ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq
cis-regulatory elements

Sequence

atgc intronic sequence ATGC exonic sequence

GCACTCTCCAGAAGGATCCACTATGGGAAGTTTGTGGCAGAGGCCAAGTTTCAAGAGTCCCCTGAAGCTTACACGCCAGCCATAATAGCCCAAgtctgcttttgttccaactattagtatttctagtactactattttcatttattttttattttatttcagagtttcagaacaaaatgatatttcgattcatttgaaaaatatatctatttctcgtcacatttggcaaaattcag

Basic information

species	Zea mays
transcript	GRMZM2G124365_T01
intron #	5
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G124365_T01 (Zea mays), 5'ss of exon 5
lower sequence: LOC_Os01g55870.1 (Oryza sativa), 5'ss of exon 5

GCACTCTCCAGAAGGATCCACTATGGGAAGTTTGTGGCAGAGGCCAAGTTTCAAGAGTCCCCTGAAGCTTACACGCCAGCCATAATAGCCCAAgtctgc-ttttgttcca----actattagtatttctagtactac-tattttcatttattttttattttatttcagagtttcagaacaaaatgatatttcgattcatttgaaaaatatatctatttctcgtcacatttggcaaaattcag
|| ||||||| ||| || |||||||| ||||||||||||||||| |||||||||||||| ||||||||||||| ||| || |||||||| || || ||  || ||||       |  ||  || ||| |  |   |   |  |  |||   | | | || |  | ||    || ||    | || | | ||   |  |||    ||      ||| || |  | |  | |||  || |||||
GCGCTCTCCAAAAGAATTCACTATGGTAAGTTTGTGGCAGAGGCTAAGTTTCAAGAGTCTCCTGAAGCTTACATGCCTGCGATAATAGCACAGgtttgtgttctgttttgctgtataatctgtctttatcatgggaagcaaataaattccatgtgttttcttgtacattactttaggtacatatcaaagttgagtctattatgcaagcgg--ctaattattttta--tctgg-gaatttcag

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|67040651|gb|CO466906.1|CO466906

EST:     CCAAGTTTCAAGAGTCCCCTGAAGCTTACACGCCAGCCATAATAGCCCAA                         GACCGTGATCAACTCATGAACCTTCT-ACATATGAAACGGTGGAGCGTGCT
genomic: CCAAGTTTCAAGAGTCCCCTGAAGCTTACACGCCAGCCATAATAGCCCAAgtctgctttt ... caaaattcagGACCGTGATCAACTCATGAACCTTCTCACATATGAAACGGTGGAGCGTGCT

EST: gi|32842440|gb|CD982121.1|CD982121

EST:     CCAAGTTTCAAGAGTCCCCTGAAGCTTACACGCCAGCCATAATAGCCCAA                         GACCGTGATCAACTCATGAACCTTCTCACATATGAAACGGTGGAGCGTGCT
genomic: CCAAGTTTCAAGAGTCCCCTGAAGCTTACACGCCAGCCATAATAGCCCAAgtctgctttt ... caaaattcagGACCGTGATCAACTCATGAACCTTCTCACATATGAAACGGTGGAGCGTGCT

EST: gi|32842677|gb|CD982358.1|CD982358

EST:     CCAAGTTTCAAGAGTCCCCTGAAGCTTACACGCCAGCCATAATAGCCCAA                         GACCGTGATCAACTCATGAACCTTCTCACATATGAAACGGTGGAGCGTGCT
genomic: CCAAGTTTCAAGAGTCCCCTGAAGCTTACACGCCAGCCATAATAGCCCAAgtctgctttt ... caaaattcagGACCGTGATCAACTCATGAACCTTCTCACATATGAAACGGTGGAGCGTGCT

EST: gi|67040128|gb|CO466383.1|CO466383

EST:     CA-GTTTCAAGAGTCCCCTGAAGCTTACACGCCAGCCATAATAGCCCCCA                         GACCGTGATCA-CTCATGAACCTTCTC-CATATGAAACGGTGGAGCGTGC
genomic: CAAGTTTCAAGAGTCCCCTGAAGCTTACACGCCAGCCATAATAGCCCA-Agtctgctttt ... caaaattcagGACCGTGATCAACTCATGAACCTTCTCACATATGAAACGGTGGAGCGTGC

EST: gi|32851768|gb|CD991449.1|CD991449

EST:     CCAAGTTTCAAGAGTCCCCTGAAGCTTACACGCCAGCCATAATAGCCCAA                         GACCGTGATCAACTCATGAACCTTCTCACATATGAAACGGTGGAGCGTGCT
genomic: CCAAGTTTCAAGAGTCCCCTGAAGCTTACACGCCAGCCATAATAGCCCAAgtctgctttt ... caaaattcagGACCGTGATCAACTCATGAACCTTCTCACATATGAAACGGTGGAGCGTGCT

EST: gi|67041520|gb|CO467775.1|CO467775

EST:     CCAAGTTTCAAGAGTCCCCTGAAGCTTACACGCCAGCCATAATAGCCCCA                         GACCGTGATCAACTCATGAAACTTCTCACA
genomic: CCAAGTTTCAAGAGTCCCCTGAAGCTTACACGCCAGCCATAATAGCCCAAgtctgctttt ... caaaattcagGACCGTGATCAACTCATGAACCTTCTCACA

EST: gi|32842515|gb|CD982196.1|CD982196

EST:     CCAAGTTTCAAGAGTCCCCTGAAGCTTACACGCCAGCCATAATAGCCCAA                         GACCGTGATCAACTCATGAACCTTCTCACATATGAAACGGTGGAGCGTGCT
genomic: CCAAGTTTCAAGAGTCCCCTGAAGCTTACACGCCAGCCATAATAGCCCAAgtctgctttt ... caaaattcagGACCGTGATCAACTCATGAACCTTCTCACATATGAAACGGTGGAGCGTGCT

EST: gi|149077331|gb|EE166010.2|EE166010

EST:     CCAAGTTTCAAGAGTCCCCTGAAGCTTACACGCCAGCCATAATAGCCCAA                         GACCGTGATCAACTCATGAACCTTTTCACATATGAAACGGTGGAGCGTGCT
genomic: CCAAGTTTCAAGAGTCCCCTGAAGCTTACACGCCAGCCATAATAGCCCAAgtctgctttt ... caaaattcagGACCGTGATCAACTCATGAACCTTCTCACATATGAAACGGTGGAGCGTGCT

EST: gi|32842445|gb|CD982126.1|CD982126

EST:     CCAAGTTTCAAGAGTCCCCTGAAGCTTACACGCCAGCCATAATAGCCCAA                         GACCGTGATCAACTCATGAACCTTCTCACATATGAAACGGTGGAGCGTGCT
genomic: CCAAGTTTCAAGAGTCCCCTGAAGCTTACACGCCAGCCATAATAGCCCAAgtctgctttt ... caaaattcagGACCGTGATCAACTCATGAACCTTCTCACATATGAAACGGTGGAGCGTGCT

EST: gi|37396226|gb|CF635400.1|CF635400

EST:     CCAAGTTTCAAGAGTCCCCTGAAGCTTACACGCCAGCCATAATAGCCCAA                         GAGCGTGATCAACTCATGAACCTTCTCACATATGAAACGGTGGAGCGTGCT
genomic: CCAAGTTTCAAGAGTCCCCTGAAGCTTACACGCCAGCCATAATAGCCCAAgtctgctttt ... caaaattcagGACCGTGATCAACTCATGAACCTTCTCACATATGAAACGGTGGAGCGTGCT

EST: gi|71302286|gb|DR787262.1|DR787262

EST:     CCAAGTTTCAAGAGTCCCCTGAAGCTTACACGCCAGCCATAATAGCCCAA                         GACCGTGATCAACTCATGAACCTTCTCACATATGAAACGGTGGAGCGTGCT
genomic: CCAAGTTTCAAGAGTCCCCTGAAGCTTACACGCCAGCCATAATAGCCCAAgtctgctttt ... caaaattcagGACCGTGATCAACTCATGAACCTTCTCACATATGAAACGGTGGAGCGTGCT

EST: gi|148931381|gb|EC874300.2|EC874300

EST:     CCAAGTTTCAAGAGTCCCCTGAAGCTTACACGCCAGCCATAATAGCCCCA                         GACCGTGATCAACTCATGAACCTTCTCACATATGAA
genomic: CCAAGTTTCAAGAGTCCCCTGAAGCTTACACGCCAGCCATAATAGCCCAAgtctgctttt ... caaaattcagGACCGTGATCAACTCATGAACCTTCTCACATATGAA

EST: gi|148996150|gb|EE035419.2|EE035419

EST:     CAAGTTTTCA-GAGTCCCCTGAAGCTTACACGCCAGCCATAATAGCCCCA                         GACCGTGATCAACTCATGAACCTTCTCACATA
genomic: CAAGTTT-CAAGAGTCCCCTGAAGCTTACACGCCAGCCATAATAGCCCAAgtctgctttt ... caaaattcagGACCGTGATCAACTCATGAACCTTCTCACATA

EST: gi|149077332|gb|EE166011.2|EE166011

EST:     CCAAGTTTCAAGAGTCCCCTGAAGCTTACACGCCAGCCATAATAGCCCAA                         GACCGTGATCAACTCATGAACCTTCTCACATATGAAACGGTGAAGCGTGCT
genomic: CCAAGTTTCAAGAGTCCCCTGAAGCTTACACGCCAGCCATAATAGCCCAAgtctgctttt ... caaaattcagGACCGTGATCAACTCATGAACCTTCTCACATATGAAACGGTGGAGCGTGCT

EST: gi|32842205|gb|CD981886.1|CD981886

EST:     CCAAGTTTCAAGAGTCCCCTGAAGCTTACACGCCAGCCATAATAGCCCAA                         GACCGTGATCAACTCATGAACCTTCTCACATATGCACCGGTGGAGCGTGCT
genomic: CCAAGTTTCAAGAGTCCCCTGAAGCTTACACGCCAGCCATAATAGCCCAAgtctgctttt ... caaaattcagGACCGTGATCAACTCATGAACCTTCTCACATATGAAACGGTGGAGCGTGCT

EST: gi|211089061|gb|FL455585.1|FL455585

EST:     CCAAGTTTCAAGAGTCCCCTGAAGCTTACACGCCAGCCATAATAGCCCAA                         GACCGTGATCAACTCATGAACCTTCTCACATATGAAACGGTGGAGCGTGCT
genomic: CCAAGTTTCAAGAGTCCCCTGAAGCTTACACGCCAGCCATAATAGCCCAAgtctgctttt ... caaaattcagGACCGTGATCAACTCATGAACCTTCTCACATATGAAACGGTGGAGCGTGCT

EST: gi|32851767|gb|CD991448.1|CD991448

EST:     CCAAGTTTCAAGAGTCCCCTGAAGCTTACACGCCAGCCATAATAGCCCAA                         GACCGTGATCAACTCATGAACCTTCTCACATATGAAACGGTGGAGCGTGCT
genomic: CCAAGTTTCAAGAGTCCCCTGAAGCTTACACGCCAGCCATAATAGCCCAAgtctgctttt ... caaaattcagGACCGTGATCAACTCATGAACCTTCTCACATATGAAACGGTGGAGCGTGCT

EST: gi|32842783|gb|CD982464.1|CD982464

EST:     CCAAGTTTCAAGAGTCCCCTGAAGCTTACACGCCAGCCATAATAGCCCAA                         GACCGTGATCAACTCATGAACCTTCTCACATATGAAACGGTGGAGCGTGCT
genomic: CCAAGTTTCAAGAGTCCCCTGAAGCTTACACGCCAGCCATAATAGCCCAAgtctgctttt ... caaaattcagGACCGTGATCAACTCATGAACCTTCTCACATATGAAACGGTGGAGCGTGCT

EST: gi|211304784|gb|FL143333.1|FL143333

EST:     CCAAGTTTCAAGAGTCCCCTGAAGCTTACACGCCAGCCATAATAGCCCAA                         GACCGTGATCAACTCATGAACCTTCTCACATATGAAACGGTGGAGCGTGCT
genomic: CCAAGTTTCAAGAGTCCCCTGAAGCTTACACGCCAGCCATAATAGCCCAAgtctgctttt ... caaaattcagGACCGTGATCAACTCATGAACCTTCTCACATATGAAACGGTGGAGCGTGCT

EST: gi|32842791|gb|CD982472.1|CD982472

EST:     CCAAGTTTCAAGAGTCCCCTGAAGCTTACACGCCAGCCATAATAGCCCAA                         GACCGTGATCAACTCATGAACCTTCTCACATATGAAACGGTGGAGCGTGCT
genomic: CCAAGTTTCAAGAGTCCCCTGAAGCTTACACGCCAGCCATAATAGCCCAAgtctgctttt ... caaaattcagGACCGTGATCAACTCATGAACCTTCTCACATATGAAACGGTGGAGCGTGCT

EST: gi|71302288|gb|DR787263.1|DR787263

EST:     CCAAGTTTCAAGAGTCCCCTGAAGCTTACACGCCAGCCATAATAGCCCAA                         GACCGTGATCAACTCATGAACCTTCTCACATATGAAACGGTGGAGCGTGCT
genomic: CCAAGTTTCAAGAGTCCCCTGAAGCTTACACGCCAGCCATAATAGCCCAAgtctgctttt ... caaaattcagGACCGTGATCAACTCATGAACCTTCTCACATATGAAACGGTGGAGCGTGCT

EST: gi|32842617|gb|CD982298.1|CD982298

EST:     CCAAGTTTCAAGAGTCCCCTGAAGCTTACACGCCAGCCATAATAGCCCAA                         GACCGTGATCAACTCATGACCCTTCTCACATATGAACCGGTGGAGCGTGCT
genomic: CCAAGTTTCAAGAGTCCCCTGAAGCTTACACGCCAGCCATAATAGCCCAAgtctgctttt ... caaaattcagGACCGTGATCAACTCATGAACCTTCTCACATATGAAACGGTGGAGCGTGCT

EST: gi|211304786|gb|FL143335.1|FL143335

EST:     CCAAGTTTCAAGAGTCCCCTGAAGCTTACACGCCAGCCATAATAGCCCAA                         GACCGTGATCAACTCATGAACCTTCTCACATATGAAACGGGNGGAGCGTGC
genomic: CCAAGTTTCAAGAGTCCCCTGAAGCTTACACGCCAGCCATAATAGCCCAAgtctgctttt ... caaaattcagGACCGTGATCAACTCATGAACCTTCTCACATATGAAACGGT-GGAGCGTGC

EST: gi|32842684|gb|CD982365.1|CD982365

EST:     CCAAGTTTCAAGAGTCCCCTGAAGCTTACACGCCAGCCATAATAGCCCAA                         GACCGTGATCAACTCATGAACCTTCTCACATATGAAACGGTGGAGCGTGCT
genomic: CCAAGTTTCAAGAGTCCCCTGAAGCTTACACGCCAGCCATAATAGCCCAAgtctgctttt ... caaaattcagGACCGTGATCAACTCATGAACCTTCTCACATATGAAACGGTGGAGCGTGCT

EST: gi|89763811|gb|DY690849.1|DY690849

EST:     CCA-GTTTCAAGAGTCCCCTGAAGCTTACACGCCAGCCATAATAGCCCAA                         GACCGTGATCAACTCATGAACCTTCTCACATATGAAACGGTGGAGCGTGCT
genomic: CCAAGTTTCAAGAGTCCCCTGAAGCTTACACGCCAGCCATAATAGCCCAAgtctgctttt ... caaaattcagGACCGTGATCAACTCATGAACCTTCTCACATATGAAACGGTGGAGCGTGCT

EST: gi|67010340|gb|CO439089.1|CO439089

EST:     CCAAGTTTCAAGAGTCCCCTGAAGCTTACACGCCAGCCATAATAGCCCAA                         GACCGTGATCAACTCATGAACCTTCTCACATATGAAACGGTGGAGCGTGCT
genomic: CCAAGTTTCAAGAGTCCCCTGAAGCTTACACGCCAGCCATAATAGCCCAAgtctgctttt ... caaaattcagGACCGTGATCAACTCATGAACCTTCTCACATATGAAACGGTGGAGCGTGCT

EST: gi|32842553|gb|CD982234.1|CD982234

EST:     CCAAGTTTCAAGAGTCCCCTGAAGCTTACACGCCAGCCATAATAGCCCAA                         GACCGTGATCAACTCATGAACCTTCTCACATATGAAACGGTGGAGCGTGCT
genomic: CCAAGTTTCAAGAGTCCCCTGAAGCTTACACGCCAGCCATAATAGCCCAAgtctgctttt ... caaaattcagGACCGTGATCAACTCATGAACCTTCTCACATATGAAACGGTGGAGCGTGCT

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), 46 (downstream exon)
Score: 34

GCACTCTCCAGAAGGATCCACTATGGGAAGTTTGTGGCAGAGGCCAAGTTTCAAGAGTCCCCTGAAGCTTACACGCCAGCCATAATAGCCCAAgtctgctttt ... caaaattcagGACCGTGATCAACTCATGAACCTTCTCACATATGAAACGGTGGAGCGTGCTATCGAACACAGGGTGGAGGCCAAAGCCAAGATCTTCGGGCAAGAGGTGA

Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 132

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 151

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 324

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GCACTCTCCAGAAGGATCCACTATGGGAAGTTTGTGGCAGAGGCCAAGTTTCAAGAGTCCCCTGAAGCTTACACGCCAGCCATAATAGCCCAAgtctgcttttgttccaactattagtatttctagtactactattttcatttattttttattttatttcagagtttcagaacaaaatgatatttcgattcatttgaaaaatatatctatttctcgtcacatttggcaaaattcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC