ERISdb: a Database of Plant Splice Sites

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

Sequence

atgc intronic sequence ATGC exonic sequence

gtatgaggctctctaaaattatttcttccataattcatttgtatatcctcagaataattgttaaattttgctaatgtatctatgttttcatgttgacgctgttgcttccagAGCACAAACTTTTCATTGGAATGCTTCCAAAAAATGTAACAGATGCTGAAATGACTGATTTATTTTCGCAATATGGGAACATCAAGGATTTGCAAATTTT

Basic information

species	Oryza sativa
transcript	LOC_Os05g30980.1
intron #	3
splice site	3'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: LOC_Os05g30980.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G128809_T01 (Zea mays), 3'ss of exon 3

gtatgaggctctctaaaattatttcttccataattcatttgtatatcctcagaataattgttaaattttgctaatgtatctatgttttcatgt-tgacgctgttgcttccagAGCACAAACTTTTCATTGGAATGCTTCCAAAAAATGTAACAGATGCTGAAATGACTGATTTATTTTCGCAATATGGGAACATCAAGGATTTGCAAATTTT
|||||||||||   |||||| | || ||    ||| ||   | |||   |||  | ||| ||   |  |  |   |  | |    |   |||| | |  ||||| |||||||||||||| || ||  |||||||||| ||||||||||||||||||||||||||||  |||||||||||  |||||||||| |||||||||||||| |||||
gtatgaggctcctcaaaattgtatcatc----atttata-atgtatttgcaggttgatt-ttggctcgttttttagatttttcactgatatgtgttatactgttacttccagAGCACAAGCTCTTTGTTGGAATGCTACCAAAAAATGTAACAGATGCTGAAATGATAGATTTATTTTCAAAATATGGGAATATCAAGGATTTGCAGATTTT

upper sequence: LOC_Os05g30980.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G177001_T02 (Zea mays), 3'ss of exon 3

gtatgaggctctctaaaattatttcttccataattcatttgtatatcctcagaataattgttaaattttgctaatgtatctatgttttcatgt-tgacgctgttgcttccagAGCACAAACTTTTCATTGGAATGCTTCCAAAAAATGTAACAGATGCTGAAATGACTGATTTATTTTCGCAATATGGGAACATCAAGGATTTGCAAATTTT
||||||||||    |||||| | || ||    |||  |   | |||   |||  | ||| ||   ||    |   | || |    |   |||| | |  ||||| |||||||||||||| || ||| |||||||||| || |||||||||||| ||||||||||||| |||||||||||  ||||||| || || |||||||| || ||| |
gtatgaggcttctcaaaattgtatcatc----atttgta-atgtattagcaggttgatt-ttggcttggtttttagaattttcactgatatgtgttatactgttacttccagAGCACAAGCTCTTCGTTGGAATGCTCCCCAAAAATGTAACACATGCTGAAATGACGGATTTATTTTCAAAATATGGAAATATAAAGGATTTACAGATTCT

upper sequence: LOC_Os05g30980.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GLYMA19G39300.1 (Glycine max), 3'ss of exon 3

-------------gtatgaggctctctaaaattatttcttcc--ataa-ttcatttgtatatcctcagaataatt---gttaaattttgctaatgtatctatgttttcatgt-tgacgctgttgcttccagAGCACAAACTTTTCATTGGAATGCTTCCAAAAAATGTAACAGATGCTGAAATGACTGATTTATTTTCGCAATATGGGAACATCAAGGATTTGCAAATTTT
              ||| |     |  ||||||||||    |  |||| ||  || | |||| |    | |  ||   | || |||  | | |||  |  ||   |   | | ||  |   |||  |||||| |||||||| |||||||| ||||||||||| |||||  | || | ||||||  ||| | | || ||  | ||||| |  || |||||||| ||||||||
gtataaaatgtttttattatttaatgaaaaattattttcagctgataaatttcttagcatatgccagaattgctttgtgctatattgaggtcatgccttgataagtagttttctgtggtccttgaatccagAACACAAACTCTTCATTGGCATGCTTCCAAAGAATGTTTCTGAAGTTGAAATATCTGCTCTTTTCTCCAAGTATGGAACTATAAAGGATTTACAAATTTT

upper sequence: LOC_Os05g30980.1 (Oryza sativa), 3'ss of exon 3
lower sequence: AT1G03457.2 (Arabidopsis thaliana), 3'ss of exon 3

-----------------gtatgaggctctctaa------aattatttcttccataattcatttgtatatcctcagaataattgttaaattttg---ctaatgtatctatgttttcatgttgac-gctgttgct-tccagAGCACAAACTTTTCATTGGAATGCTTCCAAAAAATGTAACAGATGCTGAAATGACTGATTTATTTTCGCAATATGGGAACATCAAGGATTTGCAAATTTT
                 |  ||| |   |||||      ||  | |||||   |  ||  |||  | |   |      | || |||| |||||   | |||  || |      |  | ||||| | |  |||  ||||||||||||||||||| | || ||||||||||| |||||  | ||  ||||| |       ||||| ||  ||||                           
gtacgcaaaatgcttctgagtgatgaagtctaagcaccaaaagagttctttttttctttctttccagagtttggtcgcattttttaatttttgataccaatcaatttgatagATGTTCTTGACTGTTCGTGCAATCCAGAGCACAAACTTTTCGTCGGTATGCTTCCAAAGAATGTCTCTGAAACTGAAGTCCAGTCCTTATTCTCTGAATA---------------------------

upper sequence: LOC_Os05g30980.1 (Oryza sativa), 3'ss of exon 3
lower sequence: AT1G03457.1 (Arabidopsis thaliana), 3'ss of exon 3

-----------------gtatgaggctctctaa------aattatttcttccataattcatttgtatatcctcagaataattgttaaattttg---ctaatgtatctatgttttcatgttgac-gctgttgct-tccagAGCACAAACTTTTCATTGGAATGCTTCCAAAAAATGTAACAGATGCTGAAATGACTGATTTATTTTCGCAATATGGGAACATCAAGGATTTGCAAATTTT
                 |  ||| |   |||||      ||  | |||||   |  ||  |||  | |   |      | || |||| |||||   | |||  || |      |  | ||||| | |  |||  ||||||||||||||||||| | || ||||||||||| |||||  | ||  ||||| |       ||||| ||  |||| || | ||| |||||| | || ||| |
gtacgcaaaatgcttctgagtgatgaagtctaagcaccaaaagagttctttttttctttctttccagagtttggtcgcattttttaatttttgataccaatcaatttgatagatgttcttgactgttcgtgcaatccagAGCACAAACTTTTCGTCGGTATGCTTCCAAAGAATGTCTCTGAAACTGAAGTCCAGTCCTTATTCTCTGAATACGGAACCATTAAGGATCTACAGATTCT

upper sequence: LOC_Os05g30980.1 (Oryza sativa), 3'ss of exon 3
lower sequence: EFJ23463 (Selaginella moellendorffii), 3'ss of exon 3

gtatgaggctctctaaaattatttcttccataattcatttgtatatcctcagaataattgttaaattt-tgctaatgtatctatgttttcatgttgacgctgttgcttccagAGCACAAACTTTTCATTGGAATGCTTCCAAAAAATGTAACAGATGCTGAAATGACTGATTTATTTTCGCAATATGGGAACATCAAGGATTTGCAAATTTT
                                                    | |  || |     |  ||||  | | || |   ||   |  |    ||| |  |  ||||||||||||| |||||||||||||| ||||||   || || || || ||| |   |||| | || ||| | ||||| |||||||||||  | ||| |  |
--------------------------------------------------gtactgtttttcccgctcgtgcttttct-tccacacttgacttatagttctggtcttctcagAGCACAAACTCTTCATTGGAATGCTACCAAAATCCGTCACGGAGGCCGAAGTCCGTGATGTGTTCTCGGAGTATGGAAACATCAAGGAGCTACAAGTCAT

upper sequence: LOC_Os05g30980.1 (Oryza sativa), 3'ss of exon 3
lower sequence: EFJ11518 (Selaginella moellendorffii), 3'ss of exon 3

gtatgaggctctctaaaattatttcttccataattcatttgtatatcctcagaataattgttaaattttgctaatgtatctatgttttcatgttgacgctgttgcttccagAGCACAAACTTTTCATTGGAATGCTTCCAAAAAATGTAACAGATGCTGAAATGACTGATTTATTTTCGCAATATGGGAACATCAAGGATTTGCAAATTTT
                              || |   ||| | | |   | |        |   | ||| ||      || |   ||   |  |    |||    |  ||||||||||||| |||||||||||||| ||||||   || || || || ||| |   |||| | || ||| | ||||| |||||||||||  | ||| |  |
-----------------------------gtactgtttttttttttttcccgc-------tcgtacttttct------tccacacttgacttatagttctggacttctcagAGCACAAACTCTTCATTGGAATGCTACCAAAATCCGTCACGGAGGCCGAAGTCCGTGATGTGTTCTCGGAGTATGGAAACATCAAGGAGCTACAAGTCAT

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|88350464|gb|CI654287.1|CI654287

EST:     TTCAAGTCCATTGCAAGTGAAATATGCTGATGGAGAGTTGGAAAGACTGG                         AGCACAAACTTTTCATTGGAATGCTTCCAAAAAATGTAACAGATGCTGAAA
genomic: TTCAAGTCCATTGCAAGTGAAATATGCTGATGGAGAGTTGGAAAGACTGGgtatgaggct ... ttgcttccagAGCACAAACTTTTCATTGGAATGCTTCCAAAAAATGTAACAGATGCTGAAA

EST: gi|88350481|gb|CI654304.1|CI654304

EST:     TTCAAGTCCATTGCAAGTGAAATATGCTGATGGAGAGTTGGAAAGACTGG                         AGCACAAACTTTCCATTGGAATGCTTCCAAAAAATGTAACAGATGCTGAAA
genomic: TTCAAGTCCATTGCAAGTGAAATATGCTGATGGAGAGTTGGAAAGACTGGgtatgaggct ... ttgcttccagAGCACAAACTTTTCATTGGAATGCTTCCAAAAAATGTAACAGATGCTGAAA

EST: gi|58685255|gb|CK073942.1|CK073942

EST:     TTCAAGTCCATTGCAAGTGAAATATGCTGATGGAGAGTTGGAAAGACTGG                         AGCACAAACTTTTCATTGGAATGCTTCCAAAAAATGTAACAGATGCTGAAA
genomic: TTCAAGTCCATTGCAAGTGAAATATGCTGATGGAGAGTTGGAAAGACTGGgtatgaggct ... ttgcttccagAGCACAAACTTTTCATTGGAATGCTTCCAAAAAATGTAACAGATGCTGAAA

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: 52 (upstream exon), 70 (downstream exon)
Score: 7

GCTTCAAGTCCATTGCAAGTGAAATATGCTGATGGAGAGTTGGAAAGACTGGgtatgaggct ... ttgcttccagAGCACAAACTTTTCATTGGAATGCTTCCAAAAAATGTAACAGATGCTGAAATGACTGATTTATTTTCGCAATATGGGAACATCAAGGATTTGCAAATTTT

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atgc intronic sequence ATGC exonic sequence

Intronic sequence truncated to 55 bases.

attgttaaattttgctaatgtatctatgttttcatgttgacgctgttgcttccagAGCACAAACTTTTCATTGGAATGCTTCCAAAAAATGTAACAGATGCTGAAATGACTGATTTATTTTCGCAATATGGGAACATCAAGGATTTGCAAATTTT