ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq

Sequence

atgc intronic sequence ATGC exonic sequence

AAGCTTCATTGACATCAAAGATTCCACTGGTATCGAGGATAAAGAATTGAGACGAACATTGCAATCTCTTGCATGTGGTAAAGTTCGGGTTCTCCAAAAGgtgtgttcctttttttttgccccatcgtcattttgcattttcagtatgcagcttctttaattgtaacctttgttttcag

Basic information

species	Zea mays
transcript	AC155496.2_FGT009
intron #	13
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: AC155496.2_FGT009 (Zea mays), 5'ss of exon 13
lower sequence: LOC_Os03g57290.1 (Oryza sativa), 5'ss of exon 13

AAGCTTCATTGACATCAAAGATTCCACTGGTATCGAGGATAAAGAATTGAGACGAACATTGCAATCTCTTGCATGTGGTAAAGTTCGGGTTCTCCAAAAGgtgtgttcctttttttttgccccatcgtcattttgcattttcagtatgcagcttctttaattgtaacctttgttttcag
||||||| | || ||||| || || |||||||| ||||||||||||||| || ||||  ||||||| |||||||| |||||||||||||||||||||||||||||   |||| ||||   || |  |||    |  |||||||||| ||||||| || | |||| || ||| |||||||
AAGCTTCCTCGATATCAAGGAATCGACTGGTATTGAGGATAAAGAATTGCGAAGAACGCTGCAATCACTTGCATGCGGTAAAGTTCGGGTTCTCCAAAAGgtgtggctctttatttt-atccaaatgtctaacta-attttcagta-gcagcttgttcagttgtcacttttattttcag

upper sequence: AC155496.2_FGT009 (Zea mays), 5'ss of exon 13
lower sequence: GLYMA15G10030.2 (Glycine max), 5'ss of exon 13

AAGCTTCATTGACATCAAAGATTCCACTGGTATCGAGGATAAAGAATTGAGACGAACATTGCAATCTCTTGCATGTGGTAAAGTTCGGGTTCTCCAAAAGgtgtgttcctttttttttgccccatcgtcattttgcattttcagta------tgcagcttctttaa---ttgtaacctttgttttcag-----------------
||||||    || ||||| || || |||||||| ||||  || ||||||||| | ||  ||||||| ||||||||||| |||||||| || || |||||||||||||  |  |  ||||    ||   || |||  | |||  ||       |   | |||||| |   || |||  ||  ||  |                   
AAGCTTTCAAGATATCAAGGACTCTACTGGTATAGAGGGCAAGGAATTGAGAAGGACTCTGCAATCACTTGCATGTGGAAAAGTTCGTGTCCTACAAAAGgtgtgtttgtaatcatttggagaattaccagtttataatttttgttaattactatggtttcttttaattttctaatgttgattccctttgttgaacatgcaacag

upper sequence: AC155496.2_FGT009 (Zea mays), 5'ss of exon 13
lower sequence: GLYMA08G10180.1 (Glycine max), 5'ss of exon 13

AAGCTTCATTGACATCAAAGATTCCACTGGTATCGAGGATAAAGAATTGAGACGAACATTGCAATCTCTTGCATGTGGTAAAGTTCGGGTTCTCCAAAAGgtgtgttcctttttttttgccccatcgtcattttgcattttcagtatgcagcttc--tttaattgtaacctttgttttcag-----------------------
|||  |    || ||||||||| | |||||||| ||||| || ||| ||||||| |   ||||||| || || |||||||||||||| || || |||||||||||||  |  |  ||||    ||   || | |  |  ||  || || |  |    | |   | ||   |||| | |                          
AAGTCTTCAAGATATCAAAGATGCTACTGGTATTGAGGACAAGGAACTGAGACGGATTCTGCAATCACTAGCTTGTGGTAAAGTTCGTGTCCTACAAAAGgtgtgtttgtaatcatttgtagaatttccaatatataacttttgtttgtaattatggtctctgtatattttttgatatttttccctttaatgaacatgcaacag

upper sequence: AC155496.2_FGT009 (Zea mays), 5'ss of exon 13
lower sequence: GLYMA05G27240.1 (Glycine max), 5'ss of exon 13

AAGCTTCATTGACATCAAAGATTCCACTGGTATCGAGGATAAAGAATTGAGACGAACATTGCAATCTCTTGCATGTGGTAAAGTTCGGGTTCTCCAAAAGgtgtgttcctttttttttgccccatcgtcattttgcattttcagtatgcagct----tctttaattgtaacct-ttgttttcag--------------------
|||  |    || ||||||||| | |||||||| ||||| || ||| | ||| | ||  ||||||| || || |||||||||||||| || || |||||||||||||  |  |  ||||    ||   ||   | || |||   | |  | ||    |||     | |  |   ||||||||                      
AAGTCTTCAAGATATCAAAGATGCTACTGGTATTGAGGACAAGGAACTCAGAAGGACTCTGCAATCACTAGCTTGTGGTAAAGTTCGTGTCCTACAAAAGgtgtgtttgtaatcatttgaagaatttccaacatacaatttttatttataactatggtctccgtatatttctcattgttttcccctttaatgaccatgcaacag

upper sequence: AC155496.2_FGT009 (Zea mays), 5'ss of exon 13
lower sequence: GLYMA13G29010.1 (Glycine max), 5'ss of exon 14

AAGCTTCATTGACATCAAAGATTCCACTGGTATCGAGGATAAAGAATTGAGACGAACATTGCAATCTCTTGCATGTGGTAAAGTTCGGGTTCTCCAAAAGgtgtgttcctttttttttgccccatcgtcattttgca----ttttcagta--tgcagcttctttaa---ttgtaacctttgttttcag-----------------
||||||    || ||||| || || |||||||| ||||| || ||| ||||| | ||  ||||||| ||||||||||| |||||||| || || |||||||||||||     |  ||||    ||   || |||  |    |||| | |   |   | |||||| |   || |||  ||  ||  |                   
AAGCTTTCAAGATATCAAGGACTCTACTGGTATAGAGGACAAGGAACTGAGAAGGACTCTGCAATCACTTGCATGTGGAAAAGTTCGTGTCCTACAAAAGgtgtgtttgcaatcatttggagaattaccagtttataattttttttaattactatggtttcttttaattttctaatgttgattccctttgttgaacatgcaacag

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|32847176|gb|CD986857.1|CD986857

EST:     GACGAACATTGCAATCTCTTGCATGTGGTAAAGTTCGGGTTCTCCAAAAG                         ATACCAAAAGGGAGAGATGTAGAAGATAAGGATGAATTTGTATTCAATGAA
genomic: GACGAACATTGCAATCTCTTGCATGTGGTAAAGTTCGGGTTCTCCAAAAGgtgtgttcct ... ttgttttcagATACCAAAAGGGAGAGATGTAGAAGATAAGGATGAATTTGTATTCAATGAA

EST: gi|5901302|gb|AW042402.1|AW042402

EST:     GACGAACACTGCAATCTCTTGCATGTGGTAAAGTTCGGGTTCTCCAAAAG                         ATACCAAAAGGGAGAGATGTAGAAAATAAGGATGAATTTGTATTCAATGAA
genomic: GACGAACATTGCAATCTCTTGCATGTGGTAAAGTTCGGGTTCTCCAAAAGgtgtgttcct ... ttgttttcagATACCAAAAGGGAGAGATGTAGAAGATAAGGATGAATTTGTATTCAATGAA

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: 162

AAGCTTCATTGACATCAAAGATTCCACTGGTATCGAGGATAAAGAATTGAGACGAACATTGCAATCTCTTGCATGTGGTAAAGTTCGGGTTCTCCAAAAGgtgtgttcct ... ttgttttcagATACCAAAAGGGAGAGATGTAGAAGATAAGGATGAATTTGTATTCAATGAAGATTTTAGTGCTCCTCTCTACCGCATAAAG

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 86

Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 80