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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AAAGAACTTTCTATCAAATGAGGACCCTGATTTAAGAGCAAAAGCTTGCAGTGCAATTGGCAACATGTGCCGCCACAGTTCCTACTTCTACAGTTCACTTgtaagaaaatattttattcacatttggactattgtagagatatttaaccttgttttccgcgaacag

Basic information

species Oryza sativa
transcript LOC_Os12g24550.1
intron # 20
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os12g24550.1 (Oryza sativa), 5'ss of exon 20
lower sequence: GRMZM2G062524_T02 (Zea mays), 5'ss of exon 19
AAAGAACTTTCTATCAAATGAGGACCCTGATTTAAGAGCAAAAGCTTGCAGTGCAATTGGCAACATGTGCCGCCACAGTTCCTACTTCTACAGTTCACTTgtaagaaaatattt-tattcacatt------tggact---attgta-----gagatatttaacct--tgttttccgcgaacag
 ||||||||  |||||||||  ||||||||| |||| ||||||||||| ||||| |||||||||||||||||||| || |||||||| ||  |  |||||||||| |||||| | ||||  || |       |||||   | ||||     |  ||||| |   |  |||| || |   ||||
GAAGAACTTCTTATCAAATGGAGACCCTGATATAAGGGCAAAAGCTTGTAGTGCCATTGGCAACATGTGCCGCCATAGCTCCTACTTTTATGGCCCACTTgtaaggaaatatgtatattttcactgctttgcggactgaaactgtatgccagtaatattaactttgctgttgtctggttacag

upper sequence: LOC_Os12g24550.1 (Oryza sativa), 5'ss of exon 20
lower sequence: GLYMA10G22860.1 (Glycine max), 5'ss of exon 18
AAAGAACTTTCTATCAAATGAGGACCCTGATTTAAGAGCAAAAGCTTGCAGTGCAATTGGCAACATGTGCCGCCACAGTTCCTACTTCTACAGTTCACTTgtaag-----aaaatattt-tattcacatttggacta--ttgtagagatatttaaccttgttttccgcgaa-cag-------------------------
 ||  | ||||| ||| | ||||| ||  || |  | || ||||||||||||||  |||| |||||||| || || ||| |||| || || ||||||||||||||     |||||| |  ||||  |  | ||| ||  || || | |||   ||  ||         ||| ||                          
GAAAGATTTTCTTTCACACGAGGATCCCAATATGCGTGCCAAAGCTTGCAGTGCTCTTGGAAACATGTGTCGTCATAGTGCCTATTTTTATAGTTCACTTgtaagtattaaaaataatggtatttgccctcggagtactttataaacataacgaaaattaaaaaggaagaaacaatgatatttcgtttgatgaaagctac

upper sequence: LOC_Os12g24550.1 (Oryza sativa), 5'ss of exon 20
lower sequence: Vv16s0039g02400.t01 (Vitis vinifera), 5'ss of exon 19
AAAGAACTTTCTATCAAATGAGGACCCTGATTTAAGAGCAAAAGCTTGCAGTGCAATTGGCAACATGTGCCGCCACAGTTCCTACTTCTACAGTTCACTTgtaagaaaatattttattcacatttggactattgtagagatatttaaccttgttttccgcgaacag-----------------------------------
 | | | |||||  |  |||| || ||  || || ||||||||||||| ||||| || ||||||||||| || ||||||||||| |||||  ||||||| ||||| ||  |   ||  | | ||     |||| | ||    | ||||  | | ||  |   |                                      
GAGGGAGTTTCTTACTCATGAAGATCCCAATGTACGAGCAAAAGCTTGTAGTGCTATAGGCAACATGTGTCGGCACAGTTCCTATTTCTATGGTTCACTGgtaagtaataacagtaggctccttcactatattctggac-cctataactgtttgtttagaatatcaccatctgcaaattattctgcttctggctgaccaaa

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|88689953|gb|CI734032.1|CI734032
EST:     GTGCAATTGGCAACATGTGCCGCCACAGTTCCTACTTCTACAGTTCACTT                         GCAACAAATAAGGTAATTGAGCTGGTAGTTGACAGATGCTCTGACCCGGAC
genomic: GTGCAATTGGCAACATGTGCCGCCACAGTTCCTACTTCTACAGTTCACTTgtaagaaaat ... ccgcgaacagGCAACAAATAAGGTAATTGAGCTGGTAGTTGACAGATGCTCTGACCCGGAC
EST: gi|88690870|gb|CI734949.1|CI734949
EST:     GTGCAATTGGCAACATGTGCCGCCACAGTTCCTACTTCTACAGTTCACTT                         GCAACAAATAAGGTAATTGAGCTGGTAGTTGACAGATGCTCTGACCCGGAC
genomic: GTGCAATTGGCAACATGTGCCGCCACAGTTCCTACTTCTACAGTTCACTTgtaagaaaat ... ccgcgaacagGCAACAAATAAGGTAATTGAGCTGGTAGTTGACAGATGCTCTGACCCGGAC
EST: gi|58677169|gb|CK065856.1|CK065856
EST:     GTGCAATTGGCAACATGTGCCGCCACAGTTCCTACTTCTACAGTTCACTT                         GCAACAAATAAGGTAATTGAGCTGGTAGTTGACAGATGCTCTGACCCGGAG
genomic: GTGCAATTGGCAACATGTGCCGCCACAGTTCCTACTTCTACAGTTCACTTgtaagaaaat ... ccgcgaacagGCAACAAATAAGGTAATTGAGCTGGTAGTTGACAGATGCTCTGACCCGGAC
EST: gi|88691368|gb|CI733951.1|CI733951
EST:     GTGCAATTGGCAACATGTGCCGCCACAGTTCCTACTTCTACAGTTCACTT                         GCAACAAATAAGGTAATTGAGCTGGTAGTTGACAGATGCTCTGACCCGGAC
genomic: GTGCAATTGGCAACATGTGCCGCCACAGTTCCTACTTCTACAGTTCACTTgtaagaaaat ... ccgcgaacagGCAACAAATAAGGTAATTGAGCTGGTAGTTGACAGATGCTCTGACCCGGAC
EST: gi|88690741|gb|CI734820.1|CI734820
EST:     GTGCAATTGGCAACATGTGCCGCCACAGTTCCTACTTCTACAGTTCACTT                         GCAACAAATAAGGTAATTGAGCTGGTAGTTGACAGATGCTCTGACCCGGAC
genomic: GTGCAATTGGCAACATGTGCCGCCACAGTTCCTACTTCTACAGTTCACTTgtaagaaaat ... ccgcgaacagGCAACAAATAAGGTAATTGAGCTGGTAGTTGACAGATGCTCTGACCCGGAC
EST: gi|88689600|gb|CI733176.1|CI733176
EST:     GTGCAATTGGCAACATGTGCCGCCACAGTTCCTACTTCTACAGTTCACTT                         GCAACAAATAAGGTAATTGAGCTGGTAGTTGACAGATGCTCTGACCCGGAC
genomic: GTGCAATTGGCAACATGTGCCGCCACAGTTCCTACTTCTACAGTTCACTTgtaagaaaat ... ccgcgaacagGCAACAAATAAGGTAATTGAGCTGGTAGTTGACAGATGCTCTGACCCGGAC
EST: gi|88690572|gb|CI734651.1|CI734651
EST:     GTGCAATTGGCAACATGTGCCGCCACAGTTCCTACTTCTACAGTTCACTT                         GCAACAAATAAGGTAATTGAGCTGGTAGTTGACAGATGCTCTGACCCGGAC
genomic: GTGCAATTGGCAACATGTGCCGCCACAGTTCCTACTTCTACAGTTCACTTgtaagaaaat ... ccgcgaacagGCAACAAATAAGGTAATTGAGCTGGTAGTTGACAGATGCTCTGACCCGGAC

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: 56 (upstream exon), 34 (downstream exon)
Score: 4

AAAGAACTTTCTATCAAATGAGGACCCTGATTTAAGAGCAAAAGCTTGCAGTGCAATTGGCAACATGTGCCGCCACAGTTCCTACTTCTACAGTTCACTTgtaagaaaat ... ccgcgaacagGCAACAAATAAGGTAATTGAGCTGGTAGTTGACAGATGCTCTGACCCGGACAAGCGCACTCGGAAGTTTGCATGCTTTGCT




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