ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq

Sequence

atgc intronic sequence ATGC exonic sequence

GTACCGCATCGACCGCAACCAAGTCACCTGGGACGTCTACAACGCCAAGCTCAGGTCCCTCGGCATCCTCGTCAAGGCCCGCAACTTCCTCGTCTTTCAGgtttctccatttgttcccttggtcattgtatattcctgataatttaaagtttccagtctcgggtttaagtagggcagggaaactgtccatttgcactgcag

Basic information

species	Zea mays
transcript	GRMZM5G899800_T01
intron #	1
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM5G899800_T01 (Zea mays), 5'ss of exon 1
lower sequence: LOC_Os12g44390.1 (Oryza sativa), 5'ss of exon 1

GTACCGCATCGACCGCAACCAAGTCACCTGGGACGTCTACAACGCCAAGCTCAGGTCCCTCGGCATCCTCGTCAAGGCCCGCAACTTCCTCGTCTTTCAGgtt---tctccatttgttcccttggtcattgtata-ttcctgataatttaaagtttccagtctcgggtttaagtagggcagggaaactgtccatttgcactgcag
|||||| |||||| ||   |  ||||||||||||| |||||||||||| ||||| ||||| ||||||||||||||||| ||||| ||||||||||| |||||    | ||| |   ||  | |  || |  || |  ||||      ||||   ||  |      |   ||| ||       |||  |  |||||||||| ||||
GTACCGGATCGACGGCCGTCTCGTCACCTGGGACGACTACAACGCCAAACTCAGATCCCTGGGCATCCTCGTCAAGGCTCGCAATTTCCTCGTCTTCCAGgtcagatgtccctaatttaacattttcctcatacaactcctccctgattaa---ttata----tagcactaaataaatttatgaa--ttaccatttgcaccgcag

upper sequence: GRMZM5G899800_T01 (Zea mays), 5'ss of exon 1
lower sequence: GLYMA13G18470.1 (Glycine max), 5'ss of exon 1

GTACCGCATCGACCGCAACCAAGTCACCTGGGACGTCTACAACGCCAAGCTCAGGTCCCTCGGCATCCTCGTCAAGGCCCGCAACTTCCTCGTCTTTCAGgtttctccatttgttcccttggtcattgtatattcctga---taatttaaagtttccagtctcgggttta-agtagggcagggaaactgtccatttgcactgcag
|||||||||||||     ||  ||||  ||||||  |||||||  ||  || | |||||||||||| |||||||| || ||||| ||| | |||||||||||| || | |   |||  ||   | || | |     | |   |  || ||  | |   || |    | |  |  ||     ||  | | |   |||  |      
GTACCGCATCGACGAATCCCTTGTCAATTGGGACACCTACAACAACAGACTTAAGTCCCTCGGCATTCTCGTCAAAGCTCGCAATTTCTTGGTCTTTCAGgtt-ctgcttcgcttcttttcccctttttgtgcaattaacttttgttgaagctctattgttttacttctccaaaagcttgaggtgaatataagtttctatg----

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|89758718|gb|DY687797.1|DY687797

EST:     TCAGGTCCCTCGGCATCCTCGTCAAGGCCCGCAACTTCCTCGTCTTTCAG                         GGTGATGTAGAATCCATTGCCTCCAAGAACCCCAAGGAGCTCACCGCTCTC
genomic: TCAGGTCCCTCGGCATCCTCGTCAAGGCCCGCAACTTCCTCGTCTTTCAGgtttctccat ... tgcactgcagGGTGATGTAGAATCCATTGCCTCCAAGAACCCCAAGGAGCTCACCGCTCTC

EST: gi|30306655|gb|CD001328.1|CD001328

EST:     TCAGGTCCCTCGGCATCCTCGTCAAGGCCCGCAACTTCCTCGTCTTTCAG                         GGTGATGTAGAATCCATTGCCTCCAAGAACCCCAAGGAGCTCACCGCTCTC
genomic: TCAGGTCCCTCGGCATCCTCGTCAAGGCCCGCAACTTCCTCGTCTTTCAGgtttctccat ... tgcactgcagGGTGATGTAGAATCCATTGCCTCCAAGAACCCCAAGGAGCTCACCGCTCTC

EST: gi|60344129|gb|DN211102.1|DN211102

EST:     TCAGGTCCCTCGGCATCCTCGTCAAGGCCCGCAACTTCCTCGTCTTTCAG                         GGTGATGTAGAATCCATTGCCTCCAAGAACCCCAAGGAGCTCACCGCTCTC
genomic: TCAGGTCCCTCGGCATCCTCGTCAAGGCCCGCAACTTCCTCGTCTTTCAGgtttctccat ... tgcactgcagGGTGATGTAGAATCCATTGCCTCCAAGAACCCCAAGGAGCTCACCGCTCTC

EST: gi|50336483|gb|CO531609.1|CO531609

EST:     TCAGGTCCCTCGGCATCCTCGTCAAGGCCCGCAACTTCCTCGTCTTTCAG                         GGTGATGTAGAATCCATTGCCTCCAAGAACCCCAAGGAGCTCACCGCTCTC
genomic: TCAGGTCCCTCGGCATCCTCGTCAAGGCCCGCAACTTCCTCGTCTTTCAGgtttctccat ... tgcactgcagGGTGATGTAGAATCCATTGCCTCCAAGAACCCCAAGGAGCTCACCGCTCTC

EST: gi|60336873|gb|DN203846.1|DN203846

EST:     TCAGGTCCCTCGGCATCCTCGTCAAGGCCCGCAACTTCCTCGTCTTTCAG                         GGTGATGTAGAATCCATTGCCTCCAAGAACCCCAAGGAGCTCACCGCTCTC
genomic: TCAGGTCCCTCGGCATCCTCGTCAAGGCCCGCAACTTCCTCGTCTTTCAGgtttctccat ... tgcactgcagGGTGATGTAGAATCCATTGCCTCCAAGAACCCCAAGGAGCTCACCGCTCTC

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: 356

GTACCGCATCGACCGCAACCAAGTCACCTGGGACGTCTACAACGCCAAGCTCAGGTCCCTCGGCATCCTCGTCAAGGCCCGCAACTTCCTCGTCTTTCAGgtttctccat ... tgcactgcagGGTGATGTAGAATCCATTGCCTCCAAGAACCCCAAGGAGCTCACCGCTCTCCTGGAGCAGATCTCAGGCTCTGATGAGCTTAGGAGGGAGTATGACGAGC

Block sizes: 48 (upstream exon), 47 (downstream exon)
Score: 109

Block sizes: 49 (upstream exon), 46 (downstream exon)
Score: 102