ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq

Sequence

atgc intronic sequence ATGC exonic sequence

GAGAAATATGTATTCAAACACCCTCAACCTAAGCGGCCCAAGTCACTGCGGATATATGAATCACATGTTGGAATGAGTAGCCCGgtatgcccataagctacaaatttttttctgtgcttattgtttagtccctcatggtccataccgattgtgtaatatttttaacatccaattgttcacattt...

Basic information

species	Zea mays
transcript	GRMZM2G073054_T01
intron #	9
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G073054_T02 (Zea mays), 5'ss of exon 9
lower sequence: LOC_Os04g33460.1 (Oryza sativa), 5'ss of exon 9

GAGAAATATGTATTCAAACACCCTCAACCTAAGCGGCCCAAGTCACTGCGGATATATGAATCACATGTTGGAATGAGTAGCCCGgtatgcccataagctacaaatttttt--tctgtgcttattgt-ttagtccctcatggtccataccgattgtgtaatatttttaacatccaattgttcacattt
|| |||||||||||| |||| ||||||||||| || || || || ||||||||||||||||||||| |||||||||||||||||||||||| ||||| ||  ||| ||||    | |  || |||| ||    |||  |   |  |   || ||                                 
GAAAAATATGTATTCCAACATCCTCAACCTAAACGACCAAATTCGCTGCGGATATATGAATCACATATTGGAATGAGTAGCCCGgtatgccnataagttattaatattttgacttttcttttttgtcttgaaacctttttcgctttgtagaatgcnnnnnnnnnnnnnnnnnnnnnnnnnnnnn---

upper sequence: GRMZM2G073054_T02 (Zea mays), 5'ss of exon 9
lower sequence: AT5G03650.1 (Arabidopsis thaliana), 5'ss of exon 9

GAGAAATATGTATTCAAACACCCTCAACCTAAGCGGCCCAAGTCACTGCGGATATATGAATCACATGTTGGAATGAGTAGCCCGgtatgcccataagctacaaatttttttctgtgcttattgtttagtccctcatggtc-cataccga----ttgtgtaatattttta-acatccaattgttcacattt--------------------------------------------------------------------------------------------
||||| |||||||||||||| |||||||| ||| | || ||||| ||  |||| |||||| |||||||||| ||||||||| |||| ||    |  ||| |   || | ||   |  ||||  ||| |||| | |        |||| |     | | |||  | |  | |   |  | ||||    | |                                                                                            
GAGAAGTATGTATTCAAACATCCTCAACCAAAGAGACCTAAGTCGCTAAGGATTTATGAAGCACATGTTGGCATGAGTAGCACGgtgtgtgtctg-gctcc---ttgtcttaaataattatgttttggtccttaacatctgtgtaccaagcttctttataacgtatcaatatgccacactgttggtttgttcagtatgtttgtttgactataataacatagatcccaatttctggatatttctctatatcacgtgaataatgtcagtgtacttgttatgcag

upper sequence: GRMZM2G073054_T02 (Zea mays), 5'ss of exon 9
lower sequence: AT2G36390.1 (Arabidopsis thaliana), 5'ss of exon 9

GAGAAATATGTATTCAAACACCCTCAACCTAAGCGGCCCAAGTCACTGCGGATATATGAATCACATGTTGGAATGAGTAGCCCGgtatgcccataagctacaaatttttttctgtgcttatt--gtttagtccctcatggtccataccgattgtgtaa--tatttttaacatccaattgttcacattt
|| |||||||  |||||||| ||||  || |||   ||||  || ||||| |||||||||||||||||||||||||||||  |||||||    |   ||   |  ||      ||  | | |  ||| |     |||  | | |        || |||  ||  ||| ||||  || |  ||| |   
GATAAATATGCGTTCAAACATCCTCGTCCAAAGAAACCCACATCGCTGCGTATATATGAATCACATGTTGGAATGAGTAGTACGgtatgtttcttt-ctcttatcttggaatggtaatcactaagttcataatgtcactgacaaaggtagaagtttaaactacatttgacatgaaaattctcata---

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|211263679|gb|FL032932.1|FL032932

EST:     GGCCAAAGTCACTGNGGATATATGAATCACATGTTGGAATGAGTAGCCCG                         GAACCAAAGATAAATACCTATGCTAACTTCAGAGATGAGGTGCTTCCAAGA
genomic: GGCCCAAGTCACTGCGGATATATGAATCACATGTTGGAATGAGTAGCCCGgtatgcccat ... tgttacacagGAACCAAAGATAAATACATATGCTAACTTCAGAGATGAGGTGCTTCCAAGA

EST: gi|87155797|gb|DY400586.1|DY400586

EST:     GGCCCAAGTCACTGCGGATATATGAATCACATGTTGGAATGAGTAGCCCG                         GAACCAAAGATAAATACATATGCTAACTTCAGAGATGAGGTGCTTCCAAGA
genomic: GGCCCAAGTCACTGCGGATATATGAATCACATGTTGGAATGAGTAGCCCGgtatgcccat ... tgttacacagGAACCAAAGATAAATACATATGCTAACTTCAGAGATGAGGTGCTTCCAAGA

EST: gi|26558524|gb|CA830759.1|CA830759

EST:     GGCCCAAGTCACTGCGGATATATGAATCACATGTTGGAATGAGTAGCCCG                         GAACCAAAGATAAATACATATGCTAACTTCAGAGATGAGGTGCTTCCAAGA
genomic: GGCCCAAGTCACTGCGGATATATGAATCACATGTTGGAATGAGTAGCCCGgtatgcccat ... tgttacacagGAACCAAAGATAAATACATATGCTAACTTCAGAGATGAGGTGCTTCCAAGA

EST: gi|67022129|gb|CO450878.1|CO450878

EST:     GGCCCAAGTCACTGCGGATATATGAATCACATGTTGGAATGAGTAGCCCG                         GAACCAAAGATAAATACATATGCTAACTTCAGAGATGAGGTGCTTCCAAGA
genomic: GGCCCAAGTCACTGCGGATATATGAATCACATGTTGGAATGAGTAGCCCGgtatgcccat ... tgttacacagGAACCAAAGATAAATACATATGCTAACTTCAGAGATGAGGTGCTTCCAAGA

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: 1466

GAGAAATATGTATTCAAACACCCTCAACCTAAGCGGCCCAAGTCACTGCGGATATATGAATCACATGTTGGAATGAGTAGCCCGgtatgcccat ... tgttacacagGAACCAAAGATAAATACATATGCTAACTTCAGAGATGAGGTGCTTCCAAGAATTAAAAAGCTTGGATACAATGCAGTACAGATAATGGCAATCCAGGAAC

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 243

Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 18