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

gtaacttttcctagttcagtaatatagtagtactagttagtagtccttcctacacttaactgatgtaaaaaatgtgatcccctcttttcagGCTCAGCAATTGAATAAGGATATCTTCGAAACTATTTACTTTCATTCTCTGAAAGCTTCCGCTGAGCTTGCTGGTAAAGAAGGTCCCTATGAAACATATG

Basic information

species	Oryza sativa
transcript	LOC_Os06g07210.1
intron #	11
splice site	3'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: LOC_Os06g07210.1 (Oryza sativa), 3'ss of exon 11
lower sequence: GRMZM2G304362_T01 (Zea mays), 3'ss of exon 11

gtaacttttcctagttcagtaatatagtagtactagttagtagtccttcctacacttaactgatgtaaaaaatgtgatcccctcttttcagGCTCAGCAATTGAATAAGGATATCTTCGAAACTATTTACTTTCATTCTCTGAAAGCTTCCGCTGAGCTTGCTGGTAAAGAAGGTCCCTATGAAACATATG
||| |||||| |   || |||    || | ||       ||  || || ||  |  ||  |||| |  || |  || |    |||||||||||||| || |||||||||||||| ||||||||||| |||| |||| ||||||||||||| ||||| ||||||| ||||||||||||||||||||||||||
gtaccttttcatttctccgtagctcagcattaaccacctgt--tcttttctgtaactagttgatatgtaacaaatggttttatcttttcagGCTCAACAGTTGAATAAGGATATATTCGAAACTATCTACTATCATGCTCTGAAAGCTTCTGCTGAACTTGCTGCTAAAGAAGGTCCCTATGAAACATATG

upper sequence: LOC_Os06g07210.1 (Oryza sativa), 3'ss of exon 11
lower sequence: GRMZM2G340527_T01 (Zea mays), 3'ss of exon 11

gtaacttttcctagttcagtaatatagtagtactagttagtagtccttcctacacttaactgatgtaaaaaatgtgatcccctcttttcagGCTCAGCAATTGAATAAGGATATCTTCGAAACTATTTACTTTCATTCTCTGAAAGCTTCCGCTGAGCTTGCTGGTAAAGAAGGTCCCTATGAAACATATG
||| |||| | |   |  |||    |  | ||    |  ||  ||||| ||  | |||  |||| |  || |  || |    | |||||||||||| || |||||||||||||| || |||||||| |||| |||| |||||||| |||| ||||| ||||||| ||||||||||||||||||||||||||
gtacctttccatttctatgtagctcatcattaaccatatgt--tcctttctgtaattagttgatatgtaacaaatggttttatattttcagGCTCATCAGTTGAATAAGGATATATTTGAAACTATCTACTATCATGCTCTGAAATCTTCTGCTGAACTTGCTGTTAAAGAAGGTCCCTATGAAACATATG

upper sequence: LOC_Os06g07210.1 (Oryza sativa), 3'ss of exon 11
lower sequence: GLYMA05G32070.1 (Glycine max), 3'ss of exon 11

----gtaacttttcctagttcagtaatatagtagtactagttagtagtccttcctacacttaactgatgtaaaaaatgtgatcccctcttttcagGCTCAGCAATTGAATAAGGATATCTTCGAAACTATTTACTTTCATTCTCTGAAAGCTTCCGCTGAGCTTGCTGGTAAAGAAGGTCCCTATGAAACATATG
     |||| |||    |     |  |  |     | |      |||   ||| |  | || |  | | |     |  ||          | ||||||||||| ||||| |||||||| || || ||||| |||| |||| | || ||| ||||  ||||  | ||||  |||||||||||||||||||||||| 
gtaaataacatttatgggactgctttttcatctacaatttaagctagaggttcatcaatttgatagttttcctggacatggga-------tgcagGCTCAGCAGTTGAACAAGGATATATTTGAGACTATATACTATCATGCACTAAAAACTTCATCTGAATTGGCTGCAAAAGAAGGTCCCTATGAAACATATA

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|88274010|gb|CI394416.1|CI394416

EST:     GGTTGGCAGATACTTTCATATTACTTGGCATGCCATTTGATTCACCAGAG                         GCTCAGCAATTGAATAAGGATATCTTCGAAACTATTTACTTTCATTCTCTG
genomic: GGTTGGCAGATACTTTCATATTACTTGGCATGCCATTTGATTCACCAGAGgtaacttttc ... ctcttttcagGCTCAGCAATTGAATAAGGATATCTTCGAAACTATTTACTTTCATTCTCTG

EST: gi|58656327|gb|CK045007.1|CK045007

EST:     GGTTGGCAGATACTGTCATATTACTTGGCATGCCATTTGATTCACCAGAG                         GCTCAGCAATTGAATAAGGATATCTTCGAAACTATTTACTTTCATTCTCTG
genomic: GGTTGGCAGATACTTTCATATTACTTGGCATGCCATTTGATTCACCAGAGgtaacttttc ... ctcttttcagGCTCAGCAATTGAATAAGGATATCTTCGAAACTATTTACTTTCATTCTCTG

EST: gi|66918260|gb|CX105108.1|CX105108

EST:     GGTTGGCAGATACTTTCATATTACTTGGCATGCCATTTGATTCACCAGAG                         GCTCAGCAATTGAATAAGGATATCTTCGAAACTATTTACTTTCATTCTCTG
genomic: GGTTGGCAGATACTTTCATATTACTTGGCATGCCATTTGATTCACCAGAGgtaacttttc ... ctcttttcagGCTCAGCAATTGAATAAGGATATCTTCGAAACTATTTACTTTCATTCTCTG

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: 72 (upstream exon), 73 (downstream exon)
Score: 2

CGCAAAAAGATCAAATATGCGGCACAGGCCAATTGGCATTGGTGTTCAAGGGTTGGCAGATACTTTCATATTACTTGGCATGCCATTTGATTCACCAGAGgtaacttttc ... ctcttttcagGCTCAGCAATTGAATAAGGATATCTTCGAAACTATTTACTTTCATTCTCTGAAAGCTTCCGCTGAGCTTGCTGGTAAAGAAGGTCCCTATGAAACATATG

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atgc intronic sequence ATGC exonic sequence

Intronic sequence truncated to 55 bases.

ttagtagtccttcctacacttaactgatgtaaaaaatgtgatcccctcttttcagGCTCAGCAATTGAATAAGGATATCTTCGAAACTATTTACTTTCATTCTCTGAAAGCTTCCGCTGAGCTTGCTGGTAAAGAAGGTCCCTATGAAACATATG

                     aactgat  putative branch site (score: 2)
                                      tgatcccctcttttc  putative PPT
                          atgtaaaaaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaacttttcctagttcagtaatatagtagtactagttagtagtccttcctacacttaactgatgtaaaaaatgtgatcccctcttttcagGCTCAGCAATTGAATAAGGATATCTTCGAAACTATTTACTTTCATTCTCTGAAAGCTTCCGCTGAGCTTGCTGGTAAAGAAGGTCCCTATGAAACATATG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG