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

...atagataccccattttcagatataatggaatgttcctctctagttttcttttattgtctacaacgtagagcttattaccaacttatgtttttccctctagTTTGTTGAGACAGGAATTGAACTAGGAAACAACTTCTCTGAAGTCATAGCTCCTCAAGACGTGGCAGTCTATGGTGCCCTTTGTGCACTTGCTTCTTTTG

Basic information

species	Zea mays
transcript	GRMZM2G062210_T01
intron #	2
splice site	3'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G062210_T02 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os03g02540.1 (Oryza sativa), 3'ss of exon 2

-atag-atacc--ccattttcagatataatggaatgttcctctctagttttcttttattgtctacaacgtagagcttattaccaacttatgtttttccctctagTTTGTTGAGACAGGAATTGAACTAGGAAACAACTTCTCTGAAGTCATAGCTCCTCAAGACGTGGCAGTCTATGGTGCCCTTTGTGCACTTGCTTCTTTTG
 || | ||  |  | ||| | |  ||    | | |||   |    |  | || | |  | | |  | | ||||  ||  | |  | || |  | | || |  |||||||||||||||||  ||||||||||||||| |  ||||||||||||||||| ||||| || || |||||||||||||||||||||||||||||||| |
aatgggatgtcaacaattgtgaagtactccgta-tgtatttactcatatgtcatgttctttgt-tagcatagaatttgctgctgaatttt--tctcccttaaagTTTGTTGAGACAGGACATGAACTAGGAAACAATTATTCTGAAGTCATAGCTCCACAAGATGTTGCTGTCTATGGTGCCCTTTGTGCACTTGCTTCTTTCG

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|60401615|gb|DN234422.1|DN234422

EST:     CAGGATTAGCCAACTTGGAAACAAAGAAATACAAATTTGCTGCTCGTAAG                         TTTGTTGAGACAGGAATTGAACTAGGAAACAACTTCTCTGAAGTCATAGCT
genomic: CAGGATTAGCCAACTTGGAAACAAAGAAATACAAATTTGCTGCTCGTAAGgttagtcacc ... ttccctctagTTTGTTGAGACAGGAATTGAACTAGGAAACAACTTCTCTGAAGTCATAGCT

EST: gi|32797927|gb|CD950163.1|CD950163

EST:     CAGGATTAGCCAACTTGGAAACAAAGAAATACAAATTTGCTGCTCGTAAG                         TTTGCTGAGACAGGAATTGAACTAGGAAACAACTTCTCTGAAGTCATAGCT
genomic: CAGGATTAGCCAACTTGGAAACAAAGAAATACAAATTTGCTGCTCGTAAGgttagtcacc ... ttccctctagTTTGTTGAGACAGGAATTGAACTAGGAAACAACTTCTCTGAAGTCATAGCT

EST: gi|22819870|gb|BU499960.1|BU499960

EST:     CAGGATTAGCCAACTTGGAAACAAAGAAATACAAATTTGCTGCTCGTAAG                         TTTGTTGAGACAGGAATTGAACTAGGAAACAACTTCTCTGAAGTCATAGCT
genomic: CAGGATTAGCCAACTTGGAAACAAAGAAATACAAATTTGCTGCTCGTAAGgttagtcacc ... ttccctctagTTTGTTGAGACAGGAATTGAACTAGGAAACAACTTCTCTGAAGTCATAGCT

EST: gi|60401180|gb|DN233987.1|DN233987

EST:     CAGGATTAGCCAACTTGGAAACAAAGAAATACAAATTTGCTGCTCGTAAG                         TTTGTTGAGACAGGAATTGAACTAGGAAACAACTTCTCTGAAGTCATAGCT
genomic: CAGGATTAGCCAACTTGGAAACAAAGAAATACAAATTTGCTGCTCGTAAGgttagtcacc ... ttccctctagTTTGTTGAGACAGGAATTGAACTAGGAAACAACTTCTCTGAAGTCATAGCT

EST: gi|20811311|gb|BQ295789.1|BQ295789

EST:     CAGGATTAGCCAACTTGGAAACAAAGAAATACAAATTTGCTGCTCGTAAG                         TTTGTTGAGACAGGAATTGAACTAGGAAACAACTTCTCTGAAGTCATAGCT
genomic: CAGGATTAGCCAACTTGGAAACAAAGAAATACAAATTTGCTGCTCGTAAGgttagtcacc ... ttccctctagTTTGTTGAGACAGGAATTGAACTAGGAAACAACTTCTCTGAAGTCATAGCT

EST: gi|5847125|gb|AW000204.1|AW000204

EST:     CAGGATTAGCCAACTTGGAAACAAAGAAATACAAATTTGCTGCTCGTAAG                         TTTGTTGAGACAGGAATTGAACTAGGAAACAACTTCTCTGAAGTCATAGCT
genomic: CAGGATTAGCCAACTTGGAAACAAAGAAATACAAATTTGCTGCTCGTAAGgttagtcacc ... ttccctctagTTTGTTGAGACAGGAATTGAACTAGGAAACAACTTCTCTGAAGTCATAGCT

EST: gi|71775377|gb|DR973255.1|DR973255

EST:     CAGGATTAGCCAACTTGGAAACAAAGAAATACAAATTTGCTGCTCGTAAG                         TTTGTTGAGACAGGAATTGAACTAGGAAACAACTTCTCTGAAGTCATAGCT
genomic: CAGGATTAGCCAACTTGGAAACAAAGAAATACAAATTTGCTGCTCGTAAGgttagtcacc ... ttccctctagTTTGTTGAGACAGGAATTGAACTAGGAAACAACTTCTCTGAAGTCATAGCT

EST: gi|18660332|gb|BM500807.1|BM500807

EST:     TACAAATTTGCTGCTCGTAAG                         TTTGTTGAGACAGGAATTGAACTAGGAAACAACTTCTCTGAAGTCATAGCT
genomic: TACAAATTTGCTGCTCGTAAGgttagtcacc ... ttccctctagTTTGTTGAGACAGGAATTGAACTAGGAAACAACTTCTCTGAAGTCATAGCT

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), 48 (downstream exon)
Score: 218

AACCCCCGACTCTCTGGATCCTACCATTGTTGCAAAGCTGAAGGCAGCTGCAGGATTAGCCAACTTGGAAACAAAGAAATACAAATTTGCTGCTCGTAAGgttagtcacc ... ttccctctagTTTGTTGAGACAGGAATTGAACTAGGAAACAACTTCTCTGAAGTCATAGCTCCTCAAGACGTGGCAGTCTATGGTGCCCTTTGTGCACTTGCTTCTTTTG

Block sizes: 46 (upstream exon), 47 (downstream exon)
Score: 150

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 186

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 202

atgc intronic sequence ATGC exonic sequence

Intronic sequence truncated to 55 bases.

ttcttttattgtctacaacgtagagcttattaccaacttatgtttttccctctagTTTGTTGAGACAGGAATTGAACTAGGAAACAACTTCTCTGAAGTCATAGCTCCTCAAGACGTGGCAGTCTATGGTGCCCTTTGTGCACTTGCTTCTTTTG

                                    cttatgtttttccctc  CT-rich tract
                                     ttatgttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
atagataccccattttcagatataatggaatgttcctctctagttttcttttattgtctacaacgtagagcttattaccaacttatgtttttccctctagTTTGTTGAGACAGGAATTGAACTAGGAAACAACTTCTCTGAAGTCATAGCTCCTCAAGACGTGGCAGTCTATGGTGCCCTTTGTGCACTTGCTTCTTTTG

- - - - - - - - - - - - - - - tgttcct
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ttatgtt