ERISdb: a Database of Plant Splice Sites

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

Sequence

atgc intronic sequence ATGC exonic sequence

...tatctaaattttaatttcattttgttgttgatatcgttctgcatctctcctttctgcatatcttctgatttaacaatatcacaacaaacgttgtttgcagCTTTGCAAGATTGATTCTGAGGGCAAGGCGAGGAAGGTCGTAGGCTGCTCCTGCGTCGTTGTCAAGGTAGATAATTGATTACCCACCATACTACTTCAAA

Basic information

species	Oryza sativa
transcript	LOC_Os07g12650.4
intron #	3
splice site	3'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: LOC_Os07g12650.4 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G132929_T03 (Zea mays), 3'ss of exon 2

tatctaaattttaatttcattttgttgttgatatcgttctgcatctctcctttctgcatatcttctgatttaacaata-tcacaacaaacgttgt-ttgcagCTTTGCAAGATTGATTCTGAGGGCAAGGCGAGGAAGGTCGTAGGCTGCTCCTGCGTCGTTGTCAAGGTAGATAATTGATTACCCACCATACTACTTCAAA
|  || |   | |  ||| |    ||| |  |     |  |||    |    | |  |  |  | | |  | | | || ||  ||||| | |  |  || ||||||||||||| || ||||||||||||||||||||||| |||||||||||||| || |||||||||                                  
ttgctgagcatgacattcttcactttgct--ttgtacttggcactaattgcatttcaacgttatgtaaagtgagattaatcttaacaaccttcatactgtagCTTTGCAAGATCGACTCTGAGGGCAAGGCGAGGAAGGTTGTAGGCTGCTCCTGTGTTGTTGTCAAG----------------------------------

upper sequence: LOC_Os07g12650.4 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G132929_T01 (Zea mays), 3'ss of exon 1

tatctaaattttaatttcattttgttgttgatatcgttctgcatctctcctttctgcatatcttctgatttaacaata-tcacaacaaacgttgt-ttgcagCTTTGCAAGATTGATTCTGAGGGCAAGGCGAGGAAGGTCGTAGGCTGCTCCTGCGTCGTTGTCAAGGTAGATAATTGATTACCCACCATACTACTTCAAA
|  || |   | |  ||| |    ||| |  |     |  |||    |    | |  |  |  | | |  | | | || ||  ||||| | |  |  || ||||||||||||| || ||||||||||||||||||||||| |||||||||||||| || |||||||||||   ||  | ||| || ||  ||||||| ||| 
ttgctgagcatgacattcttcactttgct--ttgtacttggcactaattgcatttcaacgttatgtaaagtgagattaatcttaacaaccttcatactgtagCTTTGCAAGATCGACTCTGAGGGCAAGGCGAGGAAGGTTGTAGGCTGCTCCTGTGTTGTTGTCAAGGTGAGTATATCATTTCCTACGGTACTACTACAAG

upper sequence: LOC_Os07g12650.4 (Oryza sativa), 3'ss of exon 3
lower sequence: AT2G32060.1 (Arabidopsis thaliana), 3'ss of exon 3

tatctaaattttaatttcattttgttgttgatatcgttctgcatctctcctttctgcatatcttctgatttaacaatatcacaacaaacgttgtttgcagCTTTGCAAGATTGATTCTGAGGGCAAGGCGAGGAAGGTCGTAGGCTGCTCCTGCGTCGTTGTCAAGGTAGATAATTGATTACCCACCATACTACTTCAAA
    ||| || |  |    |||| |  ||||     |       ||||||| |  | |   |||      |||| | || |     ||  ||| |||||||||||||||||||||||||||||||| || |||||||| || || ||||| ||  ||||  |||||                                  
---gtaagttgtcttccttttttatccttgaagcttt-------ctctcctctaaggaagactttgatggtaacta-ataatcttcaat-ttggttgcagCTTTGCAAGATTGATTCTGAGGGCAATGCAAGGAAGGTTGTTGGATGCTCATGTCTCGTGATCAAG----------------------------------

upper sequence: LOC_Os07g12650.4 (Oryza sativa), 3'ss of exon 3
lower sequence: AT1G15930.2 (Arabidopsis thaliana), 3'ss of exon 3

---------tatctaaat-tttaatttcattttgttgttgatatcgttctg-----catctctcctttctgcatatcttctgatttaacaatatcacaacaaacgtt----gtt--tgcagCTTTGCAAGATTGATTCTGAGGGCAAGGCGAGGAAGGTCGTAGGCTGCTCCTGCGTCGTTGTCAAGGTAGATAATTGATTACCCACCATACTACTTCAAA
         | | |   | ||||||      |  |  |  ||| | |  ||     ||  |   | | ||  ||   |  |   ||| ||||  || |   ||  ||    |||  ||||||| |||||||||||||||||||| || || |||||||| || || ||||| ||  | |||||||||                                  
gtaagtctatgttttcctctttaatactgactcttcatatataccttattgtcgctcagtttatcctcctaaatgaatgtttggttatcaatggcaaattgaatctttgatgttgttgcagCTCTGCAAGATTGATTCTGAGGGTAATGCCAGGAAGGTTGTTGGATGCTCATGTCTTGTTGTCAAG----------------------------------

upper sequence: LOC_Os07g12650.4 (Oryza sativa), 3'ss of exon 3
lower sequence: EFJ26130 (Selaginella moellendorffii), 3'ss of exon 2

tatctaaattttaatttcattttgttgttgatatcgttctgcatctctcctttctgcatatcttctgatttaacaatatcacaacaaacgttgtttgcagCTTTGCAAGATTGATTCTGAGGGCAAGGCGAGGAAGGTCGTAGGCTGCTCCTGCGTCGTTGTCAAGGTAGATAATTGATTACCCACCATACTACTTCAAA
                                     |  || || ||  |   |    |  ||||   | ||   | || |    | |     ||||||||||||||||| || || || ||||||||  | |||||||| |||||||||||||| ||  ||  |                                  
------------------------------------gtaagcttcccttttccttctccaagttct--ctcaaacttttcgctttgatc-----ttgcagCTTTGCAAGATCGACTCCGAAGGCAAGGCTCGAAAGGTCGTCGGCTGCTCCTGCGTGGTGATCCGG----------------------------------

upper sequence: LOC_Os07g12650.4 (Oryza sativa), 3'ss of exon 3
lower sequence: EFJ10812 (Selaginella moellendorffii), 3'ss of exon 2

tatctaaattttaatttcattttgttgttgatatcgttctgcatctctcctttctgcatatcttctgatttaacaatatcacaacaaacgttgtttgcagCTTTGCAAGATTGATTCTGAGGGCAAGGCGAGGAAGGTCGTAGGCTGCTCCTGCGTCGTTGTCAAGGTAGATAATTGATTACCCACCATACTACTTCAAA
                                        | |    ||| || | |   |  ||  | ||  |   | |    |      |  ||||||||||||||||| || || || ||||||||  | |||||||| |||||||||||||| ||  ||  |                                  
----------------------------------------gtaagcttcccttttcc---ttctccaagttctctcaaacttttcgctttgttcttgcagCTTTGCAAGATCGACTCCGAAGGCAAGGCTCGAAAGGTCGTCGGCTGCTCCTGCGTGGTGATCCGG----------------------------------

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|55432687|gb|CV729364.1|CV729364

EST:     TTCACCTCGTTACCGTGCCTAGTGCTAAAACTCTTGGCGAGTGGGCAGGG                         CTTTGCAAGATTGATTCTGAGGGCAAGGCGAGGAAGGTCGTAGGCTGCTCC
genomic: TTCACCTCGTTACCGTGCCTAGTGCTAAAACTCTTGGCGAGTGGGCAGGGgtgagataca ... ttgtttgcagCTTTGCAAGATTGATTCTGAGGGCAAGGCGAGGAAGGTCGTAGGCTGCTCC

EST: gi|88358899|gb|CI619403.1|CI619403

EST:     TTCACCTCGTTAC-GTGCCTAGTGCTAAAACTCTTGGCGAGTGGGCAGGG                         CCTTTGCAAGATTGATTCTGAGGGCAAGGC
genomic: TTCACCTCGTTACCGTGCCTAGTGCTAAAACTCTTGGCGAGTGGGCAGGGgtgagataca ... ttgtttgcagC-TTTGCAAGATTGATTCTGAGGGCAAGGC

EST: gi|58586800|gb|CF985108.1|CF985108

EST:     TTCACCTCGTTACCGTGCCTAGTGCTAAAACTCTTGGCGAGTGGGCAGGG                         CTTTGCAAGATTGATTCTGAGGGCAAGGCGAGGAAGGTCGTAGGCTGCTCC
genomic: TTCACCTCGTTACCGTGCCTAGTGCTAAAACTCTTGGCGAGTGGGCAGGGgtgagataca ... ttgtttgcagCTTTGCAAGATTGATTCTGAGGGCAAGGCGAGGAAGGTCGTAGGCTGCTCC

EST: gi|218485304|gb|FG956287.1|FG956287

EST:     TTCACCTCGTTACCGTGCCTAGTGCTAAAACTCTTGGCGAGTGGGCAGGG                         CTTTGCAAGATTGATT
genomic: TTCACCTCGTTACCGTGCCTAGTGCTAAAACTCTTGGCGAGTGGGCAGGGgtgagataca ... ttgtttgcagCTTTGCAAGATTGATT

EST: gi|427734|gb|D23869.1|D23869

EST:     TTCACCTCGTTACCGTGCCTAGTGCTAAAACTCTTGGCGAGTNGGCAGGG                         CTTTGCAAGATTGATTCTGAGGG
genomic: TTCACCTCGTTACCGTGCCTAGTGCTAAAACTCTTGGCGAGTGGGCAGGGgtgagataca ... ttgtttgcagCTTTGCAAGATTGATTCTGAGGG

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: 59 (upstream exon), 49 (downstream exon)
Score: 26

CCAGCCTGATTATGTCAAGTTGGTCAAGGCACTCTGCGCTGAGCACAATGTTCACCTCGTTACCGTGCCTAGTGCTAAAACTCTTGGCGAGTGGGCAGGGgtgagataca ... ttgtttgcagCTTTGCAAGATTGATTCTGAGGGCAAGGCGAGGAAGGTCGTAGGCTGCTCCTGCGTCGTTGTCAAGGTAGATAATTGATTACCCACCATACTACTTCAAA

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atgc intronic sequence ATGC exonic sequence

Intronic sequence truncated to 55 bases.

tctcctttctgcatatcttctgatttaacaatatcacaacaaacgttgtttgcagCTTTGCAAGATTGATTCTGAGGGCAAGGCGAGGAAGGTCGTAGGCTGCTCCTGCGTCGTTGTCAAGGTAGATAATTGATTACCCACCATACTACTTCAAA