ERISdb: a Database of Plant Splice Sites

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

Sequence

atgc intronic sequence ATGC exonic sequence

gtctactttttttttcttagtgtaaaagattgcaactgtgagtacaatttcaggactgacttttgcaatgttcacttttctcagAACAAATGTAATGTGGGGTATGCTTTTATCAATATGACTGATCCGCAGCACATAATCCCATTCTATAAG

Basic information

species	Oryza sativa
transcript	LOC_Os05g01240.3
intron #	11
splice site	3'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: LOC_Os05g01240.2 (Oryza sativa), 3'ss of exon 12
lower sequence: GRMZM2G156956_T02 (Zea mays), 3'ss of exon 13

gtctactttttttttcttagtgtaaaagattgcaactgtgagtacaatt--tcaggactgacttttgcaatgttcacttttctcagAACAAATGTAATGTGGGGTATGCTTTTATCAATATGACTGATCCGCAGCACATAATCCCATTCTATAAG
      | | |  || |  |||| || | ||| ||||   |||   |||  |  || |||||| |||   ||||  |||| ||||||| |||||||| ||||| ||||| || ||||||||||| ||||| ||||| ||| | ||||| || |||
-----gtatgtcattatgtgtgtgaagg-ttggaacttgtagtgagattaatagggtctgactcttgtggtgtttgctttcctcagAATAAATGTAACGTGGGATATGCATTCATCAATATGACGGATCCACAGCAGATAGTTCCATTTTACAAG

upper sequence: LOC_Os05g01240.2 (Oryza sativa), 3'ss of exon 12
lower sequence: GLYMA06G17250.1 (Glycine max), 3'ss of exon 10

------------------------------------------gtctactttttttttcttagtgtaaaagattgcaactgtgagtacaatttcaggactgacttttgcaatgttcacttttctcagAACAAATGTAATGTGGGGTATGCTTTTATCAATATGACTGATCCGCAGCACATAATCCCATTCTATAAG
                                          |     |  ||  |||||    |||| ||  |||| | | | |    ||  | | |  | || | |||       |  |  ||||||||||||||||| || ||||| || |||||||||| ||||||    || || || |||||| |  ||
gtatttgccaattgatttcaaggcaagtatttatttggacttgctagttgcttgattctttacttaaatgaa-gcaattataaatgtgtttctaagGC--AATTCTACAAA------TGGTTGCAGAACAAATGTAATGTTGGCTATGCATTCATCAATATGATTGATCCTGGACAAATTATTCCATTCCACCAG

upper sequence: LOC_Os05g01240.2 (Oryza sativa), 3'ss of exon 12
lower sequence: AT5G61960.2 (Arabidopsis thaliana), 3'ss of exon 11

-----------gtctacttttttttt----------cttagt--gtaaaagattgcaactgtgagtacaatttcaggactgacttttgcaatgttcacttttc---tcagAACAAATGTAATGTGGGGTATGCTTTTATCAATATGACTGATCCGCAGCACATAATCCCATTCTATAAG
             |||| |||||| |          |||| |  | | |    |  |  | |  |||   |   |  ||   ||  |  ||| ||  | | ||   |||||||||||| |||||||| |||||||| |||||| | | ||| ||  |  | ||  ||||||| | ||||
gcaagcaggcgtcctaccttttttatataagaaagtcttattaagcagacacgtagaggttttggtattttgcaataacgatctaatctaatcttaccctgtcatttcagAACAAATGCAATGTGGGATATGCTTTCATCAATCTTATTGAACCTGAAAAGATTGTCCCATTTTTTAAG

upper sequence: LOC_Os05g01240.2 (Oryza sativa), 3'ss of exon 12
lower sequence: Vv17s0000g00240.t01 (Vitis vinifera), 3'ss of exon 12

-------------gtctactttttttttcttagtgtaa-aagattgcaactgtga-gtaca-atttcaggactgacttttgcaatgttcacttttctcagAACAAATGTAATGTGGGGTATGCTTTTATCAATATGACTGATCCGCAGCACATAATCCCATTCTATAAG
             |  |   ||   |||||| | | || || ||  ||  ||  |  | || || || |    | |||||   |  |||   |||  ||||||||||| |||||||| ||||||||| |||| |||| |||||| |  || ||  | |||||| || ||
gtaagtaaatcttgcatggattgaatttctttggggaagaaaatcacatatgacatatgcacatatctgattcgcctttttgcaaattc-tgttttgcagAACAAATGCAATGTGGGCTATGCTTTTGTCAACATGATTGATCCTCTTCATATTGTTCCATTCCATCAG

upper sequence: LOC_Os05g01240.2 (Oryza sativa), 3'ss of exon 12
lower sequence: Vv01s0150g00090.t01 (Vitis vinifera), 3'ss of exon 13

---------------------------------------------------------------------------------------gtctactttttttttctta-gtgtaaaagattgcaactg-tgagtacaatttcaggactgacttttgcaatgttcacttttctcagAACAAATGTAATGTGGGGTATGCTTTTATCAATATGACTGATCCGCAGCACATAATCCCATTCTATAAG
                                                                                        |  |||||   || |||  |||| | | | | ||  || |   |||   ||      | | | ||  | |  |   ||||  ||||||||||| ||||| |||||||| |||||||| ||||| |||||    || || || ||||||||| ||
gcaagtgcattttttaccagaaagaaatgcttttatcatgtagagtggggatgatgattgagggaggaatcactattaccatttaaatttcactttggcttccttgtgtgttatacaattcatttggtctatacccctttttatttaattatttaatttatttatttttgcagAACAAATGCAATGTAGGGTATGCCTTTATCAACATGACCGATCCTTGCCAGATTATTCCATTCTATCAG

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|58602954|gb|CK013482.1|CK013482

EST:     AGAACCACCGTGGAACCTACGATTTCATCTATCTCCCAATTGATTTTAAG                         AACCAATGTAATGTGGGGTATGCT
genomic: AGAACCACCGTGGAACCTACGATTTCATCTATCTCCCAATTGATTTTAAGgtctactttt ... cttttctcagAACAAATGTAATGTGGGGTATGCT

EST: gi|33381398|gb|CF196741.1|CF196741

EST:     AGAACCACCGTGGAACCTACGATTTCATCTATCTCCCAATTGATTTTAAG                         AACAAATGTAATGTGGGGTATGCTTTTATCAATATGACTGATCCGCAGCAC
genomic: AGAACCACCGTGGAACCTACGATTTCATCTATCTCCCAATTGATTTTAAGgtctactttt ... cttttctcagAACAAATGTAATGTGGGGTATGCTTTTATCAATATGACTGATCCGCAGCAC

EST: gi|29674666|gb|CB670941.1|CB670941

EST:     AGAACCACCGTGGAACCTACGATTTCATCTATCTCCCAATTGATTTTAAG                         AACAAATGTAATGTGGGCGTATGCTTTTATCAATATGACTGATCCGCAGCA
genomic: AGAACCACCGTGGAACCTACGATTTCATCTATCTCCCAATTGATTTTAAGgtctactttt ... cttttctcagAACAAATGTAATGTGGG-GTATGCTTTTATCAATATGACTGATCCGCAGCA

EST: gi|29674667|gb|CB670942.1|CB670942

EST:     TTGATTTTAAG                         AACAAATGTAATGTGGGGTATGCTTTTATCAATATGACTGATCCGCAGCAC
genomic: TTGATTTTAAGgtctactttt ... cttttctcagAACAAATGTAATGTGGGGTATGCTTTTATCAATATGACTGATCCGCAGCAC

EST: gi|218489237|gb|FG949713.1|FG949713

EST:     AGAACCACCGTGGAACCTACGATTTCATCTATCTCCCAATTGATTTTAAG                         AACAAATGTAATGTGGGGTATGCTTTTATCAATATGACTGATCCGCAGCAC
genomic: AGAACCACCGTGGAACCTACGATTTCATCTATCTCCCAATTGATTTTAAGgtctactttt ... cttttctcagAACAAATGTAATGTGGGGTATGCTTTTATCAATATGACTGATCCGCAGCAC

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: 72 (upstream exon), 66 (downstream exon)
Score: 12

GTACAACTGTAAGCTGCTTTTGGCTGTCATTGATGAGAACCACCGTGGAACCTACGATTTCATCTATCTCCCAATTGATTTTAAGgtctactttt ... cttttctcagAACAAATGTAATGTGGGGTATGCTTTTATCAATATGACTGATCCGCAGCACATAATCCCATTCTATAAG

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atgc intronic sequence ATGC exonic sequence

Intronic sequence truncated to 55 bases.

ttgcaactgtgagtacaatttcaggactgacttttgcaatgttcacttttctcagAACAAATGTAATGTGGGGTATGCTTTTATCAATATGACTGATCCGCAGCACATAATCCCATTCTATAAG