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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATACCAAAGAAAGGGAAGATTTATTCAGTGAATGAAGGGAATGCGAAAAATTGGGACGAGCCTACCGCAAAgtacgcgctacttatgttttcagaatagtgtacttcctgaagaacctgagctaaaatctacaacaatcatttacag

Basic information

species Oryza sativa
transcript LOC_Os01g64660.4
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g64660.3 (Oryza sativa), 5'ss of exon 7
lower sequence: GLYMA16G28310.1 (Glycine max), 5'ss of exon 9
ATACCAAAGAAAGGGAAGATTTATTCAGTGAATGAAGGGAATGCGAAAAATTGGGACGAGCCTACCGCAAAgtacgcgctactt--atgttttcagaatagtgt-acttcctgaagaacctgagctaaaatctacaacaatcatttacag--------
|| ||||||||||| || |||||||||||||||||||| ||||| ||||| |||||    ||||| || | ||| |    | ||   || | | | |||  | | |    ||   | |  |  |  ||  |    |   ||  || ||          
ATCCCAAAGAAAGGTAAAATTTATTCAGTGAATGAAGGAAATGCCAAAAACTGGGATCGTCCTACTGCTACgtatgtttgaattcagtgatcttataatgttttcaggcactagtgcatatttgtcaatcttgtaattcatttttcacttcttctcag

upper sequence: LOC_Os01g64660.3 (Oryza sativa), 5'ss of exon 7
lower sequence: EFJ18090 (Selaginella moellendorffii), 5'ss of exon 8
ATACCAAAGAAAGGGAAGATTTATTCAGTGAATGAAGGGAATGCGAAAAATTGGGACGAGCCTACCGCAAAgtacgcgctacttatgttttcagaatagtgtacttcctgaagaacctgagctaaaatctacaacaatcatttacag
||||||||||| || || |||||||| |||||||| || ||||| || || ||||||||||| ||   |  ||| |       | |  |||   || |||  |  |  |||   |    ||                          
ATACCAAAGAAGGGAAAAATTTATTCCGTGAATGAGGGCAATGCAAAGAACTGGGACGAGCCCACTAGATTgtaagtttagtgttttctttttaaaaagta-agattttgatttatgacag--------------------------

upper sequence: LOC_Os01g64660.3 (Oryza sativa), 5'ss of exon 7
lower sequence: EFJ36627 (Selaginella moellendorffii), 5'ss of exon 7
ATACCAAAGAAAGGGAAGATTTATTCAGTGAATGAAGGGAATGCGAAAAATTGGGACGAGCCTACCGCAAAgtacgcgctacttatgttttcagaatagtgtacttcctgaagaacctgagctaaaatctacaacaatcatttacag
||||||||||| || || |||||||| |||||||| || ||||| || || ||||||||||| ||   |  ||| |       | |  |||   || |||  |  |  ||  |||       |   || ||  |||           
ATACCAAAGAAGGGAAAAATTTATTCCGTGAATGAGGGCAATGCAAAGAACTGGGACGAGCCCACTAGATTgtaagtttggtattttcttttcaaaaagta-agattttggtgaatta----tttgatttatgacag----------

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|38470545|gb|CF954676.1|CF954676
EST:     AGTGAATGAAGGGAATGCGAAAAATTGGGACGAGCCTACCGCAAA                         GTTTGTGGAGAAGTGCAAGTTCCCTAAGGATGGTTCATCACCTAAATCCTT
genomic: AGTGAATGAAGGGAATGCGAAAAATTGGGACGAGCCTACCGCAAAgtacgcgcta ... tcatttacagGTTTGTGGAGAAGTGCAAGTTCCCTAAGGATGGTTCATCACCTAAATCCTT
EST: gi|29686739|gb|CB683014.1|CB683014
EST:     TATTCAGTGAATGAAGGGAATGCGAAAAATTGGGACGAGCCTACCGCAAA                         GTTTGTGGAGAAGTGCAAGTTCCCTAAGGATGGTTCATCACCTAAATCCTT
genomic: TATTCAGTGAATGAAGGGAATGCGAAAAATTGGGACGAGCCTACCGCAAAgtacgcgcta ... tcatttacagGTTTGTGGAGAAGTGCAAGTTCCCTAAGGATGGTTCATCACCTAAATCCTT
EST: gi|29621610|gb|CB626621.1|CB626621
EST:     TATTCAGTGAATGAAGGGAATGCGAAAAATTGGGACGAGCCTACCGCAAA                         GTTTGTGGAGAAGTGCAAGTTCCCTAAGGATGGTTCATCACCTAAATCCTT
genomic: TATTCAGTGAATGAAGGGAATGCGAAAAATTGGGACGAGCCTACCGCAAAgtacgcgcta ... tcatttacagGTTTGTGGAGAAGTGCAAGTTCCCTAAGGATGGTTCATCACCTAAATCCTT
EST: gi|58588683|gb|CF986991.1|CF986991
EST:     TATTCAGTGAATGAAGGGAATGCGAAAAATTGGGACGAGCCTACCGCAAA                         G-TTGTGGAGAAGTGCAAGTTCCCTAAGGATGGTTCATCACCTAAATCCTT
genomic: TATTCAGTGAATGAAGGGAATGCGAAAAATTGGGACGAGCCTACCGCAAAgtacgcgcta ... tcatttacagGTTTGTGGAGAAGTGCAAGTTCCCTAAGGATGGTTCATCACCTAAATCCTT
EST: gi|29613014|gb|CB618027.1|CB618027
EST:     TATTCAGTGAATGAAGGGAATGCGAAAAATTGGGACGAGCCTACCGCAAA                         GTTTGTGGAGAAGTGCAAGTTCCCTAAGGATGGTTCATCACCTAAATCCTT
genomic: TATTCAGTGAATGAAGGGAATGCGAAAAATTGGGACGAGCCTACCGCAAAgtacgcgcta ... tcatttacagGTTTGTGGAGAAGTGCAAGTTCCCTAAGGATGGTTCATCACCTAAATCCTT
EST: gi|29617760|gb|CB622772.1|CB622772
EST:     TATTCAGTGAATGAAGGGAATGCGAAAAATTGGGACGAGCCTACCGCAAA                         GTTTGTGGAGAAGTGCAAGTTCCCTAAGGATGGTTCATCACCTAAATCCTT
genomic: TATTCAGTGAATGAAGGGAATGCGAAAAATTGGGACGAGCCTACCGCAAAgtacgcgcta ... tcatttacagGTTTGTGGAGAAGTGCAAGTTCCCTAAGGATGGTTCATCACCTAAATCCTT
EST: gi|38473796|gb|CF957928.1|CF957928
EST:     TATTCAGTGAATGAAGGGAATGCGAAAAATTGGGACGAGCCTACCGCAAA                         GTTTGTGGAGAAGTGCAAGTTCCCTAAGGATGGTTCATCACCTAAATCCTT
genomic: TATTCAGTGAATGAAGGGAATGCGAAAAATTGGGACGAGCCTACCGCAAAgtacgcgcta ... tcatttacagGTTTGTGGAGAAGTGCAAGTTCCCTAAGGATGGTTCATCACCTAAATCCTT
EST: gi|33820806|gb|CF336207.1|CF336207
EST:     TATTCAGTGAATGAAGGGAATGCGAAAAATTGGGACGAGCCTACCGCAAA                         GTTTGTGGAGAAGTGCAAGTTCCCTAAGGATGGTTCATCACCTAAATCCTT
genomic: TATTCAGTGAATGAAGGGAATGCGAAAAATTGGGACGAGCCTACCGCAAAgtacgcgcta ... tcatttacagGTTTGTGGAGAAGTGCAAGTTCCCTAAGGATGGTTCATCACCTAAATCCTT
EST: gi|27546650|gb|CA764792.2|CA764792
EST:     TATTCAGTGAATGAAGGGAATGCGAAAAATTGGGACGAGCCTACCGCAAA                         GTTTGTGGAGAAGTGCAAGTTCCCTAAGGATGGTTCATCACCTAAATCCTT
genomic: TATTCAGTGAATGAAGGGAATGCGAAAAATTGGGACGAGCCTACCGCAAAgtacgcgcta ... tcatttacagGTTTGTGGAGAAGTGCAAGTTCCCTAAGGATGGTTCATCACCTAAATCCTT
EST: gi|89198621|gb|CI016706.1|CI016706
EST:     ACGAGCCTACCGCAAA                         GTTTGTGGAGAAGTGCAAGTTCCCTAAGGATGGTTCATCACCTAAATCCTT
genomic: ACGAGCCTACCGCAAAgtacgcgcta ... tcatttacagGTTTGTGGAGAAGTGCAAGTTCCCTAAGGATGGTTCATCACCTAAATCCTT
EST: gi|29682614|gb|CB678889.1|CB678889
EST:     TATTCAGTGAATGAAGGGAATGCGAAAAATTGGGACGAGCCTACCGCAAA                         GTTTGTGGAGAAGTGCAAGTTCCCTAAGGATGGTTCATCACCTAAATCCTT
genomic: TATTCAGTGAATGAAGGGAATGCGAAAAATTGGGACGAGCCTACCGCAAAgtacgcgcta ... tcatttacagGTTTGTGGAGAAGTGCAAGTTCCCTAAGGATGGTTCATCACCTAAATCCTT

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: 71 (upstream exon), 66 (downstream exon)
Score: 44

ATACCAAAGAAAGGGAAGATTTATTCAGTGAATGAAGGGAATGCGAAAAATTGGGACGAGCCTACCGCAAAgtacgcgcta ... tcatttacagGTTTGTGGAGAAGTGCAAGTTCCCTAAGGATGGTTCATCACCTAAATCCTTGAGATACATTGGAAG




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