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

gtccgtcatcactggagcgttctctatcttccctgaatttttgcttacacgcaacttgctacaaattattcgtctgcagTTCATGATGGCCAACGGTGCACTGGTCCGTGTACTCATCCACACGAGTGTGACAAAGTATCTGAATTTCAAGGCTGTCGACGGCAGCTTCGTGTACAACA

Basic information

species	Oryza sativa
transcript	LOC_Os03g16900.1
intron #	3
splice site	3'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: LOC_Os03g16900.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G084440_T01 (Zea mays), 3'ss of exon 3

gtccgtca-tcactggag--cgttctct--atct-tccctgaatttttgcttacacgcaacttgctacaaa-------ttattcgtctgcagTTCATGATGGCCAACGGTGCACTGGTCCGTGTACTCATCCACACGAGTGTGACAAAGTATCTGAATTTCAAGGCTGTCGACGGCAGCTTCGTGTACAACA
||| || | | |   |||  ||  ||||  |||| || ||| |  | |   ||| | |  |   ||| | |       | ||  || | |||||||||||||| ||||| || |||||||| || || |||| ||| || ||||| |||||||| || ||||||||||| ||||| ||||| ||||||||||
gtctgttaattagccgagatcgacctctcgatctatcgctggagctatatataccccctcccccctatagagaatgactgatgagtttacagTTCATGATGGCAAACGGCGCGCTGGTCCGCGTCCTGATCCGCACCAGCGTGACCAAGTATCTCAACTTCAAGGCTGTTGACGGGAGCTTTGTGTACAACA

upper sequence: LOC_Os03g16900.1 (Oryza sativa), 3'ss of exon 3
lower sequence: Vv00s0313g00050.t01 (Vitis vinifera), 3'ss of exon 3

--------------------gtccgtcatcactggagcgttctctatcttccctgaatttttgcttacacgcaacttgctacaaat-tattcgtctgcagTTCATGATGGCCAACGGTGCACTGGTCCGTGTACTCATCCACACGAGTGTGACAAAGTATCTGAATTTCAAGGCTGTCGACGGCAGCTTCGTGTACAACA
                    |    |  | |     |  | |  ||  ||   | |     |  ||  |   |   |  ||    | ||| | |   ||||| ||||||||||| |||||  |||| || || ||||||||||| | ||| || || || ||||||||||||||||| || || || || ||||||||||
aatatcagcatgttgttcaagcaacttgttatctaggtatccattaggtttgtttagcacattgttctagttattgtcttaattttctatgccttgacagTTTATGATGGCCAATGGTGCCTTGGTTCGGGTTCTCATCCACACTAATGTTACCAAATACCTGAATTTCAAGGCTGTGGATGGTAGTTTTGTGTACAACA

upper sequence: LOC_Os03g16900.1 (Oryza sativa), 3'ss of exon 3
lower sequence: Vv03s0017g00490.t01 (Vitis vinifera), 3'ss of exon 2

---------gtcc-gtcatcactggagcgttctctatcttccctgaattt-ttgcttacacgcaact-tgctacaaattattcgtctgc----------agTTCATGATGGCCAACGGTGCACTGGTCCGTGTACTCATCCACACGAGTGTGACAAAGTATCTGAATTTCAAGGCTGTCGACGGCAGCTTCGTGTACAACA
         |||  | || ||    | |   |   || | ||   | ||  ||   |   | || || ||||  ||||| ||  |||            |||||||||||||||| ||||   |||||||||| |||||||||||   ||| || ||||| || ||||||||||| || || || || || ||||||||||
atagttgctgtcttggcaacatattatccaaccaaatgtgccactagttcattttctgtgcacatctatgctg-aaattctttttctatgtactctgatagTTCATGATGGCCAATGGTGGTTTGGTCCGTGTTCTCATCCACACTGATGTTACTAAGTACCTAAATTTCAAGGCCGTGGATGGTAGTTTTGTGTACAACA

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|44666775|gb|CR280209.1|CR280209

EST:     CTGAACATCTGGGTGTCAACAAGGAGTACAATGTTGACATGGTTCCCAAG                         TTCATGATGGCCAACGGTGCACTGGTCCGTGTACTCATCCACACGAGTGTG
genomic: CTGAACATCTGGGTGTCAGCAAGGAGTACAATGTTGACATGGTTCCCAAGgtccgtcatc ... tcgtctgcagTTCATGATGGCCAACGGTGCACTGGTCCGTGTACTCATCCACACGAGTGTG

EST: gi|2428398|gb|C72861.1|C72861

EST:     CTGAACATCTGGGTGTCAGCAAGGAGTACAATGTTGACATGGTTCCCAAG                         TTCATGATGGCCAACGGTGCACTGGTCCGTGTACTCATCCACACGAGTTTN
genomic: CTGAACATCTGGGTGTCAGCAAGGAGTACAATGTTGACATGGTTCCCAAGgtccgtcatc ... tcgtctgcagTTCATGATGGCCAACGGTGCACTGGTCCGTGTACTCATCCACACGAGTGTG

EST: gi|88391356|gb|CI598174.1|CI598174

EST:     CTGAACATCTGGGTGTCAGCAAGGAGTACAATGTTGACATGGTTCCCAAG                         TTCATGATGGCCAACGGTGCACTGGTCCGTGTACTCATCCACA
genomic: CTGAACATCTGGGTGTCAGCAAGGAGTACAATGTTGACATGGTTCCCAAGgtccgtcatc ... tcgtctgcagTTCATGATGGCCAACGGTGCACTGGTCCGTGTACTCATCCACA

EST: gi|88405323|gb|CI586144.1|CI586144

EST:     CTGAACATCTGGGTGTCAGCAAGGAGTACAATGTTGACATGGTTCCCAAG                         TTCATGATGGCCAACGGTGCACTGGTCCGTGTACTCATCCACACGAGTGTG
genomic: CTGAACATCTGGGTGTCAGCAAGGAGTACAATGTTGACATGGTTCCCAAGgtccgtcatc ... tcgtctgcagTTCATGATGGCCAACGGTGCACTGGTCCGTGTACTCATCCACACGAGTGTG

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: 44 (upstream exon), 66 (downstream exon)
Score: 25

CTCTGGAAGAGATTCAAAGGCAACGAGACCGCTCCTGAACATCTGGGTGTCAGCAAGGAGTACAATGTTGACATGGTTCCCAAGgtccgtcatc ... tcgtctgcagTTCATGATGGCCAACGGTGCACTGGTCCGTGTACTCATCCACACGAGTGTGACAAAGTATCTGAATTTCAAGGCTGTCGACGGCAGCTTCGTGTACAACA

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atgc intronic sequence ATGC exonic sequence

Intronic sequence truncated to 55 bases.

tatcttccctgaatttttgcttacacgcaacttgctacaaattattcgtctgcagTTCATGATGGCCAACGGTGCACTGGTCCGTGTACTCATCCACACGAGTGTGACAAAGTATCTGAATTTCAAGGCTGTCGACGGCAGCTTCGTGTACAACA

                 tgcttac  putative branch site (score: 25)
                                            ttcgtct  putative PPT
                                   tacaaattatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtccgtcatcactggagcgttctctatcttccctgaatttttgcttacacgcaacttgctacaaattattcgtctgcagTTCATGATGGCCAACGGTGCACTGGTCCGTGTACTCATCCACACGAGTGTGACAAAGTATCTGAATTTCAAGGCTGTCGACGGCAGCTTCGTGTACAACA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGCT