ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq

Sequence

atgc intronic sequence ATGC exonic sequence

CCAAAGAGTCCAAGAGCGGTTCTTTGTTTGGAGGTTTTCCATCCCTGGAGGAACGAGATAAGTCTTATGACATAAAAGACTCGATGACTGTACATTGTGGgtatgcctatacatttcatatgatttatctcgagatcatgtaatggtcgtctacaattatcagtatctcttttgctgtagctaacctactgtttgtttccag

Basic information

species	Zea mays
transcript	GRMZM5G891056_T02
intron #	3
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM5G891056_T01 (Zea mays), 5'ss of exon 4
lower sequence: LOC_Os01g19870.1 (Oryza sativa), 5'ss of exon 3

CCAAAGAGTCCAAGAGCGGTTCTTTGTTTGGAGGTTTTCCATCCCTGGAGGAACGAGATAAGTCTTATGACATAAAAGACTCGATGACTGTACATTGTGGgtatgcctatacatttcatatgattta---tctcgagatc-atgtaatggtcgtctaca--------attatcagtatctct------tttgc--tgtagctaacct--actgtttgtttccag
| |||||||| ||   |||||||||||||||||||| ||||||  |||| || ||||| ||||||||||||||||||||||| ||||| || |||||||||||||  || | |  |||| || ||||   |||  | ||| || | ||     ||||||        | ||| | |   | |      ||| |  |||| || | ||  ||||  | ||| |||
CAAAAGAGTCAAACCACGGTTCTTTGTTTGGAGGTTATCCATCATTGGAAGAGCGAGACAAGTCTTATGACATAAAAGACTCAATGACGGTTCATTGTGGgtatgtttacatagctcatctgctttagcttctgcacatctatatgataactatctacagaagtacaaatattaatgcattttaatagtttacaatgtaactgaactttactgcat-ttttcag

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|211516010|gb|FL160576.1|FL160576

EST:     GAACGAGATAAGTCTTATGACATAAAAGACTCGATGAGTGTACATTGTGG                         ATTTGTAAGAGGGAAGGTACCTGGT
genomic: GAACGAGATAAGTCTTATGACATAAAAGACTCGATGACTGTACATTGTGGgtatgcctat ... ttgtttccagATTTGTAAGAGGGAAGGTACCTGGT

EST: gi|211516003|gb|FL160569.1|FL160569

EST:     GAACGAGATAAGTCTTATGACATAAAAGACTCGATGAGTGTACATTGTGG                         ATTTGTAAGAGGGA
genomic: GAACGAGATAAGTCTTATGACATAAAAGACTCGATGACTGTACATTGTGGgtatgcctat ... ttgtttccagATTTGTAAGAGGGA

EST: gi|211516006|gb|FL160572.1|FL160572

EST:     GAACGAGATAAGTCTTATGACATAAAAGACTCGATGAGTGTACATTGTGG                         ATTTGTCAGAGCGAAGG
genomic: GAACGAGATAAGTCTTATGACATAAAAGACTCGATGACTGTACATTGTGGgtatgcctat ... ttgtttccagATTTGTAAGAGGGAAGG

EST: gi|211516012|gb|FL160578.1|FL160578

EST:     AACGAGANTA-GTCTTATGACATAAAAGACTCGATGAGTGTACATTGTGG                         ATTTGTAAGAGGGAAGGTACCTGGTCTTAATACTGGGTTTGACATAGATGA
genomic: AACGAGA-TAAGTCTTATGACATAAAAGACTCGATGACTGTACATTGTGGgtatgcctat ... ttgtttccagATTTGTAAGAGGGAAGGTACCTGGTCTTAATACTGGGTTTGACATAGATGA

EST: gi|211516002|gb|FL160568.1|FL160568

EST:     GAACGAGATAAGTCTTATGACATAAAAGACTCGATGAGTGTACATTGTGG                         ATTTGTAAGAGGGA
genomic: GAACGAGATAAGTCTTATGACATAAAAGACTCGATGACTGTACATTGTGGgtatgcctat ... ttgtttccagATTTGTAAGAGGGA

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: 45 (upstream exon), 47 (downstream exon)
Score: 45

CCAAAGAGTCCAAGAGCGGTTCTTTGTTTGGAGGTTTTCCATCCCTGGAGGAACGAGATAAGTCTTATGACATAAAAGACTCGATGACTGTACATTGTGGgtatgcctat ... ttgtttccagATTTGTAAGAGGGAAGGTACCTGGTCTTAATACTGGGTTTGACATAGATGAAGCTGATCATTCTGAGATGCAGCTGTGCCAGAGTACAGTTGTTGCCTCT

Block sizes: 46 (upstream exon), 46 (downstream exon)
Score: 9

Block sizes: 43 (upstream exon), 49 (downstream exon)
Score: 18