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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaacacagtgtttagcgacgattatgcatggtgaaatactgttaattctagatcaactataatctggattcactgtgctatttgagcttttgaccaactttctagttctttggatacagcgtcttattagtataccatcttactgacattgtaatacctttgaccatgctagGTTGTTTTGGATTCGCACCGCTGGGTTCCGATGCCATCTGTTGGCTTTGTAGCAAATGGTGTTGTCGATGACACTTCTGATGATGTGACTCCACCTTCTG

Basic information

species Zea mays
transcript AC235544.1_FGT004
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AC235544.1_FGT004 (Zea mays), 3'ss of exon 9
lower sequence: LOC_Os12g35290.1 (Oryza sativa), 3'ss of exon 9
gtaacacagtgtttagcgacgattatgcatggtgaaatactgttaattctagatcaactataatctggattcactgtgctatttgagcttttgaccaactttctagttctttggatacagcgtcttattagtataccatcttactgacattgtaatacctttgaccatgctagGTTGTTTTGGATTCGCACCGCTGGGTTCCGATGCCATCTGTTGGCTTTGTAGCAAATGGTGTTGTCGATGACACTTCTGATGATGTGACTCCACCTTCTG
                                                                     || |||  |   ||| |||| | | |||  |||  |  | | |    | |   ||||  |   | |  || ||| |  ||   |  ||||||  | |||| ||||||||| ||||||| || || |||||||| ||||||||||||||||||||||| ||||| ||||| ||||| ||||||||||||||||| || |||||||
---------------------------------------------------------------------tttacttagtgttttcagctgtagtccacattttcaaatgtct----atactttcttcctcaaacattattttaatttcaccattttaccttctatcatgttagGTTGTTCTGGATTCACATCGTTGGGTTCCAATGCCATCTGTTGGCTTTGTAGCGAATGGAGTTGTGGATGAGACTTCTGATGATGTGACGCCGCCTTCTG
















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|67014331|gb|CO443080.1|CO443080
EST:     TTCTAAATTTATTCTCAAAGAATATGAGTATGGCGGTTGAAAATTTTCAG                         GTTGTTTTGGATTCGCACCGCTGGGTTCCGATGCCATCTGTTGGCTTTGTA
genomic: TTCTAAATTTATTCTCAAAGAATATGAGTATGGCGGTTGAAAATTTTCAGgtaacacagt ... accatgctagGTTGTTTTGGATTCGCACCGCTGGGTTCCGATGCCATCTGTTGGCTTTGTA




















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: 46 (upstream exon), 47 (downstream exon)
Score: 48

CGCGGTTCTAAATTTATTCTCAAAGAATATGAGTATGGCGGTTGAAAATTTTCAGgtaacacagt ... accatgctagGTTGTTTTGGATTCGCACCGCTGGGTTCCGATGCCATCTGTTGGCTTTGTAGCAAATGGTGTTGTCGATGACACTTCTGATGATGTGACTCCACCTTCTG


Block sizes: 35 (upstream exon), 43 (downstream exon)
Score: 25

CGCGGTTCTAAATTTATTCTCAAAGAATATGAGTATGGCGGTTGAAAATTTTCAGgtaacacagt ... accatgctagGTTGTTTTGGATTCGCACCGCTGGGTTCCGATGCCATCTGTTGGCTTTGTAGCAAATGGTGTTGTCGATGACACTTCTGATGATGTGACTCCACCTTCTG


Block sizes: 33 (upstream exon), 48 (downstream exon)
Score: 28

CGCGGTTCTAAATTTATTCTCAAAGAATATGAGTATGGCGGTTGAAAATTTTCAGgtaacacagt ... accatgctagGTTGTTTTGGATTCGCACCGCTGGGTTCCGATGCCATCTGTTGGCTTTGTAGCAAATGGTGTTGTCGATGACACTTCTGATGATGTGACTCCACCTTCTG


Block sizes: 37 (upstream exon), 43 (downstream exon)
Score: 42

CGCGGTTCTAAATTTATTCTCAAAGAATATGAGTATGGCGGTTGAAAATTTTCAGgtaacacagt ... accatgctagGTTGTTTTGGATTCGCACCGCTGGGTTCCGATGCCATCTGTTGGCTTTGTAGCAAATGGTGTTGTCGATGACACTTCTGATGATGTGACTCCACCTTCTG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agcgtcttattagtataccatcttactgacattgtaatacctttgaccatgctagGTTGTTTTGGATTCGCACCGCTGGGTTCCGATGCCATCTGTTGGCTTTGTAGCAAATGGTGTTGTCGATGACACTTCTGATGATGTGACTCCACCTTCTG
      ttattagtata  TA-rich tract