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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCTGCTGATACACAAGTCATTTCGGACTATATACGTTATTTCCTCCACCAACACACgtaagtttgttcttcatacacaacttaacagtattcgatctttcatttgatgaataaatatactgaatgatacttaaattctctttgaacaatatgatggtatacaattacttgagatatctgacatgcgaggtagttgatgctaaagttaccctcctatgcag

Basic information

species Zea mays
transcript GRMZM2G374881_T02
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G374881_T02 (Zea mays), 5'ss of exon 3
lower sequence: LOC_Os06g04800.1 (Oryza sativa), 5'ss of exon 3
GCTGCTGATACACAAGTCATTTCGGACTATATACGTTATTTCCTCCACCAACACACgtaagtttgttctt---catacacaacttaacagtattcgatctttcattt---gatgaataaa--tatactgaatgat---------acttaaattctctttgaacaatatgatggtata-caattacttgagatatctgacatgcgaggtagttgatgctaaagttaccctcc-tatgcag
||||| || ||||||||||||||||| ||| |||| ||||| ||||||||||||||||||||||||||||    |   | ||  || |  |    | ||| || |||   | | | ||       |||||||||          ||||| ||| || || |  || |   ||   ||  | |||||    |||| ||   ||| || |||   |||||||| || |||||  | |||||
GCTGCCGACACACAAGTCATTTCGGAATATGTACGCTATTTTCTCCACCAACACACgtaagtttgttcttgtgtaattataatatatctattaatgctctctccttttaagctaagtaggatggcactgaatgaacaataataaacttagatt-tcattaattaacacagtgaactagtagttactgtgaatatttgctgtgcaagatagcccatgctaaattttccctcgatttgcag

upper sequence: GRMZM2G374881_T02 (Zea mays), 5'ss of exon 3
lower sequence: LOC_Os02g53060.1 (Oryza sativa), 5'ss of exon 3
GCTGCTGATACACAAGTCATTTCGGACTATATACGTTATTTCCTCCACCAACACACgtaagtttgttcttcatacacaacttaacagtattcgatctttcatttgatgaataaatatactgaatgatacttaaattctctttgaacaatatgatggtatac-aattacttgagatatctgacatgcgaggtagttgatgctaaagttaccctcc-tatgcag
||||||||||||||||| ||||| || ||| |||| ||||| |||||||||||||||||||||    | |       ||   || ||                    ||| || |    |||||||       | |||   |     ||||  || | ||| | ||||| || | || |||  ||| ||  |||| |||||||| || |||||| | | |||
GCTGCTGATACACAAGTAATTTCCGATTATGTACGCTATTTTCTCCACCAACACACgtaagttgtccccttg-----aagcgaatag--------------------gaagaagt----tgaatga-------actcttcat-----atatattgttctactagttactggaaacatttgatgtgcaagacagttcatgctaaattttccctccattttcag

upper sequence: GRMZM2G374881_T02 (Zea mays), 5'ss of exon 3
lower sequence: LOC_Os02g53060.2 (Oryza sativa), 5'ss of exon 3
GCTGCTGATACACAAGTCATTTCGGACTATATACGTTATTTCCTCCACCAACACACgtaagtttgttcttcatacacaacttaacagtattcgatctttcatttgatgaataaatatactgaatgatacttaaattctctttgaacaatatgatggtatacaattacttgagatatctgacatgcgaggtagttgatgctaaagttaccctcctatgcag
||||||||||||||||| ||||| || ||| |||| ||||| ||||||||||||||||||||| || |     |  | | |    || | | ||     |  || ||  |||  | |                                                                                                       
GCTGCTGATACACAAgtaatttccgattatgtacgctattttctccaccaacacacgtaagtt-gtccccttgaagcgaataggaagaagttgaatgaactcttcatatatat-tgt-------------------------------------------------------------------------------------------------------

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|211274177|gb|FK988507.1|FK988507
EST:     GATACACAAGTCATTTCGGACTATATACGTTATTTCCTCCACCAACACAC                         AATCCAGCTTGGACAACCAGCTACTGTTAAAGTTGCAGCTAACTTGATTAG
genomic: GATACACAAGTCATTTCGGACTATATACGTTATTTCCTCCACCAACACACgtaagtttgt ... tcctatgcagAATCCAGCTTGGACAACCAGCTACTGTTAAAGTTGCAGCTAACTTGATTAG
EST: gi|211272373|gb|FK988497.1|FK988497
EST:     GATACACAAGTCATTTCGGACTATATACGTTATTTCCTCCACCAACACAC                         AATCCAGCTTGGACAACCAGCTACTGTTAAAGTTGCAGCTAACTTGATTAG
genomic: GATACACAAGTCATTTCGGACTATATACGTTATTTCCTCCACCAACACACgtaagtttgt ... tcctatgcagAATCCAGCTTGGACAACCAGCTACTGTTAAAGTTGCAGCTAACTTGATTAG
EST: gi|71320622|gb|DR797046.1|DR797046
EST:     GTCATTTCGGACTATATACGTTATTTCCTCCACCAACACAC                         AATCCAGCTTGGACAACCAGCTACTGTTAAAGTTGCAGCTAACTTGATTAG
genomic: GTCATTTCGGACTATATACGTTATTTCCTCCACCAACACACgtaagtttgt ... tcctatgcagAATCCAGCTTGGACAACCAGCTACTGTTAAAGTTGCAGCTAACTTGATTAG
EST: gi|211274173|gb|FK988503.1|FK988503
EST:     GATACACAAGTCATTTCGGACTATATACGTTATTTCCTCCACCAACACAC                         AATCCAGCTTGGACAACCAGCTACTGTTAAAGTTTGCAGCTAACTTGATTA
genomic: GATACACAAGTCATTTCGGACTATATACGTTATTTCCTCCACCAACACACgtaagtttgt ... tcctatgcagAATCCAGCTTGGACAACCAGCTACTGTTAAAGTT-GCAGCTAACTTGATTA
EST: gi|78543575|gb|DV621073.1|DV621073
EST:     GATACACAAGTCATTTCGGACTATGTACGTTATTTCCTCCACCAACACAC                         AATCCAGCTTGGACAACCAGCTACTGTTAAAGTTGCAGCTAACTTGATTAG
genomic: GATACACAAGTCATTTCGGACTATATACGTTATTTCCTCCACCAACACACgtaagtttgt ... tcctatgcagAATCCAGCTTGGACAACCAGCTACTGTTAAAGTTGCAGCTAACTTGATTAG
EST: gi|32806791|gb|CD959025.1|CD959025
EST:     GATACACAAGTCATTTCGGACTATATACGTTATTTCCTCCACCAACACAC                         AATCCAGCTTGGACAACCAGCTACTGTTA
genomic: GATACACAAGTCATTTCGGACTATATACGTTATTTCCTCCACCAACACACgtaagtttgt ... tcctatgcagAATCCAGCTTGGACAACCAGCTACTGTTA
EST: gi|50338298|gb|CO533424.1|CO533424
EST:     GATACACAAGTCATTTCGGACTATATACGTTATTTCCTCCACCAACACAC                         AATCCAGCTTGGACAACCAGCTACTGTTAAAGTTGCAGCTAACTTGATTAG
genomic: GATACACAAGTCATTTCGGACTATATACGTTATTTCCTCCACCAACACACgtaagtttgt ... tcctatgcagAATCCAGCTTGGACAACCAGCTACTGTTAAAGTTGCAGCTAACTTGATTAG
EST: gi|211274176|gb|FK988506.1|FK988506
EST:     GATACACAAGTCATTTCGGACTATATACGTTATTTCCTCCACCAACACAC                         AATCCAGCTYGGAACAACCAGCTACTGTTAAAGTTGCAGCTTAACTTGATT
genomic: GATACACAAGTCATTTCGGACTATATACGTTATTTCCTCCACCAACACACgtaagtttgt ... tcctatgcagAATCCAGCTTGGA-CAACCAGCTACTGTTAAAGTTGCAGCT-AACTTGATT
EST: gi|78109399|gb|DV527815.1|DV527815
EST:     GATACACAAGTCATTTCGGACTATATACGTTATTTCCTCCACCAACACAC                         AATCCAGCTTGGACAACCAGCTACTGTTAAAGTTGCAGCTAACTTGATTAG
genomic: GATACACAAGTCATTTCGGACTATATACGTTATTTCCTCCACCAACACACgtaagtttgt ... tcctatgcagAATCCAGCTTGGACAACCAGCTACTGTTAAAGTTGCAGCTAACTTGATTAG
EST: gi|37380555|gb|CF627096.1|CF627096
EST:     ATACACAAGTCATTTCGGACTATGTACGTTATTTCCTCCACCAAACACAC                         AATCCAGCTTGGACAACCAGCTACTGTTAAAGTTGCAGCTAACTTGATTA
genomic: ATACACAAGTCATTTCGGACTATATACGTTATTTCCTCCACC-AACACACgtaagtttgt ... tcctatgcagAATCCAGCTTGGACAACCAGCTACTGTTAAAGTTGCAGCTAACTTGATTA
EST: gi|91049302|gb|EB159720.1|EB159720
EST:     GATACACAAGTCATTTCGGACTATATACGTTATTTCCTCCACCAACACAC                         AATCCAGCTTGGACAACCAGCTACTGTTAAAGTTGCAGCTAACTTGATTAG
genomic: GATACACAAGTCATTTCGGACTATATACGTTATTTCCTCCACCAACACACgtaagtttgt ... tcctatgcagAATCCAGCTTGGACAACCAGCTACTGTTAAAGTTGCAGCTAACTTGATTAG
EST: gi|211272372|gb|FK988496.1|FK988496
EST:     GATACACAAGTCATTTCGGACTATATACGTTATTTCCTCCACCAACACAC                         AATCCAGCTTGGACAACCAGCTACTGTTAAAGTTGCAGCTAACTTGATTAG
genomic: GATACACAAGTCATTTCGGACTATATACGTTATTTCCTCCACCAACACACgtaagtttgt ... tcctatgcagAATCCAGCTTGGACAACCAGCTACTGTTAAAGTTGCAGCTAACTTGATTAG
EST: gi|76915113|gb|DV165828.1|DV165828
EST:     GATACACAAGTCATTTCGGACTATATACGTTATTTCCTCCACCAACACAC                         AATCCAGCTTGGACAACCAGCTACTGTTAAAGTTGCAGCTAACTTGATTAG
genomic: GATACACAAGTCATTTCGGACTATATACGTTATTTCCTCCACCAACACACgtaagtttgt ... tcctatgcagAATCCAGCTTGGACAACCAGCTACTGTTAAAGTTGCAGCTAACTTGATTAG
EST: gi|211272370|gb|FK988494.1|FK988494
EST:     GATACACAAGTCATTTCGGACTATATACGTTATTTCCTCCACCAACACAC                         AATCCAGCT-GGACAACCAGCT
genomic: GATACACAAGTCATTTCGGACTATATACGTTATTTCCTCCACCAACACACgtaagtttgt ... tcctatgcagAATCCAGCTTGGACAACCAGCT
EST: gi|211274172|gb|FK988502.1|FK988502
EST:     GATACACAAGTCATTTCGGACTATATACCTTATTTCCTCCACCAACACAC                         AATCCAGCTTGGACAACCAGCTACTGTTAAAGTTGCAGCTAACTTGA
genomic: GATACACAAGTCATTTCGGACTATATACGTTATTTCCTCCACCAACACACgtaagtttgt ... tcctatgcagAATCCAGCTTGGACAACCAGCTACTGTTAAAGTTGCAGCTAACTTGA
EST: gi|91872633|gb|EB402590.1|EB402590
EST:     GATACACAAGTCATTTCGGACTATATACGTTATTTCCTCCACCAACACAC                         AATCCAGCTTGGACAACCAGCTACTGTTAAAGTTGCAGCTAACTTGATTAG
genomic: GATACACAAGTCATTTCGGACTATATACGTTATTTCCTCCACCAACACACgtaagtttgt ... tcctatgcagAATCCAGCTTGGACAACCAGCTACTGTTAAAGTTGCAGCTAACTTGATTAG
EST: gi|78109398|gb|DV527814.1|DV527814
EST:     GATACACAAGTCATTTCGGACTATATACGTTATTTCCTCCACCAACACAC                         AATCCAGCTTGGACAACCAGCTACTGTTAAAGTTGCAGCTAACTTGATTAG
genomic: GATACACAAGTCATTTCGGACTATATACGTTATTTCCTCCACCAACACACgtaagtttgt ... tcctatgcagAATCCAGCTTGGACAACCAGCTACTGTTAAAGTTGCAGCTAACTTGATTAG
EST: gi|211272369|gb|FK988493.1|FK988493
EST:     GATACACAAGTCATTTCGGACTATATACGTTATTTCCTCCACCAACACAC                         AATCCAGCTTGGACAACCAGCTACTGTTAAAGTTGCAGCTAACTTGATTAG
genomic: GATACACAAGTCATTTCGGACTATATACGTTATTTCCTCCACCAACACACgtaagtttgt ... tcctatgcagAATCCAGCTTGGACAACCAGCTACTGTTAAAGTTGCAGCTAACTTGATTAG
EST: gi|37378375|gb|CF625874.1|CF625874
EST:     GATACACAAGTCATTTCGGACTATGTACGTTATTTCCTCCACCAACACAC                         AATCCAGCTTGGACAACCAGCTACTGTTAAAGTTGCAGCTAACTTGATTAG
genomic: GATACACAAGTCATTTCGGACTATATACGTTATTTCCTCCACCAACACACgtaagtttgt ... tcctatgcagAATCCAGCTTGGACAACCAGCTACTGTTAAAGTTGCAGCTAACTTGATTAG
EST: gi|211274170|gb|FK988500.1|FK988500
EST:     GATACACAAGTCATTTCGGACTATATACGTTATTTCCTCCACCAACACAC                         AATCCAGCTTGGACAACCAGCTACTGTTAAAGTTGCAGCTAACTTGAT
genomic: GATACACAAGTCATTTCGGACTATATACGTTATTTCCTCCACCAACACACgtaagtttgt ... tcctatgcagAATCCAGCTTGGACAACCAGCTACTGTTAAAGTTGCAGCTAACTTGAT
EST: gi|211274174|gb|FK988504.1|FK988504
EST:     GATACACAAGTCATTTCGGACTATATACGTTATTTCCTCCACCAACACAC                         AATCCAGCTTGGACAACCAGCTACTGTTAAAGTTGCAGCTAACTTGATTAG
genomic: GATACACAAGTCATTTCGGACTATATACGTTATTTCCTCCACCAACACACgtaagtttgt ... tcctatgcagAATCCAGCTTGGACAACCAGCTACTGTTAAAGTTGCAGCTAACTTGATTAG
EST: gi|148967409|gb|EE018635.2|EE018635
EST:     GATACACAAGTCATTTCGGACTATATACGTTATTTCCTCCACCAACACAC                         AATCCAGCTTGGACAACCAGCTACTGTTAAAGTTGCAGCTAACTTGATTAG
genomic: GATACACAAGTCATTTCGGACTATATACGTTATTTCCTCCACCAACACACgtaagtttgt ... tcctatgcagAATCCAGCTTGGACAACCAGCTACTGTTAAAGTTGCAGCTAACTTGATTAG

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: 202

GCTGCTGATACACAAGTCATTTCGGACTATATACGTTATTTCCTCCACCAACACACgtaagtttgt ... tcctatgcagAATCCAGCTTGGACAACCAGCTACTGTTAAAGTTGCAGCTAACTTGATTAGGTTGCTAGCTTATCAGAATAAG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 172

GCTGCTGATACACAAGTCATTTCGGACTATATACGTTATTTCCTCCACCAACACACgtaagtttgt ... tcctatgcagAATCCAGCTTGGACAACCAGCTACTGTTAAAGTTGCAGCTAACTTGATTAGGTTGCTAGCTTATCAGAATAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 152

GCTGCTGATACACAAGTCATTTCGGACTATATACGTTATTTCCTCCACCAACACACgtaagtttgt ... tcctatgcagAATCCAGCTTGGACAACCAGCTACTGTTAAAGTTGCAGCTAACTTGATTAGGTTGCTAGCTTATCAGAATAAG


Block sizes: 48 (upstream exon), 47 (downstream exon)
Score: 229

GCTGCTGATACACAAGTCATTTCGGACTATATACGTTATTTCCTCCACCAACACACgtaagtttgt ... tcctatgcagAATCCAGCTTGGACAACCAGCTACTGTTAAAGTTGCAGCTAACTTGATTAGGTTGCTAGCTTATCAGAATAAG