ERISdb: a Database of Plant Splice Sites

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

Sequence

atgc intronic sequence ATGC exonic sequence

gttagatgcatttgtattttctttactcagatattttgtccactttattaggttgcctgacgaaatgttttcttttagGCATGTGCATCTCTAGAACCAAATTATCAGCCTCCTGTAACATTCGTGGTTGTCCAAAAGCGTCACCATACAAGACTCTTCGCAAACAATCACAAAGACA

Basic information

species	Oryza sativa
transcript	LOC_Os06g39640.1
intron #	17
splice site	3'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: LOC_Os06g39640.1 (Oryza sativa), 3'ss of exon 17
lower sequence: GRMZM2G079080_T02 (Zea mays), 3'ss of exon 17

gttagatgcatttgtat-tttctttactcagatattttgtccactttattaggttgcctgacgaaatgttttcttttagGCATGTGCATCTCTAGAACCAAATTATCAGCCTCCTGTAACATTCGTGGTTGTCCAAAAGCGTCACCATACAAGACTCTTCGCAAACAATCACAAAGACA
||| | |||||||  || ||| |||| ||     || |   | | ||||   |||  || || |   ||||| ||  ||||||||||||| |||||||||||||| ||||||||||||||||| ||||| || ||||| ||||| ||||||||||| || ||||| |||||||||||||
gttgggtgcattttaatgtttttttattc-----ttctaagctccttat--agtttactaactag-cgtttttttccagGCATGTGCATCCCTAGAACCAAATTACCAGCCTCCTGTAACATTTGTGGTGGTTCAAAAACGTCATCATACAAGACTATTTGCAAATAATCACAAAGACA

upper sequence: LOC_Os06g39640.1 (Oryza sativa), 3'ss of exon 17
lower sequence: AC189879.3_FGT003 (Zea mays), 3'ss of exon 16

gttagatgcatttgtattttctttactcagatattttgt-ccactttattaggttgcctgacgaaatgttttcttttagGCATGTGCATCTCTAGAACCAAATTATCAGCCTCCTGTAACATTCGTGGTTGTCCAAAAGCGTCACCATACAAGACTCTTCGCAAACAATCACAAAGACA
||| | |||||||   |||| ||     |  | || |   || ||| ||   |||  || || |  || || |||| ||||||| ||||| |||||||||||||| ||||||||||||||||| ||||| || ||||| ||||| ||||| ||||| ||  ||||||||||||||||||
gttgggtgcatttaattttttttcttctaattcttctaagccccttcatagagtttactaactag-tgcttactttcagGCATGCGCATCCCTAGAACCAAATTACCAGCCTCCTGTAACATTTGTGGTGGTTCAAAAACGTCATCATACGAGACTATTTACAAACAATCACAAAGACA

upper sequence: LOC_Os06g39640.1 (Oryza sativa), 3'ss of exon 17
lower sequence: GLYMA06G23920.1 (Glycine max), 3'ss of exon 17

gttagatgcatttgtattttcttta-ctcagatattttgtccactttattaggttgcctgacgaaatgttttctttt-------agGCATGTGCATCTCTAGAACCAAATTATCAGCCTCCTGTAACATTCGTGGTTGTCCAAAAGCGTCACCATACAAGACTCTTCGCAAACAATCACAAAGACA
  ||  || |     |     |||| |  || |||  | |  | |    | |  | ||| |  |    | |||||||       |||| ||||||||| | ||||| | ||| || ||||| |||||||| ||  |||| ||||| || || || || ||||||||||||||||||||  | ||||
-gtacctggaaaaaaaaacaatttagcaaagttataatttttattactgtggcattcctcaatattcttattctttttgtgtatagGCTTGTGCATCTTTGGAACCTAGTTACCAACCTCCAGTAACATTTGTTATTGTTCAAAAACGGCATCACACTAGACTCTTCGCAAACAATCATGATGACA

upper sequence: LOC_Os06g39640.1 (Oryza sativa), 3'ss of exon 17
lower sequence: GLYMA20G28970.1 (Glycine max), 3'ss of exon 18

gttagatgcatttgtattttctttactcagatattttgtccactttattaggttgc-ctgacgaaatgttttcttttagGCATGTGCATCTCTAGAACCAAATTATCAGCCTCCTGTAACATTCGTGGTTGTCCAAAAGCGTCACCATACAAGACTCTTCGCAAACAATCACAAAGACA
|| ||   || ||    |   | ||| |   | || |    |  | |      ||  ||||  |  | | |   | ||||||||||| ||  |||||||||| || |||||||| ||||||||| | ||||| |||||  | || |||||  |  | || ||||||||  |||  ||||
gtcaggatcactttctctcattatacacttgttttcttattatgtcaaagatatgttctgagaagttatatctgtgtagGCATGTGCTTCCTTAGAACCAAACTACCAGCCTCCAGTAACATTCATAGTTGTGCAAAAAAGACATCATACCCGGTTATTTGCAAACAACTACAGGGACA

upper sequence: LOC_Os06g39640.1 (Oryza sativa), 3'ss of exon 17
lower sequence: AT5G43810.2 (Arabidopsis thaliana), 3'ss of exon 17

-------gttagatgcatt---tgtattttctttactcagatatt--ttgtccactttattaggttgcctgacgaaatgttttcttttagGCATGTGCATCTCTAGAACCAAATTATCAGCCTCCTGTAACATTCGTGGTTGTCCAAAAGCGTCACCATACAAGACTCTTCGCAAACAATCACAAAGACA
        ||   |||||    || | |   |   |    |  ||       || ||||     | |      |   ||| ||  ||||||| |||||||| || ||||| ||||||||||| || || |||||| | ||||| || ||||||||||| ||  |  | || || || ||||||  |||||
gtaaaaacttttgtgcatagcatgaaatgaatccgccacaaagttagcaaaacattttacataatcggaaacgggtttgtgtttgtttagGCTTGTGCATCGCTTGAACCGAATTATCAGCCACCGGTGACATTCATAGTTGTACAGAAGCGTCACCACACTCGTTTGTTTGCTAATAATCACCGAGACA

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|29636941|gb|CB641950.1|CB641950

EST:     ATGAGTTGGATGCTATCCGCAAG                         GCATGTGCATCTCTAGAACCAAATTATCAGCCTCCTGTAACATTCGTGGTT
genomic: ATGAGTTGGATGCTATCCGCAAGgttagatgca ... tttcttttagGCATGTGCATCTCTAGAACCAAATTATCAGCCTCCTGTAACATTCGTGGTT

EST: gi|29674861|gb|CB671136.1|CB671136

EST:     AAGGCCAATTCTACCAAGTTCTCCTCTATGAGTTGGATGCTATCCGCAAG                         GCATGTGCATCTCTAGAACCAAATTATCAGCCTCCTGTAACATTCGTGGTT
genomic: AAGGCCAATTCTACCAAGTTCTCCTCTATGAGTTGGATGCTATCCGCAAGgttagatgca ... tttcttttagGCATGTGCATCTCTAGAACCAAATTATCAGCCTCCTGTAACATTCGTGGTT

EST: gi|29636972|gb|CB641981.1|CB641981

EST:     AAGGCCAATTCTACCAAGTTCTCCTCTATGAGTTGGATGCTATCCGCAAG                         GCATGTGCATGTCTAGAACCAAATTATCAGCCTCCTGTAACATTCGTGGTT
genomic: AAGGCCAATTCTACCAAGTTCTCCTCTATGAGTTGGATGCTATCCGCAAGgttagatgca ... tttcttttagGCATGTGCATCTCTAGAACCAAATTATCAGCCTCCTGTAACATTCGTGGTT

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: 53 (upstream exon), 36 (downstream exon)
Score: 7

GGATGGTGTCAGTGAAGGCCAATTCTACCAAGTTCTCCTCTATGAGTTGGATGCTATCCGCAAGgttagatgca ... tttcttttagGCATGTGCATCTCTAGAACCAAATTATCAGCCTCCTGTAACATTCGTGGTTGTCCAAAAGCGTCACCATACAAGACTCTTCGCAAACAATCACAAAGACA

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atgc intronic sequence ATGC exonic sequence

Intronic sequence truncated to 55 bases.

tactcagatattttgtccactttattaggttgcctgacgaaatgttttcttttagGCATGTGCATCTCTAGAACCAAATTATCAGCCTCCTGTAACATTCGTGGTTGTCCAAAAGCGTCACCATACAAGACTCTTCGCAAACAATCACAAAGACA