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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTTAATCATACAAAAAGGGCGCTGCATAATTACCTTATAACAAAACTTTATAGgtgagaatacttatttgctcttatttagaacacaacctattacatgttaagcaaaagataatttatgcactatggctttacaactttgctccaaactcttaaatatattgcccaattcag

Basic information

species Zea mays
transcript GRMZM2G129155_T01
intron # 18
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G129155_T01 (Zea mays), 5'ss of exon 18
lower sequence: LOC_Os01g69130.2 (Oryza sativa), 5'ss of exon 18
GTTAATCATACAAAAAGGGCGCTGCATAATTACCTTATAACAAAACTTTATAGgtgagaatacttatttgctcttatttagaacacaacctattacatgttaagcaaaagataatttatgcactatggctttacaactttgctccaaactcttaaatatattgcccaattcag
||||| || |||||| ||| ||||||||||||||||||||| || |||||||||||||   |    |||   || || || |  | ||  | | | | | |            ||  || |  |||  | || |||    |||  |   | ||  || ||| |    |     
GTTAACCACACAAAACGGGAGCTGCATAATTACCTTATAACTAAGCTTTATAGgtgagggaagccttttctactcatatacattataatgtttcaaacgctggatgtttccctataaatccgttataacatttcaaac--gctggatgtttttgtatgtatcgttgcag----
















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|211024339|gb|FL478389.1|FL478389
EST:     AATCATACAAAAAGGGCGCTGCATAATTACCTTATAACAAAACTTTATAG                         AGATGATCTTTTGGAAGACTTGCTCAAAGAACCTGATGAGATAACCATAAA
genomic: AATCATACAAAAAGGGCGCTGCATAATTACCTTATAACAAAACTTTATAGgtgagaatac ... cccaattcagAGATGATCTTTTGGAAGACTTGCTCAAAGAACCTGATGAGATAACCATAAA
EST: gi|32847928|gb|CD987609.1|CD987609
EST:     AATCATACAAAAAGGGCGCTGCATAATTACCTTATAACAAAACTTTATAG                         AGATGATCTTTTGGAAGACTTGCT-AAAGAACCTGATGAGAT
genomic: AATCATACAAAAAGGGCGCTGCATAATTACCTTATAACAAAACTTTATAGgtgagaatac ... cccaattcagAGATGATCTTTTGGAAGACTTGCTCAAAGAACCTGATGAGAT
EST: gi|88758145|gb|DY542286.1|DY542286
EST:     AATCATACAAAAAGGGCGCTGCATAATTACCTTATAACAAAACTTTATAG                         AGATGATCTTTTGGAAGACTTGCTCAAAGAACCTGATGAGATAACCATAAA
genomic: AATCATACAAAAAGGGCGCTGCATAATTACCTTATAACAAAACTTTATAGgtgagaatac ... cccaattcagAGATGATCTTTTGGAAGACTTGCTCAAAGAACCTGATGAGATAACCATAAA
EST: gi|37420874|gb|CF648134.1|CF648134
EST:     AATCATACAAAAAGGGCGCTGCATAATTACCTTATAACAAAACTTTATAA                         AGATGATCTTTTGGAAGACTTGCTCAAAGAACCTGATGAGATAACCATAAA
genomic: AATCATACAAAAAGGGCGCTGCATAATTACCTTATAACAAAACTTTATAGgtgagaatac ... cccaattcagAGATGATCTTTTGGAAGACTTGCTCAAAGAACCTGATGAGATAACCATAAA
EST: gi|33097482|gb|CF057442.1|CF057442
EST:     AATCATACAAAAAGGGCGCTGCATAATTACCTTATAACAAAACTTTATAG                         AGATGATCTTTTGAAAGACTTGCTCAAAGAACCTGATGAGATAACCATAAA
genomic: AATCATACAAAAAGGGCGCTGCATAATTACCTTATAACAAAACTTTATAGgtgagaatac ... cccaattcagAGATGATCTTTTGGAAGACTTGCTCAAAGAACCTGATGAGATAACCATAAA

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), 49 (downstream exon)
Score: 82

GTTAATCATACAAAAAGGGCGCTGCATAATTACCTTATAACAAAACTTTATAGgtgagaatac ... cccaattcagAGATGATCTTTTGGAAGACTTGCTCAAAGAACCTGATGAGATAACCATAAAGAGGAAGCAGATACGTGAAAATCTCAAGGTCCTTCAACAAGCTTACAAA


Block sizes: 48 (upstream exon), 47 (downstream exon)
Score: 79

GTTAATCATACAAAAAGGGCGCTGCATAATTACCTTATAACAAAACTTTATAGgtgagaatac ... cccaattcagAGATGATCTTTTGGAAGACTTGCTCAAAGAACCTGATGAGATAACCATAAAGAGGAAGCAGATACGTGAAAATCTCAAGGTCCTTCAACAAGCTTACAAA


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 98

GTTAATCATACAAAAAGGGCGCTGCATAATTACCTTATAACAAAACTTTATAGgtgagaatac ... cccaattcagAGATGATCTTTTGGAAGACTTGCTCAAAGAACCTGATGAGATAACCATAAAGAGGAAGCAGATACGTGAAAATCTCAAGGTCCTTCAACAAGCTTACAAA


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 92

GTTAATCATACAAAAAGGGCGCTGCATAATTACCTTATAACAAAACTTTATAGgtgagaatac ... cccaattcagAGATGATCTTTTGGAAGACTTGCTCAAAGAACCTGATGAGATAACCATAAAGAGGAAGCAGATACGTGAAAATCTCAAGGTCCTTCAACAAGCTTACAAA