ERISdb: a Database of Plant Splice Sites

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

Sequence

atgc intronic sequence ATGC exonic sequence

gtatgttctctattacttggaattatctatcaaaagcattctcactaatttcttatgatttcatgcaattatttcaaatgttaaatcttcttatagCAGGTGAAATTTTTAGATATGTGGGAACCAGCTATTTTGGCAATAAAGAGGGAAGGCTACAGTATTAAATGTACTGGTCAGCGTGGTGTTGTTCTCACAG

Basic information

species	Oryza sativa
transcript	LOC_Os01g01800.1
intron #	17
splice site	3'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: LOC_Os01g01800.1 (Oryza sativa), 3'ss of exon 17
lower sequence: GRMZM2G036206_T01 (Zea mays), 3'ss of exon 17

gtatgttctctattacttggaattatctatcaa---aagcattctcactaatttcttatgatttcatg-caattatttcaaatgttaaatcttcttatagCAGGTGAAATTTTTAGATATGTGGGAACCAGCTATTTTGGCAATAAAGAGGGAAGGCTACAGTATTAAATGTACTGGTCAGCGTGGTGTTGTTCTCACAG
   | | |||| | | ||| ||| |   ||  |   |   ||||| | || |||||| |||| |||   ||   || | || | || |||   |  | ||||||| | ||||||||| || |||||||||||| || | ||||||||||||||||| ||||| |||||||||| ||| |||||||||||| |  ||||||
--gtatgctctgtcatttgcaatcacacattcactcatcaattcttattactttcttctgatgtcacaacaccgatctgaactattgaattccccaacagCAGGTCAGATTTTTAGACATATGGGAACCAGCTGTTCTAGCAATAAAGAGGGAAGGTTACAGCATTAAATGTAATGGGCAGCGTGGTGTTCTAATCACAG

upper sequence: LOC_Os01g01800.1 (Oryza sativa), 3'ss of exon 17
lower sequence: Vv07s0130g00420.t01 (Vitis vinifera), 3'ss of exon 17

-----------------------------gtatg-ttctctattacttggaattatctatcaaaagcattctcactaatttcttatgatttcatgcaattatttcaaatg-------ttaaatcttcttata--gCAGGTGAAATTTTTAGATATGTGGGAACCAGCTATTTTGGCAATAAAGAGGGAAGGCTACAGTATTAAATGTACTGGTCAGCGTGGTGTTGTTCTCACAG---
                              |||  |||| | ||  |     ||  |||||||| |  || |||  ||  | |  |  ||| ||   |   | | |||          | |||||| | ||   |||||    || | | ||||| ||||||||||||| |||||| || ||||||||||| ||||| || || |||||||| |   |||||| |||  || | |   
gtatgactattacaacaaatacccctagtttataattctttgttgatcttgttttgctatcaaa-gtcttatcaggaacatatgtttttttaatttcaccttcttaaagagcttagcctgaatcttttaattttgcagGCTGGATATCTTGATATATGGGAACCAGCTACTTTGGCCATTAAGAGGGAAGGTTACAGCATCAAGTGTACTGGACCTAGTGGTGCTGTAGTCTCTGAGA

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|86437315|gb|CI119037.1|CI119037

EST:     TTAAGAGAACTCTTGAAACTGGTCATGTATCTTATGAAGTCCAACTACCT                         CAGGTGAAATTTTTAGATATGTGGGAACCAGCTATTTTGGCAATAAAGAGG
genomic: TTAAGAGAACTCTTGAAACTGGTCATGTATCTTATGAAGTCCAACTACCTgtatgttctc ... cttcttatagCAGGTGAAATTTTTAGATATGTGGGAACCAGCTATTTTGGCAATAAAGAGG

EST: gi|29628866|gb|CB633877.1|CB633877

EST:     TTAAGAGAACTCTTGAAACTGGTCATGTATCTTATGAAGTCCAACTACCT                         CAGGTGAAATTTTTAGATATGTGGGAACCAGCTATTTTGGCAATAAAGAGG
genomic: TTAAGAGAACTCTTGAAACTGGTCATGTATCTTATGAAGTCCAACTACCTgtatgttctc ... cttcttatagCAGGTGAAATTTTTAGATATGTGGGAACCAGCTATTTTGGCAATAAAGAGG

EST: gi|32947857|gb|BP184429.1|BP184429

EST:     TTAAGAGAACTCTTGAAACTGGTCATGTATCTTATGAAGTCCAACTACCT                         CAGGTGAAATTTTTAGATATGTGGGAACCAGCTATTTTGGCAATAAAGAGG
genomic: TTAAGAGAACTCTTGAAACTGGTCATGTATCTTATGAAGTCCAACTACCTgtatgttctc ... cttcttatagCAGGTGAAATTTTTAGATATGTGGGAACCAGCTATTTTGGCAATAAAGAGG

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: 65 (upstream exon), 42 (downstream exon)
Score: 11

ATCCTGAAACAAAGGAGCTTATTAAGAGAACTCTTGAAACTGGTCATGTATCTTATGAAGTCCAACTACCTgtatgttctc ... cttcttatagCAGGTGAAATTTTTAGATATGTGGGAACCAGCTATTTTGGCAATAAAGAGGGAAGGCTACAGTATTAAATGTACTGGTCAGCGTGGTGTTGTTCTCACAG

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atgc intronic sequence ATGC exonic sequence

Intronic sequence truncated to 55 bases.

tcactaatttcttatgatttcatgcaattatttcaaatgttaaatcttcttatagCAGGTGAAATTTTTAGATATGTGGGAACCAGCTATTTTGGCAATAAAGAGGGAAGGCTACAGTATTAAATGTACTGGTCAGCGTGGTGTTGTTCTCACAG