ERISdb: a Database of Plant Splice Sites

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

Sequence

atgc intronic sequence ATGC exonic sequence

gtatcatttctggaagtcaaagacatgcaacacatgttatggtccataagtaacttcatttactttaactctatctcagggcaacataatttattgtcttctgcattcatcttaatcccatctattcatgctgtgcttgtttttcaaagttatctttttgccaattgtttaccatgatgattttttttcagGTCATTGTATCAAGAATGCGATACATATCATCACAAACAGAACGTTCAATTCGGTTTGTTGGTTTATCAACAGCATTAGCCAATGCTCG

Basic information

species	Oryza sativa
transcript	LOC_Os03g11470.1
intron #	12
splice site	3'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: LOC_Os03g11470.1 (Oryza sativa), 3'ss of exon 12
lower sequence: GLYMA06G21970.1 (Glycine max), 3'ss of exon 14

gtatcatttctggaagtcaaagacatgcaacacatgttatggtccataagtaacttcatttactttaactctatctcagggcaacataatttattgtcttctgcattcatcttaatcccatctattcatgctgtgcttgtttttcaaagt---tatctttttgccaattgttta-ccatgatgattttt--tttcagGTCATTGTATCAAGAATGCGATACATATCATCACAAACAGAACGTTCAATTCGGTTTGTTGGTTTATCAACAGCATTAGCCAATGCTCG
                                                                                                |  |||  | |  | ||||  |  ||| | |||  | |   |||||||     |   ||  |  |     | || | |     |  |||||||  ||  |||| ||||| || || ||| ||||||||||||| |||||||||||| || | |||||||| ||| | || |||||  | || |||||| |
-----------------------------------------------------------------------------------------------ctactctttactagtgttaa--ctttctgtgcatattataactgttttttgtgctatatagatactctttgagtgctgaattgaggagatttttgtttctagGTTATTGTTTCTAGGATGAGATACATATCATCCCAAACAGAACGTGCAGTACGGTTTGTAGGTCTTTCTACAGCTCTGGCTAATGCTGG

upper sequence: LOC_Os03g11470.1 (Oryza sativa), 3'ss of exon 12
lower sequence: Vv17s0000g07230.t01 (Vitis vinifera), 3'ss of exon 19

gtatcatttctggaagtcaaagacatgcaacacatgttatggtccataagtaacttcatttactttaactctatctcagggcaacataatttattgtcttctgcattcatcttaatcccatctattcatgctgtgcttgtttttcaaagttatctttttgccaattgtttaccatgatgattttttttcagGTCATTGTATCAAGAATGCGATACATATCATCACAAACAGAACGTTCAATTCGGTTTGTTGGTTTATCAACAGCATTAGCCAATGCTCG
                                                                                       ||  | || | ||    | ||||| | ||   |       |     || ||  |  | |  || |  |  |||  |||        |  |   |||   | ||||| ||||| ||||| ||| ||||||||||||||||||||||  |  || | |||||||| ||  | ||||| || ||||| |||||  |
-------------------------------------------------------------------------------------taaagctgttatgtt----aatcatcctcattttagtagcctacaaactgttt--tcataactgtaacttacttgtaaatctcaccaaagaactgtttgactccagGTTATTGTTTCAAGGATGAGATACATATCATCACAAACAGAGAGGACAGTGCGGTTTGTAGGACTTTCAACTGCTTTAGCAAATGCAGG

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|88574279|gb|CI666048.1|CI666048

EST:     GATGAGATACACCTTCTTGGAGCTGACCGTGGCCCTATTCTCGAG                         GTCATTGTATCAAGAATGCGATACATATCATCACAAACAGAACGTTCAATT
genomic: GATGAGATACACCTTCTTGGAGCTGACCGTGGCCCTATTCTCGAGgtatcatttc ... tttttttcagGTCATTGTATCAAGAATGCGATACATATCATCACAAACAGAACGTTCAATT

EST: gi|88329922|gb|CI651599.1|CI651599

EST:     AGATGAGATACACCTTCTTGGAGCTGACCGTGGCCCTATTCTCGAG                         GTCATTGTATCAAGAATGCGATACATATCATCACAAACAGAACGTNCAATT
genomic: AGATGAGATACACCTTCTTGGAGCTGACCGTGGCCCTATTCTCGAGgtatcatttc ... tttttttcagGTCATTGTATCAAGAATGCGATACATATCATCACAAACAGAACGTTCAATT

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: 66 (upstream exon), 59 (downstream exon)
Score: 9

GTTGGGCTCATGATATTAGATGAGATACACCTTCTTGGAGCTGACCGTGGCCCTATTCTCGAGgtatcatttc ... tttttttcagGTCATTGTATCAAGAATGCGATACATATCATCACAAACAGAACGTTCAATTCGGTTTGTTGGTTTATCAACAGCATTAGCCAATGCTCG

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atgc intronic sequence ATGC exonic sequence

Intronic sequence truncated to 55 bases.

ttgtttttcaaagttatctttttgccaattgtttaccatgatgattttttttcagGTCATTGTATCAAGAATGCGATACATATCATCACAAACAGAACGTTCAATTCGGTTTGTTGGTTTATCAACAGCATTAGCCAATGCTCG