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

...acttttttttatgcattcttagtcatggttgttttggtggtatttgatattttctatgcacctcttattgatacggtaaacatataaaatctttccccagGGAGTTGCCATGCCTGCGATGAATAATATTCTTTCGAAATGGGTTCCTGTATCAGAGAGGAGCAGATCATTGGCTCTCGTGTATAGTGGAATGTACCTTG

Basic information

species	Oryza sativa
transcript	LOC_Os01g17240.1
intron #	3
splice site	3'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: LOC_Os01g17240.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G092793_T01 (Zea mays), 3'ss of exon 3

---------acttttttttatgcatt-cttagtcatggttgttttggtggtatttgatattttctatgcacctcttattgatacggtaaacatataaaatctttccccagGGAGTTGCCATGCCTGCGATGAATAATATTCTTTCGAAATGGGTTCCTGTATCAGAGAGGAGCAGATCATTGGCTCTCGTGTATAGTGGAATGTACCTTG
          |    || | ||  || ||||  | ||  ||||||  |     |||||||  || || ||||| |   |||||    ||||||||| | |||| || ||||| ||||| |||||||| ||||| |||||||||||||||||||||||||||||||||||||||||||||||| |||| ||||| ||||||||||||||||
tgacaattggcgaacttctttgagttgcttaaacctgcatgttttttta----ttgatatcatcgatacacctttc--tgata----aaacatatacactcttgcctcagGGGGTTGCAATGCCTGCAATGAACAATATTCTTTCGAAATGGGTTCCTGTATCAGAGAGGAGCAGATCATTGTCTCTTGTGTACAGTGGAATGTACCTTG

upper sequence: LOC_Os01g17240.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GLYMA11G26510.1 (Glycine max), 3'ss of exon 3

---acttttttttatgcattcttagtcatggttgttttggtggtatttgatattttctatgcacctcttattga-tacggtaaacatataaaatctttccccagGGAGTTGCCATGCCTGCGATGAATAATATTCTTTCGAAATGGGTTCCTGTATCAGAGAGGAGCAGATCATTGGCTCTCGTGTATAGTGGAATGTACCTTG
   | |||| |  ||   || ||  || || |  |  |    || | ||||   ||   | ||  |     | | | |  |   | | |    ||  |  | |||| ||||| ||||| || |||||||||||||| || |||||||||||||| |||||||| || |||||| | || || || || ||||| ||||| ||||
ttaagttttgtccattttttatttatcttgatgatgatacaagtttctgatgactttcttccatatggacctaacttcttttggccttt----tccctttctagGGTGTTGCTATGCCAGCCATGAATAATATTCTGTCAAAATGGGTTCCTGTGTCAGAGAGAAGTAGATCACTAGCGCTGGTCTACAGTGGCATGTATCTTG

upper sequence: LOC_Os01g17240.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GLYMA18G07320.1 (Glycine max), 3'ss of exon 4

acttttttttatgcattc--ttagtcatggttgttttggtggtatttgatattttctatgcacctcttattgatacggtaaacatataaaatctttcccc----agGGAGTTGCCATGCCTGCGATGAATAATATTCTTTCGAAATGGGTTCCTGTATCAGAGAGGAGCAGATCATTGGCTCTCGTGTATAGTGGAATGTACCTTG
  |   |||| | ||||   ||  ||  | |  |  || |   ||||| |  |  || |    ||   ||    ||   |  | | |      || |||     |||| ||||| ||||| || |||||||||||| | || |||||||||||||| |||||| | || |||||| | || || || || ||||| ||||| ||||
--taggttttgttcatttgatttatctagttgatgatgatacaatttggtgataacttt----cttccatatggacctcactctttttggcctttaccctttgtagGGTGTTGCTATGCCAGCCATGAATAATATTTTGTCAAAATGGGTTCCTGTGTCAGAGCGAAGTAGATCACTAGCGCTGGTCTACAGTGGCATGTATCTTG

upper sequence: LOC_Os01g17240.1 (Oryza sativa), 3'ss of exon 3
lower sequence: AT2G29650.2 (Arabidopsis thaliana), 3'ss of exon 3

acttttttttatgcattcttagtcatggttgttttggtggtatttgatattttctatgcacctcttattgatacggtaaacatataaaatctttccccagGGAGTTGCCATGCCTGCGATGAATAATATTCTTTCGAAATGGGTTCCTGTATCAGAGAGGAGCAGATCATTGGCTCTCGTGTATAGTGGAATGTACCTTG
     ||| |    | ||||||| ||| | | | |    || |  ||   ||| | ||      | |  |     ||||      |      ||| |||||| ||||| |||||||| |||||||||||  | ||||| |||||||||||   |||||| ||||||||| | || || || || || |||||||||||||
----gtttgtgattactcttagtgatgttagatat--cagtctcgga---tttgtgtgtgttgataa--ggagaagtaagttctcatttgtgttctccagGGTGTTGCAATGCCTGCTATGAATAATATATTGTCGAAGTGGGTTCCTGTGCAAGAGAGAAGCAGATCACTCGCGCTTGTTTACAGCGGAATGTACCTTG

upper sequence: LOC_Os01g17240.1 (Oryza sativa), 3'ss of exon 3
lower sequence: Vv06s0004g06220.t01 (Vitis vinifera), 3'ss of exon 3

acttttttttatgcattcttagtcatggttgttttggtggtatttgatattttctat---gcacctcttattgatacggtaaacatataaaatctttccccagGGAGTTGCCATGCCTGCGATGAATAATATTCTTTCGAAATGGGTTCCTGTATCAGAGAGGAGCAGATCATTGGCTCTCGTGTATAGTGGAATGTACCTTG
 | | |  ||    | | |  |  ||  || || | || |  |   ||   |||| |    || |   || ||| |   |   | | |       |    ||||| ||||| |||||||| |||||||||||||| || || |||||||||||||||||||| || ||||| |||||  | ||||| ||||| ||||||||||
-cctgtaattgattactgtaggatataatttttcttgttgggtaaaatgagttctttttgacaacaaatactgaaattttg--cttctttggctctctttcagGGTGTTGCTATGCCTGCAATGAATAATATTCTCTCAAAGTGGGTTCCTGTATCAGAGAGAAGTAGATCGTTGGCATTAGTGTACAGTGGGATGTACCTTG

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|58689321|gb|CK078008.1|CK078008

EST:     TGGGGTTACCATTCCTCCTTGTGACCCGTGCTTTCATGGGAGTTGGTGAG                         GGAGTTGCCATGCCTGCGATGAATAATATTCTTTCGAAATGGGTTCCTGTA
genomic: TGGGGTTACCATTCCTCCTTGTGACCCGTGCTTTCATGGGAGTTGGTGAGgtgagcattt ... ctttccccagGGAGTTGCCATGCCTGCGATGAATAATATTCTTTCGAAATGGGTTCCTGTA

EST: gi|29656073|gb|CB652348.1|CB652348

EST:     TGGGGTTACCATTCCTCCTTGTGACCCGTGCTTTCATGGGAGTTGGTGAG                         GGAGTTGCCATGCCTGCGATGAATAATATTCTTTCGAAATGGGTTCCTGTA
genomic: TGGGGTTACCATTCCTCCTTGTGACCCGTGCTTTCATGGGAGTTGGTGAGgtgagcattt ... ctttccccagGGAGTTGCCATGCCTGCGATGAATAATATTCTTTCGAAATGGGTTCCTGTA

EST: gi|66913930|gb|CX100778.1|CX100778

EST:     TGGGGTTACCATTCCTCCTTGTGACCCGTGCTTTCATGGGAGTTGGTGAG                         GGAGTTGCCATGCCTGCGATGAATAATATTCTTTCGAAATGGGTTCCTGTA
genomic: TGGGGTTACCATTCCTCCTTGTGACCCGTGCTTTCATGGGAGTTGGTGAGgtgagcattt ... ctttccccagGGAGTTGCCATGCCTGCGATGAATAATATTCTTTCGAAATGGGTTCCTGTA

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: 75 (upstream exon), 55 (downstream exon)
Score: 17

CGTCATTTGGTGGTCGATAGCCACAGCTCTTACGCCTTTTGCGGCGAAGCTGGGGTTACCATTCCTCCTTGTGACCCGTGCTTTCATGGGAGTTGGTGAGgtgagcattt ... ctttccccagGGAGTTGCCATGCCTGCGATGAATAATATTCTTTCGAAATGGGTTCCTGTATCAGAGAGGAGCAGATCATTGGCTCTCGTGTATAGTGGAATGTACCTTG

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atgc intronic sequence ATGC exonic sequence

Intronic sequence truncated to 55 bases.

gatattttctatgcacctcttattgatacggtaaacatataaaatctttccccagGGAGTTGCCATGCCTGCGATGAATAATATTCTTTCGAAATGGGTTCCTGTATCAGAGAGGAGCAGATCATTGGCTCTCGTGTATAGTGGAATGTACCTTG

                    tattgat  putative branch site (score: 17)
                                            tctttcccc  putative PPT
                               taaacatataaaatct  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
acttttttttatgcattcttagtcatggttgttttggtggtatttgatattttctatgcacctcttattgatacggtaaacatataaaatctttccccagGGAGTTGCCATGCCTGCGATGAATAATATTCTTTCGAAATGGGTTCCTGTATCAGAGAGGAGCAGATCATTGGCTCTCGTGTATAGTGGAATGTACCTTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGATCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGTGGA
- - - - - -tgcattc
- - - - - - - - - - - -catggtt
- - - - - - - - - - - - - - - - - tggtggt
- - - - - - - - - - - - - - - - - - - - - - - - - - -ctatgca