ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq
cis-regulatory elements

Sequence

atgc intronic sequence ATGC exonic sequence

ACTGGATAATACTGTAACTAAGCAGCCAGATTACAGGCTGTATGTGATCCATAAATTGAAGCATTTGCGTTTGCTGGATTTCAAGAAAGTGAAACAACAGgtgagcaatatcttttggcgtataaagacgttgaaatgttaacgtttgcattcatttttagctttatgagcatctgtcacacattttttgcattgccgtc...

Basic information

species	Zea mays
transcript	GRMZM2G021742_T01
intron #	4
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G021742_T01 (Zea mays), 5'ss of exon 4
lower sequence: LOC_Os02g13990.3 (Oryza sativa), 5'ss of exon 4

ACTGGATAATACTGTAACTAAGCAGCCAGATTACAGGCTGTATGTGATCCATAAATTGAAGCATTTGCGTTTGCTGGATTTCAAGAAAGTGAAACAACAGgtgagcaata------tcttttggcgtataaagacgttgaaatgttaacgtttgcattcatttttagctttatgagcatctgtcacacattttttgcattgccgtc
||| |||||||||||||| ||||||||||| ||| || ||||||||||||||||||||||||||||||| |||||||||||||||||||||||||||||||| ||||||       |  |||  | | |||| | |||    | | ||  ||   | ||||||  ||  |||      |   ||    | ||| || |    |   
ACTTGATAATACTGTAACCAAGCAGCCAGACTACCGGTTGTATGTGATCCATAAATTGAAGCATTTGCGGTTGCTGGATTTCAAGAAAGTGAAACAACAGgttagcaatgctgaggttctttttcatgtaaatatgtttttgtatgaaatttgttaatcattt--agtcttagttttgttc-tcttgaagtttctgtaaaaac---

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|60343545|gb|DN210518.1|DN210518

EST:     ATAAATTGAAGCATTTGCGTTTGCTGGATTTCAAGAAAGTGAAACAACAG                         GAGAGAGTTGCGGCAGCGAAAAAGTTCCACTCAAAGGAAGCAGAGGAAGAG
genomic: ATAAATTGAAGCATTTGCGTTTGCTGGATTTCAAGAAAGTGAAACAACAGgtgagcaata ... tgctttgtagGAGAGAGTTGCGGCAGCGAAAAAGTTCCACTCAAAGGAAGCAGAGGAAGAG

EST: gi|211426972|gb|FK970233.1|FK970233

EST:     ATAAATTGAAGCATTTGCGTTTGCTGGATTTCAAGAAAGTGAAACAACAG                         GAGAGAGTTGCGGCAGCGAAAAAGTTCCACTCNAAGGAAGCAGAGGAAGAG
genomic: ATAAATTGAAGCATTTGCGTTTGCTGGATTTCAAGAAAGTGAAACAACAGgtgagcaata ... tgctttgtagGAGAGAGTTGCGGCAGCGAAAAAGTTCCACTCAAAGGAAGCAGAGGAAGAG

EST: gi|5268366|gb|AI770330.1|AI770330

EST:     ATAAATTGAAGCATTTGCGTTTGCTGGATTTCAAGAAAGTGAAACAACAG                         GAGAGAGTTGCGGCAGCGAANAAGTTCCACTCAAAGGAAGCAGAGGAAGAG
genomic: ATAAATTGAAGCATTTGCGTTTGCTGGATTTCAAGAAAGTGAAACAACAGgtgagcaata ... tgctttgtagGAGAGAGTTGCGGCAGCGAAAAAGTTCCACTCAAAGGAAGCAGAGGAAGAG

EST: gi|76918345|gb|DV167252.1|DV167252

EST:     ATAAATTGAAGCATTTGCGTTTGCTGGATTTCAAGAAAGTGAAACAACAG                         GAGAGAGTTGCGGCAGCGAAAAAGTTCCACTCAAAGGAAGCAGAGGAAGAG
genomic: ATAAATTGAAGCATTTGCGTTTGCTGGATTTCAAGAAAGTGAAACAACAGgtgagcaata ... tgctttgtagGAGAGAGTTGCGGCAGCGAAAAAGTTCCACTCAAAGGAAGCAGAGGAAGAG

EST: gi|31364592|gb|CD448947.1|CD448947

EST:     ATAAATTGAAGCATTTGCGTTTGCTAGATTTCAAGAAAGTGAAACAACAG                         GAGAGAGTTGCGGCAGCGAAAAAGTTCCACTCAAAGGAAGCAAAGGAAGAG
genomic: ATAAATTGAAGCATTTGCGTTTGCTGGATTTCAAGAAAGTGAAACAACAGgtgagcaata ... tgctttgtagGAGAGAGTTGCGGCAGCGAAAAAGTTCCACTCAAAGGAAGCAGAGGAAGAG

EST: gi|4226387|gb|AI396494.1|AI396494

EST:     ATAAATTGAAGCATTTGCGTTTGCTGGATTTCAAGAAAGTGAAACAACAG                         GAGAGAGTTGCGGCAGCGAAAAAGTTCCACTCAAAGGAAGCAGAGGAAGAG
genomic: ATAAATTGAAGCATTTGCGTTTGCTGGATTTCAAGAAAGTGAAACAACAGgtgagcaata ... tgctttgtagGAGAGAGTTGCGGCAGCGAAAAAGTTCCACTCAAAGGAAGCAGAGGAAGAG

EST: gi|113701906|gb|EE679410.1|EE679410

EST:     ATAAATTGAAGCATTTGCGTTTGCTGGATTTCAAGAAAGTGAAACAACAG                         GAGAGAGTTGCGGCAGCGAAAAAGTTCCACTCAAAGGAAGCAGAGGAAGAG
genomic: ATAAATTGAAGCATTTGCGTTTGCTGGATTTCAAGAAAGTGAAACAACAGgtgagcaata ... tgctttgtagGAGAGAGTTGCGGCAGCGAAAAAGTTCCACTCAAAGGAAGCAGAGGAAGAG

EST: gi|71761635|gb|DR959572.1|DR959572

EST:     ATAAATTGAAGCATTTGCGTTTGCTGGATTTCAAGAAAGTGAAACAACAG                         GAGAGAGTTGCGGCAGCGAAAAAGTTCCACTCAAAGGAAGCAGAGGAAGAG
genomic: ATAAATTGAAGCATTTGCGTTTGCTGGATTTCAAGAAAGTGAAACAACAGgtgagcaata ... tgctttgtagGAGAGAGTTGCGGCAGCGAAAAAGTTCCACTCAAAGGAAGCAGAGGAAGAG

EST: gi|211242314|gb|FL469535.1|FL469535

EST:     TTCAAGAAAGTGAAACACCAG                         GAGAGAGTTGCGGCAGCGAAAAAGTTCCACTCAAAGGAAGCAGAGGAAGAG
genomic: TTCAAGAAAGTGAAACAACAGgtgagcaata ... tgctttgtagGAGAGAGTTGCGGCAGCGAAAAAGTTCCACTCAAAGGAAGCAGAGGAAGAG

EST: gi|71317917|gb|DR795718.1|DR795718

EST:     ATAAATTGAAGCATTTGCGTTTGCTGGATTTCAAGAAAGTGAAACAACAG                         GAGAGAGTTGCGGCAGCGAAAAAGTTCCACTCAAAGGAAGCAGAGGAAGAG
genomic: ATAAATTGAAGCATTTGCGTTTGCTGGATTTCAAGAAAGTGAAACAACAGgtgagcaata ... tgctttgtagGAGAGAGTTGCGGCAGCGAAAAAGTTCCACTCAAAGGAAGCAGAGGAAGAG

EST: gi|4226377|gb|AI396484.1|AI396484

EST:     ATAAATTGAAGCATTTGCGTTTGCTGGATTTCAAGAAAGTGAAACAACAG                         GAGAGAGTTGCGGCAGCGAAAAAGTTCCACTCAAAGGAAGCAGAGGAAGAG
genomic: ATAAATTGAAGCATTTGCGTTTGCTGGATTTCAAGAAAGTGAAACAACAGgtgagcaata ... tgctttgtagGAGAGAGTTGCGGCAGCGAAAAAGTTCCACTCAAAGGAAGCAGAGGAAGAG

EST: gi|31364112|gb|CD448467.1|CD448467

EST:     ATTTGCGTTTGCTAGATTTCAAGAAAGTGAACCAACAG                         GAGAGAGTTGCGCCAGCG-AAAAGTTCCCACTCAAAGGAAGCAGAGGAAGA
genomic: ATTTGCGTTTGCTGGATTTCAAGAAAGTGAAACAACAGgtgagcaata ... tgctttgtagGAGAGAGTTGCGGCAGCGAAAAAGTT-CCACTCAAAGGAAGCAGAGGAAGA

EST: gi|71317919|gb|DR795719.1|DR795719

EST:     ATAAATTGAAGCATTTGCGTTTGCTGGATTTCAAGAAAGTGAAACAACAG                         GAGAGAGTTGCGGCAGCGAAAAAGTTCCACTCAAAGGAAGCAGAGGAAGAG
genomic: ATAAATTGAAGCATTTGCGTTTGCTGGATTTCAAGAAAGTGAAACAACAGgtgagcaata ... tgctttgtagGAGAGAGTTGCGGCAGCGAAAAAGTTCCACTCAAAGGAAGCAGAGGAAGAG

EST: gi|60397657|gb|DN230473.1|DN230473

EST:     ATAAATTGAAGCATTTGCGTTTGCTGGATTTCAAGAAAGTGAAACAACAG                         GAGAGAGTTGCGGCAGCGAAAAAGTTCCACTCAAAGGAAGCAGAGGAAGAG
genomic: ATAAATTGAAGCATTTGCGTTTGCTGGATTTCAAGAAAGTGAAACAACAGgtgagcaata ... tgctttgtagGAGAGAGTTGCGGCAGCGAAAAAGTTCCACTCAAAGGAAGCAGAGGAAGAG

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: 205

ACTGGATAATACTGTAACTAAGCAGCCAGATTACAGGCTGTATGTGATCCATAAATTGAAGCATTTGCGTTTGCTGGATTTCAAGAAAGTGAAACAACAGgtgagcaata ... tgctttgtagGAGAGAGTTGCGGCAGCGAAAAAGTTCCACTCAAAGGAAGCAGAGGAAGAGGCAAAGAAGGTGCCTGCCAAAACGTTTACTCCTGGTCTGCCTGATGCTC

Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 103

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 103

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 64

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ACTGGATAATACTGTAACTAAGCAGCCAGATTACAGGCTGTATGTGATCCATAAATTGAAGCATTTGCGTTTGCTGGATTTCAAGAAAGTGAAACAACAGgtgagcaatatcttttggcgtataaagacgttgaaatgttaacgtttgcattcatttttagctttatgagcatctgtcacacattttttgcattgccgtc

- - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA