ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq
PPT, BS, UA-tract
cis-regulatory elements

Sequence

atgc intronic sequence ATGC exonic sequence

gtaaattcttgtgctcgatatgaaactcgtcggtttattcaagttatcgtccgcgtttcatattggtagctgtttgcgttgttctgtgcagGAGCCACAACTGACGGCGTGCGAGCCATTTGATGTCTATGCGAAGCCCTTCTCCCTATGACGTGTTCATAGTATTGCCCAATGTACTATATATCTCCTCC

Basic information

species	Zea mays
transcript	GRMZM2G035928_T01
intron #	4
splice site	3'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G035928_T01 (Zea mays), 3'ss of exon 4
lower sequence: Vv15s0021g00990.t01 (Vitis vinifera), 3'ss of exon 6

-------gtaaattcttgtgctcgatatgaaactc-gtcggtttattca-agttatcgtccg-cgtttcatattggtagctgtttgcgttgttctgtg-cagGAGCCACAACTGACGGCGTGCGAGCCATTTGATGTCTATGCGAAGCCCTTCTCCCTATGACGTGTTCATAGTATTGCCCAATGTACTATATATCTCCTCC--
         |||||  | || | | | ||||| |  ||   |  |  || |||||  |  |  |   | | ||      ||||||   |||||  ||  |||||||||||| |||| || ||| ||||||||||||| ||| | || || ||||||||||||  | ||||| || |        ||   ||| |      |   
agcagattcaaatttctttg-tagttttgaaattttgttcataaaagcagagttaatgatcatcaacttaaatgttcttctgtttat-ttgtttggtaacagGAGCCACAATTGACAGCCTGCCAGCCATTTGATGTGTATACAAAACCATTCTCCCTATGAT-TATTCAT-GTGTGTGTAGCGGTTGAATAAAGTCGAACAGA

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|91053235|gb|EB163653.1|EB163653

EST:     TTACAATGCTTCTTACTGGAGGGAGCCTTTCTGCTGGTGGTCTGAGACAG                         GAGCCACAACTGACGGCGTGCGAGCCATTTGATGTCTATGCGAAGCCCTTC
genomic: TTACAATGCTTCTTACTGGAGGGAGCCTTTCTGCTGGTGGTCTGAGACAGgtaaattctt ... ttctgtgcagGAGCCACAACTGACGGCGTGCGAGCCATTTGATGTCTATGCGAAGCCCTTC

EST: gi|91048638|gb|EB159056.1|EB159056

EST:     TTACAATGCTTCTTACTGGAGGGAGCCTTTCTGCTGGTGGTCTGAGACAG                         GAGCCACAACTGACGGCGTGCGAGCCATTTGATGTCTATGCGAAGCCCTTC
genomic: TTACAATGCTTCTTACTGGAGGGAGCCTTTCTGCTGGTGGTCTGAGACAGgtaaattctt ... ttctgtgcagGAGCCACAACTGACGGCGTGCGAGCCATTTGATGTCTATGCGAAGCCCTTC

EST: gi|47962618|gb|CN845327.1|CN845327

EST:     TTACAATGCTTCTTACTGGAGGGAGCCTTTCTGCTGGTGGTCTGAGACAG                         GAGCCACAACTGACGGCGTGCGAGCCATTTGATGTCTATGCGAAGCCCTTC
genomic: TTACAATGCTTCTTACTGGAGGGAGCCTTTCTGCTGGTGGTCTGAGACAGgtaaattctt ... ttctgtgcagGAGCCACAACTGACGGCGTGCGAGCCATTTGATGTCTATGCGAAGCCCTTC

EST: gi|91875164|gb|EB405121.1|EB405121

EST:     TTACAATGCTTTTTACTGGAGGGAGCCTTTTTGTTGGTGGTTTGAGACAG                         GAGCCACAACTGACGGCGTGGGAGCCATTTGATGTTTATGCGAAGCCCTTC
genomic: TTACAATGCTTCTTACTGGAGGGAGCCTTTCTGCTGGTGGTCTGAGACAGgtaaattctt ... ttctgtgcagGAGCCACAACTGACGGCGTGCGAGCCATTTGATGTCTATGCGAAGCCCTTC

EST: gi|71759837|gb|DR957774.1|DR957774

EST:     TTACAATGCTTCTTACTGGAGGGAGCCTTTCTGCTGGTGGTTTGAGACAG                         GAGCCACAACTGACGGCGTGCGAGCCATTTGATGTTTATGGGAAGCCCTTC
genomic: TTACAATGCTTCTTACTGGAGGGAGCCTTTCTGCTGGTGGTCTGAGACAGgtaaattctt ... ttctgtgcagGAGCCACAACTGACGGCGTGCGAGCCATTTGATGTCTATGCGAAGCCCTTC

EST: gi|93016581|gb|EB642101.1|EB642101

EST:     TTACAATGCTTCTTACTGGAGGGAGCCTTTCTGTTGGTGGTTTGAGACAG                         GAGCCACAACTGACGGCGTGCGAGCCATTTGATGTTTATGCGAAGCCCTTC
genomic: TTACAATGCTTCTTACTGGAGGGAGCCTTTCTGCTGGTGGTCTGAGACAGgtaaattctt ... ttctgtgcagGAGCCACAACTGACGGCGTGCGAGCCATTTGATGTCTATGCGAAGCCCTTC

EST: gi|211123433|gb|FL433083.1|FL433083

EST:     TTACAATGCTTCTTACTGGAGGGAGCCTTTCTGCTGGTGGTCTGAGACAG                         GAGCCMCAACTGACGGCGTGCGAGCCATTTRATGTCTATGCGAAGCCCTTC
genomic: TTACAATGCTTCTTACTGGAGGGAGCCTTTCTGCTGGTGGTCTGAGACAGgtaaattctt ... ttctgtgcagGAGCCACAACTGACGGCGTGCGAGCCATTTGATGTCTATGCGAAGCCCTTC

EST: gi|94478480|gb|EB707438.1|EB707438

EST:     TTAAAATGTTTTTTATTGGAGGGAGCCTTTTTGTTGGTGGTTTGAGACAG                         GAGCCACAACTGACGGCGTGCGAGCCATTTGATGTCTATGCGAAGCCCTTC
genomic: TTACAATGCTTCTTACTGGAGGGAGCCTTTCTGCTGGTGGTCTGAGACAGgtaaattctt ... ttctgtgcagGAGCCACAACTGACGGCGTGCGAGCCATTTGATGTCTATGCGAAGCCCTTC

EST: gi|148976593|gb|EE025939.2|EE025939

EST:     TTACAATGCTTCTTACTGGAGGGAGCCTTTCTGCTGGTGGTTTGAGACAG                         GAGCCACAACTGACGGCGTGCGAGCCATTTGATGTCTATGCGAAGCCCTTC
genomic: TTACAATGCTTCTTACTGGAGGGAGCCTTTCTGCTGGTGGTCTGAGACAGgtaaattctt ... ttctgtgcagGAGCCACAACTGACGGCGTGCGAGCCATTTGATGTCTATGCGAAGCCCTTC

EST: gi|50337462|gb|CO532588.1|CO532588

EST:     TTACAATGCTTCTTACTGGAGGGAGCCTTTCTGCTGGTGGTCTGAGACAG                         GAGCCACAACTGACGGCGTGCGAGCCATTTGATGTCTATGCGAAGCCCTTC
genomic: TTACAATGCTTCTTACTGGAGGGAGCCTTTCTGCTGGTGGTCTGAGACAGgtaaattctt ... ttctgtgcagGAGCCACAACTGACGGCGTGCGAGCCATTTGATGTCTATGCGAAGCCCTTC

EST: gi|91055205|gb|EB165623.1|EB165623

EST:     TTACAATGCTTCTTACTGGAGGGAGCCTTTTTGTTGGTGGTTTGAGACAG                         GAGCCACAACTGACGGCGTGCGAGCCATTTGATGTTTATGCGAAGCCCTTC
genomic: TTACAATGCTTCTTACTGGAGGGAGCCTTTCTGCTGGTGGTCTGAGACAGgtaaattctt ... ttctgtgcagGAGCCACAACTGACGGCGTGCGAGCCATTTGATGTCTATGCGAAGCCCTTC

EST: gi|78079402|gb|DV507814.1|DV507814

EST:     TTACAATGCTTCTTACTGGAGGGAGCCTTTCTGCTGGTGGTCTGAGACAG                         GAGCCACAACTGACGGCGTGCGAGCCATTTGATGTCTATGCGAAGCCCTTC
genomic: TTACAATGCTTCTTACTGGAGGGAGCCTTTCTGCTGGTGGTCTGAGACAGgtaaattctt ... ttctgtgcagGAGCCACAACTGACGGCGTGCGAGCCATTTGATGTCTATGCGAAGCCCTTC

EST: gi|78082242|gb|DV510654.1|DV510654

EST:     TTACAATGCTTCTTACTGGAGGGAGCCTTTCTGCTGGTGGTTTGAGACAG                         GAGCCACAACTGACGGCGTGCGAGCCATTTGATGTTTATGCGAAGCCCTTC
genomic: TTACAATGCTTCTTACTGGAGGGAGCCTTTCTGCTGGTGGTCTGAGACAGgtaaattctt ... ttctgtgcagGAGCCACAACTGACGGCGTGCGAGCCATTTGATGTCTATGCGAAGCCCTTC

EST: gi|76911371|gb|DV164249.1|DV164249

EST:     TTACAATGCTTCTTACTGGAGGGAGCCTTTCTGCTGGTGGTTTGAGACAG                         GAGCCACAACTGACGGCGTGCGAGCCATTTGATGTCTATGCGAAGCCCTTC
genomic: TTACAATGCTTCTTACTGGAGGGAGCCTTTCTGCTGGTGGTCTGAGACAGgtaaattctt ... ttctgtgcagGAGCCACAACTGACGGCGTGCGAGCCATTTGATGTCTATGCGAAGCCCTTC

EST: gi|89246802|gb|DY618589.1|DY618589

EST:     TTACAATGCTTCTTACTGGAGGGAGCCTTTCTGTTGGTGGTTTGAGACAG                         GAGCCACAACTGACGGCGTGCGAGCCATTTGATGTTTATGCGAAGCCCTTC
genomic: TTACAATGCTTCTTACTGGAGGGAGCCTTTCTGCTGGTGGTCTGAGACAGgtaaattctt ... ttctgtgcagGAGCCACAACTGACGGCGTGCGAGCCATTTGATGTCTATGCGAAGCCCTTC

EST: gi|91049155|gb|EB159573.1|EB159573

EST:     TTACAATGCTTTTTACTGGAGGGAGCCTTTTTGCTGGTGGTTTGAGACAG                         GAGCCACAACTGACGGCGTGCGAGCCATTTGATGTTTATGCGAAGCCCTTC
genomic: TTACAATGCTTCTTACTGGAGGGAGCCTTTCTGCTGGTGGTCTGAGACAGgtaaattctt ... ttctgtgcagGAGCCACAACTGACGGCGTGCGAGCCATTTGATGTCTATGCGAAGCCCTTC

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: 48 (upstream exon), 49 (downstream exon)
Score: 44

CAACACAGGTGACTCAGCGGGTGTAGGTGGCGGTGCTGTTACATCACTAATTACAATGCTTCTTACTGGAGGGAGCCTTTCTGCTGGTGGTCTGAGACAGgtaaattctt ... ttctgtgcagGAGCCACAACTGACGGCGTGCGAGCCATTTGATGTCTATGCGAAGCCCTTCTCCCTATGACGTGTTCATAGTATTGCCCAATGTACTATATATCTCCTCC

Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 73

Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 68

Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 44

atgc intronic sequence ATGC exonic sequence

Intronic sequence truncated to 55 bases.

attcaagttatcgtccgcgtttcatattggtagctgtttgcgttgttctgtgcagGAGCCACAACTGACGGCGTGCGAGCCATTTGATGTCTATGCGAAGCCCTTCTCCCTATGACGTGTTCATAGTATTGCCCAATGTACTATATATCTCCTCC

                                          ttgttct  CT-rich tract
                   tttcatatt  TA-rich tract

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaaattcttgtgctcgatatgaaactcgtcggtttattcaagttatcgtccgcgtttcatattggtagctgtttgcgttgttctgtgcagGAGCCACAACTGACGGCGTGCGAGCCATTTGATGTCTATGCGAAGCCCTTCTCCCTATGACGTGTTCATAGTATTGCCCAATGTACTATATATCTCCTCC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTCCTC