ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq
PPT, BS, UA-tract
cis-regulatory elements

Sequence

atgc intronic sequence ATGC exonic sequence

gtgtgttcctaagtgtacttgcagttatttaatgttttgtgtagtccatttcagtgttccatgctggaatgattatcatctccatggtgtctgactacctttgttgcagGCTTCCTGATGGATCTCTTATGGAGATTACAAAAGTCTACCCATTGGATGCAGTTTTTGACTCTCCTGAGGATGTTCCTGATGAT

Basic information

species	Oryza sativa
transcript	LOC_Os09g10600.1
intron #	4
splice site	3'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: LOC_Os09g10600.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G079256_T01 (Zea mays), 3'ss of exon 4

gtgtgttcctaagtgtacttgcagttatttaatgttttgtg--tagtcca---tttcagtgttccatgctggaatgattatcatctccatggtgtctgactacctttgttgcagGCTTCCTGATGGATCTCTTATGGAGATTACAAAAGTCTACCCATTGGATGCAGTTTTTGACTCTCCTGAGGATGTTCCTGATGAT
         | |||| | |  ||||  ||| | | |||| |  || |  |   || |  | |||||     |  |  |  | |||    || |||    ||       || |||||| |||||||||||||||||||||||| | ||||| || ||| |||| ||||||| |||| | ||||||||||||||||| |||
--------gtgagtgcattaacagtagtttgaggctttgagcataattgaagtttcctttattccacttcagtgtt-tcttgatcgaactgatgttatccttttgactttacagGCTACCTGATGGATCTCTTATGGAGATTGCTAAAGTATATCCACTGGACGCAGTTTATGACACCCCTGAGGATGTTCCTGAAGAT

upper sequence: LOC_Os09g10600.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GLYMA11G10770.1 (Glycine max), 3'ss of exon 4

gtgtgttcctaagtgtacttgcagttatttaatgttttgtgtagtccatttcagtgttccatgctggaatg-attatcatctccatggtgtctgactacctttgttgcagGCTTCCTGATGGATCTCTTATGGAGATTACAAAAGTCTACCCATTGGATGCAGTTTTTGACTCTCCTGAGGATGTTCCTGATGAT
                           | | | |||   |   ||   |     | ||   || | || |   | ||  | |   |  |     ||||  ||  || |||  | || ||||| || || ||||||||||| ||||| || |||||||||||||||||||||  || ||| ||||| || || |||
--------------------------gtatgacgttaaatactgt---tactgattttgtttgttagactatgtgatgctattgctaataagaaactatatt--ttccagATTACCAGATGGTTCGCTGATGGAGATTACCAAAGTTTATCCATTGGATGCAGTTTTTGACAATCTTGATGATGTGCCAGAAGAT

upper sequence: LOC_Os09g10600.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GLYMA12G03060.1 (Glycine max), 3'ss of exon 5

gtgtgttcctaagtgtacttgcagttatttaatgttttgtgtagtccatttcagtgttccatgctggaatgattatcatctccatggtgtctgactacctttgttgcagGCTTCCTGATGGATCTCTTATGGAGATTACAAAAGTCTACCCATTGGATGCAGTTTTTGACTCTCCTGAGGATGTTCCTGATGAT
                           | | |  ||   |   |    |     | ||   || | || |   |      |   |  |     ||||   |  || |||  | || ||||| ||  | ||||||||||| ||||| || |||||||||||||||||||||  ||| || ||||| ||||| |||
--------------------------gtatgacattaaatactgc---tgctgattttgtttgtttgactatgtgatgctttgctaataagaaactataat--ttccagATTACCAGATGGCTCGATGATGGAGATTACCAAAGTTTATCCATTGGATGCAGTTTTTGACAATCCCGATGATGTGCCTGAAGAT

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|58658677|gb|CK047357.1|CK047357

EST:     AACATATTTGAGACAAGCTTGAGGCGTGGGAAGTTTGACGAATCACGAAA                         GCTTCCTGATGGATC
genomic: AACATATTTGAGACAAGCTTGAGGCGTGGGAAGTTTGACGAATCACGAAAgtgtgttcct ... tttgttgcagGCTTCCTGATGGATC

EST: gi|29670466|gb|CB666741.1|CB666741

EST:     AACATATTTGAGACAAGCTTGAGGCGTGGGAAGTTTGACGAATCACGAAA                         GCTTCCTGATGGATCTCTTATGGAGATTACAAAAGTCTACCCATTGGATGC
genomic: AACATATTTGAGACAAGCTTGAGGCGTGGGAAGTTTGACGAATCACGAAAgtgtgttcct ... tttgttgcagGCTTCCTGATGGATCTCTTATGGAGATTACAAAAGTCTACCCATTGGATGC

EST: gi|29640101|gb|CB645110.1|CB645110

EST:     AACATATTTGAGACAAGCTTGAGGCGTGGGAAGTTTGACGAATCACGAAA                         GCTTCCTGATGGATCTCTTATGGAGATTACAAAAGTCTACCCATTGGATGC
genomic: AACATATTTGAGACAAGCTTGAGGCGTGGGAAGTTTGACGAATCACGAAAgtgtgttcct ... tttgttgcagGCTTCCTGATGGATCTCTTATGGAGATTACAAAAGTCTACCCATTGGATGC

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: 56 (upstream exon), 62 (downstream exon)
Score: 20

GCACTGAACATATTTGAGACAAGCTTGAGGCGTGGGAAGTTTGACGAATCACGAAAgtgtgttcct ... tttgttgcagGCTTCCTGATGGATCTCTTATGGAGATTACAAAAGTCTACCCATTGGATGCAGTTTTTGACTCTCCTGAGGATGTTCCTGATGAT

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atgc intronic sequence ATGC exonic sequence

Intronic sequence truncated to 55 bases.

tgttccatgctggaatgattatcatctccatggtgtctgactacctttgttgcagGCTTCCTGATGGATCTCTTATGGAGATTACAAAAGTCTACCCATTGGATGCAGTTTTTGACTCTCCTGAGGATGTTCCTGATGAT

                                  gtctgac  putative branch site (score: 20)
                                        ctaccttt  CT-rich tract
             aatgattat  TA-rich tract

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgtgttcctaagtgtacttgcagttatttaatgttttgtgtagtccatttcagtgttccatgctggaatgattatcatctccatggtgtctgactacctttgttgcagGCTTCCTGATGGATCTCTTATGGAGATTACAAAAGTCTACCCATTGGATGCAGTTTTTGACTCTCCTGAGGATGTTCCTGATGAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGATG