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

...aacgaattagcctgtccaacaacaaaaaaagttaacccactatctgtgagtagtgttttactgtatgattgcatccttgttctctctgtgcctgcaccagATTGCTCCCAACGGCTGGGCGGAAGGAGAATGCCGAGGGAAGGCTGGCTGGTTTCCGGCTGCCTATGTTGAGAGGCGCGAGAATATCCCCCCGAATAAAG

Basic information

species	Zea mays
transcript	GRMZM2G179459_T01
intron #	9
splice site	3'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G179459_T01 (Zea mays), 3'ss of exon 9
lower sequence: LOC_Os07g32460.1 (Oryza sativa), 3'ss of exon 9

aacgaattagcctgtccaacaacaaaaaaagttaacccactat-ctgtgagtagtgttttactgtatgattgcatccttgttctctctgtgcctgcaccagATTGCTCCCAACGGCTGGGCGGAAGGAGAATGCCGAGGGAAGGCTGGCTGGTTTCCGGCTGCCTATGTTGAGAGGCGCGAGAATATCCCCCCGAATAAAG
 |   ||| | |   | |||||          |   | | |    |  ||      |   | | ||  ||   ||     ||   | |||  |||| | |||||||||| || || ||||| ||||||||||||   |||  ||| || ||||| ||||||||||| || |||||||| || |||||||| || || ||||
-atcgattggtccaacaaacaatggtgctgaattgtctagtgcattaagacctcaatccaaatttaccatctaattgccttttcatttgtatctgctctagATTGCTCCGAATGGTTGGGCCGAAGGAGAATGCAAGGGGGTGGCAGGATGGTTCCCGGCTGCCTACGTGGAGAGGCGTGAAAATATCCCGCCAAACAAAG

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|87155526|gb|DY400315.1|DY400315

EST:     CGGAGAAGGAACTGAGCTTAATTGTTGGCGATTATGTTGTTGTTCGTCAG                         ATTGCTCCCAACGGCTGGGCGGAAGGAGAATGCCGAGGGAAGGCTGGGTGG
genomic: CGGAGAAGGAACTGAGCTTAATTGTTGGCGATTATGTTGTTGTTCGTCAGgtcagtgtgc ... cctgcaccagATTGCTCCCAACGGCTGGGCGGAAGGAGAATGCCGAGGGAAGGCTGGCTGG

EST: gi|110957807|gb|EE177859.1|EE177859

EST:     CGGAGAAGGAACTGAGCTTAATTGTTGGCGATTATGTTGTTGTTCGTCAG                         ATTGCTCCCAACGGCTGGGCGGAAGGAGAATGCCGAGGGAAGGCTGGCTGG
genomic: CGGAGAAGGAACTGAGCTTAATTGTTGGCGATTATGTTGTTGTTCGTCAGgtcagtgtgc ... cctgcaccagATTGCTCCCAACGGCTGGGCGGAAGGAGAATGCCGAGGGAAGGCTGGCTGG

EST: gi|60337938|gb|DN204911.1|DN204911

EST:     CGGAGAAGGAACTGAGCTTAATTGTTGGCGATTATGTTGTTGTTCGTCAG                         ATTGCTCCCAACGGCTGGGCGGAAGGAGAATGCCGAGGGAAGGCTGGCTGG
genomic: CGGAGAAGGAACTGAGCTTAATTGTTGGCGATTATGTTGTTGTTCGTCAGgtcagtgtgc ... cctgcaccagATTGCTCCCAACGGCTGGGCGGAAGGAGAATGCCGAGGGAAGGCTGGCTGG

EST: gi|18168054|gb|BM337894.1|BM337894

EST:     CGGAGAAGGAACTGAGCTTAATTGTTGGCGATTATGTTGTTGTTCGTCAG                         ATTGCTCCCAACGGCTGGGCGGAAGGAGAATGCCGAGGGAAGGCTGGCTGG
genomic: CGGAGAAGGAACTGAGCTTAATTGTTGGCGATTATGTTGTTGTTCGTCAGgtcagtgtgc ... cctgcaccagATTGCTCCCAACGGCTGGGCGGAAGGAGAATGCCGAGGGAAGGCTGGCTGG

EST: gi|60351503|gb|DN218476.1|DN218476

EST:     CGGAGAAGGAACTGAGCTTAATTGTTGGCGATTATGTTGTTGTTCGTCAG                         ATTGCTCCCAACGGCTGGGCGGAAGGAGAATGCCGAGGGAAGGCTGGCTGG
genomic: CGGAGAAGGAACTGAGCTTAATTGTTGGCGATTATGTTGTTGTTCGTCAGgtcagtgtgc ... cctgcaccagATTGCTCCCAACGGCTGGGCGGAAGGAGAATGCCGAGGGAAGGCTGGCTGG

EST: gi|33097796|gb|CF057756.1|CF057756

EST:     CGGAGAAGGAACTGAGCTTAATTGTTGGCGATTATGCTGTTGTTCGTCAG                         ATTGCTCCCAACGGCTGGGCGGAAGGAGAATGCCGAGGGAAGGCTGGCTGG
genomic: CGGAGAAGGAACTGAGCTTAATTGTTGGCGATTATGTTGTTGTTCGTCAGgtcagtgtgc ... cctgcaccagATTGCTCCCAACGGCTGGGCGGAAGGAGAATGCCGAGGGAAGGCTGGCTGG

EST: gi|91048362|gb|EB158780.1|EB158780

EST:     CGGAGAAGGAACTGAGCTTAATTGTTGGCGATTATGTTGTTGTTCGTCAG                         ATTGCTCCCAACGGCTGGGCGGAAGGAGAATGCCGAGGGAAGGCTGGCTGG
genomic: CGGAGAAGGAACTGAGCTTAATTGTTGGCGATTATGTTGTTGTTCGTCAGgtcagtgtgc ... cctgcaccagATTGCTCCCAACGGCTGGGCGGAAGGAGAATGCCGAGGGAAGGCTGGCTGG

EST: gi|60340975|gb|DN207948.1|DN207948

EST:     CGGAGAAGGAACTGAGCTTAATTGTTGGCGATTATGTTGTTGTTCGTCAG                         ATTGCTCCCAACGGCTGGGCGGAAGGAGAATGCCGAGGGAAGGCTGGCTGG
genomic: CGGAGAAGGAACTGAGCTTAATTGTTGGCGATTATGTTGTTGTTCGTCAGgtcagtgtgc ... cctgcaccagATTGCTCCCAACGGCTGGGCGGAAGGAGAATGCCGAGGGAAGGCTGGCTGG

EST: gi|213188152|gb|FM192776.1|FM192776

EST:     CGGAGAAGGAACTGAGCTTAATTGTTGGCGATTATGTTGTTGTTCGTCAG                         ATTGCTCCCAACGGCTGGGCGGAAGGAGNATGCCGAGGGANNNCTGGCTGG
genomic: CGGAGAAGGAACTGAGCTTAATTGTTGGCGATTATGTTGTTGTTCGTCAGgtcagtgtgc ... cctgcaccagATTGCTCCCAACGGCTGGGCGGAAGGAGAATGCCGAGGGAAGGCTGGCTGG

EST: gi|5566993|gb|AI881904.1|AI881904

EST:     CGGAGAAGGAACTGAGCTTAATTGTTGGCGATTATGTTGTTGTTCGTCAG                         ATTGCTCCCAACGGCTGGGCGGAAGGAGAATGCCGAGGGAAGGCTGGGTGG
genomic: CGGAGAAGGAACTGAGCTTAATTGTTGGCGATTATGTTGTTGTTCGTCAGgtcagtgtgc ... cctgcaccagATTGCTCCCAACGGCTGGGCGGAAGGAGAATGCCGAGGGAAGGCTGGCTGG

EST: gi|149032716|gb|EE154942.2|EE154942

EST:     CGGAGAAGGAACTGAGCTTAATTGTTGGCGATTATGTTGTTGTTCGTCAG                         ATTGCTCCCAACGGCTGGGCGGAAGGAGAATGCCGAGGGAAGGCTGGCTGG
genomic: CGGAGAAGGAACTGAGCTTAATTGTTGGCGATTATGTTGTTGTTCGTCAGgtcagtgtgc ... cctgcaccagATTGCTCCCAACGGCTGGGCGGAAGGAGAATGCCGAGGGAAGGCTGGCTGG

EST: gi|60344252|gb|DN211225.1|DN211225

EST:     CGGAGAAGGAACTGAGCTTAATTGTTGGCGATTATGTTGTTGTTCGTCAG                         ATTGCTCCCAACGGCTGGGCGGAAGGAGAATGCCGAGGGAAGGCTGGCTGG
genomic: CGGAGAAGGAACTGAGCTTAATTGTTGGCGATTATGTTGTTGTTCGTCAGgtcagtgtgc ... cctgcaccagATTGCTCCCAACGGCTGGGCGGAAGGAGAATGCCGAGGGAAGGCTGGCTGG

EST: gi|211532562|gb|FL475969.1|FL475969

EST:     GAACTGAGCTTAATTGTTGGCGATTATGTTGTTGTTCGTCAG                         ATTGCTCCCAACGGCTGGGCGGAAGGAGAATGCCGAGGGAAGGCTGGCTGG
genomic: GAACTGAGCTTAATTGTTGGCGATTATGTTGTTGTTCGTCAGgtcagtgtgc ... cctgcaccagATTGCTCCCAACGGCTGGGCGGAAGGAGAATGCCGAGGGAAGGCTGGCTGG

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: 295

GTAATGCATAATTTCAATGGAACCACGGAGAAGGAACTGAGCTTAATTGTTGGCGATTATGTTGTTGTTCGTCAGgtcagtgtgc ... cctgcaccagATTGCTCCCAACGGCTGGGCGGAAGGAGAATGCCGAGGGAAGGCTGGCTGGTTTCCGGCTGCCTATGTTGAGAGGCGCGAGAATATCCCCCCGAATAAAG

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 174

Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 85

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 156

atgc intronic sequence ATGC exonic sequence

Intronic sequence truncated to 55 bases.

gtgagtagtgttttactgtatgattgcatccttgttctctctgtgcctgcaccagATTGCTCCCAACGGCTGGGCGGAAGGAGAATGCCGAGGGAAGGCTGGCTGGTTTCCGGCTGCCTATGTTGAGAGGCGCGAGAATATCCCCCCGAATAAAG

                                  ttctctctgtgcct  CT-rich tract
        tgtttta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aacgaattagcctgtccaacaacaaaaaaagttaacccactatctgtgagtagtgttttactgtatgattgcatccttgttctctctgtgcctgcaccagATTGCTCCCAACGGCTGGGCGGAAGGAGAATGCCGAGGGAAGGCTGGCTGGTTTCCGGCTGCCTATGTTGAGAGGCGCGAGAATATCCCCCCGAATAAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGAGG
- - - - - - - - caacaac
- - - - - - - - - - - -aaaaaaa
- - - - - - - - - - - - - - - - - -cccacta
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ctgtatg