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

...taaacacaaaacttctccaacctaagatgctgcccatatggaatcaacacgaaattatgttttcttggtgaaatcttatctttaatctgtttggtcacagCTGCTTGGCAGAGTATTCAACATTTTGCGTGAGAACAACCCGGATCTTGCTGGTGATAGAAGAAGAACTGTTATGAGGCCCCCTCAAGTCCTCAGGGAAG

Basic information

species	Zea mays
transcript	GRMZM2G056462_T01
intron #	5
splice site	3'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G056462_T01 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os03g21550.1 (Oryza sativa), 3'ss of exon 6

-taaacacaaaact--tctccaacctaagatgctgcccatatggaatcaacacgaaattatgttt-tcttggtgaaatcttatctttaatctgtttggtcacagCTGCTTGGCAGAGTATTCAACATTTTGCGTGAGAACAACCCGGATCTTGCTGGTGATAGAAGAAGAACTGTTATGAGGCCCCCTCAAGTCCTCAGGGAAG
 |  | |    | |  | ||  |  ||     | || ||  |  ||  |  |   |||| ||||| | ||  ||||  |||    | ||||| |||||| ||||||||||||||||||||| || ||  |||||||||| || || |||||||||||||||||| ||||||||||||||||||| |||||||| || |||||||
attgatatggtattagtatctcatgtagtgctcagctcagcttcaactagtattcaattgtgtttctgttaatgaaccctt----tcaatctatttggtgacagCTGCTTGGCAGAGTATTTAATATCCTGCGTGAGAATAATCCTGATCTTGCTGGTGATAGACGAAGAACTGTTATGAGGCCTCCTCAAGTTCTTAGGGAAG

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|76291710|gb|DV031278.1|DV031278

EST:     CCACCAGATACCCTTGGGAAGGAACTGACAGAGATTATAAGTATGAAGAG                         CTGCTTGGCAGAGTATTCAACATTTTGCGTGAGAACAACCCGGATCTTGCT
genomic: CCACCAGATACCCTTGGGAAGGAACTGACAGAGATTATAAGTATGAAGAGgtacttgata ... ttggtcacagCTGCTTGGCAGAGTATTCAACATTTTGCGTGAGAACAACCCGGATCTTGCT

EST: gi|71417947|gb|DR804264.1|DR804264

EST:     CCCCCAGATACCCTTGGGAAGGAACTGACAGAGATTATAAGTATGAAGAG                         CTGCTTGGCAGAGTATTCAACATTTTGCGTGAGAACAACCCCGGATCTTTG
genomic: CCACCAGATACCCTTGGGAAGGAACTGACAGAGATTATAAGTATGAAGAGgtacttgata ... ttggtcacagCTGCTTGGCAGAGTATTCAACATTTTGCGTGAGAACAA-CCCGGATC-TTG

EST: gi|211142063|gb|FL081585.1|FL081585

EST:     CCACCAGATACCCTTGGGAAGGAACTGACAGAGATTATAAGTATGAAGAG                         CTGCTTGGCAGAGTATTCAACATTTTGCGTGAGAACAACCCGGATCTTGCT
genomic: CCACCAGATACCCTTGGGAAGGAACTGACAGAGATTATAAGTATGAAGAGgtacttgata ... ttggtcacagCTGCTTGGCAGAGTATTCAACATTTTGCGTGAGAACAACCCGGATCTTGCT

EST: gi|211142066|gb|FL081588.1|FL081588

EST:     CCACCAGATACCCTTGGGAAGGAACTGACAGAGATTATAAGTATGAAGAG                         CTGCTTGGCAGAGTATTCAACATTTTGCGTGAGAACAACCCAGATCTTGCT
genomic: CCACCAGATACCCTTGGGAAGGAACTGACAGAGATTATAAGTATGAAGAGgtacttgata ... ttggtcacagCTGCTTGGCAGAGTATTCAACATTTTGCGTGAGAACAACCCGGATCTTGCT

EST: gi|60349693|gb|DN216666.1|DN216666

EST:     CCACCAGATACCCTTGGGAAGGAACTGACAGAGATTATAAGTATGAAGAG                         CTGCTTGGCAGAGTATTCAACATTTTGCGTGAGAACAACCCGGATCTTGCT
genomic: CCACCAGATACCCTTGGGAAGGAACTGACAGAGATTATAAGTATGAAGAGgtacttgata ... ttggtcacagCTGCTTGGCAGAGTATTCAACATTTTGCGTGAGAACAACCCGGATCTTGCT

EST: gi|29577103|gb|CB617215.1|CB617215

EST:     TAAGTATGAAGAG                         CTGCTTGGCAGAGTATTCAACATTTTGCGTGAGAACAACCCGGATCTTGCT
genomic: TAAGTATGAAGAGgtacttgata ... ttggtcacagCTGCTTGGCAGAGTATTCAACATTTTGCGTGAGAACAACCCGGATCTTGCT

EST: gi|29947496|gb|CB816686.1|CB816686

EST:     CCACCAGATACCCTTGGGAAGGAACTGACAGAGATTATAAGTATGAAGAG                         CTGCTTGGCAGAGTATTCAACATTTTGCGTGAGAACAACCCGGATCTTGCT
genomic: CCACCAGATACCCTTGGGAAGGAACTGACAGAGATTATAAGTATGAAGAGgtacttgata ... ttggtcacagCTGCTTGGCAGAGTATTCAACATTTTGCGTGAGAACAACCCGGATCTTGCT

EST: gi|60338551|gb|DN205524.1|DN205524

EST:     CTTGGGAAGGAACTGACAGGAGATTATAAGTATGAAGAG                         CTGCTTGGCAGAGTATTCAACATTTTGCGTGAGAACAACCCGGATCTTGCT
genomic: CTTGGGAAGGAACTGACA-GAGATTATAAGTATGAAGAGgtacttgata ... ttggtcacagCTGCTTGGCAGAGTATTCAACATTTTGCGTGAGAACAACCCGGATCTTGCT

EST: gi|32856569|gb|CD996250.1|CD996250

EST:     CCAGCAGATACCCTTGGGAAGGAACTGACAGAGATTATAAGTATGAAGAG                         CTGCTTGGCAGAGTATTCAACATTT
genomic: CCACCAGATACCCTTGGGAAGGAACTGACAGAGATTATAAGTATGAAGAGgtacttgata ... ttggtcacagCTGCTTGGCAGAGTATTCAACATTT

EST: gi|29947331|gb|CB816599.1|CB816599

EST:     AAGGAACTGACAGAGATTATAAGTATGAAGAG                         CTGCTTGGCAGAGTATTCAACATTTTGCGTGAGAACANCCCGGATCTTGCT
genomic: AAGGAACTGACAGAGATTATAAGTATGAAGAGgtacttgata ... ttggtcacagCTGCTTGGCAGAGTATTCAACATTTTGCGTGAGAACAACCCGGATCTTGCT

EST: gi|30031975|gb|CB833826.1|CB833826

EST:     CCACCAGATACCCTTGGGAAGGAACTGACAGAGATTATAAGTATGAAGAG                         CTGCTTGGCAGAGTATTCAACATTTTGCGTGAGAACAACCCGGATCTTGCT
genomic: CCACCAGATACCCTTGGGAAGGAACTGACAGAGATTATAAGTATGAAGAGgtacttgata ... ttggtcacagCTGCTTGGCAGAGTATTCAACATTTTGCGTGAGAACAACCCGGATCTTGCT

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: 48 (upstream exon), 49 (downstream exon)
Score: 232

AGTTAGAGAGGATGAAGAAGGAGAAGGGATTGTGCTCGCTGGTGCCGCTGCCACCAGATACCCTTGGGAAGGAACTGACAGAGATTATAAGTATGAAGAGgtacttgata ... ttggtcacagCTGCTTGGCAGAGTATTCAACATTTTGCGTGAGAACAACCCGGATCTTGCTGGTGATAGAAGAAGAACTGTTATGAGGCCCCCTCAAGTCCTCAGGGAAG

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 259

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 205

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 159

atgc intronic sequence ATGC exonic sequence

Intronic sequence truncated to 55 bases.

aacacgaaattatgttttcttggtgaaatcttatctttaatctgtttggtcacagCTGCTTGGCAGAGTATTCAACATTTTGCGTGAGAACAACCCGGATCTTGCTGGTGATAGAAGAAGAACTGTTATGAGGCCCCCTCAAGTCCTCAGGGAAG

                                  ctttaat  putative branch site (score: 159)
                                        tctgttt  CT-rich tract
                         aaatcttatctttaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
taaacacaaaacttctccaacctaagatgctgcccatatggaatcaacacgaaattatgttttcttggtgaaatcttatctttaatctgtttggtcacagCTGCTTGGCAGAGTATTCAACATTTTGCGTGAGAACAACCCGGATCTTGCTGGTGATAGAAGAAGAACTGTTATGAGGCCCCCTCAAGTCCTCAGGGAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC
-aaacaca
- - - - - - - - ccaacct
- - - - - - - - - - - - -gatgctg
- - - - - - - - - - - - - - - - -ccatatg
- - - - - - - - - - - - - - - - - - - - - atcaaca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tttcttg