ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq
cis-regulatory elements

Sequence

atgc intronic sequence ATGC exonic sequence

GATGTCTACTTTGATGATGAATCAGCTGAAGTAGTAATATCTTCGTTGCGTTTGGGTGATGATCAGGACAGgtaattttgttatcgtttcgttgtcctgccgttattactattacttaactttcttatatattgtgtgttctacag

Basic information

species	Oryza sativa
transcript	LOC_Os05g51490.1
intron #	18
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: LOC_Os05g51490.1 (Oryza sativa), 5'ss of exon 18
lower sequence: GRMZM5G812498_T01 (Zea mays), 5'ss of exon 8

GATGTCTACTTTGATGATGAATCAGCTGAAGTAGTAATATCTTCGTTGCGTTTGGGTGATGATCAGGACAGgtaattttgttatcgtttcgttgtcctgccgttattactattacttaactttcttatatattgtgtgttctacag
||||||||||||||||| || ||||||||||||||||||||||| ||| ||||||| ||||||||||||||||||||    | |     |       | | ||  || |||  |   |  |  ||||||   ||||  |||| |||
GATGTCTACTTTGATGACGAGTCAGCTGAAGTAGTAATATCTTCATTGTGTTTGGGGGATGATCAGGACAGgtaattaatgtttttcagcagatctatactgtcgttgctaa-aagaagatggcttatagggtgtgcattctgcag

upper sequence: LOC_Os05g51490.1 (Oryza sativa), 5'ss of exon 18
lower sequence: GLYMA15G13580.1 (Glycine max), 5'ss of exon 18

GATGTCTACTTTGATGATGAATCAGCTGAAGTAGTAATATCTTCGTTGCGTTTGGGTGATGATCAGGACAGgtaattt---tgttatcgtt--tcgttgtcctgccg--ttattactat-tactt-aactttcttatatattgtgtgttctacag-------------------------------------------------------
|||||||| |||||||||||||| || ||||| || |||||||| ||||| ||||| ||||| || || |||||| |    ||     |||  || |     || |   ||  |||| | || || |||| || |   |  ||| |  | || ||                                                       
GATGTCTATTTTGATGATGAATCTGCAGAAGTTGTTATATCTTCTTTGCGGTTGGGAGATGACCATGAAAGgtaaatggtgtgcctctgttgatcatacatgtgtcaattttctactttgtatttgaactgtcatgcctggtgtctcatgtaaaggtctttattccaattctttcaatgtataccttagattttgctttgacacatgcag

upper sequence: LOC_Os05g51490.1 (Oryza sativa), 5'ss of exon 18
lower sequence: AT1G30470.2 (Arabidopsis thaliana), 5'ss of exon 18

GATGTCTACTTTGATGATGAATCAGCTGAAGTAGTAATATCTTCGTTGCGTTTGGGTGATGATCAGGACAGgtaattttgttatcgtttcgttgtcctgccgttattactattacttaactttc-ttatata-ttgtgtgttctacag--------------------------------------
||||||||||||||||||||||| || ||||| || ||||| || |||||  | || ||||| ||||| |||||||    | | |  ||  ||  |  |  |  ||||  ||   || | |  | | ||||  ||| |  |  |   |                                      
GATGTCTACTTTGATGATGAATCTGCAGAAGTCGTCATATCCTCCTTGCGCCTTGGAGATGACCAGGAGAGgtaatcggttcaactgttt-tttcctggtagaaatta--atccgttgattcgcatcatatgcttgagcttgatgtggtcccttaacttacgaaatataacatggtgtcgttgcag

upper sequence: LOC_Os05g51490.1 (Oryza sativa), 5'ss of exon 18
lower sequence: Vv10s0003g04630.t01 (Vitis vinifera), 5'ss of exon 18

GATGTCTACTTTGATGATGAATCAGCTGAAGTAGTAATATCTTCGTTGCGTTTGGGTGATGATCAGGACAGgtaatttt--gttatcgtttcgttgtcctgccgttat-tactat-tacttaactttcttatatattgt-----gtgttctacag----------------
||||||||||||||||||||||| |||||||| || ||||||||  |||| ||||| ||||||||||| |||||  |    |   |  ||| |   | || |   ||| |  ||  || ||||  |    | | |         |   |||  ||                
GATGTCTACTTTGATGATGAATCGGCTGAAGTTGTCATATCTTCTCTGCGATTGGGAGATGATCAGGAGAGgtaggtggaagcccttattttgaccttctccttctatatgatacctatttaaaatgaaaaaaaaaaaaaaaaagcaatctgaaggtcttctccattgtcc

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|58603505|gb|CK014033.1|CK014033

EST:     TCAGCTGAAGTAGTAATATCTTCGTTGCGTTTGGGTGATGATCAGGACAG                         CAGCTCCCTCTTTACGAATTCAAACTGGTTTACCTTTGATGGTGATAGAGG
genomic: TCAGCTGAAGTAGTAATATCTTCGTTGCGTTTGGGTGATGATCAGGACAGgtaattttgt ... tgttctacagCAGCTCCCTCTTTACGAATTCAAACTGGTTTACCTTTGATGGTGATAGAGG

EST: gi|58608385|gb|CK036418.1|CK036418

EST:     TCAGCTGAAGTAGTAATATCTTCGTTGCGTTTGGGTGATGATCAGG--A-                         CAGCTCCCTCTTTACGAATTCAAACTGGTTTACCTTTGATGGTGATAGAGG
genomic: TCAGCTGAAGTAGTAATATCTTCGTTGCGTTTGGGTGATGATCAGGACAGgtaattttgt ... tgttctacagCAGCTCCCTCTTTACGAATTCAAACTGGTTTACCTTTGATGGTGATAGAGG

EST: gi|218484458|gb|FG943361.1|FG943361

EST:     TCAGCTGAAGTAGTAATATCTTCGTTGCGTTTGGGTGATGATCAGGACAG                         CAGCTCCCTCTTT
genomic: TCAGCTGAAGTAGTAATATCTTCGTTGCGTTTGGGTGATGATCAGGACAGgtaattttgt ... tgttctacagCAGCTCCCTCTTT

EST: gi|58660503|gb|CK049183.1|CK049183

EST:     TCAGCTGAAGTAGTAATATCTTCGTTGCGTTTGGGTGATGATCAGGACAG                         CAGCTCCCTCTTTACGAATTCAAACTGGTTTACCTTTGATGGTGATAGAGG
genomic: TCAGCTGAAGTAGTAATATCTTCGTTGCGTTTGGGTGATGATCAGGACAGgtaattttgt ... tgttctacagCAGCTCCCTCTTTACGAATTCAAACTGGTTTACCTTTGATGGTGATAGAGG

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: 71 (upstream exon), 64 (downstream exon)
Score: 9

GATGTCTACTTTGATGATGAATCAGCTGAAGTAGTAATATCTTCGTTGCGTTTGGGTGATGATCAGGACAGgtaattttgt ... tgttctacagCAGCTCCCTCTTTACGAATTCAAACTGGTTTACCTTTGATGGTGATAGAGGAATAAATGACCGTTTAGCTGCCTCTGTCCCTTCTTCATCTCCCAATTCT

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Putative cis-regulatory sequences

atgc	intron	ATGC	exonic elements by Pertea et al.
ATGC	exon	atgc	putative intronic elements
		ATGC	putative exonic elements identified for retained introns

        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GATGTCTACTTTGATGATGAATCAGCTGAAGTAGTAATATCTTCGTTGCGTTTGGGTGATGATCAGGACAGgtaattttgttatcgtttcgttgtcctgccgttattactattacttaactttcttatatattgtgtgttctacag

- - - - - - - - - -  TCAGCT
- - - - - - - - - - - CAGCTG
- - - - - - - - - - -  AGCTGA
- - - - - - - - - - - -  CTGAAG