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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtattttaatgttgcagtatggtttagtcatgcacacagatttgctctttttacaattttggacataatgcagCCATGCCGGAACTTCTACGCTCAGCAAAATTGGCTGTTGAGAAAGGGCAGGCTCAAGGACGTGATGAGTCTTATGTCAAACAGTTGTCTGACTACATAAT

Basic information

species Zea mays
transcript GRMZM5G887631_T01
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G887631_T01 (Zea mays), 3'ss of exon 9
lower sequence: LOC_Os07g38760.1 (Oryza sativa), 3'ss of exon 9
gtattttaatgttgcagtatggtttagtcatgcac---acagatttgctctttt----tacaattttggacataatgcagCCATGCCGGAACTTCTACGCTCAGCAAAATTGGCTGTTGAGAAAGGGCAGGCTCAAGGACGTGATGAGTCTTATGTCAAACAGTTGTCTGACTACATAAT
|||||| ||||| |||||| ||| || | | | ||||||| ||| || | || | |||||||| ||||| ||||| ||||| || |||||||||||||||||||| |||| |||||||||||| ||||| |||||||| ||||| || ||||||||||||||
gtattt-gatgttttagtatgattttatcttttgccttatggatttgcattttaaaagtatagttccaacaacaatgcagCTATGCCTGAACTACTACGTTCTGCAAAATTGGCTGTTGAGAAGGGGCTGGCTCAAGGACGCGATGAATCTTATGTTAAACAATTATCTGACTACATAAT

upper sequence: GRMZM5G887631_T01 (Zea mays), 3'ss of exon 9
lower sequence: Vv06s0004g00500.t01 (Vitis vinifera), 3'ss of exon 9
-----------gtattttaatgttgcagtatggtttagtcatgcacacagatttgctcttttt---acaattttggacataatgcagCCATGCCGGAACTTCTACGCTCAGCAAAATTGGCTGTTGAGAAAGGGCAGGCTCAAGGACGTGATGAGTCTTATGTCAAACAGTTGTCTGACTACATAAT
| || | || || || | | || ||| ||| | | || ||| | | | |||||||||| || || || || ||||||||||| ||||| |||||||| | |||||||| ||| ||||||| ||||| || || ||||||||||| |||||
gtacaaacttcttgttcttcccccccaaaattattggg--aattttccaagttttctcaatgtgaaacgattatttctgtt-tccagCCATGCCAGAGCTACTGCGTTCAGCAAAATTAGCTGTGGAGAAAGGTCTAGCTCAAGGTCGTAATGAGTCATATGTTAAGCAATTGTCTGACTATATAAT
















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|32937524|gb|CF042343.1|CF042343
EST:     ACTGCTGAAGTTTTACTTCCATGAGGAAGTCAGGAGAGCTGCTGTTGCGG                         CCATGCCGGAACTTCTACGCTCAGCAAAATTGGCTGTTGAGAAAGGGCAGG
genomic: TCTGCTGAAGTTTTACTTCCATGAGGAAGTCAGGAGAGCTGCTGTTGCGGgtattttaat ... cataatgcagCCATGCCGGAACTTCTACGCTCAGCAAAATTGGCTGTTGAGAAAGGGCAGG
EST: gi|32937521|gb|CF042340.1|CF042340
EST:     ACTGCTGAAGTTTTACTTCCATGAGGAAGTCAGGAGAGCTGCTGTTGCGG                         CCATGCCGGAACTTCTACGCTCAGCAAAATTGGCTGTTGAGAAAGGGCAGG
genomic: TCTGCTGAAGTTTTACTTCCATGAGGAAGTCAGGAGAGCTGCTGTTGCGGgtattttaat ... cataatgcagCCATGCCGGAACTTCTACGCTCAGCAAAATTGGCTGTTGAGAAAGGGCAGG
EST: gi|71770782|gb|DR968719.1|DR968719
EST:     TCTGCTGAAGTTTTACTTCCATGAGGAAGTCAGGAGAGCTGCTGTTGCGG                         CCATGCCGGAACTTCTACGCTCAGCAAAATTGGCTGTTGAGAAAGGGCAGG
genomic: TCTGCTGAAGTTTTACTTCCATGAGGAAGTCAGGAGAGCTGCTGTTGCGGgtattttaat ... cataatgcagCCATGCCGGAACTTCTACGCTCAGCAAAATTGGCTGTTGAGAAAGGGCAGG
EST: gi|32935366|gb|CF040178.1|CF040178
EST:     ACTGCTGAAGTTTTACTTCCATGAGGAAGTCAGGAGAGCTGCTGTTGCGG                         CCATGCCGGAACTTCTACGCTCAGCAAAATTGGCTGTTGAGAAAGGGCAGG
genomic: TCTGCTGAAGTTTTACTTCCATGAGGAAGTCAGGAGAGCTGCTGTTGCGGgtattttaat ... cataatgcagCCATGCCGGAACTTCTACGCTCAGCAAAATTGGCTGTTGAGAAAGGGCAGG
EST: gi|32935549|gb|CF040361.1|CF040361
EST:     ACTGCTGAAGTTTTACTTCCATGAGGAAGTCAGGAGAGCTGCTGTTGCGG                         CCATGCCGGAACTTCTACGCTCAGCAAAATTGGCTGTTGAGAAAGGGCAGG
genomic: TCTGCTGAAGTTTTACTTCCATGAGGAAGTCAGGAGAGCTGCTGTTGCGGgtattttaat ... cataatgcagCCATGCCGGAACTTCTACGCTCAGCAAAATTGGCTGTTGAGAAAGGGCAGG
EST: gi|32850147|gb|CD989828.1|CD989828
EST:     ACTGCTGAAGTTTTACTTCCATGAGGAAGTCAGGAGAGCTGCTGTTGCGG                         CCATGCCGGAACTTCTACGCTCAGCAAAATTGGCTGTTGAGAAAGGGCAGG
genomic: TCTGCTGAAGTTTTACTTCCATGAGGAAGTCAGGAGAGCTGCTGTTGCGGgtattttaat ... cataatgcagCCATGCCGGAACTTCTACGCTCAGCAAAATTGGCTGTTGAGAAAGGGCAGG
EST: gi|32937789|gb|CF042608.1|CF042608
EST:     ACTGCTGAAGTTTTACTTCCATGAGGAAGTCAGGAGAGCTGCTGTTGCGG                         CCATGCCGGAACTTCTACGCTCAGCAAAATTGGCTGTTGAGAAAGGGCAGG
genomic: TCTGCTGAAGTTTTACTTCCATGAGGAAGTCAGGAGAGCTGCTGTTGCGGgtattttaat ... cataatgcagCCATGCCGGAACTTCTACGCTCAGCAAAATTGGCTGTTGAGAAAGGGCAGG
EST: gi|32850586|gb|CD990267.1|CD990267
EST:     ACTGCTGAAGTTTTACTTCCATGAGGAAGTCAGGAGAGCTGCTGTTGCGG                         CCATGCCGGAACTTCTACGCTCAGCAAAATTGGCTGTTGAGAAAGGGCAGG
genomic: TCTGCTGAAGTTTTACTTCCATGAGGAAGTCAGGAGAGCTGCTGTTGCGGgtattttaat ... cataatgcagCCATGCCGGAACTTCTACGCTCAGCAAAATTGGCTGTTGAGAAAGGGCAGG

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 4 RNA-Seq libraries.


Block sizes: 48 (upstream exon), 46 (downstream exon)
Score: 100

GTTGCCCCAACGTTGGTTCCTCTGCTGAAGTTTTACTTCCATGAGGAAGTCAGGAGAGCTGCTGTTGCGGgtattttaat ... cataatgcagCCATGCCGGAACTTCTACGCTCAGCAAAATTGGCTGTTGAGAAAGGGCAGGCTCAAGGACGTGATGAGTCTTATGTCAAACAGTTGTCTGACTACATAAT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 127

GTTGCCCCAACGTTGGTTCCTCTGCTGAAGTTTTACTTCCATGAGGAAGTCAGGAGAGCTGCTGTTGCGGgtattttaat ... cataatgcagCCATGCCGGAACTTCTACGCTCAGCAAAATTGGCTGTTGAGAAAGGGCAGGCTCAAGGACGTGATGAGTCTTATGTCAAACAGTTGTCTGACTACATAAT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 179

GTTGCCCCAACGTTGGTTCCTCTGCTGAAGTTTTACTTCCATGAGGAAGTCAGGAGAGCTGCTGTTGCGGgtattttaat ... cataatgcagCCATGCCGGAACTTCTACGCTCAGCAAAATTGGCTGTTGAGAAAGGGCAGGCTCAAGGACGTGATGAGTCTTATGTCAAACAGTTGTCTGACTACATAAT


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 70

GTTGCCCCAACGTTGGTTCCTCTGCTGAAGTTTTACTTCCATGAGGAAGTCAGGAGAGCTGCTGTTGCGGgtattttaat ... cataatgcagCCATGCCGGAACTTCTACGCTCAGCAAAATTGGCTGTTGAGAAAGGGCAGGCTCAAGGACGTGATGAGTCTTATGTCAAACAGTTGTCTGACTACATAAT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atggtttagtcatgcacacagatttgctctttttacaattttggacataatgcagCCATGCCGGAACTTCTACGCTCAGCAAAATTGGCTGTTGAGAAAGGGCAGGCTCAAGGACGTGATGAGTCTTATGTCAAACAGTTGTCTGACTACATAAT
                           tctttttacaatttt  TA-rich tract