ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq

Sequence

atgc intronic sequence ATGC exonic sequence

AAGTTTCTCAAATTTGGCTGATGTTTGGACTAAGGAAATAGAAGCAAACTCAACAAACAAAGACTGCATAAAAATGCTTGTTGGAAACAAAGTTGACAAGgtaccatctctgccagaaacttgattgttatttctttcctgaaacattgtgtctcatctaagaatttcttaataccttttgttactacataagtggcact...

Basic information

species	Zea mays
transcript	GRMZM2G075051_T01
intron #	4
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G075051_T01 (Zea mays), 5'ss of exon 4
lower sequence: LOC_Os10g31830.1 (Oryza sativa), 5'ss of exon 4

AAGTTTCTCAAATTTGGCTGATGTTTGGACTAAGGAAATAGAAGCAAACTCAACAAACAAAGACTGCATAAAAATGCTTGTTGGAAACAAAGTTGACAAGgtaccatctctgccagaaacttgattgtt-------------atttct-----ttcctgaa----acattgtgtctca----tctaagaatttcttaatac-cttttgttactacataagtggcact------------------------------------------------------------------
||| ||| ||||| ||||||| || |||| ||||||||||||  || ||||| |||||||||||||||||||||||||||||||||||||| |||||||||||| || |   | |   | ||  || ||               | ||     |||||||     |  || | | |||    |  |||    |  || ||  |  || | |   | |||||  ||                                                                    
AAGCTTCACAAATCTGGCTGAAGTATGGAGTAAGGAAATAGAGTCACACTCATCAAACAAAGACTGCATAAAAATGCTTGTTGGAAACAAAATTGACAAGgtactatttggccaaagtagttatttctttgaaaaaaaaagtgatcctggctgttcctgagttttagcttttatttcattgattcaagttcattatagtatgcccttttcagcccttaagttccatcgatttcataaaatactgttgaacatctcatgggagcatagttgattttgatggttctatctttcag

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|71439178|gb|DR820228.1|DR820228

EST:     CAACAAACAAAGACTGCATAAAAATGCTTGTTGGAAACAAAGTTGACAAG                         GATGATGAAAGAATGGTCACAAAAGAGGAAGGTCTTGCTTTTGCTGAAGAA
genomic: CAACAAACAAAGACTGCATAAAAATGCTTGTTGGAAACAAAGTTGACAAGgtaccatctc ... catcttgtagGATGATGAAAGAATGGTCACAAAAGAGGAAGGTCTTGCTTTTGCTGAAGAA

EST: gi|101387421|gb|EB815726.1|EB815726

EST:     CAACAAACAAAGACTGCATAAAAATGCTTGTTGGAAACAAAGTTGACAAG                         GATGATGAAAGAATGGTCACAAAAGAGGAAGGTCTTGCTTTTGCTGAAGAA
genomic: CAACAAACAAAGACTGCATAAAAATGCTTGTTGGAAACAAAGTTGACAAGgtaccatctc ... catcttgtagGATGATGAAAGAATGGTCACAAAAGAGGAAGGTCTTGCTTTTGCTGAAGAA

EST: gi|5005772|gb|AI711834.1|AI711834

EST:     CAACAAACAAAGACTGCATAAAAATGCTTGTTGGAAACAAAGTTGACAAG                         GATGATGAAAGAATGGTCACAAAAGAGGAAGGTCTTGCTTTTGCTGAAGAA
genomic: CAACAAACAAAGACTGCATAAAAATGCTTGTTGGAAACAAAGTTGACAAGgtaccatctc ... catcttgtagGATGATGAAAGAATGGTCACAAAAGAGGAAGGTCTTGCTTTTGCTGAAGAA

EST: gi|47962623|gb|CN845332.1|CN845332

EST:     CAACAAACAAAGACTGCATAAAAATGCTTGTTGGAAACAAAGTTGACAAG                         GATGATGAAAGAATGGTCACAAAGGAGGAAGGTCTTGCTTTTGCTGAAGAA
genomic: CAACAAACAAAGACTGCATAAAAATGCTTGTTGGAAACAAAGTTGACAAGgtaccatctc ... catcttgtagGATGATGAAAGAATGGTCACAAAAGAGGAAGGTCTTGCTTTTGCTGAAGAA

EST: gi|78106734|gb|DV525152.1|DV525152

EST:     CAACAAACAAAGACTGCATAAAAATGCTTGTTGGAAACAAAGTTGACAAG                         GATGATGAAAGAATGGTCACAAAAGAGGAAGGTCTTGCTTTTGCTGAAGAA
genomic: CAACAAACAAAGACTGCATAAAAATGCTTGTTGGAAACAAAGTTGACAAGgtaccatctc ... catcttgtagGATGATGAAAGAATGGTCACAAAAGAGGAAGGTCTTGCTTTTGCTGAAGAA

EST: gi|101387258|gb|EB815646.1|EB815646

EST:     CACCAAACAAAGACTGCATAAAAATGCTTGTTGGAAACAAAGTTGACAAG                         GATGATGAAAGAATGGTCACAAAAGAGGAAGGTCTTGCTTTTGCTGAAGAA
genomic: CAACAAACAAAGACTGCATAAAAATGCTTGTTGGAAACAAAGTTGACAAGgtaccatctc ... catcttgtagGATGATGAAAGAATGGTCACAAAAGAGGAAGGTCTTGCTTTTGCTGAAGAA

EST: gi|211236984|gb|FL432200.1|FL432200

EST:     CAACAAACAAAGACTGCATAAAAATGCTTGTTGGAAACAAAGTTGACAAG                         GATGATGAAAGAATGGTCACAAAAGAGGAAGGTCTTGCTTTTGCTGAAGAA
genomic: CAACAAACAAAGACTGCATAAAAATGCTTGTTGGAAACAAAGTTGACAAGgtaccatctc ... catcttgtagGATGATGAAAGAATGGTCACAAAAGAGGAAGGTCTTGCTTTTGCTGAAGAA

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: 177

AAGTTTCTCAAATTTGGCTGATGTTTGGACTAAGGAAATAGAAGCAAACTCAACAAACAAAGACTGCATAAAAATGCTTGTTGGAAACAAAGTTGACAAGgtaccatctc ... catcttgtagGATGATGAAAGAATGGTCACAAAAGAGGAAGGTCTTGCTTTTGCTGAAGAATATGGATGTCTGTTTCTTGAGAGCAGTGCAAAAACACGAGAAAACGTTG

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 105

Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 178