ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq

Sequence

atgc intronic sequence ATGC exonic sequence

CTGAGAGGTTTCGAGTTTGCTAAAGCGGTTACTCTTGTTGCTGAGCCGTTCACATTGGATAATGGCCTTCTCACCCCAACATTCAAGgtaaagctcatttgctctgttagaggcgaccccgataccaaatcactgacctgctgacactccacctcaacgcttctgtacctgtag

Basic information

species	Zea mays
transcript	GRMZM2G059381_T01
intron #	22
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G059381_T03 (Zea mays), 5'ss of exon 9
lower sequence: AT5G27600.1 (Arabidopsis thaliana), 5'ss of exon 22

CTGAGAGGTTTCGAGTTTGCTAAAGCGGTTACTCTTGTTGCTGAGCCGTTCACATTGGATAATGGCCTTCTCACCCCAACATTCAAGgtaaagctcatttgctctgttagaggcgaccccgataccaaatcactg--acctgct---gacactccacctcaacgcttctgtacctgtag------
 ||||||| || |||||||| || || || ||| | ||  | || || ||||| ||||| ||||| |||||||| ||||||||||||||||  || |    |  |||   ||  ||  |||  |  ||||   ||  || | |    ||  ||| |  |||    |  |  | || |        
TTGAGAGGGTTTGAGTTTGCAAAGGCTGTGACTTTGGTGCCAGAACCATTCACCTTGGAGAATGGACTTCTCACACCAACATTCAAGgtaa--ctaaacaacaatgt-gaagttgaaaccgcaatgaaatttttgttacttacctcggaatctctaattcatgtgtggtaaaacttttctaacag

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|60399365|gb|DN232179.1|DN232179

EST:     TTGCTGAGCCGTTCACATTGGATAATGGCCTTCTCACCCCAACATTCAAG                         GTCAAGAGGCCGCAAGCCAAAGCATACTTTGCAAAAGAGATCTCAGACATG
genomic: TTGCTGAGCCGTTCACATTGGATAATGGCCTTCTCACCCCAACATTCAAGgtaaagctca ... gtacctgtagGTCAAGAGGCCGCAAGCCAAAGCATACTTTGCAAAAGAGATCTCAGACATG

EST: gi|60395514|gb|DN228384.1|DN228384

EST:     TTGCTGAGCCATTCTCATTGGACAATGGCCTTCTCACCCCAACATTCAAG                         GTCAAGAGGCCGCAAGCCAAAGCATACTTTGCAAAAGAAATCTCAGACATG
genomic: TTGCTGAGCCGTTCACATTGGATAATGGCCTTCTCACCCCAACATTCAAGgtaaagctca ... gtacctgtagGTCAAGAGGCCGCAAGCCAAAGCATACTTTGCAAAAGAGATCTCAGACATG

EST: gi|93283329|gb|EB675593.1|EB675593

EST:     TTGCTGAGCCGTTCACATTGGATAATGGCCTTCTCACCCCAACATTCAAG                         GTCAAGAGGCCGCAAGCCAAAGCATACTTTGCAAAAGAGATCTCAGACATG
genomic: TTGCTGAGCCGTTCACATTGGATAATGGCCTTCTCACCCCAACATTCAAGgtaaagctca ... gtacctgtagGTCAAGAGGCCGCAAGCCAAAGCATACTTTGCAAAAGAGATCTCAGACATG

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), 37 (downstream exon)
Score: 60

CTGAGAGGTTTCGAGTTTGCTAAAGCGGTTACTCTTGTTGCTGAGCCGTTCACATTGGATAATGGCCTTCTCACCCCAACATTCAAGgtaaagctca ... gtacctgtagGTCAAGAGGCCGCAAGCCAAAGCATACTTTGCAAAAGAGATCTCAGACATGTATGCACGGTTGCTAGAGACAGAGTTAGCTAGGTCGAAGTTGTAACTTG

Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 122

Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 42