ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq
cis-regulatory elements

Sequence

atgc intronic sequence ATGC exonic sequence

TACCAAACTGCAAAGGCTGCTCTTGAGTTAGGTTCTTCCTATGCACCAGGCGATTCAAGGTTTACCCGTCTATTGAAGGAATGTGATGAGTGCATTGCTGgtgagcaaaattaacttcagaagttagtatataatacaacagtatgtgtgggggtatgtggtgtgtgtgtgggtggggtgggggggtgggtggggggatt...

Basic information

species	Zea mays
transcript	GRMZM2G149704_T02
intron #	3
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G149704_T02 (Zea mays), 5'ss of exon 3
lower sequence: LOC_Os01g43540.1 (Oryza sativa), 5'ss of exon 3

TACCAAACTGCAAAGGCTGCTCTTGAGTTAGGTTCTTCCTATGCACCAGGCGATTCAAGGTTTACCCGTCTATTGAAGGAATGTGATGAGTGCATTGCTGgtgagcaaaattaacttcagaagttagtatataatacaacagtatgtgtgggggtatgtggtgtgtgtgtgggtggggtgggggggtgggtggggggatt--------
|| ||||||||||| || |||||||| || ||||  || |  ||| | || || ||||||||||| || ||| ||||||| ||||||||| ||||||||||| |||    |   | |  ||    | |   |  |     | ||  | ||  |   |||| | | | | |   |||||        |  ||| |   |          
TATCAAACTGCAAAAGCAGCTCTTGAATTGGGTTACTCGTTCGCATCTGGTGACTCAAGGTTTACTCGCCTAATGAAGGAGTGTGATGAGCGCATTGCTGgtaagc----tgtccctttgagtccattgcttggt----taatacatttgcagtattgtgttatatttttacctggggcataccattacgtgagactaccatattata

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|211045632|gb|FL292671.1|FL292671

EST:     CGATTCAAGGTTTACCCGTCTATTGAAGGAATGTGATGAGCGCATTGCTG                         AGGAATCTAGCCAGGCACCAGCAAAGAATGTCGATGCTCCTGTAGCTGCTA
genomic: CGATTCAAGGTTTACCCGTCTATTGAAGGAATGTGATGAGTGCATTGCTGgtgagcaaaa ... ttgtgtccagAGGAATCTAGCCAGGCACCAGCAAAGAATGTCGAGGCTCCTGTAGCTGCTA

EST: gi|78080588|gb|DV509000.1|DV509000

EST:     CGATTCAAGGTTTACCCGTCTATTGAAGGAATGTGATGAGTGCATTGCTG                         AGGAATCTAGCCAGGCACCAGCAAAGAATGTCGAGGCTCCTGTAGCTGCTA
genomic: CGATTCAAGGTTTACCCGTCTATTGAAGGAATGTGATGAGTGCATTGCTGgtgagcaaaa ... ttgtgtccagAGGAATCTAGCCAGGCACCAGCAAAGAATGTCGAGGCTCCTGTAGCTGCTA

EST: gi|211045637|gb|FL292676.1|FL292676

EST:     CGATTCAAGGTTTACCCGTCTATTGAAGGAATGTGATGAGCGCATTGCTG                         AGGAATCTAGCCAGGCACCAGCAAAGAATGTCGATGCTCCTGTAGCTGCTA
genomic: CGATTCAAGGTTTACCCGTCTATTGAAGGAATGTGATGAGTGCATTGCTGgtgagcaaaa ... ttgtgtccagAGGAATCTAGCCAGGCACCAGCAAAGAATGTCGAGGCTCCTGTAGCTGCTA

EST: gi|89757539|gb|DY687098.1|DY687098

EST:     CGATTCAAGGTTTACCCGTCTATTGAAGGAATGTGATGAGTGCATTGCTG                         AGGAATCTAGCCAGGCACCAGCAAAGAATGTCGAGGCTCCTGTAGCTGCTA
genomic: CGATTCAAGGTTTACCCGTCTATTGAAGGAATGTGATGAGTGCATTGCTGgtgagcaaaa ... ttgtgtccagAGGAATCTAGCCAGGCACCAGCAAAGAATGTCGAGGCTCCTGTAGCTGCTA

EST: gi|149076474|gb|EE165099.2|EE165099

EST:     CGATTCAAGGTTTACCCGTCTATTGAAGGAATGTGATGAGTGCATTGCTG                         AGGAATCTAGCCAGGCACCAGCAAAGAATGTCGAGGCTCCTGTAGCTGCTA
genomic: CGATTCAAGGTTTACCCGTCTATTGAAGGAATGTGATGAGTGCATTGCTGgtgagcaaaa ... ttgtgtccagAGGAATCTAGCCAGGCACCAGCAAAGAATGTCGAGGCTCCTGTAGCTGCTA

EST: gi|211042677|gb|FL292666.1|FL292666

EST:     CGATTCAAGGTTTACCCGTCTATTGAAGGAATGTGATGAGCGCATTGCTG                         AGGAATCTAGCCAGGCACCAGCAAAAGAATGTCGAGGCTCCTGTAGCTG
genomic: CGATTCAAGGTTTACCCGTCTATTGAAGGAATGTGATGAGTGCATTGCTGgtgagcaaaa ... ttgtgtccagAGGAATCTAGCCAGGCACCAGCAAA-GAATGTCGAGGCTCCTGTAGCTG

EST: gi|29947233|gb|CB816549.1|CB816549

EST:     CGATTCAAGGTTTACCCGTCTATTGAAGGAATGTGATGAGTGCATTGCTG                         AGGAATCTAGCCAGGCACCAGCAAAGAATGTCGAGGCTCCTGTAGCTGCTA
genomic: CGATTCAAGGTTTACCCGTCTATTGAAGGAATGTGATGAGTGCATTGCTGgtgagcaaaa ... ttgtgtccagAGGAATCTAGCCAGGCACCAGCAAAGAATGTCGAGGCTCCTGTAGCTGCTA

EST: gi|149104781|gb|EE290244.2|EE290244

EST:     CGATTCAAGGTTTACCCGTCTATTGAAGGAATGTGATGAGTGCATTGCTG                         AGGAATCTAGCCAGGCACCAGCAAAGAATGTCGAGGCTCCTGTAGCTGCTA
genomic: CGATTCAAGGTTTACCCGTCTATTGAAGGAATGTGATGAGTGCATTGCTGgtgagcaaaa ... ttgtgtccagAGGAATCTAGCCAGGCACCAGCAAAGAATGTCGAGGCTCCTGTAGCTGCTA

EST: gi|211045636|gb|FL292675.1|FL292675

EST:     CGATTCAAGGTTTACCCGTCTATTGAAGGAATGTGATGAGCGCATTGCTG                         AGGAATCTAGCCAGGCAC
genomic: CGATTCAAGGTTTACCCGTCTATTGAAGGAATGTGATGAGTGCATTGCTGgtgagcaaaa ... ttgtgtccagAGGAATCTAGCCAGGCAC

EST: gi|211045634|gb|FL292673.1|FL292673

EST:     CGATTCAAGGTTTACCCGTCTATTGAAGGAATGTGATGAGCGCATTGCTG                         AGGAATCTAGCCAGGCACCAGCAAAGAATGTCGA
genomic: CGATTCAAGGTTTACCCGTCTATTGAAGGAATGTGATGAGTGCATTGCTGgtgagcaaaa ... ttgtgtccagAGGAATCTAGCCAGGCACCAGCAAAGAATGTCGA

EST: gi|148975634|gb|EE025764.2|EE025764

EST:     CGATTCAAGGTTTACCCGTCTATTGAAGGAATGTGATGAGTGCATTGCTG                         AAGAATCTAGCCAGGCACCAGCAAAGAATGTCGAGGCTCCTGTAGCTGCTA
genomic: CGATTCAAGGTTTACCCGTCTATTGAAGGAATGTGATGAGTGCATTGCTGgtgagcaaaa ... ttgtgtccagAGGAATCTAGCCAGGCACCAGCAAAGAATGTCGAGGCTCCTGTAGCTGCTA

EST: gi|211045630|gb|FL292669.1|FL292669

EST:     CGATTCAAGGTTTACCCGTCTATTGAAGGAATGTGATGAGCGCATTGCTG                         AGGAATCTAGCCAGGCACCAGCAAAGAATGTCGATGCTCCTGTAGCTGCTA
genomic: CGATTCAAGGTTTACCCGTCTATTGAAGGAATGTGATGAGTGCATTGCTGgtgagcaaaa ... ttgtgtccagAGGAATCTAGCCAGGCACCAGCAAAGAATGTCGAGGCTCCTGTAGCTGCTA

EST: gi|31612314|gb|CD568936.1|CD568936

EST:     CGATTCAAGGTTTACCCGTCTATTGAAGGAATGTGATGAGTGCATTGCTG                         AGGAATCTAGCCAGGCACCAGCAAAGAATGTCGAGGCTCCTGTAGCTGCTA
genomic: CGATTCAAGGTTTACCCGTCTATTGAAGGAATGTGATGAGTGCATTGCTGgtgagcaaaa ... ttgtgtccagAGGAATCTAGCCAGGCACCAGCAAAGAATGTCGAGGCTCCTGTAGCTGCTA

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: 95

TACCAAACTGCAAAGGCTGCTCTTGAGTTAGGTTCTTCCTATGCACCAGGCGATTCAAGGTTTACCCGTCTATTGAAGGAATGTGATGAGTGCATTGCTGgtgagcaaaa ... ttgtgtccagAGGAATCTAGCCAGGCACCAGCAAAGAATGTCGAGGCTCCTGTAGCTGCTACTGTTGAGGACAAGGAGGATGTCGCAAATATGGATAATACACCGCCAGT

Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 51

Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 90

Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 33

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TACCAAACTGCAAAGGCTGCTCTTGAGTTAGGTTCTTCCTATGCACCAGGCGATTCAAGGTTTACCCGTCTATTGAAGGAATGTGATGAGTGCATTGCTGgtgagcaaaattaacttcagaagttagtatataatacaacagtatgtgtgggggtatgtggtgtgtgtgtgggtggggtgggggggtgggtggggggatt

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAA