ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq
PPT, BS, UA-tract

Sequence

atgc intronic sequence ATGC exonic sequence

gtactgaaagcaccctctcctcgtcatttgattgcaattgatttcttgttcttcaacattagcatactttgcttgaggcttcaatttccaatttttaatttcagCTGCTGCTGCATCTCTATGTGTTCAAGTAAAGGGAGCCATACCCAGCATGCCTGACCGAAAATCAGTAATGGACCTTCTGGAATCTGTTCAGGTTGAATA

Basic information

species	Oryza sativa
transcript	LOC_Os01g47550.1
intron #	3
splice site	3'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: LOC_Os01g47550.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G178346_T02 (Zea mays), 3'ss of exon 1

gtactgaaagcaccctctcctcgtcatttgattgcaattgatttcttgttcttcaacattagcatactttgcttgaggcttcaatttccaatttttaatttcagCTGCTGCTGCATCTCTATGTGTTCAAGTAAAGGGAGCCATACCCAGCATGCCTGACCGAAAATCAGTAATGGACCTTCTGGAATCTGTTCAGGTTGAATA
|||| |||| |||   ||| ||   ||||||  |  | || |||| |              |||| |||   ||||    |   | | |  |  | |||  |||||||||| || ||||| ||||||| ||||||||| || |||||||||||||||||| ||||||| || ||| | ||||||||||||||    || |||||
gtac-gaaaccacgtcctcttcaatatttgaccg--actggtttcctt-------------gcat-cttgatttgatagct---tctacgttcctgaatcccagCTGCTGCCGCCTCTCTGTGTGTTCGAGTAAAGGGGGCTATACCCAGCATGCCTGACAGAAAATCGGTGATGAAGCTTCTGGAATCTGTGGGAGTCGAATA

upper sequence: LOC_Os01g47550.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GLYMA13G33850.1 (Glycine max), 3'ss of exon 3

gtactgaaagcaccctctcctcgtcatttgattgcaattgatttcttgttcttcaacattagcatactttgcttgaggcttcaatttccaatttttaatttcagCTGCTGCTGCATCTCTATGTGTTCAAGTAAAGGGAGCCATACCCAGCATGCCTGACCGAAAATCAGTAATGGACCTTCTGGAATCTGTTCAGGTTGAATA
                    |      | || |||||||  ||| || ||  |  |||||    |  || |    | | | | |  |   || ||      |||||||||| || | ||| ||||||||||| |||||||||   ||||||||||||||  | |||||                                    
-----------------gtgtgtatggtggaatgcaattc-ttttttctttctagacatt--tctctttggaaaaatgttcctaactatgatgttctgcaacagCTGCTGCAGCTTGTCTCTGTGTTCAAGTGAAGGGAGCCTCTCCCAGCATGCCTGATAGGAAATCT-----------------------------------

upper sequence: LOC_Os01g47550.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GLYMA15G38510.1 (Glycine max), 3'ss of exon 3

gtactgaaagcaccctctcctcgtcatttgattgcaattgatttcttgttcttcaacattagcatactttgcttgaggcttcaatttccaatttttaatttcagCTGCTGCTGCATCTCTATGTGTTCAAGTAAAGGGAGCCATACCCAGCATGCCTGACCGAAAATCAGTAATGGACCTTCTGGAATCTGTTCAGGTTGAATA---
                    |      | || ||||| |  ||| |  ||||  ||  ||  |    || |    | | | | |  | |  | ||      |||||||||| || | ||| ||||||||||| |||||||||   ||||||||||||||  | ||||| ||  |||| |||||  | |    |||    |||||   
-----------------gtgtgtatggtggaatgcaactcttttttctttctagaattttctc---tttggaaaaatgttcctaactacgttgttctgcaacagCTGCTGCAGCTTGTCTTTGTGTTCAAGTGAAGGGAGCCTCTCCCAGCATGCCTGATAGGAAATCTGTTTTGGATCTTCTTAATT---GTCAATGAGAATACTC

upper sequence: LOC_Os01g47550.1 (Oryza sativa), 3'ss of exon 3
lower sequence: AT1G17160.2 (Arabidopsis thaliana), 3'ss of exon 3

gtactgaaagcaccctctcctcgtcatttgattgcaattgatttcttgttcttcaacattagcatactttgcttgaggcttcaatttccaatttttaatttcagCTGCTGCTGCATCTCTATGTGTTCAAGTAAAGGGAGCCATACCCAGCATGCCTGACCGAAAATCAGTAATGGACCTTCTGGAATCTG---TTCAGGTTGAATA-----------------------------
                 |  |  | | |    |  |  || |||  |   |   ||           ||||  | |  |||   ||||| ||   |     ||||||| ||||| ||||| ||||| ||||||||||| || ||||| |||||||||||||||||||| ||  || | || ||  ||| |    |  |      |||                             
----------------gtaataattagtgacataaatctggttttctaacccgtaattcagattagttttgtctca--cttt--tttccgatgcctg----cagctgcagctgcctctctttgtgtccaagtaaagGGTGCAATACCGAGCATGCCTGACCGAAAATCTGTTTTGAAGCTCCTTAAATTTAGTATCTAAAACTGATACTCTTTTCAAGTCCTCTTATCAATAAAAG

upper sequence: LOC_Os01g47550.1 (Oryza sativa), 3'ss of exon 3
lower sequence: AT1G17160.1 (Arabidopsis thaliana), 3'ss of exon 3

gtactgaaagcaccctctcctcgtcatttgattgcaattgatttcttgttcttcaacattagcatactttgcttgaggcttcaatttccaatttttaatttcagCTGCTGCTGCATCTCTATGTGTTCAAGTAAAGGGAGCCATACCCAGCATGCCTGACCGAAAATCAGTAATGGACCTTCTGGAATCTGTTCAGGTTGAATA-
                 |  |  | | |    |  |  || |||  |   |   ||           ||||  | |  |||   ||||| ||   |     ||||||| ||||| ||||| ||||| ||||||||||| || ||||| |||||||||||||||||||| ||  || | || ||  ||| |  | |  |  ||   
----------------gtaataattagtgacataaatctggttttctaacccgtaattcagattagttttgtctca--cttt--tttccgatgcCTG----CAGCTGCAGCTGCCTCTCTTTGTGTCCAAGTAAAGGGTGCAATACCGAGCATGCCTGACCGAAAATCTGTTTTGAAGCTCCTTAAATTTAGT-ATCTAAAACTG

upper sequence: LOC_Os01g47550.1 (Oryza sativa), 3'ss of exon 3
lower sequence: Vv19s0014g00180.t01 (Vitis vinifera), 3'ss of exon 3

gtactgaaagcaccctctcctcgtcat-ttgattgcaattgatttcttgttcttcaacattagcatactttgc--ttgaggcttcaatttccaatttttaattt--cagCTGCTGCTGCATCTCTATGTGTTCAAGTAAAGGGAGCCATACCCAGCATGCCTGACCGAAAATCAGTAATGGACCTTCTGGA-ATCTGTTCAGGTTGAATA
                      || |  || | ||       |  |   ||  || |  |   ||| |  |     | ||  |   |       ||   | ||   |||||||||| || ||||| ||||||||||| ||||| ||||| || |||||||||||| ||   |||||  |||| |||||  | | ||||| |         
----------------------gtaagattaactgtgtcctttcccagttttctccatgtacacatcccatataactaagtttctcacaattgcttgccatttgtacagCTGCTGCAGCTTCTCTCTGTGTTCAAGTGAAGGGGGCCATTCCAAGCATGCCTGACAGACGGTCAGTTTTGGATCTTCTACAGACCTGTTGA---------

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|58674838|gb|CK063525.1|CK063525

EST:     TGTAGCTCTAGTTGAGGGTATACCTAAGGAAGAGTGCATGAGATTTGCTG                         CTGCTGCTGCATCTCTATGTGTTCAAGTAAAGGGAGCCATACCCAGCATGC
genomic: TGTAGCTCTAGTTGAGGGTAAACCTAAGGAAGAGTGCATGAGATTTGCTGgtactgaaag ... ttaatttcagCTGCTGCTGCATCTCTATGTGTTCAAGTAAAGGGAGCCATACCCAGCATGC

EST: gi|27554267|gb|CA998167.1|CA998167

EST:     TGTAGCTCTAGTTGAGGGTAAACCTAAGGAAGAGTGCATGAGATTTGCTG                         CTGCTGCTGCATCTCTATGTGTTCAAGTAAAGGGAGCCATACCCAGCATGC
genomic: TGTAGCTCTAGTTGAGGGTAAACCTAAGGAAGAGTGCATGAGATTTGCTGgtactgaaag ... ttaatttcagCTGCTGCTGCATCTCTATGTGTTCAAGTAAAGGGAGCCATACCCAGCATGC

EST: gi|13165430|gb|AU174227.1|AU174227

EST:     AGGAAGAGTGCATGAGATTTGCTG                         CTGCTGCTGCATCTCTATGTGTTCAAGTAAAGGGAGCCATACCCAGCATGC
genomic: AGGAAGAGTGCATGAGATTTGCTGgtactgaaag ... ttaatttcagCTGCTGCTGCATCTCTATGTGTTCAAGTAAAGGGAGCCATACCCAGCATGC

EST: gi|33678571|gb|CF306810.1|CF306810

EST:     TGTAGCTCTAGTTGAGGGTAAACCTAACGAAGAGTGCATGAGATTTGCTG                         CTGCTGCTGCATCTCTATGTGTTCAAGTAAAGGGAGCCATACCCAGCATGC
genomic: TGTAGCTCTAGTTGAGGGTAAACCTAAGGAAGAGTGCATGAGATTTGCTGgtactgaaag ... ttaatttcagCTGCTGCTGCATCTCTATGTGTTCAAGTAAAGGGAGCCATACCCAGCATGC

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 1 RNA-Seqlibrary.

Block sizes: 68 (upstream exon), 72 (downstream exon)
Score: 9

GAAGTTGTTGATACGACTGGTGCCGGTGACACTTTCACCTCAGCTTTTGCTGTAGCTCTAGTTGAGGGTAAACCTAAGGAAGAGTGCATGAGATTTGCTGgtactgaaag ... ttaatttcagCTGCTGCTGCATCTCTATGTGTTCAAGTAAAGGGAGCCATACCCAGCATGCCTGACCGAAAATCAGTAATGGACCTTCTGGAATCTGTTCAGGTTGAATA

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atgc intronic sequence ATGC exonic sequence

Intronic sequence truncated to 55 bases.

tcttcaacattagcatactttgcttgaggcttcaatttccaatttttaatttcagCTGCTGCTGCATCTCTATGTGTTCAAGTAAAGGGAGCCATACCCAGCATGCCTGACCGAAAATCAGTAATGGACCTTCTGGAATCTGTTCAGGTTGAATA