ERISdb: a Database of Plant Splice Sites

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

Sequence

atgc intronic sequence ATGC exonic sequence

gtacacgttcatatcaactgagttccatctctcgattgttttactctgggaatcagtttccaaccaattcatcggttctttttcagTTGGGCCTAAAAAGTGATGGCCTCCGCATCGATAGCGGCAAGCGCATAAATTTGATAGTCCAAGGCTCACATGACTCATGACATATTTTGGCACCACGCA

Basic information

species	Oryza sativa
transcript	LOC_Os06g36590.1
intron #	19
splice site	3'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: LOC_Os06g36590.1 (Oryza sativa), 3'ss of exon 19
lower sequence: GRMZM2G169114_T01 (Zea mays), 3'ss of exon 19

gtacacgttcatatcaactgagttccatctctcgattgttttactctgggaatcagtttccaaccaattcatcggttctt---tttcagTTGGGCCTAAAAAGTGATGGCCTCCGCATCGATAGCGGCAAGCGCATAAATTTGATAGTCCAAGGCTCACATGACTCATGACATATTTTGGCACCACGCA-
||||||| ||||| ||  ||||||| ||   | ||||| |||||||| | |     || |||| ||||||||||||||||   |||||| ||||||| |||| ||||| ||||||||||||||||||||||||||||||| ||||||||||||||||||||||||||||||| |||| | |||   ||| 
gtacacgatcataccagttgagttc-attgatggattgctttactctagaa--tgtttgccaatcaattcatcggttcttccttttcagCTGGGCCTGAAAAATGATGTCCTCCGCATCGATAGCGGCAAGCGCATAAATCTGATAGTCCAAGGCTCACATGACTCATGACACATTT-GACACACTGCAA

upper sequence: LOC_Os06g36590.1 (Oryza sativa), 3'ss of exon 19
lower sequence: GRMZM2G171031_T03 (Zea mays), 3'ss of exon 19

------gtacacgttcatatcaactgagttccatctctcgattgttttactctgggaatcagtttccaaccaattcatcggttctt---tttcagTTGGGCCTAAAAAGTGATGGCCTCCGCATCGATAGCGGCAAGCGCATAAATTTGATAGTCCAAGGCTCACATGACTCATGACATATTTTGGCACCACGCA---
      ||||||| ||||| ||| ||||||| ||   ||||| ||||||||||   ||    || |||| |||||||| |||||||   |||||| |||||||||||| ||||| ||||||||| ||||||||||||||||||||| ||||||||||||||||||||||||||||||| |   ||||||   |||   
gtggaggtacacgatcataccaattgagttc-attgatcgatcgttttactcta--aagtgtttgccaatcaattcattggttcttccttttcagCTGGGCCTAAAAAATGATGTCCTCCGCATTGATAGCGGCAAGCGCATAAATCTGATAGTCCAAGGCTCACATGACTCATGACACA---TGGCACACTGCAAGC

upper sequence: LOC_Os06g36590.1 (Oryza sativa), 3'ss of exon 19
lower sequence: GRMZM2G171031_T01 (Zea mays), 3'ss of exon 19

gtacacgttcatatcaactgagttccatctctcgattgttttactctgggaatcagtttccaaccaattcatcggttctt---tttcagTTGGGCCTAAAAAGTGATGGCCTCCGCATCGATAGCGGCAAGCGCATAAATTTGATAGTCCAAGGCTCACATGACTCATGACATATTTTGGCACCACGCA
||||||| ||||| ||| ||||||| ||   ||||| ||||||||||   ||    || |||| |||||||| |||||||   |||||| |||||||||||| ||||| ||||||||| ||||||||||||||||||||| |||||||||||||||||||||||||||||                   
gtacacgatcataccaattgagttc-attgatcgatcgttttactcta--aagtgtttgccaatcaattcattggttcttccttttcagCTGGGCCTAAAAAATGATGTCCTCCGCATTGATAGCGGCAAGCGCATAAATCTGATAGTCCAAGGCTCACATGACTCATGA-------------------

upper sequence: LOC_Os06g36590.1 (Oryza sativa), 3'ss of exon 19
lower sequence: GRMZM2G171031_T02 (Zea mays), 3'ss of exon 19

gtacacgttcatatcaactgagttccatctctcgattgttttactctgggaatcagtttccaaccaattcatcggttctt---tttcagTTGGGCCTAAAAAGTGATGGCCTCCGCATCGATAGCGGCAAGCGCATAAATTTGATAGTCCAAGGCTCACATGACTCATGACATATTTTGGCACCACGCA---
||||||| ||||| ||| ||||||| ||   ||||| ||||||||||   ||    || |||| |||||||| |||||||   |||||| |||||||||||| ||||| ||||||||| ||||||||||||||||||||| ||||||||||||||||||||||||||||||| |   ||||||   |||   
gtacacgatcataccaattgagttc-attgatcgatcgttttactcta--aagtgtttgccaatcaattcattggttcttccttttcagCTGGGCCTAAAAAATGATGTCCTCCGCATTGATAGCGGCAAGCGCATAAATCTGATAGTCCAAGGCTCACATGACTCATGACACA---TGGCACACTGCAAGC

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|66917034|gb|CX103882.1|CX103882

EST:     ACCTCGGTGTTCTCTTGAGATGGTTTTCTGTTGATAGCAATCAGGTGGAG                         TTGGGCCTAAAAAGTGATGGCCTTCGCATCGATAGCGGCAAGCGCATAAAT
genomic: ACCTCGGTGTTCTCTTGAGATGGTTTTCTGTTGATAGCAATCAGGTGGAGgtacacgttc ... tctttttcagTTGGGCCTAAAAAGTGATGGCCTCCGCATCGATAGCGGCAAGCGCATAAAT

EST: gi|29661780|gb|CB658055.1|CB658055

EST:     ACCTCGGTGTTCTCTTGAGATGGTTTTCTGTTGATAGCAATCAGGTGGAG                         TTGGGCCTAAAAAGTGATGGCCTCCGCATCGATAGCGGCAAGCGCATAAAT
genomic: ACCTCGGTGTTCTCTTGAGATGGTTTTCTGTTGATAGCAATCAGGTGGAGgtacacgttc ... tctttttcagTTGGGCCTAAAAAGTGATGGCCTCCGCATCGATAGCGGCAAGCGCATAAAT

EST: gi|11544417|gb|BF475235.1|BF475235

EST:     ACCTCGGTGTTCTCTTGAGATGGTTTTCTGTTGATAGCAATCAGGTGGAG                         TTGGGCCTAAAAAGTGATGGCCTCCGCATCGATAGCGGCAAGCGCATAAAT
genomic: ACCTCGGTGTTCTCTTGAGATGGTTTTCTGTTGATAGCAATCAGGTGGAGgtacacgttc ... tctttttcagTTGGGCCTAAAAAGTGATGGCCTCCGCATCGATAGCGGCAAGCGCATAAAT

EST: gi|25806181|gb|CA762142.1|CA762142

EST:     ACCTCGGTG-TCTCTTAAGATGGTTTTCTGTTAATAGCAATCAGGTGGAG                         TTGGGCCTAAAAAGTGATGGCCTCCGCATCGATAGCGGCAAGCGCATAAAT
genomic: ACCTCGGTGTTCTCTTGAGATGGTTTTCTGTTGATAGCAATCAGGTGGAGgtacacgttc ... tctttttcagTTGGGCCTAAAAAGTGATGGCCTCCGCATCGATAGCGGCAAGCGCATAAAT

EST: gi|218489725|gb|FG964366.1|FG964366

EST:     ACCTCGGTGTTCTCTTGAGATGGTTTTCTGTTGATAGCAATCAGGTGGAG                         TTGGGCCTAAAAAGTGATGGCCTCCGCATCGATAGCGGCAAGCGCATAAAT
genomic: ACCTCGGTGTTCTCTTGAGATGGTTTTCTGTTGATAGCAATCAGGTGGAGgtacacgttc ... tctttttcagTTGGGCCTAAAAAGTGATGGCCTCCGCATCGATAGCGGCAAGCGCATAAAT

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: 54 (upstream exon), 63 (downstream exon)
Score: 10

GTAACAACACCCCTTCTATTCAAAATGATACCCGCGGTGGTCCACCTCGGTGTTCTCTTGAGATGGTTTTCTGTTGATAGCAATCAGGTGGAGgtacacgttc ... tctttttcagTTGGGCCTAAAAAGTGATGGCCTCCGCATCGATAGCGGCAAGCGCATAAATTTGATAGTCCAAGGCTCACATGACTCATGACATATTTTGGCACCACGCA

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atgc intronic sequence ATGC exonic sequence

Intronic sequence truncated to 55 bases.

tcgattgttttactctgggaatcagtttccaaccaattcatcggttctttttcagTTGGGCCTAAAAAGTGATGGCCTCCGCATCGATAGCGGCAAGCGCATAAATTTGATAGTCCAAGGCTCACATGACTCATGACATATTTTGGCACCACGCA