ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq
cis-regulatory elements

Sequence

atgc intronic sequence ATGC exonic sequence

ACTTCATCATCCAATTTTGCTGGCACAGTGGCAGGACGGAGTAACACGTGTTGATTTGGCTAAAGGGTTCTCTTTTGAGGAGTTTATGAAGgtgagctagatctatgcttcttattatgtatagctgaaacttgtactccgtgctgcagaagatatggtttttctaatcttgtgatcttggccctttgttg...

Basic information

species	Zea mays
transcript	GRMZM2G054706_T01
intron #	5
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G054706_T01 (Zea mays), 5'ss of exon 5
lower sequence: LOC_Os02g04260.1 (Oryza sativa), 5'ss of exon 5

ACTTCATCATCCAATTTTGCTGGCACAGTGGCAGGACGGAGTAACACGTGTTGATTTGGCTAAAGGGTTCTCTTTTGAGGAGTTTATGAAGgtgagctagatctatgcttcttattatgtatagctgaaacttgtact--ccgtgctgcagaagatatggttt-ttctaatcttgtgatcttggccctttgttg
   ||||||||| ||| || | |||||||||||||| ||||| |||||   ||||||| |  ||||||||||||||||||| || || |||||  |    ||| |  ||| |||| |  |  | |||||| ||  | |        ||   || |  | ||   | ||    ||||    ||  | | |  |  
GAATCATCATCCGATTCTGTTAGCACAGTGGCAGGAAGGAGTTACACGCTCTGATTTGACCGAAGGGTTCTCTTTTGAGGAATTCATAAAGgtttgtataatcaa--cttgttataacctcgatctgaaaattcaaatagtgaaaatgtgaaatacttagtaaatacttcatttgtatcattttctcatgatc-

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|60341893|gb|DN208866.1|DN208866

EST:     TAACACGTGTTGATTTGGCTAAAGGGTTCTCTTTTGAGGAGTTTATGAAG                         CGTGGTGGAAACCTTGCTATGCTTGCTGAGCGCTTCCTGCACGAGGTGGCA
genomic: TAACACGTGTTGATTTGGCTAAAGGGTTCTCTTTTGAGGAGTTTATGAAGgtgagctaga ... tgatcaacagCGTGGTGGAAACCTTGCTATGCTTGCTGAGCGCTTCCTGCACGAGGTGGCA

EST: gi|84976996|gb|DW475418.1|DW475418

EST:     TAACACGTGTTGATTTGGCTAAAGGGTTCTCTTTTGAGGAGTTTATGAAG                         CGTGGTGGAAACCTTGCTATGCTTGCTGAGCGCTTCCTGCACGAGGTGGCA
genomic: TAACACGTGTTGATTTGGCTAAAGGGTTCTCTTTTGAGGAGTTTATGAAGgtgagctaga ... tgatcaacagCGTGGTGGAAACCTTGCTATGCTTGCTGAGCGCTTCCTGCACGAGGTGGCA

EST: gi|71436327|gb|DR817377.1|DR817377

EST:     TAACACGTGTTGATTTGGCTAAAGGGTTCTCTTTTGAGGAGTTTATGAAG                         CGTGGTGGAAACCTTGCTATGCTTGCTGAGCGCTTCCTGCACGAGGTGGCA
genomic: TAACACGTGTTGATTTGGCTAAAGGGTTCTCTTTTGAGGAGTTTATGAAGgtgagctaga ... tgatcaacagCGTGGTGGAAACCTTGCTATGCTTGCTGAGCGCTTCCTGCACGAGGTGGCA

EST: gi|113704082|gb|EE681586.1|EE681586

EST:     TAACACGTGTTGATTTGGCTAAAGGGTTCTCTTTTGAGGAGTTTATGAAG                         CGTGGTGGAAACCTTGCCATGCTTGCTGAGCGCTTCCTGCACGAGGTGGCA
genomic: TAACACGTGTTGATTTGGCTAAAGGGTTCTCTTTTGAGGAGTTTATGAAGgtgagctaga ... tgatcaacagCGTGGTGGAAACCTTGCTATGCTTGCTGAGCGCTTCCTGCACGAGGTGGCA

EST: gi|32934251|gb|CF039063.1|CF039063

EST:     TAACACGTGTTGATTTGGCTAAAGGGTTCTCTTTTGAGGAGTTTATGAAG                         CGTGGTGGAAACCTTGCTATGCTTGCTGAGCGCTTCCTGCACGAGGTGGCA
genomic: TAACACGTGTTGATTTGGCTAAAGGGTTCTCTTTTGAGGAGTTTATGAAGgtgagctaga ... tgatcaacagCGTGGTGGAAACCTTGCTATGCTTGCTGAGCGCTTCCTGCACGAGGTGGCA

EST: gi|76931667|gb|DV172796.1|DV172796

EST:     TAACACGTGTTGATTTGGCTAAAGGGTTCTCTTTTGAGGAGTTTATGAAG                         CGTGGTGGAAACCTTGCTATGCTTGCTGAGCGCTTCCTGCACGAGGTGGCA
genomic: TAACACGTGTTGATTTGGCTAAAGGGTTCTCTTTTGAGGAGTTTATGAAGgtgagctaga ... tgatcaacagCGTGGTGGAAACCTTGCTATGCTTGCTGAGCGCTTCCTGCACGAGGTGGCA

EST: gi|71326889|gb|DR800102.1|DR800102

EST:     TAACACGTGTTGATTTGGCTAAAGGGTTCTCTTTTGAGGAGTTTATGAAG                         CGTGGTGGAAACCTTGCTATGCTTGCTGAGCGCTTCCTGCACGAGGTGGCA
genomic: TAACACGTGTTGATTTGGCTAAAGGGTTCTCTTTTGAGGAGTTTATGAAGgtgagctaga ... tgatcaacagCGTGGTGGAAACCTTGCTATGCTTGCTGAGCGCTTCCTGCACGAGGTGGCA

EST: gi|87153522|gb|DY398311.1|DY398311

EST:     TAACACGTGTTGATTTGGCTAAAGGGTTCTCTTTTGAGGAGTTTATGAAG                         CGTGGTGGAAACCTTGCCATGCTTGCTGAGCGCTTCCTGCACGAGGTGGCA
genomic: TAACACGTGTTGATTTGGCTAAAGGGTTCTCTTTTGAGGAGTTTATGAAGgtgagctaga ... tgatcaacagCGTGGTGGAAACCTTGCTATGCTTGCTGAGCGCTTCCTGCACGAGGTGGCA

EST: gi|76923534|gb|DV169534.1|DV169534

EST:     TAACACGTGTTGATTTGGTTAAAGGGTTTTCTTTTGAGGAGTTTATGAAG                         CGTGGTGGAAACCTTGCTATGCTTGCTGAGCGCTTCCTGCACGAGGTGGCA
genomic: TAACACGTGTTGATTTGGCTAAAGGGTTCTCTTTTGAGGAGTTTATGAAGgtgagctaga ... tgatcaacagCGTGGTGGAAACCTTGCTATGCTTGCTGAGCGCTTCCTGCACGAGGTGGCA

EST: gi|149044688|gb|EE047661.2|EE047661

EST:     TAACACGTGTTGATTTGGCTAAAGGGTTCTCTTTTGAGGAGTTTATGAAG                         CGTGGTGGAAACCTTGCTATGCTTGCTGAGCGCTTCCTGCACGAGGTGGCA
genomic: TAACACGTGTTGATTTGGCTAAAGGGTTCTCTTTTGAGGAGTTTATGAAGgtgagctaga ... tgatcaacagCGTGGTGGAAACCTTGCTATGCTTGCTGAGCGCTTCCTGCACGAGGTGGCA

EST: gi|211234326|gb|FL299527.1|FL299527

EST:     TAACACGTGTTGATTTGGCTAAAGGGTTCTCTTTTGAGGAGTTTATGAAG                         CGTGGTGGAAACCTTGCCATGCTTGCTGAGCGCTTCCTGCACGAGGTGGCA
genomic: TAACACGTGTTGATTTGGCTAAAGGGTTCTCTTTTGAGGAGTTTATGAAGgtgagctaga ... tgatcaacagCGTGGTGGAAACCTTGCTATGCTTGCTGAGCGCTTCCTGCACGAGGTGGCA

EST: gi|71428268|gb|DR809318.1|DR809318

EST:     TAACACGTGTTGATTTGGCTAAAGGGTTCTCTTTTGAGGAGTTTATGAAG                         CGTGGTGGAAACCTTGCTATGCTTGCTGAGCGCTTCCTGCACGAGGTGGCA
genomic: TAACACGTGTTGATTTGGCTAAAGGGTTCTCTTTTGAGGAGTTTATGAAGgtgagctaga ... tgatcaacagCGTGGTGGAAACCTTGCTATGCTTGCTGAGCGCTTCCTGCACGAGGTGGCA

EST: gi|76017108|gb|DT944278.1|DT944278

EST:     TAACACGTGTTGATTTGGCTAAAGGGTTCTCTTTTGAGGAGTTTATGAAG                         CGTGGTGGAAACCTTGCTATGCTTGCTGAGCGCTTCCTGCACGAGGTGGCA
genomic: TAACACGTGTTGATTTGGCTAAAGGGTTCTCTTTTGAGGAGTTTATGAAGgtgagctaga ... tgatcaacagCGTGGTGGAAACCTTGCTATGCTTGCTGAGCGCTTCCTGCACGAGGTGGCA

EST: gi|9731636|gb|BE510388.1|BE510388

EST:     TAACACGTGTTGATTTGGCTAAAGGGTTCTCTTTTGAGGAGTTTATGAAG                         CGTGGTGGAAACCTTGCCATGCTTGCTGAGCGCTTCCTGCACGAGGTGGCA
genomic: TAACACGTGTTGATTTGGCTAAAGGGTTCTCTTTTGAGGAGTTTATGAAGgtgagctaga ... tgatcaacagCGTGGTGGAAACCTTGCTATGCTTGCTGAGCGCTTCCTGCACGAGGTGGCA

EST: gi|37379721|gb|CF626613.1|CF626613

EST:     TAACACGTGTTGATTTGGCTAAAGGGTTCTCTTTTGAGGAGTTTATGAAG                         CGTGGTGGAAACCTTGCCATGCTTGCTGAGCGCTTCCTGCACGAGGTGGCA
genomic: TAACACGTGTTGATTTGGCTAAAGGGTTCTCTTTTGAGGAGTTTATGAAGgtgagctaga ... tgatcaacagCGTGGTGGAAACCTTGCTATGCTTGCTGAGCGCTTCCTGCACGAGGTGGCA

EST: gi|211462811|gb|FL454173.1|FL454173

EST:     TAACACGTGTTGATTTGGCTAAAGGGTTCTCTTTTGAGGAGTTTATGAAG                         CGTGGTGGAAACCTTGCCATGCTTGCTGAGCGCTTCCTGCACGAGGTGGCA
genomic: TAACACGTGTTGATTTGGCTAAAGGGTTCTCTTTTGAGGAGTTTATGAAGgtgagctaga ... tgatcaacagCGTGGTGGAAACCTTGCTATGCTTGCTGAGCGCTTCCTGCACGAGGTGGCA

EST: gi|21331905|gb|BQ487286.1|BQ487286

EST:     TAACACGTGTTGATTTGGCTAAAGGGTTCTCTTTTGAGGAGTTTATGAAG                         CGTGGTGGAAACCTTGCCATGCTTGCTGAGCGCTTCCTGCACGAGGTGGCA
genomic: TAACACGTGTTGATTTGGCTAAAGGGTTCTCTTTTGAGGAGTTTATGAAGgtgagctaga ... tgatcaacagCGTGGTGGAAACCTTGCTATGCTTGCTGAGCGCTTCCTGCACGAGGTGGCA

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: 242

ACTTCATCATCCAATTTTGCTGGCACAGTGGCAGGACGGAGTAACACGTGTTGATTTGGCTAAAGGGTTCTCTTTTGAGGAGTTTATGAAGgtgagctaga ... tgatcaacagCGTGGTGGAAACCTTGCTATGCTTGCTGAGCGCTTCCTGCACGAGGTGGCATTTAAGCTCTGGAAAGCGCCTAAATATGGGGCTTGAGGAGGGTATCCAG

Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 206

Block sizes: 48 (upstream exon), 48 (downstream exon)
Score: 129

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 227

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ACTTCATCATCCAATTTTGCTGGCACAGTGGCAGGACGGAGTAACACGTGTTGATTTGGCTAAAGGGTTCTCTTTTGAGGAGTTTATGAAGgtgagctagatctatgcttcttattatgtatagctgaaacttgtactccgtgctgcagaagatatggtttttctaatcttgtgatcttggccctttgttg

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG