ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq

Sequence

atgc intronic sequence ATGC exonic sequence

GTATCTCCAAACGCAAGGGAAAAATTTCTTTGGGCTTGAAGGCTCTGGTACTGATATTGTTCTGAATACGATAATTTTCAACTCATTCGTCTTCTGTCAGgtatgactattattgcagatcatttctttccgcaagtttttggttcactaaatatggatggcagcattggtgccagcatctagagtttagttagaattat...

Basic information

species	Zea mays
transcript	GRMZM5G878058_T02
intron #	4
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM5G878058_T02 (Zea mays), 5'ss of exon 4
lower sequence: LOC_Os12g39660.1 (Oryza sativa), 5'ss of exon 6

GTATCTCCAAACGCAAGGGAAAAATTTCTTTGGGCTTGAAGGCTCTGGTACTGATATTGTTCTGAATACGATAATTTTCAACTCATTCGTCTTCTGTCAGgtatgactattattgcagat-catttctttccgcaagtttttggttcactaaatatggatggcagcattggtgcca---gcatctagag-tttagttagaattat-
||||||||| |||||||||||||   | ||||| ||||| ||| ||| | ||||  |||| || ||||| || ||||||||||| || |||||||| ||||||||  ||  ||  || ||   |||||||       | || || |     | || || ||    ||  | ||||    ||||  ||||   |  | |  | |   
GTATCTCCAGACGCAAGGGAAAAGCATGTTTGGCCTTGATGGCCCTGATGCTGAAGTTGTGCTAAATACAATTATTTTCAACTCGTTTGTCTTCTGCCAGgtatgtgtaccataccaaatatgtttctttttt----tcttcggctag--gagtacgggtgttgtcaaagttgccctatgcatgcagaggcctcatcactaattca

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|211048552|gb|FL062136.1|FL062136

EST:     CTGATATTGTTCTGAATACGATAATTTTCAACTCATTCGTCTTCTGTCAG                         GTGTTCAATGAAATAAGCTCTCGGGAGATGGAGAAGATCAACGTGCTCAAG
genomic: CTGATATTGTTCTGAATACGATAATTTTCAACTCATTCGTCTTCTGTCAGgtatgactat ... gatactccagGTGTTCAATGAAATAAGCTCTCGGGAGATGGAGAAGATCAACGTGCTCAAG

EST: gi|149095267|gb|EE180895.2|EE180895

EST:     CTGATATTGTTCTGAATACGATAATTTTCAACTCATTCGTCTTCTGTCAG                         GTGTTCAATGAAATAAGCTCTCGGGAGATGGAGAAGATCAACGTGCTCAAG
genomic: CTGATATTGTTCTGAATACGATAATTTTCAACTCATTCGTCTTCTGTCAGgtatgactat ... gatactccagGTGTTCAATGAAATAAGCTCTCGGGAGATGGAGAAGATCAACGTGCTCAAG

EST: gi|211048549|gb|FL062133.1|FL062133

EST:     CTGATATTGTTCTGAATACGATAATTTTCAACTCATTCGTCTTCTGTCAG                         GTGTTCAATGAAATAAGCTCTCGGGAGATGGAGAAGATCAACGTGCTCAAG
genomic: CTGATATTGTTCTGAATACGATAATTTTCAACTCATTCGTCTTCTGTCAGgtatgactat ... gatactccagGTGTTCAATGAAATAAGCTCTCGGGAGATGGAGAAGATCAACGTGCTCAAG

EST: gi|211048550|gb|FL062134.1|FL062134

EST:     CTGATATTGTTCTGAATACGATAATTTTCAACTCATTCGTCTTCTGTCAK                         GTGTTCAATGAAATAAGCTCTCGGGAGATGGAGAAGATCAACGTGCTCAAG
genomic: CTGATATTGTTCTGAATACGATAATTTTCAACTCATTCGTCTTCTGTCAGgtatgactat ... gatactccagGTGTTCAATGAAATAAGCTCTCGGGAGATGGAGAAGATCAACGTGCTCAAG

EST: gi|211048548|gb|FL062132.1|FL062132

EST:     CTGATATTGTTCTGAATACGATAATTTTCAACTCATTCGTCTTCTGTCAG                         GTGTTCAATGAAATAAGCTCTCGGGAGATGGAGAAGATCAACGTGCTCAAG
genomic: CTGATATTGTTCTGAATACGATAATTTTCAACTCATTCGTCTTCTGTCAGgtatgactat ... gatactccagGTGTTCAATGAAATAAGCTCTCGGGAGATGGAGAAGATCAACGTGCTCAAG

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), 47 (downstream exon)
Score: 172

GTATCTCCAAACGCAAGGGAAAAATTTCTTTGGGCTTGAAGGCTCTGGTACTGATATTGTTCTGAATACGATAATTTTCAACTCATTCGTCTTCTGTCAGgtatgactat ... gatactccagGTGTTCAATGAAATAAGCTCTCGGGAGATGGAGAAGATCAACGTGCTCAAGGGCATGACAAGGAACTACGTGTTCATGGCTGTCCTCAGCAGCACGGTGA

Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 130

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 229