ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq

Sequence

atgc intronic sequence ATGC exonic sequence

GCGCATGCTTGAAGAATCTCTTGGGTCTGTCCAGAAGTCCATCCATGAGGATGTGAGAAATCTCCACATTGAACTTTTAAGACAGTTTCACATGCACGAGgtaaaatttctagctcaatatgctggggttgctttgtgcttcgagttttgattcaaatttgattttaagctgactttgttttattctcaatggcacacct...

Basic information

species	Zea mays
transcript	GRMZM2G088261_T02
intron #	9
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G088261_T03 (Zea mays), 5'ss of exon 3
lower sequence: LOC_Os09g09470.1 (Oryza sativa), 5'ss of exon 9

GCGCATGCTTGAAGAATCTCTTGGGTCTGTCCAGAAGTCCATCCATGAGGATGTGAGAAATCTCCACATTGAACTTTTAAGACAGTTTCACATGCACGAGgtaaaatttctagctcaatatgctggggttgctttgtgc-ttcgagttttgattc-aaatttgattttaagctg-actttgttttattctcaatggcacacct
||| |||||||||||||| || |||||||| |||||||||||||||||||| ||||||||||| ||||| |||||| ||||||||||||||||||| ||||||| |    |     ||    |   | ||    ||| | |||    |  | ||| |      |  |||  ||| | |  ||| || |||     ||| ||| 
GCGGATGCTTGAAGAATCCCTAGGGTCTGTTCAGAAGTCCATCCATGAGGACGTGAGAAATCTGCACATCGAACTTCTAAGACAGTTTCACATGCAAGAGgtaagacaaatcttataagcaaccatgcttatagtgtacattctttctccgcttccatgcactagattacactggattgagttctagtct-gtcagca-acc-

upper sequence: GRMZM2G088261_T03 (Zea mays), 5'ss of exon 3
lower sequence: GLYMA02G41880.1 (Glycine max), 5'ss of exon 9

GCGCATGCTTGAAGAATCTCTTGGGTCTGTCCAGAAGTCCATCCATGAGGATGTGAGAAATCTCCACATTGAACTTTTAAGACAGTTTCACATGCACGAGgtaaaatttctagctcaatatgctggggttgctttgtgcttcgagttttgattcaaatttgattttaagctgactttgttttattctcaatggcacacct
 || |  ||||||||| |||| |  ||  | ||||| ||||| || |||||| ||||||| || || |||||| |||| ||||||||||| ||||| |||||      | || ||  |  |  ||  | || |||    ||    || | ||||   | | ||  |||       |||| | ||   |||  |       
ACGGACCCTTGAAGAAACTCTGGATTCCTTTCAGAAATCCATACACGAGGATATGAGAAACCTTCATATTGAAATTTTGAGACAGTTTCATATGCAAGAGgtg-----tgtatctggaattattgatggtgattttcattt----ttgtaattcctctctaat--taa-------ttgtctcatg--caacag-------

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|91878842|gb|EB408799.1|EB408799

EST:     ATGTGAGAAATCTCCACATTGAACTTTTAAGACAGTTTCACATGCACGAG                         ATGGAAATGTCAGGCGTGCTGAACTTGGTCCTGGAAAAGGTGGAAGGCCTG
genomic: ATGTGAGAAATCTCCACATTGAACTTTTAAGACAGTTTCACATGCACGAGgtaaaatttc ... cgagaaacagATGGAAATGTCAGGCGTGCTGAACTTGGTCCTGGAAAAGGTGGAAGGCCTG

EST: gi|76280381|gb|DV019949.1|DV019949

EST:     ATGTGAGAAATCTCCACATTGAACTTTTAAGACAGTTTCACATGCACGAG                         ATGGAAATGTCAGGCGTGCTGAACTTGGTCCTGGAAAAGGTGGAAGGCCTG
genomic: ATGTGAGAAATCTCCACATTGAACTTTTAAGACAGTTTCACATGCACGAGgtaaaatttc ... cgagaaacagATGGAAATGTCAGGCGTGCTGAACTTGGTCCTGGAAAAGGTGGAAGGCCTG

EST: gi|93282882|gb|EB675146.1|EB675146

EST:     ATGTGAGAAATCTCCACATTGAACTTTTAAGACAGTTTCACATGCACGAG                         ATGGAAATGTCAGGCGTGCTGAACTTGGTCCTGGAAAAGGTGGAAGGCCTG
genomic: ATGTGAGAAATCTCCACATTGAACTTTTAAGACAGTTTCACATGCACGAGgtaaaatttc ... cgagaaacagATGGAAATGTCAGGCGTGCTGAACTTGGTCCTGGAAAAGGTGGAAGGCCTG

EST: gi|89251454|gb|DY623240.1|DY623240

EST:     ATGTGAGAAATCTCCACATTGAACTTTTAAGACAGTTTCACATGCACGAG                         ATGGAAATGTCAGGCGTGCTGAACTTGGTCCTGGAAAAGGTGGAAGGCCTG
genomic: ATGTGAGAAATCTCCACATTGAACTTTTAAGACAGTTTCACATGCACGAGgtaaaatttc ... cgagaaacagATGGAAATGTCAGGCGTGCTGAACTTGGTCCTGGAAAAGGTGGAAGGCCTG

EST: gi|86473318|gb|DY239688.1|DY239688

EST:     ATGTGAGAAATCTCCCCATTGAACTTTTAAGACAGTTTCACATGCACGAG                         ATGGAAATGTCAGGCGTGCTGAACTTGGTCCTGGAAAAGGTGGAAGGCCTG
genomic: ATGTGAGAAATCTCCACATTGAACTTTTAAGACAGTTTCACATGCACGAGgtaaaatttc ... cgagaaacagATGGAAATGTCAGGCGTGCTGAACTTGGTCCTGGAAAAGGTGGAAGGCCTG

EST: gi|88755725|gb|DY539866.1|DY539866

EST:     ATGTGAGAAATCTCCACATTGAACTTTTAAGACAGTTTCACATGCACGAG                         ATGGAAATGTCAGGCGTGCTGAACTTGGTCCTGGAAAAGGTGGAAGGCCTG
genomic: ATGTGAGAAATCTCCACATTGAACTTTTAAGACAGTTTCACATGCACGAGgtaaaatttc ... cgagaaacagATGGAAATGTCAGGCGTGCTGAACTTGGTCCTGGAAAAGGTGGAAGGCCTG

EST: gi|89251709|gb|DY623495.1|DY623495

EST:     ATGTGAGAAATCTCCACATTGAACTTTTAAGACAGTTTCACATGCACGAG                         ATGGAAATGTCAGGCGTGCTGAACTTGGTCCTGGAAAAGGTGGAAGGCCTG
genomic: ATGTGAGAAATCTCCACATTGAACTTTTAAGACAGTTTCACATGCACGAGgtaaaatttc ... cgagaaacagATGGAAATGTCAGGCGTGCTGAACTTGGTCCTGGAAAAGGTGGAAGGCCTG

EST: gi|91048721|gb|EB159139.1|EB159139

EST:     CCACATGGAACTTTTAAGACAGTTTCACATGCACGAG                         AGGGAAATGTCAGGCGTGCTGAACTTGGTCCTGGAAAAGGTGGAAGGCCGG
genomic: CCACATTGAACTTTTAAGACAGTTTCACATGCACGAGgtaaaatttc ... cgagaaacagATGGAAATGTCAGGCGTGCTGAACTTGGTCCTGGAAAAGGTGGAAGGCCTG

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), 46 (downstream exon)
Score: 61

GCGCATGCTTGAAGAATCTCTTGGGTCTGTCCAGAAGTCCATCCATGAGGATGTGAGAAATCTCCACATTGAACTTTTAAGACAGTTTCACATGCACGAGgtaaaatttc ... cgagaaacagATGGAAATGTCAGGCGTGCTGAACTTGGTCCTGGAAAAGGTGGAAGGCCTGACAAAAGAAGTGCAGCAACTAAGAAGGGAGAACCAACAGCTCAGGCAGC

Block sizes: 42 (upstream exon), 49 (downstream exon)
Score: 24

Block sizes: 46 (upstream exon), 47 (downstream exon)
Score: 61