ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq
cis-regulatory elements

Sequence

atgc intronic sequence ATGC exonic sequence

CAAGAGACTGTCAGGCTGGTGACTGGAAGAACAAATGCTACCGTTGTGGCGAAAGGGGCCATATAGAAAGAAATTGCCAGAACAGTCCAAGGAACCTCAGgtgtttattgttaacactatcagctacattccacagctatatgacacacttaagcactatattctagtgtatatcattgaatgctttcattaaagaagttgcttgctaaatatgtttag

Basic information

species	Zea mays
transcript	GRMZM2G175419_T01
intron #	5
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G175419_T01 (Zea mays), 5'ss of exon 5
lower sequence: GLYMA19G35990.1 (Glycine max), 5'ss of exon 5

CAAGAGACTGTCAGGCTGGTGACTGGAAGAACAAATGCTACCGTTGTGGCGAAAGGGGCCATATAGAAAGAAATTGCCAGAACAGTCCAAGGAACCTCAGgtgtttattgttaacactatcagctacattccacagctatatgacacacttaagcactatatt---ctagtgtatatcattgaatgctttcattaaagaagttgcttgctaaatatgtttag---
|  |||| ||  | ||||| || ||||||||||| || ||||||||||| ||||| || ||||||||||  || ||  |||||||||| |  ||    ||||      || |     |  ||      | | ||||   |      | ||||||     ||||   ||  | |  ||  ||    ||||| | | |   | ||   || | |||   | ||    
CCCGAGATTGCAAAGCTGGGGATTGGAAGAACAAGTGTTACCGTTGTGGGGAAAGAGGTCATATAGAAAAGAACTGTAAGAACAGTCCCAAAAAGTCGAGgtaggccatgatgtagtttccaaacttctgctacagtgttgatttgctcttaagatggttattgatctcttatggatt-ttatgagctttaaatcattgatttcaatgttgaattgttctaacag

upper sequence: GRMZM2G175419_T01 (Zea mays), 5'ss of exon 5
lower sequence: GLYMA03G33270.3 (Glycine max), 5'ss of exon 4

CAAGAGACTGTCAGGCTGGTGACTGGAAGAACAAATGCTACCGTTGTGGCGAAAGGGGCCATATAGAAAGAAATTGCCAGAACAGTCCAAGGAACCTCAGgt-gtttattgttaacactatcagctac-attccacagctatatgacac--acttaagcactatattctagtgtatatcattgaatgctttcattaaagaagttgcttgctaaatatgtttag---
|  |||| ||  | || || || ||||||||||| || ||||||||||| ||||| || ||||||||||  || ||  |||||||||| |  ||  | |||| |   ||  |  |   |   | || | |   |      || ||      || |    | |    |||| ||  | | ||   |   ||  || |  || ||   ||  | |||   | ||    
CCCGAGATTGCAAAGCCGGGGATTGGAAGAACAAGTGTTACCGTTGTGGGGAAAGAGGTCATATAGAAAAGAACTGTAAGAACAGTCCCAAAAAGTTGAGgtaggccataatctaatttccaaacttctacctcgtgttgatttgctcttaacatggttattgctctctaatgggttttat--gagctttaaatcattgatgtcaatt--tgaattgttctaacag

upper sequence: GRMZM2G175419_T01 (Zea mays), 5'ss of exon 5
lower sequence: Vv08s0040g02860.t01 (Vitis vinifera), 5'ss of exon 3

CAAGAGACTGTCAGGCTGGTGACTGGAAGAACAAATGCTACCGTTGTGGCGAAAGGGGCCATATAGAAAGAAATTGCCAGAACAGTCCAAGGAACCTCAGgtgtt----tattgttaacactatcagctacattccacagctata----tgacacacttaagcactatattctagtgtatatcattgaa-tgctttcat-taaagaagttgcttgctaaatatgtttag------------
|  |||| ||  | ||||| ||||||||||| || || || || ||||| ||||| || ||||| |||||||| |||||||||||||| ||||| ||||||| ||    ||| || |  ||   |    ||||| | |  ||       |||||   ||   ||   |||  |  |||  | |||   | || |    |  ||||   ||| | ||| || |   |||             
CTCGAGATTGCAAAGCTGGAGACTGGAAGAATAAGTGTTATCGGTGTGGAGAAAGAGGTCATATTGAAAGAAACTGCCAGAACAGTCCCAGGAAGCTCAGgtattctcatatggtgattacatgccaaaacatttctctcctgctgccttgacatttttttccatattatatttttgttaagcatgatactgttactgtgcaaagtttttgttagcttaaaactattatgttatattgcag

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|37421775|gb|CF648589.1|CF648589

EST:     GAAAGGGGCCATATAGAAAGAAATTGCCAGAACAGTCCAAGGAACCTCAG                         GCGTGAGAGAAGCTATTC
genomic: GAAAGGGGCCATATAGAAAGAAATTGCCAGAACAGTCCAAGGAACCTCAGgtgtttattg ... atatgtttagGCGTGAGAGAAGCTATTC

EST: gi|101391570|gb|EB817721.1|EB817721

EST:     GAAAGGGGCCATATAGAAAGAAATTGCCAGAACAGTCCAAGGAACCTCAG                         GCGTGAGAGAAGCTATTCACGGTCTCCATCCCCACGCCGAGGACGGGGCCG
genomic: GAAAGGGGCCATATAGAAAGAAATTGCCAGAACAGTCCAAGGAACCTCAGgtgtttattg ... atatgtttagGCGTGAGAGAAGCTATTCACGGTCTCCATCCCCACGCCGAGGACGGGGCCG

EST: gi|78109291|gb|DV527707.1|DV527707

EST:     GAAAGGGGCCATATAGAAAGAAATTGCCAGAACAGTCCAAGGAACCTCAG                         GCGTGAGAGAAGCTATTCACGGTCTCCATCCCCACGCCGAGGACGGGGCCG
genomic: GAAAGGGGCCATATAGAAAGAAATTGCCAGAACAGTCCAAGGAACCTCAGgtgtttattg ... atatgtttagGCGTGAGAGAAGCTATTCACGGTCTCCATCCCCACGCCGAGGACGGGGCCG

EST: gi|15208745|gb|BI430629.1|BI430629

EST:     GAAAGGGGCCATATAGAAAGAAATTGCCAGAACAGTCCAAGGAACCTCAG                         GCGTGAGAGAAGCTATTCACGGTCTCCATCCCCACGCCGAGGACGGGGCCG
genomic: GAAAGGGGCCATATAGAAAGAAATTGCCAGAACAGTCCAAGGAACCTCAGgtgtttattg ... atatgtttagGCGTGAGAGAAGCTATTCACGGTCTCCATCCCCACGCCGAGGACGGGGCCG

EST: gi|31360494|gb|CD444851.1|CD444851

EST:     GAAAGGGGCCATATAGAAAGAAATTGCCAGAACAGTCCAAGGAACCTCAG                         GCGTGAGAGAAGCTATTCACGGTCTCCATCCCCACGCCGAGGACGGGGCCG
genomic: GAAAGGGGCCATATAGAAAGAAATTGCCAGAACAGTCCAAGGAACCTCAGgtgtttattg ... atatgtttagGCGTGAGAGAAGCTATTCACGGTCTCCATCCCCACGCCGAGGACGGGGCCG

EST: gi|113808432|gb|DW929109.1|DW929109

EST:     GAAATTGCCAGAACAGTCCAAGGAACCTCAG                         GCGTGAGAGAAGCTATTCACGGTCTCCATCCCCACGCCGAGGACGGGGCCG
genomic: GAAATTGCCAGAACAGTCCAAGGAACCTCAGgtgtttattg ... atatgtttagGCGTGAGAGAAGCTATTCACGGTCTCCATCCCCACGCCGAGGACGGGGCCG

EST: gi|31360368|gb|CD444725.1|CD444725

EST:     AATTGCCAGAACAGTCCAAGGAACCTCAG                         GCGTGAGAGAAGCTATTCACGGTCTCCATCCCCACGCCGAGGACGGGGCCG
genomic: AATTGCCAGAACAGTCCAAGGAACCTCAGgtgtttattg ... atatgtttagGCGTGAGAGAAGCTATTCACGGTCTCCATCCCCACGCCGAGGACGGGGCCG

EST: gi|21809627|gb|BQ667945.1|BQ667945

EST:     GAAAGGGGCCATATAGAAAGAAATTGCCAGAACAGTCCAAGGAACCTCAG                         GCGTGAGAGAAGCTATTCACG
genomic: GAAAGGGGCCATATAGAAAGAAATTGCCAGAACAGTCCAAGGAACCTCAGgtgtttattg ... atatgtttagGCGTGAGAGAAGCTATTCACG

EST: gi|76290330|gb|DV029898.1|DV029898

EST:     GAAAGGGGCCATATAGAAAGAAATTGCCAGAACAGTCCAAGGAACCTCAG                         GCGTGAGAGAAGCTATTCACGGTCTCCATCCCCACGCCGAGGACGGGGCCG
genomic: GAAAGGGGCCATATAGAAAGAAATTGCCAGAACAGTCCAAGGAACCTCAGgtgtttattg ... atatgtttagGCGTGAGAGAAGCTATTCACGGTCTCCATCCCCACGCCGAGGACGGGGCCG

EST: gi|61118470|gb|DN559431.1|DN559431

EST:     GAAAGGGGCCATATAGAAAGAAATTGCCAGAACAGTCCAAGGAACCTCAG                         GCGTGAGAGAAGCTATTCACGGTCTCCATCCCCACGCCGAGGACGGGGCCG
genomic: GAAAGGGGCCATATAGAAAGAAATTGCCAGAACAGTCCAAGGAACCTCAGgtgtttattg ... atatgtttagGCGTGAGAGAAGCTATTCACGGTCTCCATCCCCACGCCGAGGACGGGGCCG

EST: gi|67025176|gb|CO453925.1|CO453925

EST:     GAAAGGGGCCATATAGAAAGAAATTGCCAGAACAGTCCAAGGAACCTCAG                         GCGTGAGAGAAGCTATTCACGGTCTCCATCCCCACGCCGAGGACGGGGCCG
genomic: GAAAGGGGCCATATAGAAAGAAATTGCCAGAACAGTCCAAGGAACCTCAGgtgtttattg ... atatgtttagGCGTGAGAGAAGCTATTCACGGTCTCCATCCCCACGCCGAGGACGGGGCCG

EST: gi|94473189|gb|EB702147.1|EB702147

EST:     GAAAGGGGCCATATAGAAAGAAATTGCCAGAACAGTCCAAGGAACCTCAG                         GCGTGAGAGAAGCTATTCACGGTCTCCATCCCTACGCCGAGGACGGGGCCG
genomic: GAAAGGGGCCATATAGAAAGAAATTGCCAGAACAGTCCAAGGAACCTCAGgtgtttattg ... atatgtttagGCGTGAGAGAAGCTATTCACGGTCTCCATCCCCACGCCGAGGACGGGGCCG

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: 40 (upstream exon), 49 (downstream exon)
Score: 1531

CAAGAGACTGTCAGGCTGGTGACTGGAAGAACAAATGCTACCGTTGTGGCGAAAGGGGCCATATAGAAAGAAATTGCCAGAACAGTCCAAGGAACCTCAGgtgtttattg ... atatgtttagGCGTGAGAGAAGCTATTCACGGTCTCCATCCCCACGCCGAGGACGGGGCCGCAGCCGGAGCTACAGCAGAAGCCGGAGCTATAG

Block sizes: 40 (upstream exon), 49 (downstream exon)
Score: 646

Block sizes: 40 (upstream exon), 49 (downstream exon)
Score: 516

Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 796

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CAAGAGACTGTCAGGCTGGTGACTGGAAGAACAAATGCTACCGTTGTGGCGAAAGGGGCCATATAGAAAGAAATTGCCAGAACAGTCCAAGGAACCTCAGgtgtttattgttaacactatcagctacattccacagctatatgacacacttaagcactatattctagtgtatatcattgaatgctttcattaaagaagttgcttgctaaatatgtttag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA