ERISdb: a Database of Plant Splice Sites

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

Sequence

atgc intronic sequence ATGC exonic sequence

gtacatcgtcgctgccttgctgaccaatttgcagttgttgaatttgacatgtttctctttttttgtattaagaggtgttacttctccgagctgtcttattcaaaacttctatcttgtttctacagGGAACTGTTAATAATGAGACACTTGGTTACTTCATTGGGAGGGTCTATCTTTTCCTAACACGTTTGGGTATTGATAAAAACCGGCTACGCTTCAGGCAGC

Basic information

species	Oryza sativa
transcript	LOC_Os08g42560.1
intron #	4
splice site	3'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: LOC_Os08g42560.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM5G821551_T03 (Zea mays), 3'ss of exon 4

gtacatcgtcgctgccttgctgaccaatttgcagttgttgaatttgacatgtttctctt-tttttgtattaagaggtgttacttct----ccgagctgtcttattcaaaacttctatcttgtt-tctacagGGAACTGTTAATAATGAGACACTTGGTTACTTCATTGGGAGGGTCTATCTTTTCCTAACACGTTTGGGTATTGATAAAAACCGGCTACGCTTCAGGCAGC
       ||       |||||| | | |||     | |  | ||||| |  || || || || || | || | |  || |  ||||    | |    |  || |  |  | | |  |  |||| | ||||||||||||||||||||||||||||||||||||||||||| ||||||||||||||||| ||| | ||||| ||||||||   |||| | |||||||||||||
-------gttagcaa-ttgctggcaattttctctctttccagtttgatacattccttttgttcttttgtttatatatgctttttcttaccctggatagaattgtaaactattacactactgttatttacagGGAACTGTTAATAATGAGACACTTGGTTACTTCATTGGAAGGGTCTATCTTTTCCTGACAAGCTTGGGAATTGATAAGGGCCGGTTGCGCTTCAGGCAGC

upper sequence: LOC_Os08g42560.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G041797_T01 (Zea mays), 3'ss of exon 4

gtacatcgtcgctgccttgctgaccaatttgcagttgttgaatttgacatgtttctcttt--ttttgtattaagaggtgttacttctccgagctgtcttattcaaaacttctatcttgtt----tctacagGGAACTGTTAATAATGAGACACTTGGTTACTTCATTGGGAGGGTCTATCTTTTCCTAACACGTTTGGGTATTGATAAAAACCGGCTACGCTTCAGGCAGC
       ||       |||  |  |||| |     | |  ||||| |  |  |||  |||  | || | || | | |||||  |  | |      | | ||    ||||| ||   ||||    | ||||||||||||||||||| ||||||||||||||||||||||| ||||||||||||||||| ||| | ||||| ||||||||    ||| | |||||||||||||
-------gttaacaagttgtgg--caatatttgtctttcaaatttaatctcattccttttgttcttttgtttatatgtgttgttcttaccctggatataatcttgaacttttacactgttgctatttacagGGAACTGTTAATAACGAGACACTTGGTTACTTCATTGGAAGGGTCTATCTTTTCCTGACATGCTTGGGAATTGATAAGGGTCGGTTGCGCTTCAGGCAGC

upper sequence: LOC_Os08g42560.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GLYMA08G47890.1 (Glycine max), 3'ss of exon 2

gtacatcgtcgctgccttgctgaccaatttgcagttgttgaatttgacatgtttctctttttttgtattaagaggtgttacttctccgagctgtcttattcaaaacttctatcttgtttcta-cagGGAACTGTTAATAATGAGACACTTGGTTACTTCATTGGGAGGGTCTATCTTTTCCTAACACGTTTGGGTATTGATAAAAACCGGCTACGCTTCAGGCAGC
             |    | ||      || ||    ||||| ||  |||  |  |  ||||||   ||      |  | ||||| |    | |  | |       || |    |||||    ||||||| ||| || ||||||||||||||||||||||| ||||| || ||||| ||| | || ||| | ||||| || ||  ||||  |  | || ||||| |
-------------gtaaggttggtttggtttcaag-attgaacttatcattatgatagttttttaggttt---ttttcttcttcttcttcttattctttgtgctttttatggtgtgttttggtcagGGAATTGTCAACAATGAGACACTTGGTTACTTCATCGGGAGAGTGTATCTATTCTTGACGCGTCTTGGTATAGACAAGGACCGATTGAGGTTTAGGCAAC

upper sequence: LOC_Os08g42560.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GLYMA18G53620.1 (Glycine max), 3'ss of exon 5

gtacatcgtcgctgccttgctgaccaatttgcagttgttgaatttgacatgtttctctttttttgtattaagaggtgttacttctccgagctgtcttattcaaaacttctatcttgtttcta-cagGGAACTGTTAATAATGAGACACTTGGTTACTTCATTGGGAGGGTCTATCTTTTCCTAACACGTTTGGGTATTGATAAAAACC--GGCTACGCTTCAGGCAGC-----------------
                                                             |||| ||| |    ||  | ||        | |  | ||      |  |  | |||||  | | ||||| ||| ||||||||||| |||||||| |||||||||||  | |||| | || |   |       |||  ||   |      ||| ||   |  |  |                   
------------------------------------------------------------gtttggattcaagtttgagattttgttttcttattct-ttgtgctttcatggcatgttttgatcggggaattgtgaataatgagACTCTTGGTTATTTCATTGGGAGAATGTATCATGTCTTTGTATAGACAAGTACCGACTGAGGTTTAGGCAACATCTT-GCTAATGAGATGGTCACTATGCT

upper sequence: LOC_Os08g42560.1 (Oryza sativa), 3'ss of exon 4
lower sequence: Vv01s0150g00150.t01 (Vitis vinifera), 3'ss of exon 4

gtacatcgtcgctgccttgctgaccaatttgcagt-tgttgaatttgacatgtttctctttt-tttgtattaag-aggtgttacttctccgagc-tgtcttatt-caaaacttctatcttgtttctacagGGAACTGTTAATAATGAGACACTTGGTTACTTCATTGGGAGGGTCTATCTTTTCCTAACACGTTTGGGTATTGATAAAAACCGGCTACGCTTCAGGCAGC
                           || | | | | |  |  ||||| | | | | |||| ||||||  ||  |  || | |  ||  |    |||  || |   |   ||| ||  || ||    |||||| ||| || |||||||||||||  |||||||||||||| || || || |||||||||||| | || || || ||  || || |||| ||||| ||||
----------------------gttggttcgaattctatctagattgacctttatttgttttgtttgtacaaaccaactgctccacctttgcatatgtgataatatgatggttcaatgctgatt----agGGAATTGTCAACAATGAGACACTTGCCTACTTCATTGGGAGAGTATACCTATTCCTAACACGTCTTGGCATAGACAAGGACAGGTTACGTTTCAGACAGC

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|86903796|gb|CI302442.1|CI302442

EST:     TTTCAGGGGAGTCAGCCAAGTTAGTGAAGCTTGGGGAAGCAGTTTCAAAG                         GGAACTGTTAATAATGAGACACTTGGTTACTTCATTGGGAGGGTCTATCTT
genomic: TTTCAGGGGAGTCAGCCAAGTTAGTGAAGCTTGGGGAAGCAGTTTCAAAGgtacatcgtc ... gtttctacagGGAACTGTTAATAATGAGACACTTGGTTACTTCATTGGGAGGGTCTATCTT

EST: gi|58684734|gb|CK073421.1|CK073421

EST:     TTTCAGGAGAGTCAGCCAAGTTAGTGAAGCTTGGGGAAGCAGTTTCAAAG                         GGAACTGTTAATAATGAGACACTTGGTTACTTCATTGGGAGGGTCTATCTT
genomic: TTTCAGGGGAGTCAGCCAAGTTAGTGAAGCTTGGGGAAGCAGTTTCAAAGgtacatcgtc ... gtttctacagGGAACTGTTAATAATGAGACACTTGGTTACTTCATTGGGAGGGTCTATCTT

EST: gi|88300311|gb|CI584730.1|CI584730

EST:     TTTCAGGGGAGTCAGCCAAGTTAGTGAAGCTTGGGGAAGCAGTTTCAAAG                         GGAACTGTTAATAATGAGACACTTGGTTACTTCATTGGGAGGGTCTATCTT
genomic: TTTCAGGGGAGTCAGCCAAGTTAGTGAAGCTTGGGGAAGCAGTTTCAAAGgtacatcgtc ... gtttctacagGGAACTGTTAATAATGAGACACTTGGTTACTTCATTGGGAGGGTCTATCTT

EST: gi|4715424|gb|AU056541.1|AU056541

EST:     TTTCAGGGGAGTCAGCCAAGTTAGTGAAGCTTGGGGAAGCAGTTTCAAAG                         GGAACTGTTAATAATGAGACACTTGGTTACTTCATTGGGAGGGTCTATCTT
genomic: TTTCAGGGGAGTCAGCCAAGTTAGTGAAGCTTGGGGAAGCAGTTTCAAAGgtacatcgtc ... gtttctacagGGAACTGTTAATAATGAGACACTTGGTTACTTCATTGGGAGGGTCTATCTT

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: 67 (upstream exon), 68 (downstream exon)
Score: 23

TGTTGATGTTGCTGATTTGGAGTTTTTGATGTTTCCAAGAGAGCTGCAACTTTCAGGGGAGTCAGCCAAGTTAGTGAAGCTTGGGGAAGCAGTTTCAAAGgtacatcgtc ... gtttctacagGGAACTGTTAATAATGAGACACTTGGTTACTTCATTGGGAGGGTCTATCTTTTCCTAACACGTTTGGGTATTGATAAAAACCGGCTACGCTTCAGGCAGC

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atgc intronic sequence ATGC exonic sequence

Intronic sequence truncated to 55 bases.

agaggtgttacttctccgagctgtcttattcaaaacttctatcttgtttctacagGGAACTGTTAATAATGAGACACTTGGTTACTTCATTGGGAGGGTCTATCTTTTCCTAACACGTTTGGGTATTGATAAAAACCGGCTACGCTTCAGGCAGC