ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq
cis-regulatory elements

Sequence

atgc intronic sequence ATGC exonic sequence

TCTCCAGCGCATCGTAAAGGGAGGAGCGGAGCGGCGAATTCTTGTGGTTTCCCAAGATGTCTTCTCCAAGCAAGCGCCGGGAGATGGACCTCATGAAGCTgtgaggattctggtggcgtgattcggtgattttttctataggatttcgatgcggattccttgatctgcgtttctactgcatgttgatgcctgcag

Basic information

species	Zea mays
transcript	GRMZM2G150867_T02
intron #	1
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G150867_T02 (Zea mays), 5'ss of exon 1
lower sequence: LOC_Os10g31000.1 (Oryza sativa), 5'ss of exon 1

TCTCCAGCGCATCGTAAAGGGAGGAGCGGAGCGGCGAATTCTTGTGGTT-TCCCAAGATGTCTTCTCCAAGCAAGCGCCGGGAGATGGACCTCATGAAGCTgtgaggattctggtggcgtgattcggtgattttttctataggatttcgatgcgga---------ttccttgatctgcgtttctactgcatgttgatg-cctgcag------------------------------------------------------------------------------
      | | |    |||  ||    |           || || |  || |  |||||||||||| || ||||||||||| ||||||||| | ||||||||||||||||  ||    | | |||   | ||||||| |   ||     |  | |||         || |  | | ||  | | | ||   | ||| ||  || ||                                                                               
-AGGAGGAGGAGGAGAAAAAGAAATCCAATCTTTTTCTTTTTTCTTCTTGTGTCAAGATGTCTTCCCCGAGCAAGCGCCGCGAGATGGACTTGATGAAGCTgtgaggatcttgtc--ctttatttatttattttttttggggggggggggggtggaattgtgtttttgcccggtttgattcttttctttctattggtggtctccatcgtctaatctgatgtgttgttgtttgttgttttgggggtggggggattggggattttcttggtttcttgttgttgcag

upper sequence: GRMZM2G150867_T02 (Zea mays), 5'ss of exon 1
lower sequence: GLYMA09G39370.4 (Glycine max), 5'ss of exon 1

TCTCCAGCGCATCGTAAAGGGAGGAGCGGAGCGGCGAATTCTTGTGGTTTCCCAAGA---TGTCTTCTCCAAGCAAGCGCCGGGAGATGGACCTCATGAAGCTgtgaggattctggtggcgtgattcggtgattttttctataggatttcgatgcgga---ttccttgatctgcgtttctactgcatgttgatgcctgcag
   |  ||  |  | ||| ||   |   ||    |  |  |         | ||  |   ||||||| |||||||||||||| ||||||||| | ||||| |||| |    | |  |  |   ||||    |  |||         ||   ||| ||    |||||   |||| ||      ||  | ||| |  | | ||
---CTTGCCAAAGGAAAAAGGCTAAAGAGAAACCCACACACACACACACACACAGAAATATGTCTTCCCCAAGCAAGCGCCGAGAGATGGACTTGATGAAACTgttaatcctttc-tctctcaattcatcaaagtttcaatcttttttctaatggggtctcttcctgattctgggtcctctttgtcttttgttttccgtag

upper sequence: GRMZM2G150867_T02 (Zea mays), 5'ss of exon 1
lower sequence: GLYMA07G07540.1 (Glycine max), 5'ss of exon 1

TCTCCAGCGCATCGTAAAGGGAGGAGCGGAGCGGCGAATTCTTGTGGTTTCCCAAGA----TGTCTTCTCCAAGCAAGCGCCGGGAGATGGACCTCATGAAGCTgtgaggattctggtggcgtgattcggtgattttttctataggatttcgatgcggattccttgatctgcgtttctactgcatgttgatgcctgcag-------------------------------------------
     ||    |    ||  ||  |    |    |  |     |      |  || |    ||||||||||||||||||| || ||||||||| | ||||| |||| |  || |      | |  |  | |    |||||  |   ||||| ||     ||      | |   ||   | ||  |||  | |  ||                                              
----AAGTAACTAAGGAAAAGAAAACACAACACACACACAAAGGAAAAAACAGAAAAACCATGTCTTCTCCAAGCAAGCGGCGAGAGATGGACTTGATGAAACTgtta--atcc--accacttcttctgttttccttttcccttctatttccattaaagttataattttttttttctaattgggtgtctaagtttgactcttgattctgattttgatgttagtttttttttttaattaatag

upper sequence: GRMZM2G150867_T02 (Zea mays), 5'ss of exon 1
lower sequence: GLYMA07G07540.2 (Glycine max), 5'ss of exon 1

TCTCCAGCGCAT-CGTAAAGGGAGGAGCGGAGCGGCGAATTCTTGTGGTTTCCCAAGATGTCTTCTCCAAGCAAGCGCCGGGAGATGGACCTCATGAAGCTgtgaggattctggtggcgtgattcggtgattttttctataggatttcgatgcggattccttgatctgcgtttctactgcatgttgatgcctgcag-------------------------------------------
    || | ||  |  ||||| |  | | ||    | |                    ||||||||||||||||||| || ||||||||| | ||||| |||| |  || |      | |  |  | |    |||||  |   ||||| ||     ||      | |   ||   | ||  |||  | |  ||                                              
-ACACAACACACACACAAAGGAAAAAACAGAAAAACCA--------------------TGTCTTCTCCAAGCAAGCGGCGAGAGATGGACTTGATGAAACTGTTA--ATCC--ACCACTTCTTCTgttttccttttcccttctatttccattaaagttataattttttttttctaattgggtgtctaagtttgactcttgattctgattttgatgttagtttttttttttaattaatag

upper sequence: GRMZM2G150867_T02 (Zea mays), 5'ss of exon 1
lower sequence: GLYMA18G46940.1 (Glycine max), 5'ss of exon 1

TCTCCAGCGCATCGTAAAGGGAGGAGCGGAGCGGCGAATTCTTGTGGTTTCCCAAGATGTCTTCTCCAAGCAAGCGCCGGGAGATGGACCTCATGAAGCTgtgaggattctggtggcgt--------------gattcggtgattttttctataggat---ttcgatgcggattccttgatctgcgtttctactgcatgttgatgcctgcag-
 ||  || | |    |     || |  ||| |  | ||  |            || |||||||| |||||||||||||| ||||||||| | ||||| |||| |    | |       |              | |||  |  |||| |  || || |   |||  |     |||||   |||| ||      ||  | ||     | | || 
GCTAAAGAGAAGAAAAGGCAAAGCAAGGGACCAACCAAAACACACA-CAGAGAAACATGTCTTCCCCAAGCAAGCGCCGAGAGATGGACTTGATGAAACTGttaatcctttctctctctctcaattcatcaaagtttcaatctttttgttaatggggtctcttccctttctgttcctgattctgggtcctctttgtcttttctcttccgtagg

upper sequence: GRMZM2G150867_T02 (Zea mays), 5'ss of exon 1
lower sequence: PP1S161_122V6.1 (Physcomitrella patens), 5'ss of exon 1

TCTCCAGCGCATCGTAAAGGGAGGAGCGGAGCGGCGAATTCTTGTGGTTTCCCAAGATGTCTTCTCCAAGCAAGCGCCGGGAGATGGACCTCATGAAGCTgtgaggattctggtggcgtgattcggtgattttttctataggatttcgatgcggattccttgatctgcgtttctactgcatg----ttgatgcctgcag-----
                                                        ||||| || ||||||||||| |||||||||||| | |||||||||| ||    |||||    |  || | |  |||| |    |   ||| | |  || ||   ||   ||   ||  | ||| |     ||| |    | ||     
--------------------------------------------------------ATGTCATCCCCAAGCAAGCGGCGGGAGATGGACGTGATGAAGCTgtaagtcccctggtttaattgtttgct--ttttgttggaattgttttggt--ggttttggtgcggtgtagtttcagtgcttagtttttggtattggtaggattg

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|211541025|gb|FL000900.1|FL000900

EST:     CCCAAGATGTCTTCTCCAAGCAAGCGCCGGGAGATGGACCTCATGAAGCT                         GATGATGAGCGACTACAAGGTGGATATGGTGAACGATGGGATGCAGGAGTT
genomic: CCCAAGATGTCTTCTCCAAGCAAGCGCCGGGAGATGGACCTCATGAAGCTgtgaggattc ... atgcctgcagGATGATGAGCGACTACAAGGTGGATATGGTGAACGATGGGATGCAGGAGTT

EST: gi|211541026|gb|FL000901.1|FL000901

EST:     CCCAAGATGTCTTCTCCAAGCAAGCGCCGGGAGATGGACCTCATGAAGCT                         GATGATGAGCGACTACAAGGTGGATATGGTGAACGATGGGATGCAGGAGTT
genomic: CCCAAGATGTCTTCTCCAAGCAAGCGCCGGGAGATGGACCTCATGAAGCTgtgaggattc ... atgcctgcagGATGATGAGCGACTACAAGGTGGATATGGTGAACGATGGGATGCAGGAGTT

EST: gi|15499388|gb|BI595901.1|BI595901

EST:     CCCAAGATGTCTTCTCCAAGCAAGCGCCGGGAGATGGACCTCATGAAGCT                         GATGATGAGCGACTACAAGGTGGATATGGTGAACGATGGGATGCAGGAGTT
genomic: CCCAAGATGTCTTCTCCAAGCAAGCGCCGGGAGATGGACCTCATGAAGCTgtgaggattc ... atgcctgcagGATGATGAGCGACTACAAGGTGGATATGGTGAACGATGGGATGCAGGAGTT

EST: gi|211541022|gb|FL000897.1|FL000897

EST:     CCCAAGATGTCTTCTCCAAGCAAGCGCCGGGAGATGGACCTCATGAAGCT                         GATGATGAGCGACTACAAGGTGGATATGGTGAACGATGGGATGCAGGAGTT
genomic: CCCAAGATGTCTTCTCCAAGCAAGCGCCGGGAGATGGACCTCATGAAGCTgtgaggattc ... atgcctgcagGATGATGAGCGACTACAAGGTGGATATGGTGAACGATGGGATGCAGGAGTT

EST: gi|87157692|gb|DY402481.1|DY402481

EST:     CCCAAGATGTCTTCTCCAAGCAAGCGCCGGGAGATGGACCTCATGAAGCT                         GATGATGAGCGACTACAAGGTGGATATGGTGAACGATGGGATGCAGGAGTT
genomic: CCCAAGATGTCTTCTCCAAGCAAGCGCCGGGAGATGGACCTCATGAAGCTgtgaggattc ... atgcctgcagGATGATGAGCGACTACAAGGTGGATATGGTGAACGATGGGATGCAGGAGTT

EST: gi|33103947|gb|CF063907.1|CF063907

EST:     CCCAAGATGTCTTCTCCAAGCAAGCGCCGGGAGATGGACCTCATGAAGCT                         GATGATGAGCGACTACAAGGTGGATATGGTGAACGATGGGATGCAGGAGTT
genomic: CCCAAGATGTCTTCTCCAAGCAAGCGCCGGGAGATGGACCTCATGAAGCTgtgaggattc ... atgcctgcagGATGATGAGCGACTACAAGGTGGATATGGTGAACGATGGGATGCAGGAGTT

EST: gi|23199807|gb|BU582372.1|BU582372

EST:     CCCAAGATGTCTTCTCCAAGCAAGCGCCGGGAGATGGACCTCATGAAGCT                         GATGATGAGCGACTACAAGGTGGATATGGTGAACGATGGGATGCAGGAGTT
genomic: CCCAAGATGTCTTCTCCAAGCAAGCGCCGGGAGATGGACCTCATGAAGCTgtgaggattc ... atgcctgcagGATGATGAGCGACTACAAGGTGGATATGGTGAACGATGGGATGCAGGAGTT

EST: gi|211541028|gb|FL000903.1|FL000903

EST:     CCCAAGATGTCTTCTCCAAGCAAGCGCCGGGAGATGGACCTCATGAAGCT                         GATGATGAGCGACTACAAGGTGGATATGGTGAACGATGGGATGCAGGAGTT
genomic: CCCAAGATGTCTTCTCCAAGCAAGCGCCGGGAGATGGACCTCATGAAGCTgtgaggattc ... atgcctgcagGATGATGAGCGACTACAAGGTGGATATGGTGAACGATGGGATGCAGGAGTT

EST: gi|211541020|gb|FL000895.1|FL000895

EST:     CCCAAGATGTCTTCTCCAAGCAAGCGCCGGGAGATGGACCTCATGAAGCT                         GATGATGAGCGACTACAAGGTGGATATGGTGAACGATGGGATGCAGGAGTT
genomic: CCCAAGATGTCTTCTCCAAGCAAGCGCCGGGAGATGGACCTCATGAAGCTgtgaggattc ... atgcctgcagGATGATGAGCGACTACAAGGTGGATATGGTGAACGATGGGATGCAGGAGTT

EST: gi|5439433|gb|AI820354.1|AI820354

EST:     CCCAAGATGTCTTCTCCAAGCAAGCGCCGGGAGATGGACCTCATGAAGCT                         GATGATGAGCGACTACAAGGTGGATATGGTGAACGATGGGATGCAGGAGTT
genomic: CCCAAGATGTCTTCTCCAAGCAAGCGCCGGGAGATGGACCTCATGAAGCTgtgaggattc ... atgcctgcagGATGATGAGCGACTACAAGGTGGATATGGTGAACGATGGGATGCAGGAGTT

EST: gi|211541021|gb|FL000896.1|FL000896

EST:     CCCAAGATGTCTTCTCCAAGCAAGCGCCGGGAGATGGACCTCATGAAGCT                         GATGATGAGCGACTACAAGGTGGATATGGTGAACGATGGGATCCAGGAGTT
genomic: CCCAAGATGTCTTCTCCAAGCAAGCGCCGGGAGATGGACCTCATGAAGCTgtgaggattc ... atgcctgcagGATGATGAGCGACTACAAGGTGGATATGGTGAACGATGGGATGCAGGAGTT

EST: gi|211541018|gb|FL000893.1|FL000893

EST:     CCCAAGATGTCTTCTCCAAGCAAGCGCCGGGAGATGGACCTCATGAAGCT                         GATGATGAGCGACTACAAGGTGGATATGGTGAACGATGGGATGCAGGAGTT
genomic: CCCAAGATGTCTTCTCCAAGCAAGCGCCGGGAGATGGACCTCATGAAGCTgtgaggattc ... atgcctgcagGATGATGAGCGACTACAAGGTGGATATGGTGAACGATGGGATGCAGGAGTT

EST: gi|84980137|gb|DW530486.1|DW530486

EST:     CTTCTCC-AGCAAGCGCCGGGAGATGGACCTCATGAAGCT                         GATGATGAGCGACTACAAGGTGGATATGGTGAACGATGGGATGCAGGAGTT
genomic: CTTCTCCAAGCAAGCGCCGGGAGATGGACCTCATGAAGCTgtgaggattc ... atgcctgcagGATGATGAGCGACTACAAGGTGGATATGGTGAACGATGGGATGCAGGAGTT

EST: gi|6223825|gb|AW154956.1|AW154956

EST:     -CCAAGATGTCTTTTCCAAGCAAGCGCCGGGAGATGGACCTCATGAAGCT                         GATGATGAGCGACTACAAGGTGGATATGGTGAACGATGGGATGCAGGAGTT
genomic: CCCAAGATGTCTTCTCCAAGCAAGCGCCGGGAGATGGACCTCATGAAGCTgtgaggattc ... atgcctgcagGATGATGAGCGACTACAAGGTGGATATGGTGAACGATGGGATGCAGGAGTT

EST: gi|37394410|gb|CF634479.1|CF634479

EST:     CCCAAGATGTCTTCTCCAAGCAAGCGCCGGGAGATGGACCTCATGAAGCT                         GATGATGAGCGACTACAAGGTGGATATGGTGAACGATGGGATGCAGGAGTT
genomic: CCCAAGATGTCTTCTCCAAGCAAGCGCCGGGAGATGGACCTCATGAAGCTgtgaggattc ... atgcctgcagGATGATGAGCGACTACAAGGTGGATATGGTGAACGATGGGATGCAGGAGTT

EST: gi|32911041|gb|CF015853.1|CF015853

EST:     AGATGGACCTCATGAAGCT                         GATGATGAGCGACTACAAGGTGGATATGGTGAACGATGGGATGCAGGAGTT
genomic: AGATGGACCTCATGAAGCTgtgaggattc ... atgcctgcagGATGATGAGCGACTACAAGGTGGATATGGTGAACGATGGGATGCAGGAGTT

EST: gi|211541027|gb|FL000902.1|FL000902

EST:     CCCAAGATGTCTTCTCCAAGCAAGCGCCGGGAGATGGACCTCATGAAGCT                         GATGATGAGCGACTACAAGGTGGATATGGTGAACGATGGGATGCAGGAGTT
genomic: CCCAAGATGTCTTCTCCAAGCAAGCGCCGGGAGATGGACCTCATGAAGCTgtgaggattc ... atgcctgcagGATGATGAGCGACTACAAGGTGGATATGGTGAACGATGGGATGCAGGAGTT

EST: gi|211541019|gb|FL000894.1|FL000894

EST:     CCCAAGATGTCTTCTCCAAGCAAGCGCCGGGAGATGGACCTCATGAAGCT                         GATGATGAGCGACTACAAGGTGGATATGGTGAACGATGGGATGCAGGAGTT
genomic: CCCAAGATGTCTTCTCCAAGCAAGCGCCGGGAGATGGACCTCATGAAGCTgtgaggattc ... atgcctgcagGATGATGAGCGACTACAAGGTGGATATGGTGAACGATGGGATGCAGGAGTT

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: 44 (upstream exon), 48 (downstream exon)
Score: 48

TCTCCAGCGCATCGTAAAGGGAGGAGCGGAGCGGCGAATTCTTGTGGTTTCCCAAGATGTCTTCTCCAAGCAAGCGCCGGGAGATGGACCTCATGAAGCTgtgaggattc ... atgcctgcagGATGATGAGCGACTACAAGGTGGATATGGTGAACGATGGGATGCAGGAGTTCTTTGTTGAATTTCGTGGGCCTAACGAAA

Block sizes: 48 (upstream exon), 48 (downstream exon)
Score: 56

Block sizes: 49 (upstream exon), 44 (downstream exon)
Score: 39

Block sizes: 48 (upstream exon), 48 (downstream exon)
Score: 66

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TCTCCAGCGCATCGTAAAGGGAGGAGCGGAGCGGCGAATTCTTGTGGTTTCCCAAGATGTCTTCTCCAAGCAAGCGCCGGGAGATGGACCTCATGAAGCTgtgaggattctggtggcgtgattcggtgattttttctataggatttcgatgcggattccttgatctgcgtttctactgcatgttgatgcctgcag

- - - - - - - - - - - - - - - - - - - - - - - - - -  AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGC