ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq

Sequence

atgc intronic sequence ATGC exonic sequence

GGGTACCCTTACGAAGAAATACTGAGGACATTCCACAACCAAACCGACAACGTCATGTGCTCGTATTTACCTGTATTCAATTCATTCAACTTCACCAAAGgttggtgatggtgatgtccctctctgtttctctgcttcttgctccacagaacagagcttttagctaagcaatgggacattttttttcgcag

Basic information

species	Zea mays
transcript	GRMZM2G147849_T01
intron #	4
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G147849_T01 (Zea mays), 5'ss of exon 4
lower sequence: LOC_Os03g52630.1 (Oryza sativa), 5'ss of exon 4

GGGTACCCTTACGAAGAAATACTGAGGACATTCCACAACCAAACCGACAACGTCATGTGCTCGTATTTACCTGTATTCAATTCATTCAACTTCACCAAAGgttggtgatggtgatgtccctctctgtttctctgcttcttgctccacagaacagagcttttagctaagcaatgggacattttttttcgcag
|| || |||||||||||||||||||| ||||| ||||||||||| ||||| || |||||||||||| | ||  | | ||||||||||||||| ||||||||| |||| || |     ||| || ||  |||||  || |  ||| |     || |  |   || ||| ||||||||  |||          
GGATATCCTTACGAAGAAATACTGAGAACATTTCACAACCAAACAGACAATGTTATGTGCTCGTATCTGCCGATGTACAATTCATTCAACTTTACCAAAGgtcggtgctgtt-----ccccctttgcctctctttttttctctcta---gccacaaatggaagttaaacaatgggaggtttacag------

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|211472968|gb|FL344046.1|FL344046

EST:     CGTCATGTGCTCGTATTTACCTGTATTCAATTCATTCAACTTCACCAAAG                         GAGGATTAATACAGCTCAACCATGGAAGGCCTCAACCGCTTCAGTACGCTG
genomic: CGTCATGTGCTCGTATTTACCTGTATTCAATTCATTCAACTTCACCAAAGgttggtgatg ... tttttcgcagGAGGATTAATACAGCTCAACCATGGAAGGCCTCAACCGCTTCAGTACGCTG

EST: gi|160481653|gb|EY254223.1|EY254223

EST:     CGTCATGTGCTCGTATTTACCTGTATTCAATTCATTCAACTTCACCAAAG                         GAGGATTAATACAGCTCAACCATGGAAGGCCTCAACCGCTTCAGTACGCTG
genomic: CGTCATGTGCTCGTATTTACCTGTATTCAATTCATTCAACTTCACCAAAGgttggtgatg ... tttttcgcagGAGGATTAATACAGCTCAACCATGGAAGGCCTCAACCGCTTCAGTACGCTG

EST: gi|211308480|gb|FL124618.1|FL124618

EST:     CGTCATGTGCTCGTATTTACCTGTATTCAATTCATTCAACTTCACCAAAG                         GAGGATTAATACAGCTCAACCATGGAAGGCCTCAACCGCTTCAGTACGCTG
genomic: CGTCATGTGCTCGTATTTACCTGTATTCAATTCATTCAACTTCACCAAAGgttggtgatg ... tttttcgcagGAGGATTAATACAGCTCAACCATGGAAGGCCTCAACCGCTTCAGTACGCTG

EST: gi|74239514|gb|DT647428.1|DT647428

EST:     CGTCATGTGCTCGTATTTACCTGTATTCAATTCATTCAACTTCACCAAAG                         GAGGATTAATACAGCTCAACCATGGAAGGCCTCAACCGCTTCAGTACGCTG
genomic: CGTCATGTGCTCGTATTTACCTGTATTCAATTCATTCAACTTCACCAAAGgttggtgatg ... tttttcgcagGAGGATTAATACAGCTCAACCATGGAAGGCCTCAACCGCTTCAGTACGCTG

EST: gi|211467558|gb|FL331131.1|FL331131

EST:     CGTCATGTGCTCGTATTTACCTGTATTCAATTCATTCAACTTCACCAAAG                         GAGGATTAATACAGCTCAACCATGGAAGGCCTCAACCGCTTCAGTACGCTG
genomic: CGTCATGTGCTCGTATTTACCTGTATTCAATTCATTCAACTTCACCAAAGgttggtgatg ... tttttcgcagGAGGATTAATACAGCTCAACCATGGAAGGCCTCAACCGCTTCAGTACGCTG

EST: gi|211279182|gb|FL307694.1|FL307694

EST:     CGTCATGTGCTCGTATTTACCTGTATTCAATTCATTCAACTTCACCAAAG                         GAGGATTAATACAGCTCAACCATGGAAGGCCTCAACCGCTTCAGTACGCTG
genomic: CGTCATGTGCTCGTATTTACCTGTATTCAATTCATTCAACTTCACCAAAGgttggtgatg ... tttttcgcagGAGGATTAATACAGCTCAACCATGGAAGGCCTCAACCGCTTCAGTACGCTG

EST: gi|211001820|gb|FL229076.1|FL229076

EST:     CATGTGCTCGTATTTACCTGTATTCAATTCATTCAACTTCACCAAAG                         GAGGATTAATACAGCTCAACCATGGAAGGCCTCAACCGCTTCAGTACGCTG
genomic: CATGTGCTCGTATTTACCTGTATTCAATTCATTCAACTTCACCAAAGgttggtgatg ... tttttcgcagGAGGATTAATACAGCTCAACCATGGAAGGCCTCAACCGCTTCAGTACGCTG

EST: gi|67010311|gb|CO439060.1|CO439060

EST:     CGTCATGTGCTCGTATTTACCTGTATTCAATTCATTCAACTTCACCAAAG                         GAGGATTAATACAGCTCAACCATGGAAGGCCTCAACCGCTTCAGTACGCTG
genomic: CGTCATGTGCTCGTATTTACCTGTATTCAATTCATTCAACTTCACCAAAGgttggtgatg ... tttttcgcagGAGGATTAATACAGCTCAACCATGGAAGGCCTCAACCGCTTCAGTACGCTG

EST: gi|211532037|gb|FL347050.1|FL347050

EST:     CGTCATGTGCTCGTATTTACCTGTATTCAATTCATTCAACTTCACCAAAG                         GAGGATTAATACAGCTCAACCATGGAAGGCCTCAACCGCTTCAGTACGCTG
genomic: CGTCATGTGCTCGTATTTACCTGTATTCAATTCATTCAACTTCACCAAAGgttggtgatg ... tttttcgcagGAGGATTAATACAGCTCAACCATGGAAGGCCTCAACCGCTTCAGTACGCTG

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), 48 (downstream exon)
Score: 74

GGGTACCCTTACGAAGAAATACTGAGGACATTCCACAACCAAACCGACAACGTCATGTGCTCGTATTTACCTGTATTCAATTCATTCAACTTCACCAAAGgttggtgatg ... tttttcgcagGAGGATTAATACAGCTCAACCATGGAAGGCCTCAACCGCTTCAGTACGCTGTCAACGCAGCTTTCCTTGCTTCTTTATACAGCGACTATCTTGAAGCGGC

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 206

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 119