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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtactccatgtgaattttagatcttctttgaatttacttaaatgcatagatatcgattgtgtttgtagaaaacatgccagtttccctgttaccaatgaaaaattcaaacatgttacagGAGGTCACATTCAGAGTGGACTACACAGCTCCAAATGTTGGACGAGAATTTGGTACTGTTTACCTCGGTGACAAGAATGTTGCCTACTCGATAATTGCTG

Basic information

species Oryza sativa
transcript LOC_Os02g32350.2
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g32350.2 (Oryza sativa), 3'ss of exon 3
lower sequence: AC207890.3_FGT002 (Zea mays), 3'ss of exon 2
gtactccatgtgaattttagatcttctttgaatttacttaaatgcatagatatcgattgtgtttgtagaaaacatgccagtttccctgttaccaatgaaaaattcaaacatg---ttacagGAGGTCACATTCAGAGTGGACTACACAGCTCCAAATGTTGGACGAGAATTTGGTACTGTTTACCTCGGTGACAAGAATGTTGCCTACTCGATAATTGCTG
|| || ||| |||| || | ||||||| | || |  | ||           ||  ||||| ||  |                |   | |   ||||| ||||||  ||  ||   |||||||||||||||||||||||||| || || ||||| ||| ||||||||||||| || |||||||| || ||||||||||||||||| |||||  ||||| |||
gtgctacatttgaacttcatatcttctctaaactctcgtat---------cattcattgtattctt--------------cctttttttggacaatgcaaaattataatctgctgttacagGAGGTCACATTCAGAGTGGATTATACGGCTCCTAATATTGGACGAGAATTCGGAACTGTTTATCTAGGTGACAAGAATGTTGCGTACTCAGTAATTTCTG

upper sequence: LOC_Os02g32350.2 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G136296_T02 (Zea mays), 3'ss of exon 3
gtactccatgtgaattttagatcttctttgaatttacttaaatgcatagatatcgattgtgtttgtagaaaacatgccagtttccctgttaccaatgaaaaattcaaa---catgtta-cagGAGGTCACATTCAGAGTGGACTACACAGCTCCAAATGTTGGACGAGAATTTGGTACTGTTTACCTCGGTGACAAGAATGTTGCCTACTCGATAATTGCTG
|| || ||| |||| || | |||||||  ||  |  || | ||        ||  ||||| ||                 |||   | ||  || || ||||||  ||   | ||||| |||||||||||||||| |||||| || |||||||| ||| |||||||||||||||| |||||||  ||  |||| ||||||||||| |||||  || || |||
gtgctacatttgaacttcatatcttctccgagct--ctcatat-------cattcattgtattc----------------ttttttttttgacactgcaaaattataatctcctgttaacagGAGGTCACATTCAAAGTGGATTATACAGCTCCTAATATTGGACGAGAATTTGGAACTGTTTTTCTATGTGATAAGAATGTTGCATACTCAGTAGTTTCTG
















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|29687922|gb|CB684197.1|CB684197
EST:     CATTTGCTTGGGAAAGCAGGGAGTTTCTAAGGAAACTCTGCATAGGAAAG                         GAGGTCACATTCAGAGTGGACTACACAGCTCCAAATGTTGGACGAGAATTT
genomic: CATTTGCTTGGGAAAGCAGGGAGTTTCTAAGGAAACTCTGCATAGGAAAGgtactccatg ... catgttacagGAGGTCACATTCAGAGTGGACTACACAGCTCCAAATGTTGGACGAGAATTT
EST: gi|29631511|gb|CB636520.1|CB636520
EST:     CATTTGCTTGGGAAAGCAGGGAGTTTCTAAGGAAACTCTGCATAGGAAAG                         GAGGTCACATTCAGAGTGGACTACACAGCTCCAAATGTTGGACGAGAATTT
genomic: CATTTGCTTGGGAAAGCAGGGAGTTTCTAAGGAAACTCTGCATAGGAAAGgtactccatg ... catgttacagGAGGTCACATTCAGAGTGGACTACACAGCTCCAAATGTTGGACGAGAATTT
EST: gi|6012905|gb|AU078722.1|AU078722
EST:     ATTTGCTTGGGAAAGCAGGGGAGTTTCTAAGGAAACTCTGCATAGGAAAG                         GAGGTCACATTCAGAGTGGACTACACAGCTCCAAATGTTGGACGAGAATTT
genomic: ATTTGCTTGGGAAAGCA-GGGAGTTTCTAAGGAAACTCTGCATAGGAAAGgtactccatg ... catgttacagGAGGTCACATTCAGAGTGGACTACACAGCTCCAAATGTTGGACGAGAATTT
EST: gi|58680371|gb|CK069058.1|CK069058
EST:     CATTTGCTTGGGAAAGCAGGGAGTTTCTAAGGAAACTCTGCATAGGAAAG                         GAGGTCACATTCAGAGTGGACTACACAGCTCCAAATGTTGGACGAGAATTT
genomic: CATTTGCTTGGGAAAGCAGGGAGTTTCTAAGGAAACTCTGCATAGGAAAGgtactccatg ... catgttacagGAGGTCACATTCAGAGTGGACTACACAGCTCCAAATGTTGGACGAGAATTT
EST: gi|29622580|gb|CB627591.1|CB627591
EST:     CATTTGCTTGGGAAAGCAGGGAGTTTCTAAGGAAACTCTGCATAGGAAAG                         GAGGTCACATTCAGAGTGGACTACACAGCTCCAAATGTTGGACGAGAATTT
genomic: CATTTGCTTGGGAAAGCAGGGAGTTTCTAAGGAAACTCTGCATAGGAAAGgtactccatg ... catgttacagGAGGTCACATTCAGAGTGGACTACACAGCTCCAAATGTTGGACGAGAATTT
EST: gi|29636331|gb|CB641340.1|CB641340
EST:     CATTTGCTTGGGAAAGCAGGGAGTTTCTAAGGAAACTCTGCATAGGAAAG                         GAGGTCACATTCAGAGTGGACTACACAGCTCCAAATGTTGGACGAGAATTT
genomic: CATTTGCTTGGGAAAGCAGGGAGTTTCTAAGGAAACTCTGCATAGGAAAGgtactccatg ... catgttacagGAGGTCACATTCAGAGTGGACTACACAGCTCCAAATGTTGGACGAGAATTT
EST: gi|88328058|gb|CI649856.1|CI649856
EST:     CATTTGCTTGGGAAAGCAGGGAGTTTCTAAGGAAACTCTGCATAGGAAAG                         GAGGTCANATTC
genomic: CATTTGCTTGGGAAAGCAGGGAGTTTCTAAGGAAACTCTGCATAGGAAAGgtactccatg ... catgttacagGAGGTCACATTC
EST: gi|88367108|gb|CI563872.1|CI563872
EST:     CATTTGCTTGGGAAAGCAGGGAGTTTCTAAGGAAACTCTGCATAGGAAAG                         GAGGTCACATTCAGAGTGGACTACACAGCTCCAAATGTTGGACGAGAATTT
genomic: CATTTGCTTGGGAAAGCAGGGAGTTTCTAAGGAAACTCTGCATAGGAAAGgtactccatg ... catgttacagGAGGTCACATTCAGAGTGGACTACACAGCTCCAAATGTTGGACGAGAATTT
EST: gi|117240306|gb|CT842733.1|CT842733
EST:     CATTTGCTTGGGAAAGCAGGGAGTTTCTAAGGAAACTCTGCATAGGAAAG                         GAGGTCACATTCAGAGTGGACTACACAGCTCCAAATGTTGGACGAGAATTT
genomic: CATTTGCTTGGGAAAGCAGGGAGTTTCTAAGGAAACTCTGCATAGGAAAGgtactccatg ... catgttacagGAGGTCACATTCAGAGTGGACTACACAGCTCCAAATGTTGGACGAGAATTT
EST: gi|29627292|gb|CB632303.1|CB632303
EST:     CATTTGCTTGGGAAAGCAGGGAGTTTCTAAGGAAACTCTGCATAGGAAAG                         GAGGTCACATTCAGAGTGGACTACACAGCTCCAAATGTTGGACGAGAATTT
genomic: CATTTGCTTGGGAAAGCAGGGAGTTTCTAAGGAAACTCTGCATAGGAAAGgtactccatg ... catgttacagGAGGTCACATTCAGAGTGGACTACACAGCTCCAAATGTTGGACGAGAATTT
EST: gi|88361419|gb|CI605200.1|CI605200
EST:     CATTTGCTTGGGAAAGCAGGGAGTTTCTAAGGAAACTCTGCATAGGAGAG                         GAGGTCACATTCAGAGTGGACTACACAGCTCCAAATGTTGGACGAGAATTT
genomic: CATTTGCTTGGGAAAGCAGGGAGTTTCTAAGGAAACTCTGCATAGGAAAGgtactccatg ... catgttacagGAGGTCACATTCAGAGTGGACTACACAGCTCCAAATGTTGGACGAGAATTT

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: 75 (upstream exon), 73 (downstream exon)
Score: 167

GCTCGCCGTGGTGGAGTGGATGAACCATTTGCTTGGGAAAGCAGGGAGTTTCTAAGGAAACTCTGCATAGGAAAGgtactccatg ... catgttacagGAGGTCACATTCAGAGTGGACTACACAGCTCCAAATGTTGGACGAGAATTTGGTACTGTTTACCTCGGTGACAAGAATGTTGCCTACTCGATAATTGCTG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgtagaaaacatgccagtttccctgttaccaatgaaaaattcaaacatgttacagGAGGTCACATTCAGAGTGGACTACACAGCTCCAAATGTTGGACGAGAATTTGGTACTGTTTACCTCGGTGACAAGAATGTTGCCTACTCGATAATTGCTG
                              aatgaaaaattcaaa  TA-rich tract