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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GAGGCTCGTGTATCAGACTTTGGACTCGCAAAGCTATTAGAGGACGACAAATCCCATATTACTACAATAGTTGCAGGAACATTTGGCTATCTTGCACCAGgtatgttaaaactgttctgtttcattcattgtgggaaaataacagcatataacaaatgcttaccaccttattgcatctctggattttatttatcaatatataatttcatatgctctgagctaatttgcaaaattcaaaatccag

Basic information

species Oryza sativa
transcript LOC_Os03g16010.1
intron # 12
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g16010.1 (Oryza sativa), 5'ss of exon 12
lower sequence: GRMZM5G886952_T01 (Zea mays), 5'ss of exon 12
GAGGCTCGTGTATCAGACTTTGGACTCGCAAAGCTATTAGAGGACGACAAATCCCATATTACTACAATAGTTGCAGGAACATTTGGCTATCTTGCACCAGgtatgttaaaactgttctgtttcattcattgtgggaaaataacagcatataacaaatgcttaccaccttattgcatctctggattttat----ttatcaatatataatttcatatgctctgagctaattt--gcaaaattcaaaatc-cag
||||| |||||||||||||||||||| |||||||| |||||||| ||  |||| ||||||||||||||||||||||||||||||||||| ||||||||||||||||  ||     |||||| ||| |  || ||| ||| |  || |   |||   || ||||    | || ||  ||   || ||| |    ||   || |||| |||    ||||||||||||||      | |||| | ||  | |||
GAGGCCCGTGTATCAGACTTTGGACTTGCAAAGCTTTTAGAGGATGAAGAATCACATATTACTACAATAGTTGCAGGAACATTTGGCTACCTTGCACCAGgtatgtggaagtccctctgttacatcc--tgaggggaaagagaagaaatgaacttctgtttactctttaatcgccgcttcagactttctctggttgctaaaatatcattgttaatgctctgagctaacaccaacgaaatccgaatccacag

upper sequence: LOC_Os03g16010.1 (Oryza sativa), 5'ss of exon 12
lower sequence: GRMZM2G479243_T01 (Zea mays), 5'ss of exon 12
GAGGCTCGTGTATCAGACTTTGGACTCGCAAAGCTATTAGAGGACGACAAATCCCATATTACTACAATAGTTGCAGGAACATTTGGCTATCTTGCACCAGgtatgttaaaactgttctgtttcattcattgtgggaaaataacagcatataacaaatgcttaccaccttattgcatctctggattttat----ttatcaatatataatttcatatgctctgagctaattt--gcaaaattcaaaatc-cag
||||| || ||||||||||||||||| |||||||| |||||||||||  |||||||||| |||||||||||||||||||||||||| |||||||| ||||||||||  ||   |||||| | ||| ||  | || ||||    || |   |||   || ||||    | ||| |  |   ||| ||| |    ||   || |||| | | |  ||||||||||||||  |   |||||| |||   | |||
GAGGCCCGCGTATCAGACTTTGGACTTGCAAAGCTTTTAGAGGACGAAGAATCCCATATCACTACAATAGTTGCAGGAACATTTGGTTATCTTGCGCCAGgtatgtggaagtcgttctgctacatccagaggggaaaaa----agaaatgaacttctgtttactctttaattaccgcatcggactttctctggttgctaaaatatcactgctaatgctctgagctaacatcaacaaaatccaactccacag

upper sequence: LOC_Os03g16010.1 (Oryza sativa), 5'ss of exon 12
lower sequence: AT2G35620.2 (Arabidopsis thaliana), 5'ss of exon 12
GAGGCTCGTGTATCAGACTTTGGACTCGCAAAGCTATTAGAGGACGACAAATCCCATATTACTACAATAGTTGCAGGAACATTTGGCTATCTTGCACCAGgtatgttaaaactgttctgtttcattcattgtgggaaaataacagcatataacaaatgcttaccaccttattgcatctctggattttatttatcaatatataatttcatatgctctgagctaatttgcaaaattcaaaatccag
|||||||| |||||||||||||| || || ||| | |||||||||||  |||| |||||||| || || |||||||| ||||| || ||  | || |||||||                  ||| | |    |  | || ||  || ||| ||   |  |||| | ||  | | | ||    | |   |  |   |||   | | |  | |||                               
GAGGCTCGGGTATCAGACTTTGGGCTTGCCAAGTTGTTAGAGGACGAAGAATCTCATATTACAACCATTGTTGCAGGCACATTCGGTTACTTGGCTCCAGgtac-----------------tcaattacacagtaataacaat-gcttattacttgttgttactatctgttaggacct---aaatccgtgaactcataatgagtgttttttgcag-----------------------------

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|25806103|gb|CA762064.1|CA762064
EST:     TCCCCATATTACTACAATAGTTGCAGGAACATTTGGCTATCTTGCACCAG                         AGTATATGCAAAGTGGCAGAGCCACCGAAAAGACTGACGTCTACAGTTTTG
genomic: T-CCCATATTACTACAATAGTTGCAGGAACATTTGGCTATCTTGCACCAGgtatgttaaa ... caaaatccagAGTATATGCAAAGTGGCAGAGCCACCGAAAAGACTGACGTCTACAGTTTTG
EST: gi|29629427|gb|CB634436.1|CB634436
EST:     ATCCCATATTACTACAATAGTTGCAGGAACATTTGGCTATCTTGCACCAG                         AGTATATGCAAAGTGGCAGAGCCACCGAAAAGACTGACGTCTACAGTTTTG
genomic: ATCCCATATTACTACAATAGTTGCAGGAACATTTGGCTATCTTGCACCAGgtatgttaaa ... caaaatccagAGTATATGCAAAGTGGCAGAGCCACCGAAAAGACTGACGTCTACAGTTTTG
EST: gi|86477546|gb|CI120179.1|CI120179
EST:     AACATTTGGCTATCTTGCACCAG                         AGTATATGCAAAGTGGCAGAGCCACCGAAAAGACTGACGTCTACAGTTTTG
genomic: AACATTTGGCTATCTTGCACCAGgtatgttaaa ... caaaatccagAGTATATGCAAAGTGGCAGAGCCACCGAAAAGACTGACGTCTACAGTTTTG
EST: gi|396941397|gb|HO188606.1|HO188606
EST:     ATCCCATATTACTACAATAGTTGCAGGAACATTTGGCTATCTTGCACCAG                         AGTATATGCAAAGTGGCAGAGCCACCGAAAAGACTGACGTCTACAGTTTTG
genomic: ATCCCATATTACTACAATAGTTGCAGGAACATTTGGCTATCTTGCACCAGgtatgttaaa ... caaaatccagAGTATATGCAAAGTGGCAGAGCCACCGAAAAGACTGACGTCTACAGTTTTG
EST: gi|88994832|gb|CI036413.1|CI036413
EST:     TATCTTGCACCAG                         AGTATATGCAAAGTGGCAGAGCCACCGAAAAGACTGACGTCTACAGTTTTG
genomic: TATCTTGCACCAGgtatgttaaa ... caaaatccagAGTATATGCAAAGTGGCAGAGCCACCGAAAAGACTGACGTCTACAGTTTTG
EST: gi|29625253|gb|CB630264.1|CB630264
EST:     ATCCCATATTACTACAATAGTTGCAGGAACATTTGGCTATCTTGCACCAG                         AGTATATGCAAAGTGGCAGAGCCACCGAAAAGACTGACGTCTACAGTTTTG
genomic: ATCCCATATTACTACAATAGTTGCAGGAACATTTGGCTATCTTGCACCAGgtatgttaaa ... caaaatccagAGTATATGCAAAGTGGCAGAGCCACCGAAAAGACTGACGTCTACAGTTTTG
EST: gi|14981452|gb|BI306130.1|BI306130
EST:     CCCATATTACTACAATAGTTGCAGGAACATTTGGCTATCTTGCACCAG                         AGTATATGCAAAGTGGCAGAGCCACCGAAAAGACTGACGTCTACAGTTTTG
genomic: CCCATATTACTACAATAGTTGCAGGAACATTTGGCTATCTTGCACCAGgtatgttaaa ... caaaatccagAGTATATGCAAAGTGGCAGAGCCACCGAAAAGACTGACGTCTACAGTTTTG
EST: gi|27554522|gb|CA998422.1|CA998422
EST:     ATCCCATATTACTACAATAGTTGCAGGAACATTTGGCTATCTTGCACCAG                         AGTATATGCAAAGTGGCAGAGCCACCGAAAAGACTGACGTCTACAGTTTTG
genomic: ATCCCATATTACTACAATAGTTGCAGGAACATTTGGCTATCTTGCACCAGgtatgttaaa ... caaaatccagAGTATATGCAAAGTGGCAGAGCCACCGAAAAGACTGACGTCTACAGTTTTG
EST: gi|38482222|gb|CF966274.1|CF966274
EST:     ATCCCATATTACTACAATAGTTGCAGGAACATTTGGCTATCTTGCACCAG                         AGTATATGCAAAGTGGCAGAGCCACCGAAAAGACTGACGTCTACAGTTTTG
genomic: ATCCCATATTACTACAATAGTTGCAGGAACATTTGGCTATCTTGCACCAGgtatgttaaa ... caaaatccagAGTATATGCAAAGTGGCAGAGCCACCGAAAAGACTGACGTCTACAGTTTTG
EST: gi|29629424|gb|CB634433.1|CB634433
EST:     ATCCCATATTACTACAATAGTTGCAGGAACATTTGGCTATCTTGCACCAG                         AGTATATGCAAAGTGGCAGAGCCACCGAAAAGACTGACGTCTACAGTTTTG
genomic: ATCCCATATTACTACAATAGTTGCAGGAACATTTGGCTATCTTGCACCAGgtatgttaaa ... caaaatccagAGTATATGCAAAGTGGCAGAGCCACCGAAAAGACTGACGTCTACAGTTTTG
EST: gi|29614510|gb|CB619523.1|CB619523
EST:     ATCCCATATTACTACAATAGTTGCAGGAACATTTGGCTATCTTGCACCAG                         AGTATATGCAAAGTGGCAGAGCCACCGAAAAGACTGACGTCTACAGTTTTG
genomic: ATCCCATATTACTACAATAGTTGCAGGAACATTTGGCTATCTTGCACCAGgtatgttaaa ... caaaatccagAGTATATGCAAAGTGGCAGAGCCACCGAAAAGACTGACGTCTACAGTTTTG
EST: gi|86479170|gb|CI121803.1|CI121803
EST:     ATCCCATATTACTACAATAGTTGCAGGAACATTTGGCTATCTTGCACCAG                         AGTATATGCAAAGTGGCAGAGCCACCGAAAAGACTGACGTCTACAGTTTTG
genomic: ATCCCATATTACTACAATAGTTGCAGGAACATTTGGCTATCTTGCACCAGgtatgttaaa ... caaaatccagAGTATATGCAAAGTGGCAGAGCCACCGAAAAGACTGACGTCTACAGTTTTG

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: 53 (upstream exon), 51 (downstream exon)
Score: 11

GAGGCTCGTGTATCAGACTTTGGACTCGCAAAGCTATTAGAGGACGACAAATCCCATATTACTACAATAGTTGCAGGAACATTTGGCTATCTTGCACCAGgtatgttaaa ... caaaatccagAGTATATGCAAAGTGGCAGAGCCACCGAAAAGACTGACGTCTACAGTTTTGGAGTTTTGCTACTTGAAATACTAAGCGGAAAACGACCTACTGATGCATC




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