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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TAAGCATCCACATAGGGCAGGCGGGCATCCAGGTGGGGAATTCTTGCTGGGAACTATACTGCCTCGAGCATGGCATCCAGCCGGACGGCCTCATGCCCAGgttcttctcgatcccaattcttgctcgtctgcatctcttgctgtcttttcctacttaattttgtgaaattctgatattcggatgatggttttgtcctgtt...

Basic information

species Oryza sativa
transcript LOC_Os03g11970.1
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g11970.1 (Oryza sativa), 5'ss of exon 1
lower sequence: GRMZM2G051782_T01 (Zea mays), 5'ss of exon 1
TAAGCATCCACATAGGGCAGGCGGGCATCCAGGTGGGGAATTCTTGCTGGGAACTATACTGCCTCGAGCATGGCATCCAGCCGGACGGCCTCATGCCCAGgttcttctcgatcccaattcttgctcgtctgcatctcttgctgtcttttcctacttaattttgtgaaattctgatattcggatgatggttttg--tcctgtt----
| |||||||| || |||||||| ||||||||||| ||||||||||||||||| || |||||||||||||| || |||||||| |||||||||||||||||||    | |  | ||| |||   ||| ||    ||  |     |  | ||  | ||  || |||     |||     |  ||||||  ||     ||| | |    
TCAGCATCCATATCGGGCAGGCAGGCATCCAGGTAGGGAATTCTTGCTGGGAGCTCTACTGCCTCGAGCACGGTATCCAGCCTGACGGCCTCATGCCCAGgtgaggcccctttcca-ttccaactcatcc-tttccttgagaattatgtcagattttgttctgtacttctct----ctgagatgattattccagttccagctcaga

upper sequence: LOC_Os03g11970.1 (Oryza sativa), 5'ss of exon 1
lower sequence: PP1S341_23V6.1 (Physcomitrella patens), 5'ss of exon 1
TAAGCATCCACATAGGGCAGGCGGGCATCCAGGTGGGGAATTCTTGCTGGGAACTATACTGCCTCGAGCATGGCATCCAGCCGGACGGCCTCATGCCCAGgttctt---ctcgat--cccaattcttgctcgtctgcatctcttgct-gtcttttcctacttaattttgtgaaattctgatattcggatgatggttttgtcctgtt
| |||||||||||||| ||||| || || ||||| |||||| | |||||||| || ||||| || |||||||| || ||||| || || | |||||| |||| | |    | | |    ||     ||    |  || | |  ||||   |  ||||  |   |   |     |  | | |   | |  | ||||   |    |  
TCAGCATCCACATAGGCCAGGCCGGTATTCAGGTCGGGAATGCGTGCTGGGAGCTGTACTGTCTGGAGCATGGGATTCAGCCCGATGGTCGCATGCCAAGgtacgtggattgggtggtgcaggggatggggatgggcttgtgatgcttagcagttccggcgggaccgt-----agcccggtgcccaggggttggtagcggggagg-
















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|88403229|gb|CI570970.1|CI570970
EST:     GAACTATACTGGCTCGAGCATGGCATCCAGCCGGACGGCCTCATGCCCAG                         CGACACAACTCCTGGAATTGCAAGGGATGCATTCAACACGTTCTTCAGCGA
genomic: GAACTATACTGCCTCGAGCATGGCATCCAGCCGGACGGCCTCATGCCCAGgttcttctcg ... ttgcttgcagCGACACAACTCCTGGAATTGCAAGGGATGCATTCAACACGTTCTTCAGCGA
EST: gi|88733922|gb|CI755358.1|CI755358
EST:     GAACTATACTGCCTCGAGCATGGCATCCAGCCGGACGGCCTCATGCCCAG                         CGACACAACTCCTGGAATTGCAAGGGATGCATTCAACACGTTCTTAACCGA
genomic: GAACTATACTGCCTCGAGCATGGCATCCAGCCGGACGGCCTCATGCCCAGgttcttctcg ... ttgcttgcagCGACACAACTCCTGGAATTGCAAGGGATGCATTCAACACGTTCTTCAGCGA
EST: gi|29640705|gb|CB645714.1|CB645714
EST:     GAACTATACTGCCTCGAGCATGGCATCCAGCCGGACGGCCTCATGCCCAG                         CGACACAACTCCTGGAATTGCAAGGGATGCATTCAACACGTTCTTCAGCGA
genomic: GAACTATACTGCCTCGAGCATGGCATCCAGCCGGACGGCCTCATGCCCAGgttcttctcg ... ttgcttgcagCGACACAACTCCTGGAATTGCAAGGGATGCATTCAACACGTTCTTCAGCGA
EST: gi|88308811|gb|CI654094.1|CI654094
EST:     GAACTATACTGCCTCGAGCATGGCATCCAGCCGGACGGCCTCATGCCCAG                         CGACACAACTCCTGGAATTGCAAGGGATGCATTCAACACGTTCTTCAGCGA
genomic: GAACTATACTGCCTCGAGCATGGCATCCAGCCGGACGGCCTCATGCCCAGgttcttctcg ... ttgcttgcagCGACACAACTCCTGGAATTGCAAGGGATGCATTCAACACGTTCTTCAGCGA
EST: gi|88737243|gb|CI760751.1|CI760751
EST:     GAACTATACTGCCTCGAGCATGGCATCCAGCCGGACGGCCTCATGCCCAG                         CGACACAACTCCTGGAATTGCAAGGGATGCATTCAACACGTTCTTCAGCGA
genomic: GAACTATACTGCCTCGAGCATGGCATCCAGCCGGACGGCCTCATGCCCAGgttcttctcg ... ttgcttgcagCGACACAACTCCTGGAATTGCAAGGGATGCATTCAACACGTTCTTCAGCGA
EST: gi|88356918|gb|CI620806.1|CI620806
EST:     GAACTATACTGCCTCGAGCATGGCATCCAGCCGGACGGCCTCATGCCCAG                         CGACACAACTCCTGGAATTGCAAGGGATGCATTCAACACGTTCTTCAGCGA
genomic: GAACTATACTGCCTCGAGCATGGCATCCAGCCGGACGGCCTCATGCCCAGgttcttctcg ... ttgcttgcagCGACACAACTCCTGGAATTGCAAGGGATGCATTCAACACGTTCTTCAGCGA
EST: gi|87005660|gb|CI287484.1|CI287484
EST:     GAACTATACTGCCTCGAGCATGGCATCCAGCCGGACGGCCTCATGCCCAG                         CGACACAACTCCTGGAATTGCAAGGGATGCATTCAACACGTTCTTCAGCGA
genomic: GAACTATACTGCCTCGAGCATGGCATCCAGCCGGACGGCCTCATGCCCAGgttcttctcg ... ttgcttgcagCGACACAACTCCTGGAATTGCAAGGGATGCATTCAACACGTTCTTCAGCGA
EST: gi|88825254|gb|CI775819.1|CI775819
EST:     GAACTATACTGCCTCGAGCATGGCATCCAGCCGGACGGCCTCATGCCCAG                         CGACACAACTCCTGGAATTGCAAGGGATGCATTCAACACGTTCTTCAGCGA
genomic: GAACTATACTGCCTCGAGCATGGCATCCAGCCGGACGGCCTCATGCCCAGgttcttctcg ... ttgcttgcagCGACACAACTCCTGGAATTGCAAGGGATGCATTCAACACGTTCTTCAGCGA
EST: gi|88740826|gb|CI763341.1|CI763341
EST:     GAACTATACTGCCTCGAGCATGGCATCCAGCCGGACGGCCTCATGCCCAG                         CGACACAACTCCTGGAATTGCAAGGGATGCATTCAACACGTTCTTCAGCGA
genomic: GAACTATACTGCCTCGAGCATGGCATCCAGCCGGACGGCCTCATGCCCAGgttcttctcg ... ttgcttgcagCGACACAACTCCTGGAATTGCAAGGGATGCATTCAACACGTTCTTCAGCGA
EST: gi|88742014|gb|CI765522.1|CI765522
EST:     GAACTATACTGCCTCGAGCATGGCATCCAGCCGGACGGCCTCATGCCCAG                         CGACACAACTCCTGGAATTGCAAGGGATGCATTCAACACGTTCTTCAGCGA
genomic: GAACTATACTGCCTCGAGCATGGCATCCAGCCGGACGGCCTCATGCCCAGgttcttctcg ... ttgcttgcagCGACACAACTCCTGGAATTGCAAGGGATGCATTCAACACGTTCTTCAGCGA
EST: gi|88732880|gb|CI756057.1|CI756057
EST:     GAACTATACTGCCTCGAGCATGGCATCCAGCCGGACGGCCTCATGCC-AC                         CGACACAACTCCTGGAATTGCAAGGGATGCATTCAACACGTTCTTCAGCGA
genomic: GAACTATACTGCCTCGAGCATGGCATCCAGCCGGACGGCCTCATGCCCAGgttcttctcg ... ttgcttgcagCGACACAACTCCTGGAATTGCAAGGGATGCATTCAACACGTTCTTCAGCGA
EST: gi|88294849|gb|CI604721.1|CI604721
EST:     GAACTATACTGCCTCGAGCATGGCATCCAGCCGGACGGCCTCATGCCCAG                         CGAC-CAACTCCTGGAATTGCAAGGGATGCATTCAACACGTTCTTCAGCGA
genomic: GAACTATACTGCCTCGAGCATGGCATCCAGCCGGACGGCCTCATGCCCAGgttcttctcg ... ttgcttgcagCGACACAACTCCTGGAATTGCAAGGGATGCATTCAACACGTTCTTCAGCGA
EST: gi|88391691|gb|CI600880.1|CI600880
EST:     GAACTATACTGCCTCGAGCATGGCATCCAGCCGGACGGCCTCATGCCCAG                         CGACACAACTCCTGGAATTGCAAGGGATGCATTCAACACGTTCTTCAGCGA
genomic: GAACTATACTGCCTCGAGCATGGCATCCAGCCGGACGGCCTCATGCCCAGgttcttctcg ... ttgcttgcagCGACACAACTCCTGGAATTGCAAGGGATGCATTCAACACGTTCTTCAGCGA
EST: gi|27545580|gb|CA763794.2|CA763794
EST:     GAACTATACTGCCTCGAGCATGGCATCCAGCCGGACGGCCTCATGCCCAG                         CGACACAACTCCTGGAATTGCAAGGGATGCATTCAACACGTTCTTCAGCGA
genomic: GAACTATACTGCCTCGAGCATGGCATCCAGCCGGACGGCCTCATGCCCAGgttcttctcg ... ttgcttgcagCGACACAACTCCTGGAATTGCAAGGGATGCATTCAACACGTTCTTCAGCGA
EST: gi|88735974|gb|CI759482.1|CI759482
EST:     GAACTATACTGCCTCGAGCATGGCATCCAGCCGGACGGCCTCATGCCCAG                         CGACACAACTCCTGGAATTGCAAGGGATGCATTCAACACGTTCTTCAGCGA
genomic: GAACTATACTGCCTCGAGCATGGCATCCAGCCGGACGGCCTCATGCCCAGgttcttctcg ... ttgcttgcagCGACACAACTCCTGGAATTGCAAGGGATGCATTCAACACGTTCTTCAGCGA
EST: gi|29638414|gb|CB643423.1|CB643423
EST:     GAACTATACTGCCTCGAGCATGGCATCCAGCCGGACGGCCTCATGCCCAG                         CGACACAACTCCTGGAATTGCAAGGGATGCATTCAACACGTTCTTCAGCGA
genomic: GAACTATACTGCCTCGAGCATGGCATCCAGCCGGACGGCCTCATGCCCAGgttcttctcg ... ttgcttgcagCGACACAACTCCTGGAATTGCAAGGGATGCATTCAACACGTTCTTCAGCGA
EST: gi|4715111|gb|AU056228.1|AU056228
EST:     GAACTATACTGCCTCGAGCATGGCATCCAGCCGGACGGCCTCATGCCCAG                         CGACACAACTCCTGGAATTGCAAGGGATGCATTCAACACGTTCTTCAGCGA
genomic: GAACTATACTGCCTCGAGCATGGCATCCAGCCGGACGGCCTCATGCCCAGgttcttctcg ... ttgcttgcagCGACACAACTCCTGGAATTGCAAGGGATGCATTCAACACGTTCTTCAGCGA
EST: gi|88736135|gb|CI759643.1|CI759643
EST:     GAACTATACTGCCTCGAGCATGGCATCCAGCCGGACGGCCTCATGCCCAG                         CGACANAACTCCTGGAATTGCAAGGGATGCATTCAACACGTTCTTCANCGA
genomic: GAACTATACTGCCTCGAGCATGGCATCCAGCCGGACGGCCTCATGCCCAGgttcttctcg ... ttgcttgcagCGACACAACTCCTGGAATTGCAAGGGATGCATTCAACACGTTCTTCAGCGA

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: 57 (upstream exon), 75 (downstream exon)
Score: 13

TAAGCATCCACATAGGGCAGGCGGGCATCCAGGTGGGGAATTCTTGCTGGGAACTATACTGCCTCGAGCATGGCATCCAGCCGGACGGCCTCATGCCCAGgttcttctcg ... ttgcttgcagCGACACAACTCCTGGAATTGCAAGGGATGCATTCAACACGTTCTTCAGCGAGACGAGTTCAGGCAAGCACGTCCCAAGGGCGTTGTTCGTCGACCTGGAG




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