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

...accaggagcaagcccctcctgattagtatataataatcttgtgggaatttcacgtctgaaattgtgcagttctgatcgcttttgtcattttccggagcagGTGATGTGGGCATTCTCCATTTATTTGGAAGCTGTCGCGATATTTCCACAACTTGTGTTGCTACAGCGGACAAGGAATATTGACAACCTGACTGGCCAAT

Basic information

species	Zea mays
transcript	GRMZM2G031802_T03
intron #	2
splice site	3'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G031802_T02 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os11g28340.1 (Oryza sativa), 3'ss of exon 2

--accaggagcaagcccctcctgattagtatataataatcttgtgggaattt--cacgtctgaaattgtgcagttctgatcgcttttgtcattttccggagcagGTGATGTGGGCATTCTCCATTTATTTGGAAGCTGTCGCGATATTTCCACAACTTGTGTTGCTACAGCGGACAAGGAATATTGACAACCTGACTGGCCAAT
      |  |  |       ||| || |  | |  ||   |||| | || ||   || |   | | | |||| || ||| |  |     |||| |  || |||||| ||||||||||||||||| ||||| |||||||| || ||  | || |||||||||||||||||||| || ||||||||||||||||||||||||||||
tttatggatgtgatggaagtctgttt-gcctctttta---ttgttgaaacttagtacattatagactctgcaattttgaccattcacaccattatttggggcagGTTATGTGGGCATTCTCCATATATTTAGAAGCTGTAGCAATTCTACCTCAACTTGTGTTGCTACAGCGCACGAGGAATATTGACAACCTGACTGGCCAAT

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|211525033|gb|FL310988.1|FL310988

EST:     CTTGTCTTCTTCTGGCTCTCCTCATTAATGAGAAGTTTACTTTTAGAGAG                         GTGATGTGGGCATTCTCCATTTATTTGGAAGCTGTCGCGATATTTCCACAA
genomic: CTTGTCTTCTTCTGGCTCTCCTCATTAATGAGAAGTTTACTTTTAGAGAGgtcagtgttt ... tccggagcagGTGATGTGGGCATTCTCCATTTATTTGGAAGCTGTCGCGATATTTCCACAA

EST: gi|148995872|gb|EE035110.2|EE035110

EST:     CTTGTCTTCTTCTGGCTCTCCTCATTAATGAGAAGTTTACTTTTAGAGAG                         GTGATGTGGGCATTCTCCATTTATTTGGAAGCTGTCGCGATATTTCCACAA
genomic: CTTGTCTTCTTCTGGCTCTCCTCATTAATGAGAAGTTTACTTTTAGAGAGgtcagtgttt ... tccggagcagGTGATGTGGGCATTCTCCATTTATTTGGAAGCTGTCGCGATATTTCCACAA

EST: gi|60397063|gb|DN229882.1|DN229882

EST:     CTTGTCTTCTTCTGGCTCTCCTCATTAATGAGAAGTTTACTTTTAGAGAG                         GTGATGTGGGCATTCTCCATTTATTTGGAAGCTGTCGCGATATTTCCACAA
genomic: CTTGTCTTCTTCTGGCTCTCCTCATTAATGAGAAGTTTACTTTTAGAGAGgtcagtgttt ... tccggagcagGTGATGTGGGCATTCTCCATTTATTTGGAAGCTGTCGCGATATTTCCACAA

EST: gi|5361053|gb|AI795668.1|AI795668

EST:     TTACTTTTAGAGAG                         GTGATGTGGGCATTCTCCATTTATTTGGAAGCTGTCGCGATATTTCCACAA
genomic: TTACTTTTAGAGAGgtcagtgttt ... tccggagcagGTGATGTGGGCATTCTCCATTTATTTGGAAGCTGTCGCGATATTTCCACAA

EST: gi|60359236|gb|DN226209.1|DN226209

EST:     CTTGTCTTCTTCTGGCTCTCCTCATTAATGAGAAGTTTACTTTTAGAGAG                         GTGATGTGGGCATTCTCCATTTATTTGGAAGCTGTCGCGATATTTCCACAA
genomic: CTTGTCTTCTTCTGGCTCTCCTCATTAATGAGAAGTTTACTTTTAGAGAGgtcagtgttt ... tccggagcagGTGATGTGGGCATTCTCCATTTATTTGGAAGCTGTCGCGATATTTCCACAA

EST: gi|71329461|gb|DR801451.1|DR801451

EST:     CTTGTCTTCTTCTGGCTCTCCTCATTAATGAGAAGTTTACTTTTAGAGAG                         GTGATGTGGGCATTCTCCATTTATTTGGAAGCTGTCGCGATATTTCCACAA
genomic: CTTGTCTTCTTCTGGCTCTCCTCATTAATGAGAAGTTTACTTTTAGAGAGgtcagtgttt ... tccggagcagGTGATGTGGGCATTCTCCATTTATTTGGAAGCTGTCGCGATATTTCCACAA

EST: gi|78117678|gb|DV536065.1|DV536065

EST:     CTTGTCTTCTTCTGGCTCTCCTCATTAATGAGAAGTTTACTTTTAGAGAG                         GTGATGTGGGCATTCTCCATTTATTTGGAAGCTGTCGCGATATTTCCACAA
genomic: CTTGTCTTCTTCTGGCTCTCCTCATTAATGAGAAGTTTACTTTTAGAGAGgtcagtgttt ... tccggagcagGTGATGTGGGCATTCTCCATTTATTTGGAAGCTGTCGCGATATTTCCACAA

EST: gi|8383313|gb|BE056256.1|BE056256

EST:     CTTGTCTTCTTCTGGCTCTCCTCATTAATGAGAAGTTTACTTTTAGAGAG                         GTGATGTGGGCATTCTCCATTTATTTGGAAGCTGTCGCGATATTTCCACAA
genomic: CTTGTCTTCTTCTGGCTCTCCTCATTAATGAGAAGTTTACTTTTAGAGAGgtcagtgttt ... tccggagcagGTGATGTGGGCATTCTCCATTTATTTGGAAGCTGTCGCGATATTTCCACAA

EST: gi|5847439|gb|AW000518.1|AW000518

EST:     CTTGTCTTCTTCTGGCTCTCCTCATTAATGAGAAGTTTACTTTTAGAGAG                         GTGATGTGGGCATTCTCCATTTATTTGGAAGCTGTCGCGATATTTCCACAA
genomic: CTTGTCTTCTTCTGGCTCTCCTCATTAATGAGAAGTTTACTTTTAGAGAGgtcagtgttt ... tccggagcagGTGATGTGGGCATTCTCCATTTATTTGGAAGCTGTCGCGATATTTCCACAA

EST: gi|67022873|gb|CO451622.1|CO451622

EST:     CTTGTCTTCTTCTGGCTCTCCTCATTAATGAGAAGTTTACTTTTAGAGAG                         GTGATGTGGGCATTCTCCATTTATTTGGAAGCTGTCGCGATATTTCCACAA
genomic: CTTGTCTTCTTCTGGCTCTCCTCATTAATGAGAAGTTTACTTTTAGAGAGgtcagtgttt ... tccggagcagGTGATGTGGGCATTCTCCATTTATTTGGAAGCTGTCGCGATATTTCCACAA

EST: gi|211009468|gb|FL312897.1|FL312897

EST:     CTTGTCTTCTTCTGGCTCTCCTCATTAATGAGAAGTTTACTTTTAGAGAG                         GTGATGTGGGCATTCTCCATTTATTTGGAAGCTGTCGCGATATTTCCCACA
genomic: CTTGTCTTCTTCTGGCTCTCCTCATTAATGAGAAGTTTACTTTTAGAGAGgtcagtgttt ... tccggagcagGTGATGTGGGCATTCTCCATTTATTTGGAAGCTGTCGCGATATTTCC-ACA

EST: gi|78117677|gb|DV536064.1|DV536064

EST:     CTTGTCTTCTTCTGGCTCTCCTCATTAATGAGAAGTTTACTTTTAGAGAG                         GTGATGTGGGCATTCTCCATTTATTTGGAAGCTGTCGCGATATTTCCACAA
genomic: CTTGTCTTCTTCTGGCTCTCCTCATTAATGAGAAGTTTACTTTTAGAGAGgtcagtgttt ... tccggagcagGTGATGTGGGCATTCTCCATTTATTTGGAAGCTGTCGCGATATTTCCACAA

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), 47 (downstream exon)
Score: 77

GACATATGACAAGGATCATGACACCTTTCGCCATTACGTTTTAGTGTTGCCTTGTCTTCTTCTGGCTCTCCTCATTAATGAGAAGTTTACTTTTAGAGAGgtcagtgttt ... tccggagcagGTGATGTGGGCATTCTCCATTTATTTGGAAGCTGTCGCGATATTTCCACAACTTGTGTTGCTACAGCGGACAAGGAATATTGACAACCTGACTGGCCAAT

Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 80

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 114

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

atgc intronic sequence ATGC exonic sequence

Intronic sequence truncated to 55 bases.

aatttcacgtctgaaattgtgcagttctgatcgcttttgtcattttccggagcagGTGATGTGGGCATTCTCCATTTATTTGGAAGCTGTCGCGATATTTCCACAACTTGTGTTGCTACAGCGGACAAGGAATATTGACAACCTGACTGGCCAAT

                        ttctgat  putative branch site (score: 174)
                                 cttttgtcattttcc  putative PPT
           tgaaatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
accaggagcaagcccctcctgattagtatataataatcttgtgggaatttcacgtctgaaattgtgcagttctgatcgcttttgtcattttccggagcagGTGATGTGGGCATTCTCCATTTATTTGGAAGCTGTCGCGATATTTCCACAACTTGTGTTGCTACAGCGGACAAGGAATATTGACAACCTGACTGGCCAAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAA
- caggagc
- - - - - - - cctcctg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgtgcag