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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatggggcttgtgacaatctggctgaagtttttaattcatcataaacagttattctttgtagagaaaagattgagtttttcacccattttttcatttttagGTGGCTGTTGAAATGGAATACTCTCGAAGGATCAGCACTGTAGATGGACAGAGTGCTGCTCCAACAGCAAACATGGCTGATACAAGAGTTTTAGATTATG

Basic information

species Zea mays
transcript AC207890.3_FGT002
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AC207890.3_FGT002 (Zea mays), 3'ss of exon 9
lower sequence: LOC_Os02g32350.2 (Oryza sativa), 3'ss of exon 9
------gtatggggcttgtgacaatctggctgaagtttttaattcatcataaacagttattctttgtagagaaaagattgagtttttcacccattttttcatttttagGTGGCTGTTGAAATGGAATACTCTCGAAGGATCAGCACTGTAGATGGACAGAGTGCTGCTCCAACAGCAAACATGGCTGATACAAGAGTTTTAGATTATG---------
        || ||  ||| || | ||   | ||||||       ||| | ||   ||||  |||||| || ||   ||||| |||||| ||    ||   ||||  ||||| ||||||| |||||||||||| |||||||||||||||| |||||||||         || ||| ||||||  |||||| | || ||||| |||||||         
gtatgtacataggttttgagatattccatcagaagttc------cataacaagttgttac-ctttgttgaaaatttattgattttttctcc----ttcctatttccagGTGACTGTTGAGATGGAATACTCTAGAAGGATCAGCACTGTGGATGGACAG---------CCCACAACAAACACAGCTGATGCCAGGGTTTTGGATTATGGGTCGGTTT
















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|211312966|gb|FL374721.1|FL374721
EST:     TTGCTCGTGAAGCTAAGGAGTTCTTACGCACGAGGTTGATTGGCAAACAA                         GTGGCTGTTGAAATGGAATACTCTCGAAGGATCAGCACTGTAGATGGACAG
genomic: TTGCTCGTGAAGCTAAGGAGTTCTTACGCACGAGGTTGATTGGCAAACAAgtatggggct ... tcatttttagGTGGCTGTTGAAATGGAATACTCTCGAAGGATCAGCACTGTAGATGGACAG
EST: gi|89758370|gb|DY687573.1|DY687573
EST:     TTGCTCGTGAAGCTAAGGAGTTCTTACGCACGAGGTTGATTGGCAAACAA                         GTGGCTGTTGAAATGGAATACTCTCGAAGGATCAGCACTGTAGATGGACAG
genomic: TTGCTCGTGAAGCTAAGGAGTTCTTACGCACGAGGTTGATTGGCAAACAAgtatggggct ... tcatttttagGTGGCTGTTGAAATGGAATACTCTCGAAGGATCAGCACTGTAGATGGACAG
EST: gi|67033177|gb|CO461926.1|CO461926
EST:     TTGCTCGTGAAGCTAAGGAGTTCTTACGCACGAGGTTGATTGGCAAACAA                         GTGGCTGTTGAAATGGAATACTCTCGAAGGATCAGCACTGTAGATGGACAG
genomic: TTGCTCGTGAAGCTAAGGAGTTCTTACGCACGAGGTTGATTGGCAAACAAgtatggggct ... tcatttttagGTGGCTGTTGAAATGGAATACTCTCGAAGGATCAGCACTGTAGATGGACAG

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: 236

TAGGGCTCCTAAGTTGGGCAATGCTCGTACAGATGTGAAGCCTGACCATTTTGCTCGTGAAGCTAAGGAGTTCTTACGCACGAGGTTGATTGGCAAACAAgtatggggct ... tcatttttagGTGGCTGTTGAAATGGAATACTCTCGAAGGATCAGCACTGTAGATGGACAGAGTGCTGCTCCAACAGCAAACATGGCTGATACAAGAGTTTTAGATTATG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 340

TAGGGCTCCTAAGTTGGGCAATGCTCGTACAGATGTGAAGCCTGACCATTTTGCTCGTGAAGCTAAGGAGTTCTTACGCACGAGGTTGATTGGCAAACAAgtatggggct ... tcatttttagGTGGCTGTTGAAATGGAATACTCTCGAAGGATCAGCACTGTAGATGGACAGAGTGCTGCTCCAACAGCAAACATGGCTGATACAAGAGTTTTAGATTATG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 303

TAGGGCTCCTAAGTTGGGCAATGCTCGTACAGATGTGAAGCCTGACCATTTTGCTCGTGAAGCTAAGGAGTTCTTACGCACGAGGTTGATTGGCAAACAAgtatggggct ... tcatttttagGTGGCTGTTGAAATGGAATACTCTCGAAGGATCAGCACTGTAGATGGACAGAGTGCTGCTCCAACAGCAAACATGGCTGATACAAGAGTTTTAGATTATG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 401

TAGGGCTCCTAAGTTGGGCAATGCTCGTACAGATGTGAAGCCTGACCATTTTGCTCGTGAAGCTAAGGAGTTCTTACGCACGAGGTTGATTGGCAAACAAgtatggggct ... tcatttttagGTGGCTGTTGAAATGGAATACTCTCGAAGGATCAGCACTGTAGATGGACAGAGTGCTGCTCCAACAGCAAACATGGCTGATACAAGAGTTTTAGATTATG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cagttattctttgtagagaaaagattgagtttttcacccattttttcatttttagGTGGCTGTTGAAATGGAATACTCTCGAAGGATCAGCACTGTAGATGGACAGAGTGCTGCTCCAACAGCAAACATGGCTGATACAAGAGTTTTAGATTATG
                             tttttcacccattttt  CT-rich tract
                                       attttttcattttta  TA-rich tract
















Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatggggcttgtgacaatctggctgaagtttttaattcatcataaacagttattctttgtagagaaaagattgagtttttcacccattttttcatttttagGTGGCTGTTGAAATGGAATACTCTCGAAGGATCAGCACTGTAGATGGACAGAGTGCTGCTCCAACAGCAAACATGGCTGATACAAGAGTTTTAGATTATG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGAT