTCAACTAATAACAAATCTGGCTTC                         AAGTCATTGAGAGGATGGTGACAATGGCAAGCCTGATATCAGG
genomic: AACCTGCGAGGAAGGTGTTGGGTGGTTCAACTAATAACAAATCAGGCTTCaaggtataca ... tctttgtttaCAGTCATCGAGAGGATGGTGACAATGGCAAGCCTGATATCAGG

EST: gi|116822684|gb|EC866106.1|EC866106

EST:     ACCTGCGAGGAAAGGTGTTGGGTGGTTCAACTAATAACAAATCTGGCTTC                         AAGTCATTGAGAGGATGGTGACAATGGCAAGCCTGATATCAGGTTGGTTGG
genomic: ACCTGCGAGG-AAGGTGTTGGGTGGTTCAACTAATAACAAATCAGGCTTCaaggtataca ... tctttgtttaCAGTCATCGAGAGGATGGTGACAATGGCAAGCCTGATATCAGGTTGGTTGG

EST: gi|69351419|gb|DR452128.1|DR452128

EST:     AACCTGCGAGGAAGGTGTTGGGTGGTTCAACTAATAACAAATCTGGCTTC                         AAGTCATTGAGAGGATGGTGACAATGGCAAGCCTGATATCAGGTTGGTTGG
genomic: AACCTGCGAGGAAGGTGTTGGGTGGTTCAACTAATAACAAATCAGGCTTCaaggtataca ... tctttgtttaCAGTCATCGAGAGGATGGTGACAATGGCAAGCCTGATATCAGGTTGGTTGG

EST: gi|30052497|gb|AI065786.2|AI065786

EST:     AACCTGCGAGGAAGGTGTNGGGTGGTTCAAATAATAACAAATCAGGCTTC                         AAGTCATCGAGAGGATGGTGACAATGGCAAGCCTGATATCAGGTTGGNTGG
genomic: AACCTGCGAGGAAGGTGTTGGGTGGTTCAACTAATAACAAATCAGGCTTCaaggtataca ... tctttgtttaCAGTCATCGAGAGGATGGTGACAATGGCAAGCCTGATATCAGGTTGGTTGG

EST: gi|37384218|gb|CF629167.1|CF629167

EST:     AACCTGC---GAAGGTGTTGGGTGGTTCAACTAATAACAAATCAGGCTTC                         AAGTCATCGAGAGGATGGTGACAATGGCAAGCCTGATATCAGGTTGGTTGG
genomic: AACCTGCGAGGAAGGTGTTGGGTGGTTCAACTAATAACAAATCAGGCTTCaaggtataca ... tctttgtttaCAGTCATCGAGAGGATGGTGACAATGGCAAGCCTGATATCAGGTTGGTTGG

EST: gi|16379645|gb|BI993074.1|BI993074

EST:     AACCTGCGAGGAAGGTGTTGGGTGGTTCAACTAATAACAAATCAGGCTTC                         AAGTCATCGAGAGGATGGTGACAATGGCAAGCCTGATATCAGGTTGGTTGG
genomic: AACCTGCGAGGAAGGTGTTGGGTGGTTCAACTAATAACAAATCAGGCTTCaaggtataca ... tctttgtttaCAGTCATCGAGAGGATGGTGACAATGGCAAGCCTGATATCAGGTTGGTTGG

EST: gi|93284121|gb|EB676385.1|EB676385

EST:     AACCTGCGAGGAAGGTGTTGGGTGGTTCAACTAATAACAAATCAGGCTTC                         AAGTCATCGAGAGGATGGTGACAATGGCAAGCCTGATATCAGGTTGGTTGG
genomic: AACCTGCGAGGAAGGTGTTGGGTGGTTCAACTAATAACAAATCAGGCTTCaaggtataca ... tctttgtttaCAGTCATCGAGAGGATGGTGACAATGGCAAGCCTGATATCAGGTTGGTTGG

EST: gi|60359288|gb|DN226261.1|DN226261

EST:     AACCTGCGAGGAAGGTGTTGGGTGGTTCAACTAATAACAAATCAGGCTTC                         AAGTCATCGAGAGGATGGTGACAATGGCAAGCCTGATATCAGGTTGGTTGG
genomic: AACCTGCGAGGAAGGTGTTGGGTGGTTCAACTAATAACAAATCAGGCTTCaaggtataca ... tctttgtttaCAGTCATCGAGAGGATGGTGACAATGGCAAGCCTGATATCAGGTTGGTTGG

EST: gi|211195637|gb|FL445841.1|FL445841

EST:     GGTGTTGGGTGGTTCAACTAAWTAACAAAATCAGGCTTC                         AAGTCATCGAGAGGATGGTGACAATGGCAAGCCTGATAYCAGGTTGGTTGG
genomic: GGTGTTGGGTGGTTCAACTAA-TAAC-AAATCAGGCTTCaaggtataca ... tctttgtttaCAGTCATCGAGAGGATGGTGACAATGGCAAGCCTGATATCAGGTTGGTTGG

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: 163

TGCCATGATGAGTGTAGATGAGACATTGATGTGCTCCTTCCAAATACTGAAACCTGCGAGGAAGGTGTTGGGTGGTTCAACTAATAACAAATCAGGCTTCaaggtataca ... tctttgtttaCAGTCATCGAGAGGATGGTGACAATGGCAAGCCTGATATCAGGTTGGTTGGTGAGCAGCACGCCAGTGGTCGACGGGGGGTTGTTCCATCATAATCATAT

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 191

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 157

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 126

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGCCATGATGAGTGTAGATGAGACATTGATGTGCTCCTTCCAAATACTGAAACCTGCGAGGAAGGTGTTGGGTGGTTCAACTAATAACAAATCAGGCTTCaaggtatacatcattaacatgaaaactgtttatatgtatcatgtagttagcacaatttgttgtcctataaaaatgtttggtcccttccctctagaaatga

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -catgaaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -cccttccc