ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq
cis-regulatory elements

Sequence

atgc intronic sequence ATGC exonic sequence

TTTGCCAGCAAGATATCGTGATTCAGTCCGAGCAATCACTCCTGGCTTGCCTCTTTTCCTCTATAACTACACAACCCACCAGCTTCATGGGGTATTTGAGgtgtgtgattggttatctgatttcctgattcctgcaaagcctatctcaagttgttaaacacttgttcgtttgtcatacaaaagatacttttgagctaaaa...

Basic information

species	Zea mays
transcript	GRMZM2G033117_T01
intron #	3
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G033117_T01 (Zea mays), 5'ss of exon 3
lower sequence: LOC_Os05g41930.1 (Oryza sativa), 5'ss of exon 3

TTTGCCAGCAAGATATCGTGATTCAGTCCGAGCAATCACTCCTGGCTTGCCTCTTTTCCTCTATAACTACACAACCCACCAGCTTCATGGGGTATTTGAGgtgtgtgattggttatctgatttcctgattcctgcaaagcctatc-tcaagttgttaaacacttgttcgtttgtcatacaaaagatacttttg-agctaaaa----
 ||||||||||||||||||||||||||||||||||| | ||||||  | ||||||||||||||||||||||| ||||| |||||||||||||||||||||||||||   |  ||  ||  ||| | ||| |    ||| | | |  | || ||  |||  |  | ||   |||  | || |||||| | |  | ||| |  |    
GTTGCCAGCAAGATATCGTGATTCAGTCCGAGCAATTATTCCTGGTCTACCTCTTTTCCTCTATAACTACACGACCCATCAGCTTCATGGGGTATTTGAGgtgtgt---taatttcct--ttttcagatactcataaatcatcttatgaatttcataaggagctctttacttgaaa-acgaaagatccataagcagccatgaaatt

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|60401049|gb|DN233856.1|DN233856

EST:     CTCTTTTCCTCTATAACTACACAACCCACCAGCTTCATGGGGTATTTGAG                         GCTGCCAGTTTTGGTGGGTCCAATATCGATCCTACTGCATGGGAGGATAAG
genomic: CTCTTTTCCTCTATAACTACACAACCCACCAGCTTCATGGGGTATTTGAGgtgtgtgatt ... atctgcttagGCTGCCAGTTTTGGTGGGTCCAATATCGATCCTACTGCATGGGAGGATAAG

EST: gi|148949364|gb|EC894819.2|EC894819

EST:     CTCTTTTCCTCTATAACTACACAACCCACCAGCTTCATGGGGTATTTGAG                         GCTGCCAGTTTTGGTGGGTCCAATATCGATCCTACTGCATG
genomic: CTCTTTTCCTCTATAACTACACAACCCACCAGCTTCATGGGGTATTTGAGgtgtgtgatt ... atctgcttagGCTGCCAGTTTTGGTGGGTCCAATATCGATCCTACTGCATG

EST: gi|28361820|gb|CB240176.1|CB240176

EST:     CTCTTTTCCTCTATAACTACACAACCCACCAGCTTCATGGGGTATTTGAG                         GCTGCCAGTTTTGGTGGGTCCAATATCGATCCTACTGCATGGGAGGATAAG
genomic: CTCTTTTCCTCTATAACTACACAACCCACCAGCTTCATGGGGTATTTGAGgtgtgtgatt ... atctgcttagGCTGCCAGTTTTGGTGGGTCCAATATCGATCCTACTGCATGGGAGGATAAG

EST: gi|149102652|gb|EE288009.2|EE288009

EST:     TCTTTTCCTCTANTA-CTACACAACCCACCAGCTTCATGGGGTATTTGAG                         GCTGCCAGTTTTGGTGGGGTCCA-TATCGATCCTACT
genomic: TCTTTTCCTCTA-TAACTACACAACCCACCAGCTTCATGGGGTATTTGAGgtgtgtgatt ... atctgcttagGCTGCCAGTTTTGGTGGG-TCCAATATCGATCCTACT

EST: gi|60350290|gb|DN217263.1|DN217263

EST:     TCATGGGGTATTTGAG                         GCTGCCAGTTTTGGTGGGTCCAATATCGATCTTACTGCATGGGAGGATAAG
genomic: TCATGGGGTATTTGAGgtgtgtgatt ... atctgcttagGCTGCCAGTTTTGGTGGGTCCAATATCGATCCTACTGCATGGGAGGATAAG

EST: gi|78077999|gb|DV506414.1|DV506414

EST:     CTCTTTTCCTCTATAACTACACAACCCACCAGCTTCATGGGGTATTTGAG                         GCTGCCAGTTTTGGTGGGTCCAATAT
genomic: CTCTTTTCCTCTATAACTACACAACCCACCAGCTTCATGGGGTATTTGAGgtgtgtgatt ... atctgcttagGCTGCCAGTTTTGGTGGGTCCAATAT

EST: gi|60357783|gb|DN224756.1|DN224756

EST:     TTTCCTCTATAACTACACAACCCACCAGCTTCATGGGGTATTTGAG                         GCTGCCAGTTTTGGTGGGTCCAATATCGATCCTACTGCATGGGAGGATAAG
genomic: TTTCCTCTATAACTACACAACCCACCAGCTTCATGGGGTATTTGAGgtgtgtgatt ... atctgcttagGCTGCCAGTTTTGGTGGGTCCAATATCGATCCTACTGCATGGGAGGATAAG

EST: gi|148932942|gb|EE285770.2|EE285770

EST:     CTCTTTTCCTCTATAACTACACAACCCACCAGCTTCATGGGGTATTTGAG                         GCTGCCAGTTTTTGGTGGGTCCAATATCGATCCTACTGCA
genomic: CTCTTTTCCTCTATAACTACACAACCCACCAGCTTCATGGGGTATTTGAGgtgtgtgatt ... atctgcttagGCTGCCAGTTTT-GGTGGGTCCAATATCGATCCTACTGCA

EST: gi|149079919|gb|EE168929.2|EE168929

EST:     CTCTTTTTCTCTATAACTACACAACCCACCAGCTTCATGGGGTATTTGAG                         GCTGCCAGTTTTGGTGGGGTC-AATATCGATCCTACTGCA
genomic: CTCTTTTCCTCTATAACTACACAACCCACCAGCTTCATGGGGTATTTGAGgtgtgtgatt ... atctgcttagGCTGCCAGTTTTGGTGGG-TCCAATATCGATCCTACTGCA

EST: gi|60338189|gb|DN205162.1|DN205162

EST:     CACAACCCACCAGCTTCATGGGGTA-TTGAGG                         GCTGCCAGTTTTGGTGGGTCCAATATCGATCCTACTGCATGGGAGGATAA
genomic: CACAACCCACCAGCTTCATGGGGTATTTGA-Ggtgtgtgatt ... atctgcttagGCTGCCAGTTTTGGTGGGTCCAATATCGATCCTACTGCATGGGAGGATAA

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), 46 (downstream exon)
Score: 228

TTTGCCAGCAAGATATCGTGATTCAGTCCGAGCAATCACTCCTGGCTTGCCTCTTTTCCTCTATAACTACACAACCCACCAGCTTCATGGGGTATTTGAGgtgtgtgatt ... atctgcttagGCTGCCAGTTTTGGTGGGTCCAATATCGATCCTACTGCATGGGAGGATAAGAAGTGTAAAGGTGAATCTAGATTCCCAGCGCAG

Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 175

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 179

Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 87

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TTTGCCAGCAAGATATCGTGATTCAGTCCGAGCAATCACTCCTGGCTTGCCTCTTTTCCTCTATAACTACACAACCCACCAGCTTCATGGGGTATTTGAGgtgtgtgattggttatctgatttcctgattcctgcaaagcctatctcaagttgttaaacacttgttcgtttgtcatacaaaagatacttttgagctaaaa

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - acaaaaga