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

...tcaaggttttgttggtcatcacattggttatataattccatgagatcaagcgccttttggaaataactttgtccttccatttttgttcccctgtttgcagGATAACATTCCTCGTCGCAGAAGCTTGTCTCATAGGAGGATCGGTGAGGAATGCAAAGCACACCAAGTATTTAGGCTACTACATGAAGCATGATTTGGTG

Basic information

species	Zea mays
transcript	GRMZM2G360615_T01
intron #	2
splice site	3'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G360615_T01 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os08g16130.1 (Oryza sativa), 3'ss of exon 2

tcaaggttttgttgg----tcatcacattggttatataattccatgagatcaagcgccttttggaaataactttgtccttccatttttg-ttcccctgtttgcagGATAACATTCCTCGTCGCAGAAGCTTGTCTCATAGGAGGATCGGTGAGGAATGCAAAGCACACCAAGTATTTAGGCTACTACATGAAGCATGATTTGGTG
    | ||| | |||    |||     ||  || |   |  |  ||  ||  ||   | | || | ||  |||  || |    |  | | ||  | |||| ||||||||||||| |||  ||||||||| || || || || ||||| |||||||||||  | |||||||||||| | || ||||||||||||||||| ||||| 
---cgatttagctggcatttcaaggttttcattgtgataaccattggcatttag-atcatctgaacatcccttc-tcataatgtcctggcttttcttgttcgcagGATAACATTTCTCACCGCAGAAGCCTGCCTTATTGGTGGATCTGTGAGGAATGCGTACCACACCAAGTATCTTGGTTACTACATGAAGCATGACTTGGTC

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|74244611|gb|DT652525.1|DT652525

EST:     CCCGTGCTCTCCTCCCGCGGCTGTGCCGTAACGGCATTCGTCCTCTCCTG                         GATAACATTCCTCGTCGCAGAAGCTTGTCTCATAGGAGGATCGGTGAGGAA
genomic: CCCGTGCTCTCCTCCCGCGGCTGTGCCGTAACGGCATTCGTCCTCTCCTGgtgcgtcgtg ... ctgtttgcagGATAACATTCCTCGTCGCAGAAGCTTGTCTCATAGGAGGATCGGTGAGGAA

EST: gi|26457228|gb|CA828811.1|CA828811

EST:     CCCGTGCTCTCCTCCCGCGGCTGTGCCGTAACGGCATTCGTCCTCTCCTG                         GATAACATTCCTCGTCGCAGAAGCTTGTCTCATAGGAGGATCGGTGAGGAA
genomic: CCCGTGCTCTCCTCCCGCGGCTGTGCCGTAACGGCATTCGTCCTCTCCTGgtgcgtcgtg ... ctgtttgcagGATAACATTCCTCGTCGCAGAAGCTTGTCTCATAGGAGGATCGGTGAGGAA

EST: gi|211189796|gb|FL061814.1|FL061814

EST:     CCCGTGCTCTCCTCCCGCGGCTGTGCCGTAACGGCATTCGTCCTCTCCTG                         GATAACATTCCTCGTCGCAGAAGCTTGTCTCATAGGAGGATCGGTGAGGAA
genomic: CCCGTGCTCTCCTCCCGCGGCTGTGCCGTAACGGCATTCGTCCTCTCCTGgtgcgtcgtg ... ctgtttgcagGATAACATTCCTCGTCGCAGAAGCTTGTCTCATAGGAGGATCGGTGAGGAA

EST: gi|21809527|gb|BQ667845.1|BQ667845

EST:     CCCGTGCTCTCCTCCCGCGGCTGTGCCGTAACGGCATTCGTCCTCTCCTG                         GATAACATTCCTCGTCGCAGAAGCTTGTCTCATAGGAGGATCGGTGAGGAA
genomic: CCCGTGCTCTCCTCCCGCGGCTGTGCCGTAACGGCATTCGTCCTCTCCTGgtgcgtcgtg ... ctgtttgcagGATAACATTCCTCGTCGCAGAAGCTTGTCTCATAGGAGGATCGGTGAGGAA

EST: gi|91050107|gb|EB160525.1|EB160525

EST:     CCCGTGCTCTCCTCCCGCGGCTGTGCCGTAACGGCATTCGTCCTCTCCTG                         GATAACATTCCTCGTCGCAGAAGCTTGTCTCATAGGAGGATCGGTGAGGAA
genomic: CCCGTGCTCTCCTCCCGCGGCTGTGCCGTAACGGCATTCGTCCTCTCCTGgtgcgtcgtg ... ctgtttgcagGATAACATTCCTCGTCGCAGAAGCTTGTCTCATAGGAGGATCGGTGAGGAA

EST: gi|211187401|gb|FL061802.1|FL061802

EST:     CCCGTGCTCTCCTCCCGCGGCTGTGCCGTAACGGCATTCGTCCTCTCCTG                         GATAACATTCCTCGTCGCAGAAGCTTGTCTCATAGGA---TCGGTGAGGAA
genomic: CCCGTGCTCTCCTCCCGCGGCTGTGCCGTAACGGCATTCGTCCTCTCCTGgtgcgtcgtg ... ctgtttgcagGATAACATTCCTCGTCGCAGAAGCTTGTCTCATAGGAGGATCGGTGAGGAA

EST: gi|21390150|gb|BQ528199.1|BQ528199

EST:     CCCGTGCTCTCCTCCCGCGGCTGTGCCGTAACGGCATTCGTCCTCTCCTG                         GATAACATTCCTCGTCGCAGAAGCTTGTCT
genomic: CCCGTGCTCTCCTCCCGCGGCTGTGCCGTAACGGCATTCGTCCTCTCCTGgtgcgtcgtg ... ctgtttgcagGATAACATTCCTCGTCGCAGAAGCTTGTCT

EST: gi|78543510|gb|DV621008.1|DV621008

EST:     CCCGTGCTCTCCTCCCGCGGCTGTGCCGTAACGGCATTCGTCCTCTCCTG                         GATAACATTCCTCGTCGCAGAAGCTTGTCTCATAGGAGGATCGGTGAGGAA
genomic: CCCGTGCTCTCCTCCCGCGGCTGTGCCGTAACGGCATTCGTCCTCTCCTGgtgcgtcgtg ... ctgtttgcagGATAACATTCCTCGTCGCAGAAGCTTGTCTCATAGGAGGATCGGTGAGGAA

EST: gi|211192202|gb|FL061828.1|FL061828

EST:     CCGTGCTCTCCTCCCGCGGCTGTGCCGTAACGGCATTTCGTCCTCTC-TG                         GATAACATCCCTCGTCGCAGAAGCTTGTCTCATNAGGAG-ATCGGTGANGA
genomic: CCGTGCTCTCCTCCCGCGGCTGTGCCGTAACGGCATT-CGTCCTCTCCTGgtgcgtcgtg ... ctgtttgcagGATAACATTCCTCGTCGCAGAAGCTTGTCTCAT-AGGAGGATCGGTGAGGA

EST: gi|211192206|gb|FL061832.1|FL061832

EST:     CCCGTGCTCTCCTCCCGCGGCTGTGCCGTAACGGCATTCGTCCTCTCCTG                         GATAACATTCCTCGTCGCAGAAGCTTGTCTCATAGGAGGATCGGTGAGGAA
genomic: CCCGTGCTCTCCTCCCGCGGCTGTGCCGTAACGGCATTCGTCCTCTCCTGgtgcgtcgtg ... ctgtttgcagGATAACATTCCTCGTCGCAGAAGCTTGTCTCATAGGAGGATCGGTGAGGAA

EST: gi|78074187|gb|DV502621.1|DV502621

EST:     CCCGTGCTCTCCTCCCGCGGCTGTGCCGTAACGGCATTCGTCCTCTCCTG                         GATAACATTCCTCGTCGCAGAAGCTTGTCTCATAGGAGGATCGGTGAGGAA
genomic: CCCGTGCTCTCCTCCCGCGGCTGTGCCGTAACGGCATTCGTCCTCTCCTGgtgcgtcgtg ... ctgtttgcagGATAACATTCCTCGTCGCAGAAGCTTGTCTCATAGGAGGATCGGTGAGGAA

EST: gi|101399381|gb|EB821563.1|EB821563

EST:     CCCGTGCTCTCCTCCCGCGGCTGTGCCGTAACGGCATTCGTCCTCTCCTG                         GATAACATTCCTCGTCGCAGAAGCTTGTCTCATAGGAGGATCGGTGAGGAA
genomic: CCCGTGCTCTCCTCCCGCGGCTGTGCCGTAACGGCATTCGTCCTCTCCTGgtgcgtcgtg ... ctgtttgcagGATAACATTCCTCGTCGCAGAAGCTTGTCTCATAGGAGGATCGGTGAGGAA

EST: gi|78074188|gb|DV502622.1|DV502622

EST:     CCCGTGCTCTCCTCCCGCGGCTGTGCCGTAACGGCATTCGTCCTCTCCTG                         GATAACATTCCTCGTCGCAGAAGCTTGTCTCATAGGAGGATCGGTGAGGAA
genomic: CCCGTGCTCTCCTCCCGCGGCTGTGCCGTAACGGCATTCGTCCTCTCCTGgtgcgtcgtg ... ctgtttgcagGATAACATTCCTCGTCGCAGAAGCTTGTCTCATAGGAGGATCGGTGAGGAA

EST: gi|21809526|gb|BQ667844.1|BQ667844

EST:     GCATTCGTCCTCTCCTG                         GATAACATTCCTCGTCGCAGAAGCTTGTCTCATAGGAGGATCGGTGAGGAA
genomic: GCATTCGTCCTCTCCTGgtgcgtcgtg ... ctgtttgcagGATAACATTCCTCGTCGCAGAAGCTTGTCTCATAGGAGGATCGGTGAGGAA

EST: gi|71443007|gb|DR824057.1|DR824057

EST:     CCCGTGCTCTCCTCCCGCGGCTGTGCCGCAACGGCATTCGTCCTCTCCTG                         GATAACATTCCTCGTCGCAGAAGCTTGTCTCATAGGAGGATTCGGTGAGGA
genomic: CCCGTGCTCTCCTCCCGCGGCTGTGCCGTAACGGCATTCGTCCTCTCCTGgtgcgtcgtg ... ctgtttgcagGATAACATTCCTCGTCGCAGAAGCTTGTCTCATAGGAGGAT-CGGTGAGGA

EST: gi|211189802|gb|FL061820.1|FL061820

EST:     CCCGTGCTCTCCTCCCGCGGCTGTGCCGTAACGGCATTCGTCCTCTCCTG                         GATAACATTCCTCGTCGCAGAAGCTTGTCTCATAGGAGGATCGGTGAGGAA
genomic: CCCGTGCTCTCCTCCCGCGGCTGTGCCGTAACGGCATTCGTCCTCTCCTGgtgcgtcgtg ... ctgtttgcagGATAACATTCCTCGTCGCAGAAGCTTGTCTCATAGGAGGATCGGTGAGGAA

EST: gi|211192205|gb|FL061831.1|FL061831

EST:     CCCGTGCTCTCCTCCCGCGGCTGTGCCGTAACGGCATTCGTCCTCTCCTG                         CACAACATTCCTCGTCGCAGAAGCTTGTCTCATAGGAGGATCGGTGAGGAA
genomic: CCCGTGCTCTCCTCCCGCGGCTGTGCCGTAACGGCATTCGTCCTCTCCTGgtgcgtcgtg ... ctgtttgcagGATAACATTCCTCGTCGCAGAAGCTTGTCTCATAGGAGGATCGGTGAGGAA

EST: gi|93282764|gb|EB675028.1|EB675028

EST:     CCCGTGCTCTCCTCCCGCGGCTGTGCCGTAACGGCATTCGTCCTCTCCTG                         GATAACATTCCTCGTCGCAGAAGCTTGTCTCATAGGAGGATCGGTGAGGAA
genomic: CCCGTGCTCTCCTCCCGCGGCTGTGCCGTAACGGCATTCGTCCTCTCCTGgtgcgtcgtg ... ctgtttgcagGATAACATTCCTCGTCGCAGAAGCTTGTCTCATAGGAGGATCGGTGAGGAA

EST: gi|211192208|gb|FL061834.1|FL061834

EST:     CCCGTGCTCTCCTCCCGCGGCTGTGCCGTAACGGCATTCGTCCTCTCCTG                         GATAACATTCCTCGTCGCAGAAGCTTGTCTC
genomic: CCCGTGCTCTCCTCCCGCGGCTGTGCCGTAACGGCATTCGTCCTCTCCTGgtgcgtcgtg ... ctgtttgcagGATAACATTCCTCGTCGCAGAAGCTTGTCTC

EST: gi|22521036|gb|BU079847.1|BU079847

EST:     CCCGTGCTCTCCTCCCGCGGCTGTGCCGTAACGGCATTCGTCCTCTCCTG                         GATAACATTCCTCGTCGCAGAAGCTTGTCTCATAGGAGGATCGGTGAGGAA
genomic: CCCGTGCTCTCCTCCCGCGGCTGTGCCGTAACGGCATTCGTCCTCTCCTGgtgcgtcgtg ... ctgtttgcagGATAACATTCCTCGTCGCAGAAGCTTGTCTCATAGGAGGATCGGTGAGGAA

EST: gi|211189803|gb|FL061821.1|FL061821

EST:     CCCGTGCTCTCCTCCCGCGGCTGTGCCGTAACGGCATTCGTCCTCTCCTG                         GATAACATTCCTCGTCGCAGAAGCTTGTCTCATAGGAGGATCGGTGAGGAA
genomic: CCCGTGCTCTCCTCCCGCGGCTGTGCCGTAACGGCATTCGTCCTCTCCTGgtgcgtcgtg ... ctgtttgcagGATAACATTCCTCGTCGCAGAAGCTTGTCTCATAGGAGGATCGGTGAGGAA

EST: gi|211187409|gb|FL061810.1|FL061810

EST:     CCCGTGCTCTCCTCCCGCGGCTGTGCCGTAACGGCATTCGTCCTCTCCTG                         GATAACATTCCTCGTCGCAGAAGCTTGTCTCATAGGAGGATCGGTGAGGAA
genomic: CCCGTGCTCTCCTCCCGCGGCTGTGCCGTAACGGCATTCGTCCTCTCCTGgtgcgtcgtg ... ctgtttgcagGATAACATTCCTCGTCGCAGAAGCTTGTCTCATAGGAGGATCGGTGAGGAA

EST: gi|60358833|gb|DN225806.1|DN225806

EST:     CCCGTGCTCTCCTCCCGCGGCTGTGCCGTAACGGCATTCGTCCTCTCCTG                         GATAACATTCCTCGTCGCAGAAGCTTGTCTCATAGGAGGATCGGTGAGGAA
genomic: CCCGTGCTCTCCTCCCGCGGCTGTGCCGTAACGGCATTCGTCCTCTCCTGgtgcgtcgtg ... ctgtttgcagGATAACATTCCTCGTCGCAGAAGCTTGTCTCATAGGAGGATCGGTGAGGAA

EST: gi|211189801|gb|FL061819.1|FL061819

EST:     CCCGTGCTCTCCTCCCGCGGCTGTGCCGTAACGGCATTCGTCCTCTCCTG                         GATAACATTCCTCGTCGCARAAGCTTGTCTCATAGGAGGATCGGTGAGGAA
genomic: CCCGTGCTCTCCTCCCGCGGCTGTGCCGTAACGGCATTCGTCCTCTCCTGgtgcgtcgtg ... ctgtttgcagGATAACATTCCTCGTCGCAGAAGCTTGTCTCATAGGAGGATCGGTGAGGAA

EST: gi|18661270|gb|BM501322.1|BM501322

EST:     CCCGTGCTCTCCTCCCGCGGCTGTGCCGTAACGGCATTCGTCCTCTCCTG                         GATAACATTCCTCGTCGCAGAAGCTTGTCTCATANGAGGATCGGTGAAGAA
genomic: CCCGTGCTCTCCTCCCGCGGCTGTGCCGTAACGGCATTCGTCCTCTCCTGgtgcgtcgtg ... ctgtttgcagGATAACATTCCTCGTCGCAGAAGCTTGTCTCATAGGAGGATCGGTGAGGAA

EST: gi|211189797|gb|FL061815.1|FL061815

EST:     CCCGTGCTCTCCTCCCGCGGCTGTGCCGTAACGGCATTCGTCCTCTCCTG                         GATAACATTCCTCGTCGCAGAAGC
genomic: CCCGTGCTCTCCTCCCGCGGCTGTGCCGTAACGGCATTCGTCCTCTCCTGgtgcgtcgtg ... ctgtttgcagGATAACATTCCTCGTCGCAGAAGC

EST: gi|71443008|gb|DR824058.1|DR824058

EST:     CCCGTGCTCTCCTCCCGCGGCTGTGCCGTAACGGCATTCGTCCTCTCCTG                         GATAACATTCCTCGTCGCAGAAGCTTGTCTCATAGGAGGATCGGTGAGGAA
genomic: CCCGTGCTCTCCTCCCGCGGCTGTGCCGTAACGGCATTCGTCCTCTCCTGgtgcgtcgtg ... ctgtttgcagGATAACATTCCTCGTCGCAGAAGCTTGTCTCATAGGAGGATCGGTGAGGAA

EST: gi|74239152|gb|DT647066.1|DT647066

EST:     CCCGTGCTCTCCTCCCGCGGCTGTGCCGTAACGGCATTCGTCCTCTCCTG                         GATAACATTCCTCGTCGCAGAAGCTTGTCTCATAGGAGGATCGGTGAGGAA
genomic: CCCGTGCTCTCCTCCCGCGGCTGTGCCGTAACGGCATTCGTCCTCTCCTGgtgcgtcgtg ... ctgtttgcagGATAACATTCCTCGTCGCAGAAGCTTGTCTCATAGGAGGATCGGTGAGGAA

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: 141

TGCTCCAGCAGGCCATTGTCAACGTCGCCACGTGGTGCCTCTGCTTCGGACCCGTGCTCTCCTCCCGCGGCTGTGCCGTAACGGCATTCGTCCTCTCCTGgtgcgtcgtg ... ctgtttgcagGATAACATTCCTCGTCGCAGAAGCTTGTCTCATAGGAGGATCGGTGAGGAATGCAAAGCACACCAAGTATTTAGGCTACTACATGAAGCATGATTTGGTG

Block sizes: 49 (upstream exon), 39 (downstream exon)
Score: 12

Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 29

Block sizes: 49 (upstream exon), 46 (downstream exon)
Score: 17

atgc intronic sequence ATGC exonic sequence

Intronic sequence truncated to 55 bases.

tcaagcgccttttggaaataactttgtccttccatttttgttcccctgtttgcagGATAACATTCCTCGTCGCAGAAGCTTGTCTCATAGGAGGATCGGTGAGGAATGCAAAGCACACCAAGTATTTAGGCTACTACATGAAGCATGATTTGGTG

               aaataac  putative branch site (score: 17)
                     ctttgtccttccattt  CT-rich tract
               aaataacttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tcaaggttttgttggtcatcacattggttatataattccatgagatcaagcgccttttggaaataactttgtccttccatttttgttcccctgtttgcagGATAACATTCCTCGTCGCAGAAGCTTGTCTCATAGGAGGATCGGTGAGGAATGCAAAGCACACCAAGTATTTAGGCTACTACATGAAGCATGATTTGGTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGC
- - - - -tgttggt
- - - - - - - - - - - - - - - - - -ttccatg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - ggaaataa