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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GAGGCAAATAAGAGGAACAACAACTGGCTGCCACCTCCATGGGCACTTGCCGCAATGGCTATCCTTGGATTCAACGAGTTCATGACATTGTTAAAgtatttccttctgtctactgaatcatgcatgagcatttgataagctatcgcagtgtttgaccgtactgagttctctttaatggcag

Basic information

species Oryza sativa
transcript LOC_Os01g39310.1
intron # 21
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g39310.1 (Oryza sativa), 5'ss of exon 21
lower sequence: GRMZM2G350256_T01 (Zea mays), 5'ss of exon 4
GAGGCAAATAAGAGGAACAACAACTGGCTGCCACCTCCATGGGCACTTGCCGCAATGGCTATCCTTGGATTCAACGAGTTCATGACATTGTTAAAgtatttccttctgtctactgaatcatgcatgagcat--ttgataagctatcgcagtgtttgaccgtactgagttct---ctttaatggcag
                                                    ||||| |||||||||||||||||||||| |||||| | || | ||||| | || |||||   ||| |||  |||    |  ||  ||   |||  |    |||||||   || | || |   ||| |||   ||
-------------------------------------------------TGACAATGTCTATCCTTGGATTCAACGAGTTTATGACACTATTGATgtatt-ctttttgtctgtagaaacatatatgcatgtcatttctagattattac---ttttgaccaggctaactttttcacttgaataatag

upper sequence: LOC_Os01g39310.1 (Oryza sativa), 5'ss of exon 21
lower sequence: AC196426.3_FGT007 (Zea mays), 5'ss of exon 20
GAGGCAAATAAGAGGAACAACAACTGGCTGCCACCTCCATGGGCACTTGCCGCAATGGCTATCCTTGGATTCAACGAGTTCATGACATTGTTAAAgtatttccttctgtctactgaatcatgcatgagcatttgataagctatcgcagtgtttgaccgtactgagttct---ctttaatggcag
|| |||||||||||||||||||||||||| |||||||||||||||||||| ||||||||||||||||||||||||||||| ||||||||  | | ||||||| |  ||||| | ||| ||| ||||       | |  |  ||       |||||||   || | || |   ||| |||  |||
GAAGCAAATAAGAGGAACAACAACTGGCTCCCACCTCCATGGGCACTTGCTGCAATGGCTATCCTTGGATTCAACGAGTTTATGACATTACTGAGgtatttc-tgttgtctgcagaaacatacatgcatgccagttttgg-attattacttttgaccaggctaacttttttacttgaataacag

upper sequence: LOC_Os01g39310.1 (Oryza sativa), 5'ss of exon 21
lower sequence: GRMZM5G873287_T01 (Zea mays), 5'ss of exon 3
GAGGCAAATAAGAGGAACAACAACTGGCTGCCACCTCCATGGGCACTTGCCGCAATGGCTATCCTTGGATTCAACGAGTTCATGACATTGTTAAAgtat-ttccttctgtctactgaatcatgcatgagcatttgataagctatcgcagtgtttgaccgtactgagttctc---tttaatggcag
|| |||||||||||||||||||||||||| |||||||||||||||||||| ||||||||||| ||||||||||||||||||||||||||  | | |||| ||| ||  |||| | ||| ||| ||||    |  | |  |  ||       | |||||   || | || ||   || |||  |||
GAAGCAAATAAGAGGAACAACAACTGGCTACCACCTCCATGGGCACTTGCTGCAATGGCTATTCTTGGATTCAACGAGTTCATGACATTACTGAGgtatattcttttcgtctgcagaaacatacatgcatctcagttttgg-attattacttctgaccaggctaacttttccacttgaataacag

upper sequence: LOC_Os01g39310.1 (Oryza sativa), 5'ss of exon 21
lower sequence: AT3G13870.1 (Arabidopsis thaliana), 5'ss of exon 21
GAGGCAAATAAGAGGAACAACAACTGGCTGCCACCTCCATGGGCACTTGCCGCAATGGCTATCCTTGGATTCAACGAGTTCATGACATTGTTAAAgtatttcctt----ctgtctactgaatcatgcatgagcatttgataagctatcgcagtgtttgaccgtactgagttctctttaatggcag------------
|| || ||     |||| ||||||||||||||||||||||||||| |    ||  ||| | | |||||||| || || || |||||  | |||| |||    | |    |  |||  |||||       | |  |||   |  | |||    |     ||     |  | |||   |    |||             
GAAGCTAACCGACGGAATAACAACTGGCTGCCACCTCCATGGGCAATCCTTGCCCTGGTTGTTCTTGGATTTAATGAATTTATGACTCTCTTAAGgtaccctccttgtccattcttttgaattgactcggcggctttttcatacaatcaagattccgtactcactttggctcttcgtgcctgcatctctcatggcag

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|86480387|gb|CI123020.1|CI123020
EST:     CTTGCCGCAATGGCTATCCTTGGATTCAACGAGTTCATGACATTGTTAAA                         GAATCCCCTTTACCTGGGAGTCATATTTGTTGTTTTCCTTGTTGGAAAAGC
genomic: CTTGCCGCAATGGCTATCCTTGGATTCAACGAGTTCATGACATTGTTAAAgtatttcctt ... ttaatggcagGAATCCCCTTTACCTGGGAGTCATATTTGTTGTTTTCCTTGTTGGAAAAGC
EST: gi|87022912|gb|CI269848.1|CI269848
EST:     CTTGCCGCAATGGCTATCCTTGGATTCAACGAGTTCATGACATTGTTAAA                         GAATCCCCTTTACCTGGGAGTCATATTTGTTGTTTTCCTTGTTGGAAAAGC
genomic: CTTGCCGCAATGGCTATCCTTGGATTCAACGAGTTCATGACATTGTTAAAgtatttcctt ... ttaatggcagGAATCCCCTTTACCTGGGAGTCATATTTGTTGTTTTCCTTGTTGGAAAAGC
EST: gi|86479218|gb|CI121851.1|CI121851
EST:     CTTGCCGCAATGGCTATCCTTGGATTCAACGAGTTCATGACATTGTTAAA                         GAATCCCCTTTACCTGGGAGTCATATTTGTTGTTTTCCTTGTTGGAAAAGC
genomic: CTTGCCGCAATGGCTATCCTTGGATTCAACGAGTTCATGACATTGTTAAAgtatttcctt ... ttaatggcagGAATCCCCTTTACCTGGGAGTCATATTTGTTGTTTTCCTTGTTGGAAAAGC
EST: gi|87015009|gb|CI273407.1|CI273407
EST:     TTGGATTCAACGAGGTCATGACATTGTTAAA                         GAATCCCCTTTACCTGGGAGTCATATTTGTTGTTTTCCTTGTTGGAAAAGC
genomic: TTGGATTCAACGAGTTCATGACATTGTTAAAgtatttcctt ... ttaatggcagGAATCCCCTTTACCTGGGAGTCATATTTGTTGTTTTCCTTGTTGGAAAAGC
EST: gi|88340407|gb|CI659613.1|CI659613
EST:     CTTGCCGCAATGGCTATCCTTGGATTCAACGAGTTCATGACATTGTTAAA                         GAATCCCCTTTACCTGGGAGTCATATTTGTTGTTTTCCTTGTTGGAAAAGC
genomic: CTTGCCGCAATGGCTATCCTTGGATTCAACGAGTTCATGACATTGTTAAAgtatttcctt ... ttaatggcagGAATCCCCTTTACCTGGGAGTCATATTTGTTGTTTTCCTTGTTGGAAAAGC
EST: gi|58690187|gb|CK078874.1|CK078874
EST:     CTTGCCGCAATGGCTATCCTTGGATTCAACGAGTTCATGACATTGTTAAA                         GAATCCCCTTTACCTGGGAGTCATATTTGTTGTTTTCCTTGTTGGAAAAGC
genomic: CTTGCCGCAATGGCTATCCTTGGATTCAACGAGTTCATGACATTGTTAAAgtatttcctt ... ttaatggcagGAATCCCCTTTACCTGGGAGTCATATTTGTTGTTTTCCTTGTTGGAAAAGC
EST: gi|87021432|gb|CI274039.1|CI274039
EST:     CTTGCCGCAATGGCTATCCTTGGATTCAACGAGTTCATGACATTGTTAAA                         GAATCCCCTTTACCTGGGAGTCATATTTGTTGTTTTCCTTGTTGGAAAAGC
genomic: CTTGCCGCAATGGCTATCCTTGGATTCAACGAGTTCATGACATTGTTAAAgtatttcctt ... ttaatggcagGAATCCCCTTTACCTGGGAGTCATATTTGTTGTTTTCCTTGTTGGAAAAGC
EST: gi|58661468|gb|CK050148.1|CK050148
EST:     CTTGCCGCAATGGCTATCCTTGGATTCAACGAGTTCATGACATTGTTAAA                         GAATCCCCTTTACCTGGGAGTCATATTTGTTGTTTTCCTTGTTGGAAAAGC
genomic: CTTGCCGCAATGGCTATCCTTGGATTCAACGAGTTCATGACATTGTTAAAgtatttcctt ... ttaatggcagGAATCCCCTTTACCTGGGAGTCATATTTGTTGTTTTCCTTGTTGGAAAAGC
EST: gi|29641075|gb|CB646082.1|CB646082
EST:     GTTCATGACATTGTTAAA                         GAATCCCCTTTACCTGGGAGTCATATTTGTTGTTTTCCTTGTTGGAAAAGC
genomic: GTTCATGACATTGTTAAAgtatttcctt ... ttaatggcagGAATCCCCTTTACCTGGGAGTCATATTTGTTGTTTTCCTTGTTGGAAAAGC
EST: gi|29671822|gb|CB668097.1|CB668097
EST:     CTTGCCGCAATGGCTATCCTTGGATTCAACGAGTTCATGACATTGTTAAA                         GAATCCCCTTTACCTGGGAGTCATATTTGTTGTTTTCCTTGTTGGAAAAGC
genomic: CTTGCCGCAATGGCTATCCTTGGATTCAACGAGTTCATGACATTGTTAAAgtatttcctt ... ttaatggcagGAATCCCCTTTACCTGGGAGTCATATTTGTTGTTTTCCTTGTTGGAAAAGC
EST: gi|86596902|gb|CI270698.1|CI270698
EST:     GGATTCAACGAGTTCATGACATTGTTAAA                         GAATCCCCTTTACCTGGGAGTCATATTTGTTGTTTTCCTTGTTGGAAAAGC
genomic: GGATTCAACGAGTTCATGACATTGTTAAAgtatttcctt ... ttaatggcagGAATCCCCTTTACCTGGGAGTCATATTTGTTGTTTTCCTTGTTGGAAAAGC
EST: gi|29675673|gb|CB671948.1|CB671948
EST:     CTTGCCGCAATGGCTATCCTTGGATTCAACGAGTTCATGACATTGTTAAA                         GAATCCCCTTTACCTGGGAGTCATATTTGTTGTTTTCCTTGTTGGAAAAGC
genomic: CTTGCCGCAATGGCTATCCTTGGATTCAACGAGTTCATGACATTGTTAAAgtatttcctt ... ttaatggcagGAATCCCCTTTACCTGGGAGTCATATTTGTTGTTTTCCTTGTTGGAAAAGC
EST: gi|218485492|gb|FG956827.1|FG956827
EST:     CTTGCCGCAATGGCTATCCTTGGATTCAACGAGTTCATGACATTGTTAAA                         GAATCCCCTTTACCTGGGAGTCATATTTGTTGTTTTCCTTGTTGGAAAAGC
genomic: CTTGCCGCAATGGCTATCCTTGGATTCAACGAGTTCATGACATTGTTAAAgtatttcctt ... ttaatggcagGAATCCCCTTTACCTGGGAGTCATATTTGTTGTTTTCCTTGTTGGAAAAGC
EST: gi|86482562|gb|CI125195.1|CI125195
EST:     CTTGCCGCAATGGCTATCTTTGGATTCAACGAGTTCATGACATTGTTAAA                         GAATCCCCTTTACCTGGGAGTCATATTTGTTGTTTTCCTTGTTGGAAAAGC
genomic: CTTGCCGCAATGGCTATCCTTGGATTCAACGAGTTCATGACATTGTTAAAgtatttcctt ... ttaatggcagGAATCCCCTTTACCTGGGAGTCATATTTGTTGTTTTCCTTGTTGGAAAAGC

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), 75 (downstream exon)
Score: 64

GAGGCAAATAAGAGGAACAACAACTGGCTGCCACCTCCATGGGCACTTGCCGCAATGGCTATCCTTGGATTCAACGAGTTCATGACATTGTTAAAgtatttcctt ... ttaatggcagGAATCCCCTTTACCTGGGAGTCATATTTGTTGTTTTCCTTGTTGGAAAAGCCATGTGGGTACAGCTAGACATTGCCAAGGAGTTCCAAAATGGATTT




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