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

...atgaatccaaactttcatttttatttttttacattgtgtattacctatttacctgtatctcttatgtaatcatggaacatttttttttctcaaatggcagGCATGGCAATGTATGCCTGACAGGGCATTCTCTTGGAATATACTGTCACTGTTTACAAAATCAGGAATGTTATTCTTGGAAGTGAGTCTCATAGCCTTTC

Basic information

species	Zea mays
transcript	GRMZM2G086497_T01
intron #	2
splice site	3'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G086497_T01 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os03g54920.1 (Oryza sativa), 3'ss of exon 1

---atgaatccaaactttcatttttatttttttacattgtgtattacctatttacctgtatctcttatgtaatcatgg-aacatttttttttctcaaatggcagGCATGGCAATGTATGCCTGACAGGGCATTCTCTTGGAATATACTGTCACTGTTTACAAAATCAGGAATGTTATTCTTGGAAGTGAGTCTCATAGCCTTTC
      | |    || |  ||||| ||| | | | ||  |  | ||| ||||    | | ||||||||      ||   | | ||||| |||||    |||||||| ||||||||||||||||| ||||| ||||| |||||| | ||||| |||||||| |||||||| ||||||||||||||||| ||||||||||| ||||
caagcaagttttgacct--attttaattctatcatatgctacactacatattg--ttatttctcttattcttgtataacagcctttttatttctttgttggcagGCGTGGCAATGTATGCCTGATAGGGCGTTCTCATGGAATGTGCTGTCTCTGTTTACCAAATCAGGGATGTTATTCTTGGAAGTTAGTCTCATAGCATTTC

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|71306896|gb|DR789603.1|DR789603

EST:     CGCTCCTCTGGGCCGTCGCCGTACTCAACCTCCTCTGGTGCTTCCTGCAG                         GCATGGCAATGTATGCCTGACAGGGCATTCTCTTGGAATATACTGTCACTG
genomic: CGCTCCTCTGGGCCGTCGCCGTACTCAACCTCCTCTGGTGCTTCCTGCAGgtgcggattg ... caaatggcagGCATGGCAATGTATGCCTGACAGGGCATTCTCTTGGAATATACTGTCACTG

EST: gi|211461764|gb|FL185824.1|FL185824

EST:     CGCTCCTCTGGGCCGTCGCCGTACTCAACCTCCTCTGGTGCTTCCTGCAG                         GCATGGCAATGTATGCCTGACAGGGCATTCTCTTGGAATATACTGTCACTG
genomic: CGCTCCTCTGGGCCGTCGCCGTACTCAACCTCCTCTGGTGCTTCCTGCAGgtgcggattg ... caaatggcagGCATGGCAATGTATGCCTGACAGGGCATTCTCTTGGAATATACTGTCACTG

EST: gi|211464287|gb|FL185836.1|FL185836

EST:     CGCTCCTCTGGGCCGTCGCCGTACTCAACCTCCTCTGGTGCTTCCTGCAG                         GCATGGCAATGTATGCCTGACAGGGCATTCTCTTGGAATATACTGTCACTG
genomic: CGCTCCTCTGGGCCGTCGCCGTACTCAACCTCCTCTGGTGCTTCCTGCAGgtgcggattg ... caaatggcagGCATGGCAATGTATGCCTGACAGGGCATTCTCTTGGAATATACTGTCACTG

EST: gi|93014938|gb|EB640458.1|EB640458

EST:     CGCTCCTCTGGGCCGTCGCCGTACTCAACCTCCTCTGGTGCTTCCTGCAG                         GCATGGCAATGTATGCCTGACAGGGCATTCTCTTGGAATATACTGTCACTG
genomic: CGCTCCTCTGGGCCGTCGCCGTACTCAACCTCCTCTGGTGCTTCCTGCAGgtgcggattg ... caaatggcagGCATGGCAATGTATGCCTGACAGGGCATTCTCTTGGAATATACTGTCACTG

EST: gi|76935254|gb|DV174267.1|DV174267

EST:     CGCTCCTCTGGGCCGTCGCCGTACTCAACCTCCTCTGGTGCTTCCTGCAG                         GCATGGCAATGTATGCCTGACAGGGCATTCTCTTGGAATATACTGTCACTG
genomic: CGCTCCTCTGGGCCGTCGCCGTACTCAACCTCCTCTGGTGCTTCCTGCAGgtgcggattg ... caaatggcagGCATGGCAATGTATGCCTGACAGGGCATTCTCTTGGAATATACTGTCACTG

EST: gi|149004864|gb|EE039372.2|EE039372

EST:     CGCTCCTCTGGGCCGTCGCCGTACTCAACCTCCTCTGGTGCTTCCTGCAG                         GCATGGCAATGTATGCCTGACAGGGCATTCTCTTGGAATATACTGTCACTG
genomic: CGCTCCTCTGGGCCGTCGCCGTACTCAACCTCCTCTGGTGCTTCCTGCAGgtgcggattg ... caaatggcagGCATGGCAATGTATGCCTGACAGGGCATTCTCTTGGAATATACTGTCACTG

EST: gi|211464298|gb|FL185847.1|FL185847

EST:     CGCTCCTCTGGGCCGTCGCCGTACTCAACCTCCTCTGGTGCTTCCTGCAG                         GCATGGCAATGTATGCCTGACAGAGCATTCTCTTGGAATGTACTGTCACTG
genomic: CGCTCCTCTGGGCCGTCGCCGTACTCAACCTCCTCTGGTGCTTCCTGCAGgtgcggattg ... caaatggcagGCATGGCAATGTATGCCTGACAGGGCATTCTCTTGGAATATACTGTCACTG

EST: gi|32928610|gb|CF033422.1|CF033422

EST:     CCTCCTCTGGTGCTTCCTGCAG                         GCATGGCAATGTATGCCTGACAGGGCATTCTCTTGGAATATACTGTCACTG
genomic: CCTCCTCTGGTGCTTCCTGCAGgtgcggattg ... caaatggcagGCATGGCAATGTATGCCTGACAGGGCATTCTCTTGGAATATACTGTCACTG

EST: gi|91051591|gb|EB162009.1|EB162009

EST:     CGCTCCTCTGGGCCGTCGCCGTACTCAACCTCCTCTGGTGCTTCCTGCAG                         GCATGGCAATGTATGCCTGACAGGGCATTCTCTTGGAATATACTGTCACTG
genomic: CGCTCCTCTGGGCCGTCGCCGTACTCAACCTCCTCTGGTGCTTCCTGCAGgtgcggattg ... caaatggcagGCATGGCAATGTATGCCTGACAGGGCATTCTCTTGGAATATACTGTCACTG

EST: gi|211464291|gb|FL185840.1|FL185840

EST:     CGCTCCTCTGGGCCGTCGCCGTACTCAACCTCCTCTGGTGCTTCCTGCAG                         GCATGGCAATGTATGCCTGACAGAGCATTCTCTTGGAATGTACTGTCACTG
genomic: CGCTCCTCTGGGCCGTCGCCGTACTCAACCTCCTCTGGTGCTTCCTGCAGgtgcggattg ... caaatggcagGCATGGCAATGTATGCCTGACAGGGCATTCTCTTGGAATATACTGTCACTG

EST: gi|71315913|gb|DR794644.1|DR794644

EST:     CGCTCCTCTGGGCCGTCGCCGTACTCAACCTCCTCTGGTGCTTCCTGCAG                         GCATGGCAATGTATGCCTGACAGGGCATTCTCTTGGAATATACTGTCACTG
genomic: CGCTCCTCTGGGCCGTCGCCGTACTCAACCTCCTCTGGTGCTTCCTGCAGgtgcggattg ... caaatggcagGCATGGCAATGTATGCCTGACAGGGCATTCTCTTGGAATATACTGTCACTG

EST: gi|211464297|gb|FL185846.1|FL185846

EST:     CGCTCCTCTGGGCCGTCGCCGTACTCAACCTCCTCTGGTGCTTCCTGCAG                         GCATGGCAATGTATGCC
genomic: CGCTCCTCTGGGCCGTCGCCGTACTCAACCTCCTCTGGTGCTTCCTGCAGgtgcggattg ... caaatggcagGCATGGCAATGTATGCC

EST: gi|211459239|gb|FL185809.1|FL185809

EST:     CGCTCCTCTGGGCCGTCGCCGTACTCAACCTCCTCTGGTGCTTCCTGCAG                         GCATGGCAATGTATGCCTGACAGGGCATTCTCTTGGAATATACTGTCACTG
genomic: CGCTCCTCTGGGCCGTCGCCGTACTCAACCTCCTCTGGTGCTTCCTGCAGgtgcggattg ... caaatggcagGCATGGCAATGTATGCCTGACAGGGCATTCTCTTGGAATATACTGTCACTG

EST: gi|211461766|gb|FL185826.1|FL185826

EST:     CGCTCCTCTGGGCCGTCGCCGTACTCAACCTCCTCTGGTGCTTCCTGCAG                         GCATGGCAATGTATGCCTGACAGAGCATTCTCTTGGAATGTACTGTCACTG
genomic: CGCTCCTCTGGGCCGTCGCCGTACTCAACCTCCTCTGGTGCTTCCTGCAGgtgcggattg ... caaatggcagGCATGGCAATGTATGCCTGACAGGGCATTCTCTTGGAATATACTGTCACTG

EST: gi|60355709|gb|DN222682.1|DN222682

EST:     CGCTCCTCTGGGCCGTCGCCGTACTCAACCTCCTCTGGTGCTTCCTGCAG                         GCATGGCAATGTATGCCTGACAGGGCATTCTCTTGGAATATACTGTCACTG
genomic: CGCTCCTCTGGGCCGTCGCCGTACTCAACCTCCTCTGGTGCTTCCTGCAGgtgcggattg ... caaatggcagGCATGGCAATGTATGCCTGACAGGGCATTCTCTTGGAATATACTGTCACTG

EST: gi|211459242|gb|FL185812.1|FL185812

EST:     CGCTCCTCTGGGCCGTCGCCGTACTCAACCTCCTCTGGTGCTTCCTGCAG                         GCATGGCAATGTATGCCTGANAGGGGCATTCTCTTGGGAATATACTGTCAC
genomic: CGCTCCTCTGGGCCGTCGCCGTACTCAACCTCCTCTGGTGCTTCCTGCAGgtgcggattg ... caaatggcagGCATGGCAATGTATGCCTGACAGGG-CATTCTCTTGG-AATATACTGTCAC

EST: gi|211464289|gb|FL185838.1|FL185838

EST:     CGCTCCTCTGGGCCGTCGCCGTACTCAACCTCCTCTGGTGCTTCCTGCAG                         GCATGGCAATGTATGCCTGACAGAGCATTCTCTTGGAATGTACTGTCACTG
genomic: CGCTCCTCTGGGCCGTCGCCGTACTCAACCTCCTCTGGTGCTTCCTGCAGgtgcggattg ... caaatggcagGCATGGCAATGTATGCCTGACAGGGCATTCTCTTGGAATATACTGTCACTG

EST: gi|211464286|gb|FL185835.1|FL185835

EST:     CGCTCCTCTGGGCCGTCGCCGTACTCAACCTCCTCTGGTGCTTCCTGCAG                         GCATGGCAATGTATGCCTGACAGG-CATTCT
genomic: CGCTCCTCTGGGCCGTCGCCGTACTCAACCTCCTCTGGTGCTTCCTGCAGgtgcggattg ... caaatggcagGCATGGCAATGTATGCCTGACAGGGCATTCT

EST: gi|211461759|gb|FL185819.1|FL185819

EST:     CGCTCCTCTGGGCCGTCGCCGTACTCAACCTCCTCTGGTGCTTCCTGCAG                         GCATGGCAATGTATGCCTGACAGGGCATTCTCTTGGAATATACTGTCACTG
genomic: CGCTCCTCTGGGCCGTCGCCGTACTCAACCTCCTCTGGTGCTTCCTGCAGgtgcggattg ... caaatggcagGCATGGCAATGTATGCCTGACAGGGCATTCTCTTGGAATATACTGTCACTG

EST: gi|26456832|gb|CA828415.1|CA828415

EST:     CGCTCCTCTGGGTCGTCGCCGTACTCAACCTCCTCTGGTGCTTCCTGCAG                         GCATGGCAATGTATGCCTGACAGGGCATTCTCTTGGAATATACTGTCACTG
genomic: CGCTCCTCTGGGCCGTCGCCGTACTCAACCTCCTCTGGTGCTTCCTGCAGgtgcggattg ... caaatggcagGCATGGCAATGTATGCCTGACAGGGCATTCTCTTGGAATATACTGTCACTG

EST: gi|149101732|gb|EE187869.2|EE187869

EST:     CGCTCCTCTGGGCCGTCGCCGTACTCAACCTCCTCTGGTGCTTCCTGCAG                         GCATGGCAATGTATGCCTGACAGGGCATTCTCTTGGAATATACTGTCACTG
genomic: CGCTCCTCTGGGCCGTCGCCGTACTCAACCTCCTCTGGTGCTTCCTGCAGgtgcggattg ... caaatggcagGCATGGCAATGTATGCCTGACAGGGCATTCTCTTGGAATATACTGTCACTG

EST: gi|20507680|gb|BQ279727.1|BQ279727

EST:     CGCTCCTCTGGGTCGTCGCCGTACTCAACCTCCTCTGGTGCTTCCTGCAG                         GCATGGCAATGTATGCCTGACAGGGCATTCTCTTGGAATATACTGTCACTG
genomic: CGCTCCTCTGGGCCGTCGCCGTACTCAACCTCCTCTGGTGCTTCCTGCAGgtgcggattg ... caaatggcagGCATGGCAATGTATGCCTGACAGGGCATTCTCTTGGAATATACTGTCACTG

EST: gi|78075810|gb|DV504244.1|DV504244

EST:     CGCTCCTCTGGGCCGTCGCCGTACTCAACCTCCTCTGGTGCTTCCTGCAG                         GCATGGCAATGTATGCCTGACAGGGCATTCTCTTGGAATATACTGTCACTG
genomic: CGCTCCTCTGGGCCGTCGCCGTACTCAACCTCCTCTGGTGCTTCCTGCAGgtgcggattg ... caaatggcagGCATGGCAATGTATGCCTGACAGGGCATTCTCTTGGAATATACTGTCACTG

EST: gi|211461771|gb|FL185831.1|FL185831

EST:     CGCTCCTCTGGGCCGTCGCCGTACTCAACCTCCTCTGGTGCTTCCTGCAG                         GCATGGCAATGTATGCCTGACAGGGCATTCTCTTGGAATATACTGTCACTG
genomic: CGCTCCTCTGGGCCGTCGCCGTACTCAACCTCCTCTGGTGCTTCCTGCAGgtgcggattg ... caaatggcagGCATGGCAATGTATGCCTGACAGGGCATTCTCTTGGAATATACTGTCACTG

EST: gi|91878992|gb|EB408949.1|EB408949

EST:     CGCTCCTCTGGGCCGTCGCCGTACTCAACCTCCTCTGGTGCTTCCTGCAG                         GCATGGCAATGTATGCCTGACAGGGCATTCTCTTGGAATATACTGTCACTG
genomic: CGCTCCTCTGGGCCGTCGCCGTACTCAACCTCCTCTGGTGCTTCCTGCAGgtgcggattg ... caaatggcagGCATGGCAATGTATGCCTGACAGGGCATTCTCTTGGAATATACTGTCACTG

EST: gi|211461768|gb|FL185828.1|FL185828

EST:     CGCTCCTCTGGGCCGTCGCCGTACTCAACCTCCTCTGGTGCTTCCTGCAG                         GCATGGCAATGTATGCCTGACAGGGCATTCTCTTGGAATATACTGTCACTG
genomic: CGCTCCTCTGGGCCGTCGCCGTACTCAACCTCCTCTGGTGCTTCCTGCAGgtgcggattg ... caaatggcagGCATGGCAATGTATGCCTGACAGGGCATTCTCTTGGAATATACTGTCACTG

EST: gi|211459244|gb|FL185814.1|FL185814

EST:     CGCTCCTCTGGGCCGTCGCCGTACTCAACCTCCTCTGGTGCTTCCTGCAG                         GCATGGCAATGTATGCCTGACAGAGCATTCTCTTGGAATGTACTGTCACTG
genomic: CGCTCCTCTGGGCCGTCGCCGTACTCAACCTCCTCTGGTGCTTCCTGCAGgtgcggattg ... caaatggcagGCATGGCAATGTATGCCTGACAGGGCATTCTCTTGGAATATACTGTCACTG

EST: gi|211459240|gb|FL185810.1|FL185810

EST:     CGCTCCTCTGGGCCGTCGCCGTACTCAACCTCCTCTGGTGCTTCCTGCAG                         GCATGGCAATGTATGCCTGACAGGGCATTCTCTTGGAATATACTGTCACTG
genomic: CGCTCCTCTGGGCCGTCGCCGTACTCAACCTCCTCTGGTGCTTCCTGCAGgtgcggattg ... caaatggcagGCATGGCAATGTATGCCTGACAGGGCATTCTCTTGGAATATACTGTCACTG

EST: gi|149077477|gb|EE166173.2|EE166173

EST:     CGCTCCTCTGGGCCGTCGCCGTACTCAACCTCCTCTGGTGCTTCCTGCAG                         GCATGGCAATGTATGCCTGACAGGGCATTCTCTTGGAATATACTGTCACTG
genomic: CGCTCCTCTGGGCCGTCGCCGTACTCAACCTCCTCTGGTGCTTCCTGCAGgtgcggattg ... caaatggcagGCATGGCAATGTATGCCTGACAGGGCATTCTCTTGGAATATACTGTCACTG

EST: gi|211461767|gb|FL185827.1|FL185827

EST:     CGCTCCTCTGGGCCGTCGCCGTACTCAACCTCCTCTGGTGCTTCCTGCAG                         GCATGGCAATGTATGCCTGACAG
genomic: CGCTCCTCTGGGCCGTCGCCGTACTCAACCTCCTCTGGTGCTTCCTGCAGgtgcggattg ... caaatggcagGCATGGCAATGTATGCCTGACAG

EST: gi|148963745|gb|EE014820.2|EE014820

EST:     CGCTCCTCTGGGCCGTCGCCGTACTCAACCTCCTCTGGTGCTTCCTGCAG                         GCATGGCAATGTATGCCTGACAGGGCATTCTCTTGGAATATACTGTCACTG
genomic: CGCTCCTCTGGGCCGTCGCCGTACTCAACCTCCTCTGGTGCTTCCTGCAGgtgcggattg ... caaatggcagGCATGGCAATGTATGCCTGACAGGGCATTCTCTTGGAATATACTGTCACTG

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: 116

CCGTAGGCTCAGCTACGGCCGCTCTCACGTCGTTGTCGTCGCGTACTACGCGCTCCTCTGGGCCGTCGCCGTACTCAACCTCCTCTGGTGCTTCCTGCAGgtgcggattg ... caaatggcagGCATGGCAATGTATGCCTGACAGGGCATTCTCTTGGAATATACTGTCACTGTTTACAAAATCAGGAATGTTATTCTTGGAAGTGAGTCTCATAGCCTTTC

Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 78

Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 123

Block sizes: 48 (upstream exon), 48 (downstream exon)
Score: 81

atgc intronic sequence ATGC exonic sequence

Intronic sequence truncated to 55 bases.

tatttacctgtatctcttatgtaatcatggaacatttttttttctcaaatggcagGCATGGCAATGTATGCCTGACAGGGCATTCTCTTGGAATATACTGTCACTGTTTACAAAATCAGGAATGTTATTCTTGGAAGTGAGTCTCATAGCCTTTC

                                catttttttttctc  CT-rich tract
                                 atttttttttctcaaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
atgaatccaaactttcatttttatttttttacattgtgtattacctatttacctgtatctcttatgtaatcatggaacatttttttttctcaaatggcagGCATGGCAATGTATGCCTGACAGGGCATTCTCTTGGAATATACTGTCACTGTTTACAAAATCAGGAATGTTATTCTTGGAAGTGAGTCTCATAGCCTTTC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
-tgaatcc
- - - - - - tttcatt
- - - - - - - - - - - - - - - - - - - - - - - - - - ctgtatc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - catggaa