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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaatattttgtcccttcctcttggttattgcattagttgtacttaacttattttttggattcagaatgtttattgctgcagctaaaaaagctattgtcttttgacctaaatattggctgcctctgatggatgcgctagttcttttttcgtattgattttgtattggtttttggcagATATGTAGAGCATTGGCTTACATTCATGGTACTATCGGTGTCTGCCACAGAGATATTAAGCCACAAAATCTTCTG

Basic information

species Zea mays
transcript GRMZM5G835235_T02
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G835235_T04 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os01g14860.1 (Oryza sativa), 3'ss of exon 5
gtaatattttgtcccttcctcttggttattgcattagttgtacttaacttattttttggattcagaatgtttattgctgcagctaaaaaagctattgtcttttgacctaaatattggctgcctctgatggatgcgctagttcttttttcgtattgattttgtattggtttttggcagATATGTAGAGCATTGGCTTACATTCATGGTACTATCGGTGTCTGCCACAGAGATATTAAGCCACAAAATCTTCTG
|||||||| |||    | |  ||     ||| ||           |  || || ||| || | |       | ||| || |||     | |||||  ||     | |||   | | ||   |   ||||                 || | ||| | |||| | |  || ||| ||||| ||||| ||||| |||||||| |||  ||  ||||| || |||||||||||||| |||||||| |||||||||
gtaatattctgttatgtaccttt-----ttggat-----------actttgttcttttgactta-------tgttg-tgtagc-----aggctatattcagacaaactagccagtagcataccgagatga---------------ctttgaatttagtttgaaat--ttgttgacagATTTGTAGGGCATTAGCTTACATCCATAATAGCATCGGAGTTTGCCACAGAGATATCAAGCCACAGAATCTTCTG
















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|67039601|gb|CO465856.1|CO465856
EST:     AGATGCACCAACGCATGCCACTTATTTATGTGAAGCTTTATATGTACCAG                         ATATGTAGAGCATTGGCTTACATTCATGGTACAATCGGTGTCTGCCACAGA
genomic: AGATGCACCAACGCATGCCACTTATTTATGTGAAGCTTTATATGTACCAGgtaatatttt ... tttttggcagATATGTAGAGCATTGGCTTACATTCATGGTACTATCGGTGTCTGCCACAGA
EST: gi|166413835|gb|EG065949.1|EG065949
EST:     AGATGCACCAACGCATGCCACTTATTTATGTGAAGCTTTATATGTACCAG                         ATATGTAGAGCATTGGCTTACATTC
genomic: AGATGCACCAACGCATGCCACTTATTTATGTGAAGCTTTATATGTACCAGgtaatatttt ... tttttggcagATATGTAGAGCATTGGCTTACATTC
EST: gi|211480778|gb|FL342573.1|FL342573
EST:     AGATGCACCAACGCATGCCACTTATTTATGTGAAGCTTTATATGTACCAG                         ATATGTAGAGCATTGGCTTACATTCATGGTACTATCGGTGTCTGCCACAGA
genomic: AGATGCACCAACGCATGCCACTTATTTATGTGAAGCTTTATATGTACCAGgtaatatttt ... tttttggcagATATGTAGAGCATTGGCTTACATTCATGGTACTATCGGTGTCTGCCACAGA

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), 48 (downstream exon)
Score: 179

CCTTGAGTATGTTCCGGAGACAGTTCATCGAGTTGTGAAACATCACAACAAGATGCACCAACGCATGCCACTTATTTATGTGAAGCTTTATATGTACCAGgtaatatttt ... tttttggcagATATGTAGAGCATTGGCTTACATTCATGGTACTATCGGTGTCTGCCACAGAGATATTAAGCCACAAAATCTTCTG


Block sizes: 45 (upstream exon), 48 (downstream exon)
Score: 82

CCTTGAGTATGTTCCGGAGACAGTTCATCGAGTTGTGAAACATCACAACAAGATGCACCAACGCATGCCACTTATTTATGTGAAGCTTTATATGTACCAGgtaatatttt ... tttttggcagATATGTAGAGCATTGGCTTACATTCATGGTACTATCGGTGTCTGCCACAGAGATATTAAGCCACAAAATCTTCTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 159

CCTTGAGTATGTTCCGGAGACAGTTCATCGAGTTGTGAAACATCACAACAAGATGCACCAACGCATGCCACTTATTTATGTGAAGCTTTATATGTACCAGgtaatatttt ... tttttggcagATATGTAGAGCATTGGCTTACATTCATGGTACTATCGGTGTCTGCCACAGAGATATTAAGCCACAAAATCTTCTG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 94

CCTTGAGTATGTTCCGGAGACAGTTCATCGAGTTGTGAAACATCACAACAAGATGCACCAACGCATGCCACTTATTTATGTGAAGCTTTATATGTACCAGgtaatatttt ... tttttggcagATATGTAGAGCATTGGCTTACATTCATGGTACTATCGGTGTCTGCCACAGAGATATTAAGCCACAAAATCTTCTG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tctgatggatgcgctagttcttttttcgtattgattttgtattggtttttggcagATATGTAGAGCATTGGCTTACATTCATGGTACTATCGGTGTCTGCCACAGAGATATTAAGCCACAAAATCTTCTG
                            tattgat  putative branch site (score: 94)
                                             ttttt  putative PPT
                            tattgattttgtatt  TA-rich tract