ERISdb: a Database of Plant Splice Sites

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

Sequence

atgc intronic sequence ATGC exonic sequence

gcaagttataattttaacatgctaggaagctaggcatgtccatatgtgtacctccttttcttgaccgctgttcatgccatgatgtatcttctgattctgcagAGGAGAGATGTTTATGGAGCTTGGGAACAATACCTTGGCTTGGAACATACTGACACAACACCAAAAAGGTCTTATACAGCCAATCAG

Basic information

species	Oryza sativa
transcript	LOC_Os12g30540.1
intron #	30
splice site	3'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: LOC_Os12g30540.1 (Oryza sativa), 3'ss of exon 30
lower sequence: GRMZM2G014805_T02 (Zea mays), 3'ss of exon 11

gcaagttataattttaacatgctaggaagctaggcatgtccatatgtgtacctccttttcttgaccgctgttcatgccatgatgtat--cttctgattctgcagAGGAGAGATGTTTATGGAGCTTGGGAACAATACCTTGGCTTGGAACATACTGACACAACACCAAAAAGGTCTTATACAGCCAATCAG
                 |||| |      ||   |||    | |||  ||||| || |  || ||  |  ||||| | ||||||  |  ||| | ||| | |||||||||||||| ||||| |||||||||||||||||||||||||| || || || |||||| | ||||||||||| ||||||||||||
----------------gcatg-tgatttccttatcatacttaaatgcataccttctctcattcactac-attcatac-atgatgctttgctttttattatacagAGGAGAGATGTATATGGTGCTTGGGAACAATACCTTGGCTTGGAGCACACCGATACAACATCGAAAAGGTCTTACACAGCCAATCAG

upper sequence: LOC_Os12g30540.1 (Oryza sativa), 3'ss of exon 30
lower sequence: GRMZM2G303655_T01 (Zea mays), 3'ss of exon 19

gcaagttataattttaacatgctaggaagctaggcatgtccatatgtgtacctccttttcttgaccgctgttcatgccatgatgtat--cttctgattctgcagAGGAGAGATGTTTATGGAGCTTGGGAACAATACCTTGGCTTGGAACATACTGACACAACACCAAAAAGGTCTTATACAGCCAATCAG
                 || | |       |  | |||   | |||  ||||| || || || ||   ||||||| | ||||||  |  ||| | ||| | ||| |||||||||| ||||| |||||||||||||||||||||||||| || ||||| |||||| | ||| ||||||| ||| ||||||||
----------------gcaag-tgatttcttcagaatgcttaaatgcataccttctcttgttcact-ttgttcatac-atgatgctttgctttttattatacagCGGAGAGATGTATATGGTGCTTGGGAACAATACCTTGGCTTGGAGCACACTGATACAACATCGAAACGGTCTTACACATCCAATCAG

upper sequence: LOC_Os12g30540.1 (Oryza sativa), 3'ss of exon 30
lower sequence: GLYMA20G11330.1 (Glycine max), 3'ss of exon 22

-------gcaagttataattttaacatgctaggaagctaggcatgtccatatgtgtacctccttttcttgac-cgctgttcatgccatgatgtatcttctgattctgcagAGGAGAGATGTTTATGGAGCTTGGGAACAATACCTTGGCTTGGAACATACTGACACAACACCAAAAAGGTCTTATACAGCCAATCAG
            || |||||||    |  ||  ||| ||  |    | ||||   |   |   ||| |     |  ||| | ||   ||  ||||| | ||||     |||| |||||||||||||| |||||||| ||||| ||||| ||||| ||||||||||   | || ||||| || ||| | | ||| |||
gttgagacttcattgtaattttt-tttcttaaaaagatatccg---ctatattcatgtttgaatttgtgattacattgtacttgttttg--gtatcctatgat-----agAGAAGAGATGTTTATGGTGCTTGGGAGCAATATCTTGGTTTGGAGCATACTGACAATGCTCCTAAAAGATCATATGCTGTCAACCAG

upper sequence: LOC_Os12g30540.1 (Oryza sativa), 3'ss of exon 30
lower sequence: GLYMA02G43930.1 (Glycine max), 3'ss of exon 30

-----gcaagttataattttaacatgctaggaagctaggcatgtccat--atgtgtacctccttttcttgaccgctg--ttcatgcc-atgatgtatcttctgattctgcagAGGAGAGATGTTTATGGAGCTTGGGAACAATACCTTGGCTTGGAACATACTGACACAACACCAAAAAGGTCTTATACAGCCAATCAG
        | ||||| ||  |      |         |  |  || ||  || | || |  | ||| |  |   |||  || ||||      |||||||| ||||     ||||||||||||||||||| |||||||| ||||| ||||| ||||| |||||||| |   | || ||||| || ||| | |  || |||
gtacattcatttatacttggattccttttttttttgtgataattcaattgatatttagcatcatttttatatgtctgaatttatgcttgcattgtatcttgtgat-----agAGGAGAGATGTTTATGGTGCTTGGGAGCAATATCTTGGTTTGGAGCATACTGATAATGCTCCTAAAAGATCATATGCTGTTAACCAG

upper sequence: LOC_Os12g30540.1 (Oryza sativa), 3'ss of exon 30
lower sequence: GLYMA13G16040.1 (Glycine max), 3'ss of exon 11

-------gcaagttataattttaacatgctaggaagctaggcatgtccatatgtgtacctccttttcttgaccgctgttcatgccatgatgtatcttctgattctgcagAGGAGAGATGTTTATGGAGCTTGGGAACAATACCTTGGCTTGGAACATACTGACACAACACCAAAAAGGTCTTATACAGCCAATCAG
            || |||||||    |  ||  ||| ||  ||  |  ||   |||   |  || |  | ||   ||  | ||   ||  ||||| | ||||     |||| |||||||||||||| |||||||| ||||| ||||||||||| ||||||||||   | || ||||| || ||| | | ||| |||
gttgagacttcattgtaattttt-tttcttaaaaagttatccac-tgtattcatgtttttatttgtgattac-attgcacttgttttg--gtatcctatgat-----agAGAAGAGATGTTTATGGTGCTTGGGAGCAATATCTTGGCTTGGAGCATACTGACAATGCTCCTAAAAGATCATATGCTGTCAACCAG

upper sequence: LOC_Os12g30540.1 (Oryza sativa), 3'ss of exon 30
lower sequence: GLYMA14G04890.1 (Glycine max), 3'ss of exon 30

----------gcaagttataattttaacatgctaggaagctaggcatgtccat--atgtgtacctccttttcttgaccgctg--ttcatgcc-atgatgtatcttctgattctgcagAGGAGAGATGTTTATGGAGCTTGGGAACAATACCTTGGCTTGGAACATACTGACACAACACCAAAAAGGTCTTATACAGCCAATCAG
            |   |   |||      |  |  |      |  |  || ||  || | || | || |||    |   |||  || ||||      |||||||| ||||     ||||||||||||||||||| |||||||| || || ||||||||||| ||||||||||   | || ||||| || ||| | |  || |||
gtacattcatttatacttggattccttttttttttggtttgtgataattcaattgatatttagcaccattttcatatgtctgaatttatgcttgcattgtatcttgtgat-----agAGGAGAGATGTTTATGGTGCTTGGGAGCAGTATCTTGGCTTGGAGCATACTGACAATGCTCCTAAAAGATCATATGCTGTTAACCAG

upper sequence: LOC_Os12g30540.1 (Oryza sativa), 3'ss of exon 30
lower sequence: Vv08s0032g00600.t01 (Vitis vinifera), 3'ss of exon 30

------------gcaagttataattttaac----atgctaggaagctaggcatgtccatatgtgtacctccttt---tcttgaccgctgttcatgccatgatgtatcttctgattctg--cagAGGAGAGATGTTTATGGAGCTTGGGAACAATACCTTGGCTTGGAACATACTGACACAACACCAAAAAGGTCTTATACAGCCAATCAG
              || ||||  ||||       ||||       ||  |||   |      | || |    |    | || |  |   |||  |     |||| |    | ||| ||  ||||| |||||||||||||| ||||||||||| ||||||||  |||| ||  |||| ||  | || |||||| ||||| |||| ||||||
gtgtcttaaatttaaaattatttttttcttgtgaatgccgatggcctgtgcaaaacttgtgatttatcctgatagggtttttattgaatttcgagtttaaatgttttggtttattttgttcagAGAAGAGATGTTTATGGTGCTTGGGAACAGTACCTTGGGCTGGAGCACTCTGATACTGCTCCTAAAAGGGCTTATGCAGCAAATCAG

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|86854386|gb|CI256508.1|CI256508

EST:     ATCGGCCTGAATACCTCCAGGATGTCGACGTTGTATCTGCACGTTTTCAG                         AGGAGAGATGTTTATGGAGCTTGGGAACAATACCTTGGCTTGGAACATACT
genomic: ATCGGCCTGAATACCTCCAGGATGTCGACGTTGTATCTGCACGTTTTCAGgcaagttata ... gattctgcagAGGAGAGATGTTTATGGAGCTTGGGAACAATACCTTGGCTTGGAACATACT

EST: gi|218486792|gb|FG957440.1|FG957440

EST:     ATCGGCCTGAATACCTCCAGGATGTCGACGTTGTATCTGCACGTTTTCAG                         AGGAGAGATGTTTATGGAGCTTGGGAACAATACCTTGGCTTGGAACATACT
genomic: ATCGGCCTGAATACCTCCAGGATGTCGACGTTGTATCTGCACGTTTTCAGgcaagttata ... gattctgcagAGGAGAGATGTTTATGGAGCTTGGGAACAATACCTTGGCTTGGAACATACT

EST: gi|29637182|gb|CB642191.1|CB642191

EST:     ATCGGCCTGAATACCTCCAGGATGTCGACGTTGTATCTGCACGTTTTCAG                         AGGAGAGATGTTTATGGAGCTTGGGAACAATACCTTGGCTTGGAACATACT
genomic: ATCGGCCTGAATACCTCCAGGATGTCGACGTTGTATCTGCACGTTTTCAGgcaagttata ... gattctgcagAGGAGAGATGTTTATGGAGCTTGGGAACAATACCTTGGCTTGGAACATACT

EST: gi|163925839|gb|EG712263.1|EG712263

EST:     TGTCGACGTTGTATCTGCACGTTTTCAG                         AGGAGAGATGTTTATGGAGCTTGGGAACAATACCTTGGCTTGGAACATACT
genomic: TGTCGACGTTGTATCTGCACGTTTTCAGgcaagttata ... gattctgcagAGGAGAGATGTTTATGGAGCTTGGGAACAATACCTTGGCTTGGAACATACT

EST: gi|29614413|gb|CB619426.1|CB619426

EST:     GCACGTTTTCAG                         AGGAGAGATGTTTATGGAGCTTGGGAACAATACCTTGGCTTGGAACATACT
genomic: GCACGTTTTCAGgcaagttata ... gattctgcagAGGAGAGATGTTTATGGAGCTTGGGAACAATACCTTGGCTTGGAACATACT

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: 74 (upstream exon), 73 (downstream exon)
Score: 41

TGGAAGCTTGCATTCATATCTATGAATCGGCCTGAATACCTCCAGGATGTCGACGTTGTATCTGCACGTTTTCAGgcaagttata ... gattctgcagAGGAGAGATGTTTATGGAGCTTGGGAACAATACCTTGGCTTGGAACATACTGACACAACACCAAAAAGGTCTTATACAGCCAATCAG

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atgc intronic sequence ATGC exonic sequence

Intronic sequence truncated to 55 bases.

gtacctccttttcttgaccgctgttcatgccatgatgtatcttctgattctgcagAGGAGAGATGTTTATGGAGCTTGGGAACAATACCTTGGCTTGGAACATACTGACACAACACCAAAAAGGTCTTATACAGCCAATCAG