ERISdb: a Database of Plant Splice Sites

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

Sequence

atgc intronic sequence ATGC exonic sequence

gtaagcaaactactttcgtcattgctaagtcttgactctttattgagttgatggatttgcatgaatggttctatgcctgcagCTGTGTGCAAATACGGAATTGGTTTGACTATCGTAATCATATATGTATA

Basic information

species	Oryza sativa
transcript	LOC_Os01g62080.2
intron #	6
splice site	3'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: LOC_Os01g62080.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G386991_T01 (Zea mays), 3'ss of exon 4

gtaagcaaactactttcgtcattgctaagtcttgactcttt-attgagttgatggatttgcatgaatggttctatgcctgcagCTGTGTGCAAATACGGAATTGGTTTGACTATCGTAATCATATATGTATA
||||| ||  ||| |   |  ||   |  | ||||  ||||  ||||||||||||||||||||  |||||||||||||||||| ||||||||||||||||| ||||||||||||||||||||||| ||||||
gtaagaaatttacctctcttgtt-tcacttattgatccttttgttgagttgatggatttgcatcgatggttctatgcctgcagTTGTGTGCAAATACGGAACTGGTTTGACTATCGTAATCATATTTGTATA

upper sequence: LOC_Os01g62080.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GLYMA19G35800.1 (Glycine max), 3'ss of exon 2

--------------------------------gtaagcaaactactttcgtcattgctaagtcttgactctttattgagttgatggat-ttgcatgaatggttctatgcct-gcagCTGTGTGCAAATACGGAATTGGTTTGACTATCGTAATCATATATGTATA
                                |   | | |        |  | || |   | |||  | |  ||         | || ||| || | |||||  || | | |||| |||||||| |||||||||||||||||||||| ||||||||| ||||| 
gtaagggttctttctgattctctttcattattggttgtagatgctaaaagagaatgttgtatattggttgtagatgctaaaagagaatgttgtataagtggtttcattctttgcagTTGTGTGCAGATACGGAATTGGTTTGACTATCTTAATCATATTTGTATT

upper sequence: LOC_Os01g62080.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GLYMA03G33100.1 (Glycine max), 3'ss of exon 4

gtaagcaaactactttcgtcattgctaagtcttgactctttat-tgagttgatggatttgcatgaatggttctatgcct-gcagCTGTGTGCAAATACGGAATTGGTTTGACTATCGTAATCATATATGTATA
|||||    ||  ||| ||  |   |   | |||  | |  ||   |   ||     | | || | |||||  || | | |||| ||||||||||||||||||||||||||||||||||||||||| ||||| 
gtaagggttct-ttttggttgtctttctttattggttgtagatgctaaaagagattgtggtataagtggtttcattctttgcagTTGTGTGCAAATACGGAATTGGTTTGACTATCGTAATCATATTTGTATT

upper sequence: LOC_Os01g62080.1 (Oryza sativa), 3'ss of exon 6
lower sequence: AT3G53570.4 (Arabidopsis thaliana), 3'ss of exon 6

gtaagcaaactactttcgtcattgctaagtcttgactctttattgagttgatggatttg-catgaatggttctatgcct-gcagCTGTGTGCAAATACGGAATTGGTTTGACTATCGTAATCATATATGTATA
||||| | | | ||||| || || |||  ||||  ||  || |    ||  |  |||||  || |    ||| || ||| |||| ||||||||||||||||||||||||||||||||||||||||| ||||| 
gtaagaatatttctttcctc-ttactatttcttcgctagttttaattttattacatttggtataagcttttcaattccttgcagTTGTGTGCAAATACGGAATTGGTTTGACTATCGTAATCATATTTGTATT

upper sequence: LOC_Os01g62080.1 (Oryza sativa), 3'ss of exon 6
lower sequence: Vv08s0040g02640.t01 (Vitis vinifera), 3'ss of exon 4

gtaagcaaactactttcgtcattgctaagtcttgactctttattgagttgatggattt----gcatgaatggttctatgcct-gcagCTGTGTGCAAATACGGAATTGGTTTGACTATCGTAATCATATATGTATA
||| | |  ||   |   |   || |  ||  |   | | ||     |||| |  |||    | || | | |||  || | | |||| ||||||||||||||||||||||||||||||||||||||||| ||||| 
gtacggactctctgtctctttgtgttctgttcttggt-tgtagaagtttgaagtgttttttggtataagtcgtttcattctttgcagTTGTGTGCAAATACGGAATTGGTTTGACTATCGTAATCATATTTGTATT

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|117243444|gb|CT848361.1|CT848361

EST:     GAAATTGATGTGCTTCAGAGGCTTGGGAAGCATGATTTTACTGGTAGCCG                         CTGTGTGCAAATACGGAATTGGTTTGACTATCGTAATCATATATGTATA
genomic: GAAATTGATGTGCTTCAGAGGCTTGGGAAGCATGATTTTACTGGTAGCCGgtaagcaaac ... atgcctgcagCTGTGTGCAAATACGGAATTGGTTTGACTATCGTAATCATATATGTATA

EST: gi|58694718|gb|CK083405.1|CK083405

EST:     GAAATTGATGTGCTTCAGAGGCTTGGGAAGCATGATTTTACTGGTAGCCG                         CTGTGTGCAAATACGGAATTGGTTTGACTATCGTAATCATATATGTATAGT
genomic: GAAATTGATGTGCTTCAGAGGCTTGGGAAGCATGATTTTACTGGTAGCCGgtaagcaaac ... atgcctgcagCTGTGTGCAAATACGGAATTGGTTTGACTATCGTAATCATATATGTATAGT

EST: gi|58654607|gb|CK043287.1|CK043287

EST:     GAAATTGATGTGCTTCAGAGGCTTGGGAAGCATGATTTTACTGGTAGCCG                         CTGTGTGCAAATACGGAATTGGTTTGACTATCGTAATCATATATGTATA
genomic: GAAATTGATGTGCTTCAGAGGCTTGGGAAGCATGATTTTACTGGTAGCCGgtaagcaaac ... atgcctgcagCTGTGTGCAAATACGGAATTGGTTTGACTATCGTAATCATATATGTATA

EST: gi|29665089|gb|CB661364.1|CB661364

EST:     GAAATTGATGTGCTTCAGAGGCTTGGGAAGCATGATTTTACTGGTAGCCG                         CTGTGTGCAAATACGGAATTGGTTTGACTATCGTAATCATATATGTATA
genomic: GAAATTGATGTGCTTCAGAGGCTTGGGAAGCATGATTTTACTGGTAGCCGgtaagcaaac ... atgcctgcagCTGTGTGCAAATACGGAATTGGTTTGACTATCGTAATCATATATGTATA

EST: gi|58593129|gb|CF991437.1|CF991437

EST:     GAAATTGATGTGCTTCAGAGGCTTGGGAAGCATGATTTTACTGGTAGCCG                         CTGTGTGCAAATACGGAATTG
genomic: GAAATTGATGTGCTTCAGAGGCTTGGGAAGCATGATTTTACTGGTAGCCGgtaagcaaac ... atgcctgcagCTGTGTGCAAATACGGAATTG

EST: gi|29679261|gb|CB675536.1|CB675536

EST:     GAAATTGATGTGCTTCAGAGGCTTGGGAAGCATGATTTTACTGGTAGCCG                         CTGTGTGCAAATACGGAATTGGTTTGACTATCGTAATCATATATGTATA
genomic: GAAATTGATGTGCTTCAGAGGCTTGGGAAGCATGATTTTACTGGTAGCCGgtaagcaaac ... atgcctgcagCTGTGTGCAAATACGGAATTGGTTTGACTATCGTAATCATATATGTATA

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: 61 (upstream exon), 74 (downstream exon)
Score: 22

CTATCAAAATTGTGCGCTCCCTTCAGAAATATCGAGAGGCTGCTATGATTGAAATTGATGTGCTTCAGAGGCTTGGGAAGCATGATTTTACTGGTAGCCGgtaagcaaac ... atgcctgcagCTGTGTGCAAATACGGAATTGGTTTGACTATCGTAATCATATATGTATA

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atgc intronic sequence ATGC exonic sequence

Intronic sequence truncated to 55 bases.

agtcttgactctttattgagttgatggatttgcatgaatggttctatgcctgcagCTGTGTGCAAATACGGAATTGGTTTGACTATCGTAATCATATATGTATA