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

...gatagatgtggtaccatcccagtatgctgcttgacaagtcactagtttttaacatgatcaagttcagtctctaagtttcatggtcacctctctttttcagAGCTTGCCAAGTGGCAAAACAAGCATTTGATGAGGCTCTTACTGAGATAAATTCTGGTGAGGGAGTTTACAAGGATAGCACACTTATGATGCAGCTTCTG

Basic information

species	Zea mays
transcript	GRMZM2G145213_T01
intron #	4
splice site	3'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G145213_T01 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os11g39540.1 (Oryza sativa), 3'ss of exon 4

gatagatgtggtaccatcccagtatgc---tgcttgacaagtcactagtttttaacatgatcaagttcagtctctaagtttcatggtcacctctctttttcagAGCTTGCCAAGTGGCAAAACAAGCATTTGATGAGGCTCTTACTGAGATAAATTCTG---GTGAGGGAGTTTACAAGGATAGCACACTTATGATGCAGCTTCTG
     || | |  |||| ||||  | |   |  |  || ||||  |      |   | |||  |    | ||  | ||||      |    |  ||||||||||||| |||||||||||||||||||| |||||||||||  | ||||||| || ||||   ||| ||  | ||||||||| ||||  ||||||||||||||    
---gcatcttgggccatgccagatttcacatcatccaccagtctttcaaagcttcaaagatataccataatcaatgagttagtcattttatttcctttttcagAGCTAGCCAAGTGGCAAAACAAGCACTTGATGAGGCTACTGCTGAGATTAACTCTGCTGGTGTGGAGGGTTACAAGGACAGCATGCTTATGATGCAGCTC---

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|6431859|gb|AW172063.1|AW172063

EST:     GCCCTCAATTTGTCGGTCTTCTTTTATGAGATAATGAACTCTCATGAGAG                         AGCTTGCCAAGTGGCAAAACAAGCATTTGATGAGGCTCTTACTGAGATAAA
genomic: GCCCTCAATTTGTCGGTCTTCTTTTATGAGATAATGAACTCTCATGAGAGgtcactcatc ... tctttttcagAGCTTGCCAAGTGGCAAAACAAGCATTTGATGAGGCTCTTACTGAGATAAA

EST: gi|74234408|gb|DT642322.1|DT642322

EST:     GCCCTCAATTTGTCGGTCTTCTTTTATGAGATAATGAACTCTCATGAGAG                         AGCTTGCCAAGTGGCAAAACAAGCATTTGATGAGGCTCTTACTGAGATAAA
genomic: GCCCTCAATTTGTCGGTCTTCTTTTATGAGATAATGAACTCTCATGAGAGgtcactcatc ... tctttttcagAGCTTGCCAAGTGGCAAAACAAGCATTTGATGAGGCTCTTACTGAGATAAA

EST: gi|211267022|gb|FK966686.1|FK966686

EST:     GCCCTCAATTTGTCGGTCTTCTTTTATGAGATAATGAATTCTCATGAGAG                         AGCTTGCCAAGTGGCAAAACAAGCATTTGATGAGGCTCTTACTGAGATAAA
genomic: GCCCTCAATTTGTCGGTCTTCTTTTATGAGATAATGAACTCTCATGAGAGgtcactcatc ... tctttttcagAGCTTGCCAAGTGGCAAAACAAGCATTTGATGAGGCTCTTACTGAGATAAA

EST: gi|6227145|gb|AW155674.1|AW155674

EST:     GCCCTCAATTTGTCGGTCTTCTTTTATGAGATAATGAACTCTCATGAGAG                         AGCTTGCCAAGTGGCAAAACAAGCATTTGATGAGGCTCTTACTGAGATAAA
genomic: GCCCTCAATTTGTCGGTCTTCTTTTATGAGATAATGAACTCTCATGAGAGgtcactcatc ... tctttttcagAGCTTGCCAAGTGGCAAAACAAGCATTTGATGAGGCTCTTACTGAGATAAA

EST: gi|71302156|gb|DR787186.1|DR787186

EST:     GCCCTCAATTTGTCGGTCTTCTTTTATGAGATAATGAACTCTCATGAGAG                         AGCTTGCCAAGTGCCAAAA
genomic: GCCCTCAATTTGTCGGTCTTCTTTTATGAGATAATGAACTCTCATGAGAGgtcactcatc ... tctttttcagAGCTTGCCAAGTGGCAAAA

EST: gi|31353761|gb|CD438118.1|CD438118

EST:     GCCCTCAATTTGTCGGTCTTCTTTTATGAGATAATGAACTCTCATGAGAG                         AGCTTGCCAAGTGGCAAAACAAGCATTTGATGAGGCTCTTACTGAGATAAA
genomic: GCCCTCAATTTGTCGGTCTTCTTTTATGAGATAATGAACTCTCATGAGAGgtcactcatc ... tctttttcagAGCTTGCCAAGTGGCAAAACAAGCATTTGATGAGGCTCTTACTGAGATAAA

EST: gi|78093195|gb|DV521569.1|DV521569

EST:     GCCCTCAATTTGTCGGTCTTCTTTTATGAGATAATGAACTCTCATGAGAG                         AGCTTGCCAAGTGGCAAAACAAGCATTTGATGAGGCTCTTACTGAGATAAA
genomic: GCCCTCAATTTGTCGGTCTTCTTTTATGAGATAATGAACTCTCATGAGAGgtcactcatc ... tctttttcagAGCTTGCCAAGTGGCAAAACAAGCATTTGATGAGGCTCTTACTGAGATAAA

EST: gi|67020921|gb|CO449670.1|CO449670

EST:     CCCTNCA-TTTGTCGGTCTTCTTTTATGAGATAATGAACTCTCATGAGAG                         AGCTTGCCAAGTGGCAAAACAAGCATTTGATGAGGCTCTTACTGAGATAAA
genomic: CCCT-CAATTTGTCGGTCTTCTTTTATGAGATAATGAACTCTCATGAGAGgtcactcatc ... tctttttcagAGCTTGCCAAGTGGCAAAACAAGCATTTGATGAGGCTCTTACTGAGATAAA

EST: gi|101382257|gb|EB813184.1|EB813184

EST:     GCCCTCAATTTGTCGGTCTTCTTTTATGAGATAATGAACTCTCATGAGAG                         AGCTTGCCAAGTGGCAAAACAAGCATTTGATGAGGCTCTTACTGAGATAAA
genomic: GCCCTCAATTTGTCGGTCTTCTTTTATGAGATAATGAACTCTCATGAGAGgtcactcatc ... tctttttcagAGCTTGCCAAGTGGCAAAACAAGCATTTGATGAGGCTCTTACTGAGATAAA

EST: gi|44681886|gb|CK786934.1|CK786934

EST:     GCCCTCAATTTGTCGGTCTTCTTTTATGAGATAATGAACTCTCATGAGAG                         AGCTTGCCAAGTGGCAAAACAAGCATTTGATGAGGCTCTTACTGAGATAAA
genomic: GCCCTCAATTTGTCGGTCTTCTTTTATGAGATAATGAACTCTCATGAGAGgtcactcatc ... tctttttcagAGCTTGCCAAGTGGCAAAACAAGCATTTGATGAGGCTCTTACTGAGATAAA

EST: gi|71448133|gb|DR829183.1|DR829183

EST:     GCCCTCAATTTGTCGGTCTTCTTTTATGAGATAATGAACTCTCATGAGAG                         AGCTTGCCAAGTGGCAAAACAAGCATTTGATGAGGCTCTTACTGAGATAAA
genomic: GCCCTCAATTTGTCGGTCTTCTTTTATGAGATAATGAACTCTCATGAGAGgtcactcatc ... tctttttcagAGCTTGCCAAGTGGCAAAACAAGCATTTGATGAGGCTCTTACTGAGATAAA

EST: gi|71444597|gb|DR825647.1|DR825647

EST:     GCCCTCAATTTGTCGGTCTTCTTTTATGAGATAATGAACTCTCATGAGAG                         AGCTTGCCAAGTGGCAAAACAAGCATTTGATGAGGCTCTTACTGAGATAAA
genomic: GCCCTCAATTTGTCGGTCTTCTTTTATGAGATAATGAACTCTCATGAGAGgtcactcatc ... tctttttcagAGCTTGCCAAGTGGCAAAACAAGCATTTGATGAGGCTCTTACTGAGATAAA

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: 185

TTGTCGCCTCCAGTGAGCTCTCACCTGCTCACCAAATCCGGCTTGGCCTTGCCCTCAATTTGTCGGTCTTCTTTTATGAGATAATGAACTCTCATGAGAGgtcactcatc ... tctttttcagAGCTTGCCAAGTGGCAAAACAAGCATTTGATGAGGCTCTTACTGAGATAAATTCTGGTGAGGGAGTTTACAAGGATAGCACACTTATGATGCAGCTTCTG

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 111

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 170

Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 145

atgc intronic sequence ATGC exonic sequence

Intronic sequence truncated to 55 bases.

tttttaacatgatcaagttcagtctctaagtttcatggtcacctctctttttcagAGCTTGCCAAGTGGCAAAACAAGCATTTGATGAGGCTCTTACTGAGATAAATTCTGGTGAGGGAGTTTACAAGGATAGCACACTTATGATGCAGCTTCTG

 ttttaac  putative branch site (score: 145)
                                      tcacctctctttttc  putative PPT
                          taagttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gatagatgtggtaccatcccagtatgctgcttgacaagtcactagtttttaacatgatcaagttcagtctctaagtttcatggtcacctctctttttcagAGCTTGCCAAGTGGCAAAACAAGCATTTGATGAGGCTCTTACTGAGATAAATTCTGGTGAGGGAGTTTACAAGGATAGCACACTTATGATGCAGCTTCTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGCT
- - - - - - -ccatccc
- - - - - - - - - - - - -gctgctt
- - - - - - - - - - - - - - - - - - - - - - - - - - catgatc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ttcatgg