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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaatttatgtgatagctatggatcatcaagattttaattgcaatgcttcttttcaaaactgaaagcagaaagggcataggagtttggacagatattctcgtttccgttttccttaaattttttattcaatctctccctcatatttcttaaatgtcctagGAATTGTTTGAGGGGCACTATTTCTGCCAAGCTCAAAGACTGGATTTCTTTCGGCGCGCTAAGCCTTACAAAGGCAATCCAACTATTATAAG

Basic information

species Zea mays
transcript GRMZM2G073950_T01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G073950_T01 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os02g33080.2 (Oryza sativa), 3'ss of exon 2
gtaaatttatgtgatagctatggatcatcaagattttaattgcaatgcttcttttcaaaactgaaagcagaaagggcataggagtttggacagatattctcgtttccgttttccttaaattttttattcaatctctccctcatatttcttaaatgtcctagGAATTGTTTGAGGGGCACTATTTCTGCCAAGCTCAAAGACTGGATTTCTTTCGGCGCGCTAAGCCTTACAAAGGCAATCCAACTATTATAAG--------
                                 ||| |||||  ||| ||  |||    | | |   |||    ||| ||  |   |  |  || ||  |  ||    | | |  | ||| |                   |||| ||   ||||   |||||| ||||||||||||| || ||||| |||||||||||  |||| |||||||  || ||||||||||| ||||| || |||||||| || ||        
----------------------------tttcgtttaaattgttatgttttgttt---gattcagttcag----ggcctaaaaagattaatgga-atgatgatt---atgtgcactgaatct-------------------atatgtc---aatgctttagGAACTGTTTGAGGGGCAGTACTTCTGTCAAGCTCAAAGGTTGGACTTCTTTCAACGTGCTAAGCCTTATAAAGGGAACCCAACTATAATCAGGTAGGCTT

upper sequence: GRMZM2G073950_T01 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os02g33080.1 (Oryza sativa), 3'ss of exon 2
gtaaatttatgtgatagctatggatcatcaagattttaattgcaatgcttcttttcaaaactgaaagcagaaagggcataggagtttggacagatattctcgtttccgttttccttaaattttttattcaatctctccctcatatttcttaaatgtcctagGAATTGTTTGAGGGGCACTATTTCTGCCAAGCTCAAAGACTGGATTTCTTTCGGCGCGCTAAGCCTTACAAAGGCAATCCAACTATTATAAG
                                 ||| |||||  ||| ||  |||    | | |   |||    ||| ||  |   |  |  || ||  |  ||    | | |  | ||| |                   |||| ||   ||||   |||||| ||||||||||||| || ||||| |||||||||||  |||| |||||||  || ||||||||||| ||||| || |||||||| || ||
----------------------------tttcgtttaaattgttatgttttgttt---gattcagttcag----ggcctaaaaagattaatgga-atgatgatt---atgtgcactgaatct-------------------atatgtc---aatgctttagGAACTGTTTGAGGGGCAGTACTTCTGTCAAGCTCAAAGGTTGGACTTCTTTCAACGTGCTAAGCCTTATAAAGGGAACCCAACTATAATCAG
















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|211074743|gb|FL419972.1|FL419972
EST:     GTTGATTAGAGAAGCACACAAGAAAGGTGCAAAGATTGTACTCGTTCAG                         GAATTGTTTGAGGGGCACTATTTCTGCCAAGCTCAAAGACTGGATTTCTTT
genomic: GTTGATTAGAGAAGCACACAAGAAAGGTGCAAAGATTGTACTCGTTCAGgtaaatttat ... aatgtcctagGAATTGTTTGAGGGGCACTATTTCTGCCAAGCTCAAAGACTGGATTTCTTT
EST: gi|211141684|gb|FL053512.1|FL053512
EST:     GTTGATTAGAGAAGCACACAAGAAAGGTGCAAAGATTGTACTCGTTCAG                         GAATTGTTTGAGGGGCACTATTTCTGCCAAGCTCAAAGACTGGATTTCTTT
genomic: GTTGATTAGAGAAGCACACAAGAAAGGTGCAAAGATTGTACTCGTTCAGgtaaatttat ... aatgtcctagGAATTGTTTGAGGGGCACTATTTCTGCCAAGCTCAAAGACTGGATTTCTTT
EST: gi|91056600|gb|EB167018.1|EB167018
EST:     GTTGATTAGAGAAGCACACAAGAAAGGTGCAAAGATTGTACTCGTTCAG                         GAATTGTTTGAGGGGCACTATTTCTGCCAAGCTCAAAGACTGGATTTCTTT
genomic: GTTGATTAGAGAAGCACACAAGAAAGGTGCAAAGATTGTACTCGTTCAGgtaaatttat ... aatgtcctagGAATTGTTTGAGGGGCACTATTTCTGCCAAGCTCAAAGACTGGATTTCTTT
EST: gi|148953399|gb|EE152896.2|EE152896
EST:     GTTGATTAGAGAAGCACACAAGAAAGGTGCAAAGATTGTACTCGTTCAG                         GAATTGTTTGAGGGGCACTATTTCTGCCAAGCTCAAAGACTGGATTTCTTT
genomic: GTTGATTAGAGAAGCACACAAGAAAGGTGCAAAGATTGTACTCGTTCAGgtaaatttat ... aatgtcctagGAATTGTTTGAGGGGCACTATTTCTGCCAAGCTCAAAGACTGGATTTCTTT
EST: gi|78081735|gb|DV510147.1|DV510147
EST:     GTTGATTAGAGAAGCACACAAGAAAGGTGCAAAGATTGTACTCGTTCAG                         GAATTGTTTGAGGGGCACTATTTCTGCCAAGCTCAAAGACTGGATTTCTTT
genomic: GTTGATTAGAGAAGCACACAAGAAAGGTGCAAAGATTGTACTCGTTCAGgtaaatttat ... aatgtcctagGAATTGTTTGAGGGGCACTATTTCTGCCAAGCTCAAAGACTGGATTTCTTT
EST: gi|88758160|gb|DY542301.1|DY542301
EST:     GTTGATTAGAGAAGCACACAAGAAAGGTGCAAAGATTGTACTCGTTCAG                         GAATTGTTTGAGGGGCACTATTTCTGCCAAGCTCAAAGACTGGATTTCTTT
genomic: GTTGATTAGAGAAGCACACAAGAAAGGTGCAAAGATTGTACTCGTTCAGgtaaatttat ... aatgtcctagGAATTGTTTGAGGGGCACTATTTCTGCCAAGCTCAAAGACTGGATTTCTTT
EST: gi|50324199|gb|CO519325.1|CO519325
EST:     GTTGACTAGAGAAGCACACAAGAAAGGTGCAAAGATTGTACTCGTTCAG                         GAATTGTTTGAGGGGCACTATTTCTGCCAAGCTCAAAGACTGGATTTCTTT
genomic: GTTGATTAGAGAAGCACACAAGAAAGGTGCAAAGATTGTACTCGTTCAGgtaaatttat ... aatgtcctagGAATTGTTTGAGGGGCACTATTTCTGCCAAGCTCAAAGACTGGATTTCTTT
EST: gi|148939361|gb|EC883888.2|EC883888
EST:     GTTGATTAGAGAAGCACACAAGAAAGGTGCAAAGATTGTACTCGTTCAG                         GAATTGTTTGAGGGGCACTATTTCTGCCAAGCTCAAAGACTGGATTTCTTT
genomic: GTTGATTAGAGAAGCACACAAGAAAGGTGCAAAGATTGTACTCGTTCAGgtaaatttat ... aatgtcctagGAATTGTTTGAGGGGCACTATTTCTGCCAAGCTCAAAGACTGGATTTCTTT
EST: gi|78078908|gb|DV507320.1|DV507320
EST:     GTTGATTAGAGAAGCACACAAGAAAGGTGCAAAGATTGTACTCGTTCAG                         GAATTGTTTGAGGGGCACTATTTCTGCCAAGCTCAAAGACTGGATTTCTTT
genomic: GTTGATTAGAGAAGCACACAAGAAAGGTGCAAAGATTGTACTCGTTCAGgtaaatttat ... aatgtcctagGAATTGTTTGAGGGGCACTATTTCTGCCAAGCTCAAAGACTGGATTTCTTT
EST: gi|29167916|gb|CB411176.1|CB411176
EST:     G-TGATTAGAGAAGCACACAAGAAAGG-GCAAAGA-TGTACTCGTTCAG                         GAATTGTTTGAGGGGCACTATTTCTGCCAAGCTCAAAGACTGGATTTCTTT
genomic: GTTGATTAGAGAAGCACACAAGAAAGGTGCAAAGATTGTACTCGTTCAGgtaaatttat ... aatgtcctagGAATTGTTTGAGGGGCACTATTTCTGCCAAGCTCAAAGACTGGATTTCTTT
EST: gi|71417127|gb|DR803933.1|DR803933
EST:     GTTGATTAGAGAAGCACACAAGAAAGGTGCAAAGATTGTACTCGTTCAG                         GAATTGTTTGAGGGGCACTATTTCTGCCAAGCTCAAAGACTGGATTTCTTT
genomic: GTTGATTAGAGAAGCACACAAGAAAGGTGCAAAGATTGTACTCGTTCAGgtaaatttat ... aatgtcctagGAATTGTTTGAGGGGCACTATTTCTGCCAAGCTCAAAGACTGGATTTCTTT
EST: gi|211482279|gb|FL401962.1|FL401962
EST:     GTTGATTAGAGAAGCACACAAGAAAGGTGCAAAGATTGTACTCGTTCAG                         GAATTGTTTGAGGGGCACTATTTCTGCCAAGCTCAAAGACTGGATTTCTTT
genomic: GTTGATTAGAGAAGCACACAAGAAAGGTGCAAAGATTGTACTCGTTCAGgtaaatttat ... aatgtcctagGAATTGTTTGAGGGGCACTATTTCTGCCAAGCTCAAAGACTGGATTTCTTT
EST: gi|94478259|gb|EB707217.1|EB707217
EST:     GTTGATTAGAGAAGCACACAAGAAAGGTGCAAAGATTGTACTCGTTCAG                         GAATTGTTTGAGGGGCACTATTTCTGCCAAGCTCAAAGACTGGATTTCTTT
genomic: GTTGATTAGAGAAGCACACAAGAAAGGTGCAAAGATTGTACTCGTTCAGgtaaatttat ... aatgtcctagGAATTGTTTGAGGGGCACTATTTCTGCCAAGCTCAAAGACTGGATTTCTTT
EST: gi|78077686|gb|DV506120.1|DV506120
EST:     GTTGATTAGAGAAGCACACAAGAAAGGTGCAAAGATTGTACTCGTTCAG                         GAATTGTTTGAGGGGCACTATTTCTGCCAAGCTCAAAGACTGGATTTCTTT
genomic: GTTGATTAGAGAAGCACACAAGAAAGGTGCAAAGATTGTACTCGTTCAGgtaaatttat ... aatgtcctagGAATTGTTTGAGGGGCACTATTTCTGCCAAGCTCAAAGACTGGATTTCTTT

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: 49 (upstream exon), 49 (downstream exon)
Score: 170

GTTGATTAGAGAAGCACACAAGAAAGGTGCAAAGATTGTACTCGTTCAGgtaaatttat ... aatgtcctagGAATTGTTTGAGGGGCACTATTTCTGCCAAGCTCAAAGACTGGATTTCTTTCGGCGCGCTAAGCCTTACAAAGGCAATCCAACTATTATAAG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 220

GTTGATTAGAGAAGCACACAAGAAAGGTGCAAAGATTGTACTCGTTCAGgtaaatttat ... aatgtcctagGAATTGTTTGAGGGGCACTATTTCTGCCAAGCTCAAAGACTGGATTTCTTTCGGCGCGCTAAGCCTTACAAAGGCAATCCAACTATTATAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 191

GTTGATTAGAGAAGCACACAAGAAAGGTGCAAAGATTGTACTCGTTCAGgtaaatttat ... aatgtcctagGAATTGTTTGAGGGGCACTATTTCTGCCAAGCTCAAAGACTGGATTTCTTTCGGCGCGCTAAGCCTTACAAAGGCAATCCAACTATTATAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 283

GTTGATTAGAGAAGCACACAAGAAAGGTGCAAAGATTGTACTCGTTCAGgtaaatttat ... aatgtcctagGAATTGTTTGAGGGGCACTATTTCTGCCAAGCTCAAAGACTGGATTTCTTTCGGCGCGCTAAGCCTTACAAAGGCAATCCAACTATTATAAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cgttttccttaaattttttattcaatctctccctcatatttcttaaatgtcctagGAATTGTTTGAGGGGCACTATTTCTGCCAAGCTCAAAGACTGGATTTCTTTCGGCGCGCTAAGCCTTACAAAGGCAATCCAACTATTATAAG
        ttaaattttttattca  TA-rich tract