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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagttcttccataggtcaaaacttatgataagacacaattttctattaaaaaaccaagattttttaagctagttaaccttgaatacacattataacaccagaagaattgtcaccaacattagttgctgataaaagatttagatgtctattgttacttttttctgtttgcagTCTGATTGCTTTTACAATGCCGGGTGGACGGCAGATATGCGTGAAGTTGTTAGTTTCCTTCATCAAGAGTATCCTAAGGCTCCACTATTCACTGTTGGGA

Basic information

species Zea mays
transcript GRMZM2G011169_T01
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G011169_T01 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os05g35730.2 (Oryza sativa), 3'ss of exon 5
gtaagttcttccataggtcaaaacttatgataagacacaattttctattaaaaaaccaagattttttaagctagttaaccttgaatacacattataacaccagaagaattgtcaccaacattagttgctgataaaagatttagatgtctattgttact--------tttttctgtttgcagTCTGATTGCTTTTACAATGCCGGGTGGACGGCAGATATGCGTGAAGTTGTTAGTTTCCTTCATCAAGAGTATCCTAAGGCTCCACTATTCACTGTTGGGA
                                                                               ||  |  | | |||||  | ||||||  ||          |  ||||| ||| ||||  || || ||    ||||| ||        | ||| |  ||||||||||||||||| |||||||| || ||||| | |||| | |||||  |||| | || |||||||||  |||||||  |||||||| ||||  |||||||||
-----------------------------------------------------------------------------gactccaggaaa-attatgtc-ccagaatcatcaat-ttggtagcagttgatga-aaaatgttcaggtggtacttgttcctcaacctagtatttattcttgcagTCTGATTGCTTCTACAATGCTGGATGGACAGAAGATTTCCGTGAGATTGTCAATTACCTTCATCAGAAGTATCCACAGGCTCCATTATTTGCTGTTGGGA
















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|160481564|gb|EY254396.1|EY254396
EST:     GGAATGTTGTTGTAAGCAACCACAGGGGTCTTGGTGGCATCTCCATAACA                         TCTGATTGCTTTTACAATGCCGGGTGGACGGCAGATATGCGTGAAGTTGTT
genomic: GGAATGTTGTTGTAAGCAACCACAGGGGTCTTGGTGGCATCTCCATAACAgtaagttctt ... ctgtttgcagTCTGATTGCTTTTACAATGCCGGGTGGACGGCAGATATGCGTGAAGTTGTT
EST: gi|160481556|gb|EY254388.1|EY254388
EST:     GGAATGTTGTTGTAAGCAACCACAGGGGTCTTGGTGGCATCTCCATAACA                         TCTGATTGCTTTTACAATGCCGGGTGGACGGCAGATATGCGTGAAGTTGTT
genomic: GGAATGTTGTTGTAAGCAACCACAGGGGTCTTGGTGGCATCTCCATAACAgtaagttctt ... ctgtttgcagTCTGATTGCTTTTACAATGCCGGGTGGACGGCAGATATGCGTGAAGTTGTT

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: 44 (upstream exon), 49 (downstream exon)
Score: 18

TATGTGAAGCACTTGGTCTTTTCTATGGCAATCAAAGGATGGAATGTTGTTGTAAGCAACCACAGGGGTCTTGGTGGCATCTCCATAACAgtaagttctt ... ctgtttgcagTCTGATTGCTTTTACAATGCCGGGTGGACGGCAGATATGCGTGAAGTTGTTAGTTTCCTTCATCAAGAGTATCCTAAGGCTCCACTATTCACTGTTGGGA


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 26

TATGTGAAGCACTTGGTCTTTTCTATGGCAATCAAAGGATGGAATGTTGTTGTAAGCAACCACAGGGGTCTTGGTGGCATCTCCATAACAgtaagttctt ... ctgtttgcagTCTGATTGCTTTTACAATGCCGGGTGGACGGCAGATATGCGTGAAGTTGTTAGTTTCCTTCATCAAGAGTATCCTAAGGCTCCACTATTCACTGTTGGGA


Block sizes: 45 (upstream exon), 49 (downstream exon)
Score: 22

TATGTGAAGCACTTGGTCTTTTCTATGGCAATCAAAGGATGGAATGTTGTTGTAAGCAACCACAGGGGTCTTGGTGGCATCTCCATAACAgtaagttctt ... ctgtttgcagTCTGATTGCTTTTACAATGCCGGGTGGACGGCAGATATGCGTGAAGTTGTTAGTTTCCTTCATCAAGAGTATCCTAAGGCTCCACTATTCACTGTTGGGA


Block sizes: 42 (upstream exon), 49 (downstream exon)
Score: 31

TATGTGAAGCACTTGGTCTTTTCTATGGCAATCAAAGGATGGAATGTTGTTGTAAGCAACCACAGGGGTCTTGGTGGCATCTCCATAACAgtaagttctt ... ctgtttgcagTCTGATTGCTTTTACAATGCCGGGTGGACGGCAGATATGCGTGAAGTTGTTAGTTTCCTTCATCAAGAGTATCCTAAGGCTCCACTATTCACTGTTGGGA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cattagttgctgataaaagatttagatgtctattgttacttttttctgtttgcagTCTGATTGCTTTTACAATGCCGGGTGGACGGCAGATATGCGTGAAGTTGTTAGTTTCCTTCATCAAGAGTATCCTAAGGCTCCACTATTCACTGTTGGGA
       tgctgat  putative branch site (score: 31)
                                   ttacttttttctgttt  putative PPT
            ataaaagatttagat  TA-rich tract