ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq
cis-regulatory elements

Sequence

atgc intronic sequence ATGC exonic sequence

ACTTTTAGATAATAAGGAAAGCGGGGATACAGCTTGGCAGAATTTGATGGAGCGTACAACCTCCAACATGACCTACAAGGCCTGGCGGCGTGAGCCTGAGgtttgtctttccagtgggttttggaaaaaaaatttaaatgctgataatataggatattatagaaggtacttctaccacaattccgaggtggtgtataacc...

Basic information

species	Zea mays
transcript	GRMZM2G124965_T02
intron #	2
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G124965_T02 (Zea mays), 5'ss of exon 2
lower sequence: LOC_Os07g08760.2 (Oryza sativa), 5'ss of exon 1

ACTTTTAGATAATAAGGAAAGCGGGGATACAGCTTGGCAGAATTTGATGGAGCGTACAACCTCCAACATGACCTACAAGGCCTGGCGGCGTGAGCCTGAGgtttgtctttccagtgggttttggaaaaaaaatttaaatgctgataatataggatattatagaaggtacttctaccacaattccgaggtggtgtataacc--------
|||| | ||||| ||||| || ||||||||| | |||||| |||||||||| ||||| || ||||||||||| |||||||||||||| |||||||||||||| ||| || | |  || || | | ||| |||   | |||   | | |||| |    |||||   | | | |    |  |||    ||   ||||| |          
ACTTCTTGATAACAAGGAGAGTGGGGATACAACATGGCAGCATTTGATGGAACGTACCACTTCCAACATGACTTACAAGGCCTGGCGCCGTGAGCCTGAGgtatgttttccaatgggattgtaggaaagaaac--agatgtcaa-agtatatg----tatagcgtg-attgcgtaaatgattagagggccctgtattagaaataagtt

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|149083327|gb|EE172619.2|EE172619

EST:     AGCGTACAACCTCCAACATGACCTACAAGGCCTGGCGGCGTGAGCCTGAG                         GAGGGACCTATAATGTACTGCAGCCGCACTATTTTTGAGGATGCTACACCT
genomic: AGCGTACAACCTCCAACATGACCTACAAGGCCTGGCGGCGTGAGCCTGAGgtttgtcttt ... gtaattttagGAGGGACCTATAATGTACTGCAGCCGCACTATTTTTGAGGATGCTACACCT

EST: gi|71769408|gb|DR967345.1|DR967345

EST:     AGCGTACAACCTCCAACATGACCTACAAGGCCTGGCGGCGTGAGCCTGAG                         GAGGGACCTATAATGTACTGCAGCCGCACTATTTTTGAGGATGCTACACCT
genomic: AGCGTACAACCTCCAACATGACCTACAAGGCCTGGCGGCGTGAGCCTGAGgtttgtcttt ... gtaattttagGAGGGACCTATAATGTACTGCAGCCGCACTATTTTTGAGGATGCTACACCT

EST: gi|149111705|gb|EE190850.2|EE190850

EST:     AGCGTACAACCTCCAACATGACCTACAAGGCCTGGCGGCGTGAGCCTGAG                         GAGGGACCTATAATGTACTGCAGCCGCACTATTTTTGAGGATGCTACACCT
genomic: AGCGTACAACCTCCAACATGACCTACAAGGCCTGGCGGCGTGAGCCTGAGgtttgtcttt ... gtaattttagGAGGGACCTATAATGTACTGCAGCCGCACTATTTTTGAGGATGCTACACCT

EST: gi|149106183|gb|EE291871.2|EE291871

EST:     AGCGTACAACCTCCAACATGACCTACAAGGCCTGGCGGCGTGAGCCTGAG                         GAGGGACCTATAATGTACTGCAGCCGCACTATTTTTGAGGATGCTACACCT
genomic: AGCGTACAACCTCCAACATGACCTACAAGGCCTGGCGGCGTGAGCCTGAGgtttgtcttt ... gtaattttagGAGGGACCTATAATGTACTGCAGCCGCACTATTTTTGAGGATGCTACACCT

EST: gi|91055562|gb|EB165980.1|EB165980

EST:     AGCGTACAACCTCCAACATGACCTACAAGGCCTGGCGGCGTGAGCCTGAG                         GAGGGACCTATAATGTACTGCAGCCGCACTATTTTTGAGGATGCTACACCT
genomic: AGCGTACAACCTCCAACATGACCTACAAGGCCTGGCGGCGTGAGCCTGAGgtttgtcttt ... gtaattttagGAGGGACCTATAATGTACTGCAGCCGCACTATTTTTGAGGATGCTACACCT

EST: gi|71437018|gb|DR818068.1|DR818068

EST:     AGCGTACAACCTCCAACATGACCTACAAGGCCTGGCGGCGTGAGCCTGAG                         GAGGGACCTATAATGTACTGCAGCCGCACTATTTTTGAGGATGCTACACCT
genomic: AGCGTACAACCTCCAACATGACCTACAAGGCCTGGCGGCGTGAGCCTGAGgtttgtcttt ... gtaattttagGAGGGACCTATAATGTACTGCAGCCGCACTATTTTTGAGGATGCTACACCT

EST: gi|148954197|gb|EC899605.2|EC899605

EST:     AGCGTACAACCTCCAACATGACCTACAAGGCCTGGCGGCGTGAGCCTGAG                         GAGGGACCTATAATGTACTGCAGCCGCACTATTTTTGAGGATGCTACACCT
genomic: AGCGTACAACCTCCAACATGACCTACAAGGCCTGGCGGCGTGAGCCTGAGgtttgtcttt ... gtaattttagGAGGGACCTATAATGTACTGCAGCCGCACTATTTTTGAGGATGCTACACCT

EST: gi|94472323|gb|EB701281.1|EB701281

EST:     AGCGTACAACCTCCAACATGACCTACAAGGCCTGGCGGCGTGAGCCTGAG                         GAGGGACCTATAATGTACTGCAGCCGCACTATTTTTGAGGATGCTACACCT
genomic: AGCGTACAACCTCCAACATGACCTACAAGGCCTGGCGGCGTGAGCCTGAGgtttgtcttt ... gtaattttagGAGGGACCTATAATGTACTGCAGCCGCACTATTTTTGAGGATGCTACACCT

EST: gi|31354728|gb|CD439085.1|CD439085

EST:     AGCGTACAACCTCCAACATGACCTACAAGGCCTGGCGGCGTGAGCCTGAG                         GAGGGACCTATAATGTACTGCAGCCGCACTATTTTTGAGGATGCTACACCT
genomic: AGCGTACAACCTCCAACATGACCTACAAGGCCTGGCGGCGTGAGCCTGAGgtttgtcttt ... gtaattttagGAGGGACCTATAATGTACTGCAGCCGCACTATTTTTGAGGATGCTACACCT

EST: gi|93017144|gb|EB642664.1|EB642664

EST:     AGCGTACAACCTCCAACATGACCTACAAGGCCTGGCGGCGTGAGCCTGAG                         GAGGGACCTATAATGTACTGCAGCCGCACTATTTTTGAGGATGCTACACCT
genomic: AGCGTACAACCTCCAACATGACCTACAAGGCCTGGCGGCGTGAGCCTGAGgtttgtcttt ... gtaattttagGAGGGACCTATAATGTACTGCAGCCGCACTATTTTTGAGGATGCTACACCT

EST: gi|78083626|gb|DV512019.1|DV512019

EST:     AGCGTACAACCTCCAACATGACCTACAAGGCCTGGCGGCGTGAGCCTGAG                         GAGGGACCTATAATGTACTGCAGCCGCACTATTTTTGAGGATGCTACACCT
genomic: AGCGTACAACCTCCAACATGACCTACAAGGCCTGGCGGCGTGAGCCTGAGgtttgtcttt ... gtaattttagGAGGGACCTATAATGTACTGCAGCCGCACTATTTTTGAGGATGCTACACCT

EST: gi|91054396|gb|EB164814.1|EB164814

EST:     AGCGTACAACCTCCAACATGACCTACAAGGCCTGGCGGCGTGAGCCTGAG                         GAGGGACCTATAATGTACTGCAGCCGCACTATTTTTGAGGATGCTACACCT
genomic: AGCGTACAACCTCCAACATGACCTACAAGGCCTGGCGGCGTGAGCCTGAGgtttgtcttt ... gtaattttagGAGGGACCTATAATGTACTGCAGCCGCACTATTTTTGAGGATGCTACACCT

EST: gi|76015844|gb|DT943014.1|DT943014

EST:     AGCGTACAACCTCCAACATGACCTACAAGGCCTGGCGGCGTGAGCCTGAG                         GAGGGACCTATAATGTACTGCAGCCGCACTATTTTTGAGGATGCTACACCT
genomic: AGCGTACAACCTCCAACATGACCTACAAGGCCTGGCGGCGTGAGCCTGAGgtttgtcttt ... gtaattttagGAGGGACCTATAATGTACTGCAGCCGCACTATTTTTGAGGATGCTACACCT

EST: gi|86469996|gb|DY236366.1|DY236366

EST:     AGCGTACAACCTCCAACATGACCTACAAGGCCTGGCGGCGTGAGCCTGAG                         GAGGGACCTATAATGTACTGCAGCCGCACTATTTTTGAGGATGC
genomic: AGCGTACAACCTCCAACATGACCTACAAGGCCTGGCGGCGTGAGCCTGAGgtttgtcttt ... gtaattttagGAGGGACCTATAATGTACTGCAGCCGCACTATTTTTGAGGATGC

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: 86

ACTTTTAGATAATAAGGAAAGCGGGGATACAGCTTGGCAGAATTTGATGGAGCGTACAACCTCCAACATGACCTACAAGGCCTGGCGGCGTGAGCCTGAGgtttgtcttt ... gtaattttagGAGGGACCTATAATGTACTGCAGCCGCACTATTTTTGAGGATGCTACACCTGAACTGGTTAGAGATTTCTTCTGGGATGGTGATTTTCGTCTAAAGTGGG

Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 51

Block sizes: 48 (upstream exon), 46 (downstream exon)
Score: 53

Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 137

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ACTTTTAGATAATAAGGAAAGCGGGGATACAGCTTGGCAGAATTTGATGGAGCGTACAACCTCCAACATGACCTACAAGGCCTGGCGGCGTGAGCCTGAGgtttgtctttccagtgggttttggaaaaaaaatttaaatgctgataatataggatattatagaaggtacttctaccacaattccgaggtggtgtataacc

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