ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq
PPT, BS, UA-tract

Sequence

atgc intronic sequence ATGC exonic sequence

gtatgtacactgtgttctgttattggccttccatgactgcaacttatagtattcttttctctcgcttttagGTTGTCAGATGGGGTCGCTCGGTTTATGCAAACATTCAGAAATTTATACAGTTTCAGTTAACCGTCAACGTTGCAGCCTTGATTATTAACGTTGTTGCTG

Basic information

species	Oryza sativa
transcript	LOC_Os04g51610.1
intron #	26
splice site	3'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: LOC_Os04g51610.3 (Oryza sativa), 3'ss of exon 26
lower sequence: GRMZM2G140328_T03 (Zea mays), 3'ss of exon 26

-------------------------------------------------------------------------------------------------------------------------------gtatgtacactgtgttctgttattggccttccatgactgcaacttatagtattcttttctctcgcttttagGTTGTCAGATGGGGTCGCTCGGTTTATGCAAACATTCAGAAATTTATACAGTTTCAGTTAACCGTCAACGTTGCAGCCTTGATTATTAACGTTGTTGCTG
                                                                                                                                 ||||    | | || | || || ||||||    |||| |  | || || ||  |||||   |  || ||||||||||||||||||| ||||| ||||||||||| ||||| |||||||| || ||  |||| |||||||| |||||  |||| || || || |||||||
gtacgttaaggactagtttgggaacaccattttcccaaaggattttaattttccaagggaaattagttcattttcccttgggaaaaatagaaatctcttgggaaaattgagttcccaaactagccctaaatgtgt-ttatatttttttgttagccttctgctactgtagttcatggtgtttgtttct---ggcttcagGTTGTCAGATGGGGTCGTTCGGTGTATGCAAACATACAGAAGTTTATACAATTCCAACTAACGGTCAACGTCGCAGCTCTGATAATCAATGTAGTTGCTG

upper sequence: LOC_Os04g51610.3 (Oryza sativa), 3'ss of exon 26
lower sequence: GRMZM2G391042_T01 (Zea mays), 3'ss of exon 26

-----gtatgtacactgtgttctgttattggccttccatgactgcaacttatagtattcttttctctcgcttttagGTTGTCAGATGGGGTCGCTCGGTTTATGCAAACATTCAGAAATTTATACAGTTTCAGTTAACCGTCAACGTTGCAGCCTTGATTATTAACGTTGTTGCTG
      ||  | |  | | || | || || |||||     |||| |  |||| || ||  ||| |   |  || |||||||||| ||||| || ||||| ||||||||||| || || ||||||||||| ||  |||| |||||||| |||||  |||| || || || |||||||
gtacgttaactgctttatcttttcttgttagccttgtgctactgtagtttatggtgtttgttttt---ggcttcagGTTGTCAGGTGGGGCCGATCGGTGTATGCAAACATACAAAAGTTTATACAGTTCCAACTAACAGTCAACGTCGCAGCTCTGATAATCAATGTAGTTGCTG

upper sequence: LOC_Os04g51610.3 (Oryza sativa), 3'ss of exon 26
lower sequence: GLYMA13G00420.1 (Glycine max), 3'ss of exon 26

---------------------------gtatgtacactgtgttctgttattggccttccatgactgcaacttatagtattct--tttctctcgct--tttagGTTGTCAGATGGGGTCGCTCGGTTTATGCAAACATTCAGAAATTTATACAGTTTCAGTTAACCGTCAACGTTGCAGCCTTGATTATTAACGTTGTTGCTG
                            ||||||  |||  | |    ||||   ||  | |  |      ||  |  ||    ||||| | ||   || ||||||||| |||||| || || || |||||||| |||||||||||||| ||||||||| | || |||||  | |||||  |   ||| || ||||||||||
gtgtatcctatagcccgagatattattttatgtaagctgattacga--attgatgtttgaagcgtaagtggtactgcctttcaatttcttttgccaattcagGTTGTCAAATGGGGGCGGTCTGTATATGCAAATATTCAGAAATTTATCCAGTTTCAGCTTACAGTCAATATAGCAGCACTTGCTATAAATGTTGTTGCTG

upper sequence: LOC_Os04g51610.3 (Oryza sativa), 3'ss of exon 26
lower sequence: GLYMA08G23760.1 (Glycine max), 3'ss of exon 28

----------------------gtatgtacactgtgttc-tgttat-tggccttccatgactgcaacttat--agtattcttttctctcgcttt---tagGTTGTCAGATGGGGTCGCTCGGTTTATGCAAACATTCAGAAATTTATACAGTTTCAGTTAACCGTCAACGTTGCAGCCTTGATTATTAACGTTGTTGCTG
                       ||| |   |      | |||  | |||  | |     ||| || || |  |  |||  | | ||   ||||   ||||||||| | ||||| ||||| || |||||||| |||||||||||||| ||||| ||| | || || || ||||| ||  |  | || || ||||| || |
gggttttggcttaaggagagatttatttcaccaagacacgtgtcctatggattgctcaacctgtaatttgtgtaagatttctatttcattctttgtgtagGTTGTCCGCTGGGGCCGCTCTGTATATGCAAATATTCAGAAATTTATCCAGTTCCAGCTTACAGTTAATGTTGCTGCTCTTGTAATAAATGTTGTGGCAG

upper sequence: LOC_Os04g51610.3 (Oryza sativa), 3'ss of exon 26
lower sequence: GLYMA09G06890.1 (Glycine max), 3'ss of exon 25

-----------------------------------------------------------------------------------------------gtatgtacactgtgttctgttattggccttccatgactgcaacttatagtattcttttctctcgcttttagGTTGTCAGATGGGGTCGCTCGGTTTATGCAAACATTCAGAAATTTATACAGTTTCAGTTAACCGTCAACGTTGCAGCCTTGATTATTAACGTTGTTGCTG
                                                                                                |||  |      || |  ||| |       ||  ||||    | | | |  | |||   |  | || ||||||||||||||||| || || || |||||||| |||||||||||||| ||||||||| | || || || || || ||  |  | ||||| ||||||||||
gtttgtactactttgagatatttttatttgttctgttttttgccattagtagtggaaatgcactttttgaacactgattgtacaatgagaggtttatatagaagtgaggtgcatttaatattgaagcacaactgatgatgacaattgtgtttctccatggttgtagGTTGTCAGATGGGGGCGGTCTGTATATGCAAATATTCAGAAATTTATCCAGTTTCAGCTTACAGTAAATGTGGCCGCTCTAGTGATTAATGTTGTTGCTG

upper sequence: LOC_Os04g51610.3 (Oryza sativa), 3'ss of exon 26
lower sequence: GLYMA17G06520.1 (Glycine max), 3'ss of exon 28

---------------------------gtatgtacactgtgttctgttattggccttccatgactgcaacttatagtattct--tttctctcgct--tttagGTTGTCAGATGGGGTCGCTCGGTTTATGCAAACATTCAGAAATTTATACAGTTTCAGTTAACCGTCAACGTTGCAGCCTTGATTATTAACGTTGTTGCTG
                            ||||||  |||  || ||  ||||   ||  | |  |      ||  |  ||    ||||| ||||   || ||||||||| |||||| || || || |||||||| |||||||||||||| ||||||||| | || |||||  | |||||  |   ||| || ||||||||||
aggtgtatcccatagcctgatattattttatgtaagctg-attatga-attgatgtttgaagcataagtggtactgcctttcaatttctttcgccaattcagGTTGTCAAATGGGGGCGGTCTGTATATGCAAATATTCAGAAATTTATCCAGTTTCAGCTTACAGTCAATATAGCAGCACTTGCTATAAATGTTGTTGCTG

upper sequence: LOC_Os04g51610.3 (Oryza sativa), 3'ss of exon 26
lower sequence: GLYMA07G00630.2 (Glycine max), 3'ss of exon 25

---------------------------gtatgtacac-tgtgttctgttattggccttccatgactgcaacttatagtattcttttctctcgcttt-tagGTTGTCAGATGGGGTCGCTCGGTTTATGCAAACATTCAGAAATTTATACAGTTTCAGTTAACCGTCAACGTTGCAGCCTTGATTATTAACGTTGTTGCTG
                                 |||| ||| | || |   | ||    | ||         |    | |   ||||  ||  | | ||||||||| ||||||| ||||| || |||||||| |||||||||||||| ||||||||| | || || || ||||| ||  |  | || || ||||| || |
gttttggcttaaggagagatttatttcaccaagacacatgtatcctatggattgctcatcttgtaatttgtctgagatgtctatttcattctttgtgtagGTTGTCCGATGGGGCCGCTCTGTATATGCAAATATTCAGAAATTTATCCAGTTTCAGCTCACGGTTAATGTTGCTGCTCTTGTAATAAATGTTGTGGCAG

upper sequence: LOC_Os04g51610.3 (Oryza sativa), 3'ss of exon 26
lower sequence: GLYMA15G18180.1 (Glycine max), 3'ss of exon 25

------------------------------------------------------------------------------------------------gtatgtaca-ctgtgttctgttattggccttc--catgactgcaacttatagtattcttttctctcgcttttagGTTGTCAGATGGGGTCGCTCGGTTTATGCAAACATTCAGAAATTTATACAGTTTCAGTTAACCGTCAACGTTGCAGCCTTGATTATTAACGTTGTTGCTG
                                                                                                 ||| || |  || | |   ||       |    ||  ||||    | | | |  | |||   |  | || ||||||||||||||||| || || || |||||||| |||||||||||||| ||||||||| | || || || || || ||  |  | || || ||||||||||
gttagtactactttgagatattttaatttgttctgttttttgtcattagtagaagtagaaatgcactttttgaatactgattgtacaatgagaggtttatatagaattgaggtgcattgaatatttgaagcacaactgatgatgacaattgtttttctccatggttgtagGTTGTCAGATGGGGGCGGTCTGTATATGCAAATATTCAGAAATTTATCCAGTTTCAGCTTACAGTAAATGTGGCCGCTCTAGTGATAAATGTTGTTGCTG

upper sequence: LOC_Os04g51610.3 (Oryza sativa), 3'ss of exon 26
lower sequence: Vv11s0052g00320.t01 (Vitis vinifera), 3'ss of exon 28

--------------------------gtatgtacactgtgttctgtta---ttggccttccatgactgcaacttatagtattcttttctctcgcttttagGTTGTCAGATGGGGTCGCTCGGTTTATGCAAACATTCAGAAATTTATACAGTTTCAGTTAACCGTCAACGTTGCAGCCTTGATTATTAACGTTGTTGCTG
                            |||   || |  ||  | ||   |       |   ||          |  |  | | |  | | || ||||||||||||||||||| || || || |||||||| || |||||||| || ||||||||| | || || || ||||||||  | || ||||| || || || |
cgagtttgttgatcaaagtttcccttcgatgcctacagcatttggataagttgaagaagctgggatctttgtaactgttgatttctcttgttgcatttagGTTGTCAGATGGGGACGATCTGTATATGCAAATATACAGAAATTCATCCAGTTTCAGCTCACAGTTAATGTTGCAGCTCTAATAATTAATGTCGTGGCAG

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|88351169|gb|CI623391.1|CI623391

EST:     AGAGTTCTGATATTATCATCTTGGATGACAATTTTGCATCGGTCGTGAGG                         GTTGTCAGATGGGGTCGCTCGGTTTATGCAAACATTCAGAAATTTATACAG
genomic: AGAGTTCTGATATTATCATCTTGGATGACAATTTTGCATCGGTCGTGAGGgtatgtacac ... tcgcttttagGTTGTCAGATGGGGTCGCTCGGTTTATGCAAACATTCAGAAATTTATACAG

EST: gi|58594188|gb|CF992496.1|CF992496

EST:     AGAGTTCTGATATTATCATCTTGGATGACAATTTTGCATCGGTCGTGAGG                         GTTGTCAGATGGGGTCGCTCAGTTTATGCAAACATTCAGAAATTTATACAG
genomic: AGAGTTCTGATATTATCATCTTGGATGACAATTTTGCATCGGTCGTGAGGgtatgtacac ... tcgcttttagGTTGTCAGATGGGGTCGCTCGGTTTATGCAAACATTCAGAAATTTATACAG

EST: gi|218500877|gb|FG965670.1|FG965670

EST:     CAATTTTGCATCGGTCGTGAGG                         GTTGTCAGATGGGGTCGCTCGGTTTATGCAAACATTCAGAAATTTATACAG
genomic: CAATTTTGCATCGGTCGTGAGGgtatgtacac ... tcgcttttagGTTGTCAGATGGGGTCGCTCGGTTTATGCAAACATTCAGAAATTTATACAG

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: 64 (upstream exon), 74 (downstream exon)
Score: 36

GCAGATATAGGTCTCTCCATGGGCATCCAGGGAACTGAAGTTGCCAAGGAGAGTTCTGATATTATCATCTTGGATGACAATTTTGCATCGGTCGTGAGGgtatgtacac ... tcgcttttagGTTGTCAGATGGGGTCGCTCGGTTTATGCAAACATTCAGAAATTTATACAGTTTCAGTTAACCGTCAACGTTGCAGCCTTGATTATTAACGTTGTTGCTG

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atgc intronic sequence ATGC exonic sequence

Intronic sequence truncated to 55 bases.

ctgttattggccttccatgactgcaacttatagtattcttttctctcgcttttagGTTGTCAGATGGGGTCGCTCGGTTTATGCAAACATTCAGAAATTTATACAGTTTCAGTTAACCGTCAACGTTGCAGCCTTGATTATTAACGTTGTTGCTG