ERISdb: a Database of Plant Splice Sites

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

Sequence

atgc intronic sequence ATGC exonic sequence

gtgagcagcagagcagagctgtccggtggcagcctgtccgtccctttcgagacagcctcgcgcttctcttccgctgcgagtgaactggaccgaatggggcagactggttccttaactgaaatagactaactcgatcagtcgtcccagaatctaacctcgttcgatcgtctgctctgtgcagGGTACCTGATCCCCAAGGGCTGGAAAGTGCTACCTCTGTTCCGCAACATCCACCACAACCCCGACCACTTCCCCTGCCCGGAAAAGTTCGACCCGTCCCG

Basic information

species	Oryza sativa
transcript	LOC_Os02g47470.2
intron #	3
splice site	3'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: LOC_Os02g47470.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G126505_T02 (Zea mays), 3'ss of exon 3

--------gtgagcagcagagcagagctgtccggtggcagcct-gtccgtccctttcgagacagcctcgcgcttct--cttccgctgcga--gtgaactg-gaccgaatggggcagactggttccttaactgaaatagactaactcgatcagtcgtcccagaatctaacctcgttcgatcgtctgctctgtgcagGGTACCTGATCCCCAAGGGCTGGAAAGTGCTACCTCTGTTCCGCAACATCCACCACAACCCCGACCACTTCCCCTGCCCGGAAAAGTTCGACCCGTCCCG
          | |   | |  |   ||||||||   ||  ||  |  |  || ||||  |   |  | | ||| |   |  | |   |    |||  ||| |   |||  || | |   |    |||        ||  | || |  ||       | ||        ||| |   |   |   |||   |||||||||||||||||||||||||||||| ||| | || |||||||| ||||||||||||| |||||||||||||||||||||||| ||||||||||| |||||
gtgagacgtcgcgtcacggcccctcgctgtccgcccgcgcccccgcgccaccgtttcacgttggattggagctccctgcccctgtccctgtcgtgcgctgcggatgaactggacggggggacggcttcctaatcctaaccgaaatgaatagactaactcatcgctgtgccttgcctg--tgctggctggctgcagGGTACCTGATCCCCAAGGGCTGGAAGGTGTTGCCCCTGTTCCGGAACATCCACCACAGCCCCGACCACTTCCCCTGCCCGGACAAGTTCGACCCCTCCCG

upper sequence: LOC_Os02g47470.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G179147_T02 (Zea mays), 3'ss of exon 3

gtgagcagcagagcagagctgtccggtggcagcctgtccgtccctttcgagacagcctcgcgcttctcttccgctgcgagtgaactggaccgaatggggcagactggttccttaactgaaatagactaactcgatcagtcgtcccagaatctaacctcgttcgatcgtctgctctgtgcagGGTACCTGATCCCCAAGGGCTGGAAAGTGCTACCTCTGTTCCGCAACATCCACCACAACCCCGACCACTTCCCCTGCCCGGAAAAGTTCGACCCGTCCCG
                                                         || |  |  |   | ||||||  ||||||||||      || | |   |  | | |||| |||||  |   ||                 |  || || || | ||   || ||||   |||||||||||||||||||||||||||||| ||| | || |||||||| ||||||||||||| |||||||||||||||||||||||| ||||||||||| |||||
--------------------------------------------------------gtccctgtcgtgcgctgctgcggatgaactggac------ggacgggacgcgttcctaaccgaaatgaatagac-----------------agactgac-tcatccg-ctgtgtgctggctgcagGGTACCTGATCCCCAAGGGCTGGAAGGTGATGCCCCTGTTCCGGAACATCCACCACAGCCCCGACCACTTCCCCTGCCCGGAGAAGTTCGACCCCTCCCG

upper sequence: LOC_Os02g47470.1 (Oryza sativa), 3'ss of exon 3
lower sequence: EFJ30794 (Selaginella moellendorffii), 3'ss of exon 6

gtgagcagcagagcagagctgtccggtggcagcctgtccgtccctttcgagacagcctcgcgcttctcttccgctgcgagtgaactggaccgaatggggcagactggttccttaa-ctgaaatagactaactcgatcagtcgtcccagaatctaacctcgtt--cgatcgtctgctctgtgcagGGTACCTGATCCCCAAGGGCTGGAAAGTGCTACCTCTGTTCCGCAACATCCACCACAACCCCGACCACTTCCCCTGCCCGGAAAAGTTCGACCCGTCCCG
                                                                                             | |  | || |  |  |||    ||| || |       | |  ||   |     ||| ||||||   ||  |       |||| || ||||| ||| |||| |||||||||||||||||| | ||||||||| | |||||||| |||| ||||||    ||||     ||| | |||||| |||| ||| |
----------------------------------------------------------------------------------------gtaagaagttgtagcccagcccctccctctgtaacatcacggttgg--caaaagaaaaggaagctaaccgttttacccggaacttgctttg-gcagGATACGTGATTCCCAAGGGCTGGAAAGTGATGCCTCTGTTCAGAAACATCCATCACAGCCCCGAGTTTTTCCTGGAGCCGCAGAAGTTCAACCCCTCCAG

upper sequence: LOC_Os02g47470.1 (Oryza sativa), 3'ss of exon 3
lower sequence: EFJ22851 (Selaginella moellendorffii), 3'ss of exon 6

gtgagcagcagagcagagctgtccggtggcagcctgtccgtccctttcgagacagcctcgcgcttctcttccgctgcgagtgaactggaccgaatggggcagactggttccttaa-ctgaaatagactaactcgatcagtcgtcccagaatctaacctcgtt--cgatcgtctgctctgtgcagGGTACCTGATCCCCAAGGGCTGGAAAGTGCTACCTCTGTTCCGCAACATCCACCACAACCCCGACCACTTCCCCTGCCCGGAAAAGTTCGACCCGTCCCG
                                                                                             | |  | || |  |  |||    ||| || |       | |  ||   |     ||| ||||||   ||  |       |||| || ||||| ||| |||| |||||||||||||||||| | ||||||||| | |||||||| |||| ||||||    ||||     ||| | ||||||||||| ||| |
----------------------------------------------------------------------------------------gtaagaagttgtagcccagcccctccctctgtaacatcacggttgg--caaaagaaaaggaagctaaccgttttacccggaacttgctttg-gcagGATACGTGATTCCCAAGGGCTGGAAAGTGATGCCTCTGTTCAGAAACATCCATCACAGCCCCGAGTTTTTCCTGGAGCCGCAGAAGTTCGACCCCTCCAG

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|66914874|gb|CX101722.1|CX101722

EST:     CATCCTCTCCTTCACCTTCAGGGAGGCCGTGGAGGACGTGGAATACCAAG                         GGTACCTGATCCCCAAGGGCTGGAAAGTGCTACCTCTGTTCCGCAACATCC
genomic: CATCCTCTCCTTCACCTTCAGGGAGGCCGTGGAGGACGTGGAATACCAAGgtgagcagca ... ctctgtgcagGGTACCTGATCCCCAAGGGCTGGAAAGTGCTACCTCTGTTCCGCAACATCC

EST: gi|58599154|gb|CK009682.1|CK009682

EST:     CATCCTCTCCTTCACCTTCAGGGAGGCCGTGGAGGACGTGGAATACCAAG                         GGTACCTGATCCCCAAGGGCTGGAAAGTGCTACC
genomic: CATCCTCTCCTTCACCTTCAGGGAGGCCGTGGAGGACGTGGAATACCAAGgtgagcagca ... ctctgtgcagGGTACCTGATCCCCAAGGGCTGGAAAGTGCTACC

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: 56 (upstream exon), 70 (downstream exon)
Score: 13

CGGATGAAGATGACGAGCCGGGTCATCCAGGAGACGATGAGGGTGGCGTCCATCCTCTCCTTCACCTTCAGGGAGGCCGTGGAGGACGTGGAATACCAAGgtgagcagca ... ctctgtgcagGGTACCTGATCCCCAAGGGCTGGAAAGTGCTACCTCTGTTCCGCAACATCCACCACAACCCCGACCACTTCCCCTGCCCGGAAAAGTTCGACCCGTCCCG

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atgc intronic sequence ATGC exonic sequence

Intronic sequence truncated to 55 bases.

taactcgatcagtcgtcccagaatctaacctcgttcgatcgtctgctctgtgcagGGTACCTGATCCCCAAGGGCTGGAAAGTGCTACCTCTGTTCCGCAACATCCACCACAACCCCGACCACTTCCCCTGCCCGGAAAAGTTCGACCCGTCCCG