ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq
cis-regulatory elements

Sequence

atgc intronic sequence ATGC exonic sequence

TGTAACTAATGTGCTTATCTCTACTGTCAGGTGATTGCAGGACTGTGGATCCTTTCTGTTCTTGGGAGCTGCTGCAATTTCCTCACCTTGTCTTACATAGgtgattgttgttcgttaacattctttgatgcattaagaagcgttaatgtgttactcagttatggttttttgtgcag

Basic information

species	Zea mays
transcript	GRMZM2G004349_T02
intron #	2
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G004349_T02 (Zea mays), 5'ss of exon 2
lower sequence: LOC_Os05g45050.2 (Oryza sativa), 5'ss of exon 3

--TGTAACTAATGTGCTTATCTCTACTGTCAGGTGATTGCAGGACTGTGGATCCTTTCTGTTCTTGGGAGCTGCTGCAATTTCCTCACCTTGTCTTACATAGgtgattgttgttcgttaacattctttgatgcattaagaagcgttaatgtgttactcagttatggttttttgtgcag---
  | |   ||   || |  ||| || |   ||||  | |  || || ||| | || ||||||||||||||||||||||||||||| |||||||  ||||||||| ||| || |     ||||    |  |    |||  |    |     |||||| ||  ||  ||||| | |   |   
AATTTGCTTATGCTGGTCCTCTTTATTA--AGGTTGTCGTGGGTCTCTGGGTTCTCTCTGTTCTTGGGAGCTGCTGCAATTTCCTGACCTTGTTCTACATAGgtaattattttggtacaacaactgt--acaagttaccacatttagcactgttac-caactacagttttctttcttgcag

upper sequence: GRMZM2G004349_T02 (Zea mays), 5'ss of exon 2
lower sequence: LOC_Os05g45050.1 (Oryza sativa), 5'ss of exon 4

TGTAACTAATGTGCTTATCTCTACTGTCAGGTGATTGCAGGACTGTGGATCCTTTCTGTTCTTGGGAGCTGCTGCAATTTCCTCACCTTGTCTTACATAGgtgattgttgttcgttaacattctttgatgcattaagaagcgttaatgtgttactcagttatggttttttgtgcag---
                              ||  | |  || || ||| | || ||||||||||||||||||||||||||||| |||||||  ||||||||| ||| || |     ||||    |  |    |||  |    |     |||||| ||  ||  ||||| | |   |   
------------------------------GTTGTCGTGGGTCTCTGGGTTCTCTCTGTTCTTGGGAGCTGCTGCAATTTCCTGACCTTGTTCTACATAGgtaattattttggtacaacaactgt--acaagttaccacatttagcactgttac-caactacagttttctttcttgcag

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|32802019|gb|CD954255.1|CD954255

EST:     CCTTTCTGTTCTTGGGAGCTGCTGCAATTTCCTCACCTTGTCTTACATAG                         TTTTTATGGTACTGTACACTGTACCGGTCCTGTATGAGAAACATGAGGATA
genomic: CCTTTCTGTTCTTGGGAGCTGCTGCAATTTCCTCACCTTGTCTTACATAGgtgattgttg ... ttttgtgcagTTTTTATGGTACTGTACACTGTACCGGTCCTGTATGAGAAACATGAGGATA

EST: gi|211274061|gb|FL438421.1|FL438421

EST:     CTTTCTGTTCTTGGGAGCTGCTGCAATTTCCTCACC-TGTCCTTACATAG                         TTTTTATGGTACTGTACACTGTACCGGTCCTGTATGAGAAACATGAGGAT
genomic: CTTTCTGTTCTTGGGAGCTGCTGCAATTTCCTCACCTTGT-CTTACATAGgtgattgttg ... ttttgtgcagTTTTTATGGTACTGTACACTGTACCGGTCCTGTATGAGAAACATGAGGAT

EST: gi|21809730|gb|BQ668048.1|BQ668048

EST:     CCTTTCTGTTCTTGGGAGCTGCTGCAATTTCCTCACCTTGTCTTACATAG                         TTTTTATGGTACTGTACACTGTACCGGTCCTGTATGAGAAACATGAGGATA
genomic: CCTTTCTGTTCTTGGGAGCTGCTGCAATTTCCTCACCTTGTCTTACATAGgtgattgttg ... ttttgtgcagTTTTTATGGTACTGTACACTGTACCGGTCCTGTATGAGAAACATGAGGATA

EST: gi|32804285|gb|CD956521.1|CD956521

EST:     CCTTTCTGTTCTTGGGAGCTGCTGCAATTTCCTCACCTTGTCTTACATAG                         TTTTTATGGTACTGTACACTGTACCGGTCCTGTATGAGAAACATGAGGATA
genomic: CCTTTCTGTTCTTGGGAGCTGCTGCAATTTCCTCACCTTGTCTTACATAGgtgattgttg ... ttttgtgcagTTTTTATGGTACTGTACACTGTACCGGTCCTGTATGAGAAACATGAGGATA

EST: gi|9742682|gb|BE518830.1|BE518830

EST:     CCTTTCTGTTCTTGGGAGCTGCTGCAATTTCCTCACCTTGTCTTACATAG                         TTTTTATGGTACTGTACACTGTACCGGTCCTGTATGAGAAACATGAGGATA
genomic: CCTTTCTGTTCTTGGGAGCTGCTGCAATTTCCTCACCTTGTCTTACATAGgtgattgttg ... ttttgtgcagTTTTTATGGTACTGTACACTGTACCGGTCCTGTATGAGAAACATGAGGATA

EST: gi|211335930|gb|FL468894.1|FL468894

EST:     CCTTTCTGTTCTTGGGAGCTGCTGCAATTTCCTCACCTTGTCTTACATAG                         TTTTTATGGTACTGTACACTGTACCGGTCCTGTATGAGAAACATGAGGATA
genomic: CCTTTCTGTTCTTGGGAGCTGCTGCAATTTCCTCACCTTGTCTTACATAGgtgattgttg ... ttttgtgcagTTTTTATGGTACTGTACACTGTACCGGTCCTGTATGAGAAACATGAGGATA

EST: gi|94480543|gb|EB709501.1|EB709501

EST:     CCTTTCTGTTCTTGGGAGCTGCTGCAATTTCCTCACCTTGTCTTACATAG                         TTTTTATGGTACTGTACACTGTACCGGTCCTGTATGAGAAACATGAGGATA
genomic: CCTTTCTGTTCTTGGGAGCTGCTGCAATTTCCTCACCTTGTCTTACATAGgtgattgttg ... ttttgtgcagTTTTTATGGTACTGTACACTGTACCGGTCCTGTATGAGAAACATGAGGATA

EST: gi|116813218|gb|EC855637.1|EC855637

EST:     CCTTTCTGTTC-TGGGAGCTGCTGCAA-TT-CTCACC-TGTCTTACATAG                         TTTTTATGGTACTGTACACTGTACCGGTCCTGTATGAGAAACATGAGGATA
genomic: CCTTTCTGTTCTTGGGAGCTGCTGCAATTTCCTCACCTTGTCTTACATAGgtgattgttg ... ttttgtgcagTTTTTATGGTACTGTACACTGTACCGGTCCTGTATGAGAAACATGAGGATA

EST: gi|9742922|gb|BE519070.1|BE519070

EST:     CCTTTCTGTTCTTGGGAGCTGCTGCAATTTCCTCACCTTGTCTTACATAG                         TTTTTATGGTACTGTACACTGTACCGGTCCTGTATGAGAAACATGAGGATA
genomic: CCTTTCTGTTCTTGGGAGCTGCTGCAATTTCCTCACCTTGTCTTACATAGgtgattgttg ... ttttgtgcagTTTTTATGGTACTGTACACTGTACCGGTCCTGTATGAGAAACATGAGGATA

EST: gi|71759056|gb|DR956993.1|DR956993

EST:     CCTTTCTGTTCTTGGGAGCTGCTGCAATTTCCTCACCTTGTCTTACATAG                         TTTTTATGGTACTGTACACTGTACCGGTCCTGTATGAGAAACATGAGGATA
genomic: CCTTTCTGTTCTTGGGAGCTGCTGCAATTTCCTCACCTTGTCTTACATAGgtgattgttg ... ttttgtgcagTTTTTATGGTACTGTACACTGTACCGGTCCTGTATGAGAAACATGAGGATA

EST: gi|32788374|gb|CD940610.1|CD940610

EST:     CCTTTCTGTTCTTGGGAGCTGCTGCAATTTCCTCACCTTGTCTTACATAG                         TTTTTATGGTACTGTACACTGTACCGGTCCTGTATGAGAAACATGAGGACA
genomic: CCTTTCTGTTCTTGGGAGCTGCTGCAATTTCCTCACCTTGTCTTACATAGgtgattgttg ... ttttgtgcagTTTTTATGGTACTGTACACTGTACCGGTCCTGTATGAGAAACATGAGGATA

EST: gi|60358536|gb|DN225509.1|DN225509

EST:     CCTTTCTGTTCTTGGGAGCTGCTGCAATTTCCTCACCTTGTCTTACATAG                         TTTTTATGGTACTGTACACTGTACCGGTCCTGTATGAGAAACATGAGGATA
genomic: CCTTTCTGTTCTTGGGAGCTGCTGCAATTTCCTCACCTTGTCTTACATAGgtgattgttg ... ttttgtgcagTTTTTATGGTACTGTACACTGTACCGGTCCTGTATGAGAAACATGAGGATA

EST: gi|30307150|gb|CD001823.1|CD001823

EST:     CCTTTCTGTTCTTGGGAGCTGCTGCAATTTCCTCACCTTGTCTTACATAG                         TTTTTATGGTACTGTACACTGTACCGGTCCTGTATGAGAAACATGAGGATA
genomic: CCTTTCTGTTCTTGGGAGCTGCTGCAATTTCCTCACCTTGTCTTACATAGgtgattgttg ... ttttgtgcagTTTTTATGGTACTGTACACTGTACCGGTCCTGTATGAGAAACATGAGGATA

EST: gi|211274062|gb|FL438422.1|FL438422

EST:     CCTTTCTGTTCTTGGGAGCTGCTGCAATTTCCTCACCTTGTCTTACATAG                         TTTTTATGGTACTGTACACTGTACCGGTCCTGTATGAGAAACATGAGGATA
genomic: CCTTTCTGTTCTTGGGAGCTGCTGCAATTTCCTCACCTTGTCTTACATAGgtgattgttg ... ttttgtgcagTTTTTATGGTACTGTACACTGTACCGGTCCTGTATGAGAAACATGAGGATA

EST: gi|32796691|gb|CD948927.1|CD948927

EST:     CCTTTCTGTTCTTGGGAGCTGCTGCAATTTCCTCACCTTGTCTTACATAG                         TTTTTATGGTACTGTACACTGTACCGGTCCTGTATGAGAAACATGAGGATA
genomic: CCTTTCTGTTCTTGGGAGCTGCTGCAATTTCCTCACCTTGTCTTACATAGgtgattgttg ... ttttgtgcagTTTTTATGGTACTGTACACTGTACCGGTCCTGTATGAGAAACATGAGGATA

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: 412

TGTAACTAATGTGCTTATCTCTACTGTCAGGTGATTGCAGGACTGTGGATCCTTTCTGTTCTTGGGAGCTGCTGCAATTTCCTCACCTTGTCTTACATAGgtgattgttg ... ttttgtgcagTTTTTATGGTACTGTACACTGTACCGGTCCTGTATGAGAAACATGAGGATAAGGTTGATGCTTTTGGTGAGAAGGCCATGGTCGAGCTGAAGAGGTACTA

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 86

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 116

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 160

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGTAACTAATGTGCTTATCTCTACTGTCAGGTGATTGCAGGACTGTGGATCCTTTCTGTTCTTGGGAGCTGCTGCAATTTCCTCACCTTGTCTTACATAGgtgattgttgttcgttaacattctttgatgcattaagaagcgttaatgtgttactcagttatggttttttgtgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGCTGC