ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq

Sequence

atgc intronic sequence ATGC exonic sequence

GAATAACTACATCTCTGTTGGTGCTTCTGGAGCTTTATTTGGCCTGCTTGGATCCATGCTTTCTGAGCTACTCATGAACTGGACTATATACTCCAACAAGgccagtacaattaacagataaatatatactttattttatccagctgcttgatagtcatttagctcgtatacttaatttgctcttgcag

Basic information

species	Zea mays
transcript	GRMZM2G033937_T01
intron #	3
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G033937_T01 (Zea mays), 5'ss of exon 3
lower sequence: LOC_Os09g35730.1 (Oryza sativa), 5'ss of exon 3

GAATAACTACATCTCTGTTGGTGCTTCTGGAGCTTTATTTGGCCTGCTTGGATCCATGCTTTCTGAGCTACTCATGAACTGGACTATATACTCCAACAAGgccagtacaattaacagataaatatatactttattttatccagctgcttgatagtcatttagctcgtatacttaatttgctcttgcag
 |||||||||||||||||||| || ||||||||||||||||| ||||||||||| ||||||||||||||  | |||||||||||||| || ||||||||||  |||| |    | ||||  | ||| | |||    ||| ||| ||||||||  |  ||| | ||    |  ||||   |||||||||
TAATAACTACATCTCTGTTGGAGCCTCTGGAGCTTTATTTGGACTGCTTGGATCAATGCTTTCTGAGCTTATTATGAACTGGACTATTTATTCCAACAAGgttagtaaatgagatagatgcacatacatttt-cactattcagttgcttgatgtttgttttgatca---agctaatccactcttgcag

upper sequence: GRMZM2G033937_T01 (Zea mays), 5'ss of exon 3
lower sequence: GLYMA09G26610.2 (Glycine max), 5'ss of exon 3

GAATAACTACATCTCTGTTGGTGCTTCTGGAGCTTTATTTGGCCTGCTTGGATCCATGCTTTCTGAGCTACTCATGAACTGGACTATATACTCCAACAAGgccagtacaat-taacagataaatatatactttattttatccagctgcttgatagtcatttagctcgtatacttaatt--tgctcttgcag---------
 |  ||| | |||||||||||||||||||| ||| ||||||| || |||||  | |||||||| || ||  |||  ||||||| ||| ||  |||| ||||  |||| ||  | |  | |    ||    ||| | || ||    || ||| ||||  ||| |       |  | |||  || | |   |          
TAGAAACAATATCTCTGTTGGTGCTTCTGGTGCTCTATTTGGACTTCTTGGTGCAATGCTTTCAGAACTTATCACAAACTGGAGTATTTATACCAATAAGgtgagtataaagtcattggttcccatcctatttttgttttctgtgtgtttgttagttcttttgaaaaggaaaatgattaatgttatgaaaagattgacaa

upper sequence: GRMZM2G033937_T01 (Zea mays), 5'ss of exon 3
lower sequence: AT5G07250.2 (Arabidopsis thaliana), 5'ss of exon 3

GAATAACTACATCTCTGTTGGTGCTTCTGGAGCTTTATTTGGCCTGCTTGGATCCATGCTTTCTGAGCTACTCATGAACTGGACTATATACTCCAACAAGgccagtac-aattaacagat------aaatatatactttattttatccagctgcttgatagtcat----ttagctcgtatacttaatt--tgctcttgcag
 |  |||   ||||||||||| |||||||| ||| | |||||||| ||||| || ||||| ||||| ||  |||  |||||||| || ||||| |||||||  | ||| |||   |   |      ||| ||| |  | | |  |||  | ||  | ||  |  |    | |||   | |||   |||  ||| ||     
CAGAAACAGTATCTCTGTTGGAGCTTCTGGTGCTCTTTTTGGCCTCCTTGGCTCAATGCTCTCTGAACTTTTCACCAACTGGACAATCTACTCTAACAAGgttaataccaatctgcttttcatttcaaacatacaaatcactccatcatgttggctcatgtttctgatctgagcatatgtaccagattgctgcactcctg-

upper sequence: GRMZM2G033937_T01 (Zea mays), 5'ss of exon 3
lower sequence: AT5G07250.1 (Arabidopsis thaliana), 5'ss of exon 3

GAATAACTACATCTCTGTTGGTGCTTCTGGAGCTTTATTTGGCCTGCTTGGATCCATGCTTTCTGAGCTACTCATGAACTGGACTATATACTCCAACAAGgccagtacaattaacagataaatatatactttattttatccagctgcttgatagtcatttagctcgtatacttaatttgctcttgcag-----
 |  |||   ||||||||||| |||||||| ||| | |||||||| ||||| || ||||| ||||| ||  |||  |||||||| || ||||| |||||||  | |||      ||      | |  | || |      | |    ||  ||  |   || |||| | |   | || ||  | |         
CAGAAACAGTATCTCTGTTGGAGCTTCTGGTGCTCTTTTTGGCCTCCTTGGCTCAATGCTCTCTGAACTTTTCACCAACTGGACAATCTACTCTAACAAGgttaatac------caatctgcttttcatttcaaacatacaaatcactccatcatg--ttggctcatgtttctgatctgagcatatgtaccag

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|211161010|gb|FL476903.1|FL476903

EST:     CCATGCTTTCTGAGCTACTCATGAACT-GACTATATACTCCAACAAG                         GCAGCAGCTATAATAACACTCCTGTTTATAATTGCACTCAACTTGGCTATT
genomic: CCATGCTTTCTGAGCTACTCATGAACTGGACTATATACTCCAACAAGgccagtacaa ... gctcttgcagGCAGCAGCTATAATAACACTCCTGTTTATAATTGCACTCAACTTGGCTATT

EST: gi|88753280|gb|DY537421.1|DY537421

EST:     GATCCATGCTTTTTGAGCTACTCATGAACTGGACTATATACTCCAACAAG                         GCAGCAGCTATAATAACACTCCTGTTTATAATTGCACTCAACTTGGCTATT
genomic: GATCCATGCTTTCTGAGCTACTCATGAACTGGACTATATACTCCAACAAGgccagtacaa ... gctcttgcagGCAGCAGCTATAATAACACTCCTGTTTATAATTGCACTCAACTTGGCTATT

EST: gi|71304368|gb|DR788299.1|DR788299

EST:     GATCCATGCTTTCTGAGCTACTCATGAACTGGACTATATACTCCAACAAG                         GCAGCAGCTATAATAACACTCCTGTTTATAATTGCACTCAACTTGGCTATT
genomic: GATCCATGCTTTCTGAGCTACTCATGAACTGGACTATATACTCCAACAAGgccagtacaa ... gctcttgcagGCAGCAGCTATAATAACACTCCTGTTTATAATTGCACTCAACTTGGCTATT

EST: gi|149004836|gb|EE039341.2|EE039341

EST:     GATCCATGCTTTCTGAGCTACTCATGAACTGGACTATATACTCCAACAAG                         GCAGCAGCTATAATAACACTCCTGTTTATAATTGCACTCAACTTGGCTATT
genomic: GATCCATGCTTTCTGAGCTACTCATGAACTGGACTATATACTCCAACAAGgccagtacaa ... gctcttgcagGCAGCAGCTATAATAACACTCCTGTTTATAATTGCACTCAACTTGGCTATT

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: 52

GAATAACTACATCTCTGTTGGTGCTTCTGGAGCTTTATTTGGCCTGCTTGGATCCATGCTTTCTGAGCTACTCATGAACTGGACTATATACTCCAACAAGgccagtacaa ... gctcttgcagGCAGCAGCTATAATAACACTCCTGTTTATAATTGCACTCAACTTGGCTATTGGGATACTACCTCATGCTGACAACTTTGCTCACATTGGTGGATTCGCAA

Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 56

Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 21