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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gaaaaatatgccactacttactatagcccgcaatttgaaaccttgcatatgtcatttaaaattgaataacacctgagttaatatgtcttttgcgttatagTTAGTTGGCACAGATGAGGCTACTACATGCATTGGTGTTGTAATTCGCAACAACAAGACTGGAAT

Basic information

species Zea mays
transcript GRMZM2G144362_T01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G144362_T06 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os06g41390.4 (Oryza sativa), 3'ss of exon 2
gaaaaatatgc-cactacttactatagcccgcaatttgaaaccttgcatatgtcat-ttaaaattgaataacacctgagttaatatgt-cttttgcgt-tatagTTAGTTGGCACAGATGAGGCTACTACATGCATTGGTGTTGTAATTCGCAACAACAAGACTGGAAT
      | |||       || ||| |      | | | |  ||| |   ||   || | |  ||     |     |  ||||||   | ||||||| | | |||||||| |||||||||||||  ||||||||| | ||||| ||||||||||||||||||||||||||
----cttttgcatgtctgttgctaaaagttaaattattattcctggaccattcgatgtcagtatattgcactttatatgttaatccattcttttgcatctgtagTTAGTGGGCACAGATGAGGTGACTACATGCGTGGGTGTAGTAATTCGCAACAACAAGACTGGAAT

upper sequence: GRMZM2G144362_T06 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os06g41390.3 (Oryza sativa), 3'ss of exon 2
gaaaaatatgc-cactacttactatagcccgcaatttgaaaccttgcatatgtcat-ttaaaattgaataacacctgagttaatatgt-cttttgcgt-tatagTTAGTTGGCACAGATGAGGCTACTACATGCATTGGTGTTGTAATTCGCAACAACAAGACTGGAAT-----------------------------------
      | |||       || ||| |      | | | |  ||| |   ||   || | |  ||     |     |  ||||||   | ||||||| | | |||||||| |||||||||||||  ||||||||| | ||||| ||||||||||||||||||||||||||                                   
----cttttgcatgtctgttgctaaaagttaaattattattcctggaccattcgatgtcagtatattgcactttatatgttaatccattcttttgcatctgtagTTAGTGGGCACAGATGAGGTGACTACATGCGTGGGTGTAGTAATTCGCAACAACAAGACTGGAATGTAAGTGAAAAAGGAAGTGAGCATTTAAGCTGAAC
















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|91872202|gb|EB402159.1|EB402159
EST:     TCTACGTGTTCCAGCGGGAGTACGCCACGGTGGATCCGGCGCGCGTCGAG                         TTAGTTGGCACAGATGAGGCTACTACATGCATTGGTGTTGTAATTCGCAAC
genomic: TCTACGTGTTCCAGCGGGAGTACGCCACGGTGGATCCGGCGCGCGTCGAGgtgcgtggag ... tgcgttatagTTAGTTGGCACAGATGAGGCTACTACATGCATTGGTGTTGTAATTCGCAAC
EST: gi|94479450|gb|EB708408.1|EB708408
EST:     TCTACGTGTTCCAGCGGGAGTACGCCACGGTGGATCCGGCGCGCGTCGAG                         TTAGTTGGCACAGATGAGGCTACTACATGCATTGGTGTTGTAATTCGCAAC
genomic: TCTACGTGTTCCAGCGGGAGTACGCCACGGTGGATCCGGCGCGCGTCGAGgtgcgtggag ... tgcgttatagTTAGTTGGCACAGATGAGGCTACTACATGCATTGGTGTTGTAATTCGCAAC

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), 45 (downstream exon)
Score: 44

CGCGCCGGAGAGGCGGATCTCGGCAGGGCAGGAGGGGGCGCCGAAGCACGTCTACGTGTTCCAGCGGGAGTACGCCACGGTGGATCCGGCGCGCGTCGAGgtgcgtggag ... tgcgttatagTTAGTTGGCACAGATGAGGCTACTACATGCATTGGTGTTGTAATTCGCAACAACAAGACTGGAAT


Block sizes: 44 (upstream exon), 48 (downstream exon)
Score: 48

CGCGCCGGAGAGGCGGATCTCGGCAGGGCAGGAGGGGGCGCCGAAGCACGTCTACGTGTTCCAGCGGGAGTACGCCACGGTGGATCCGGCGCGCGTCGAGgtgcgtggag ... tgcgttatagTTAGTTGGCACAGATGAGGCTACTACATGCATTGGTGTTGTAATTCGCAACAACAAGACTGGAAT


Block sizes: 49 (upstream exon), 46 (downstream exon)
Score: 72

CGCGCCGGAGAGGCGGATCTCGGCAGGGCAGGAGGGGGCGCCGAAGCACGTCTACGTGTTCCAGCGGGAGTACGCCACGGTGGATCCGGCGCGCGTCGAGgtgcgtggag ... tgcgttatagTTAGTTGGCACAGATGAGGCTACTACATGCATTGGTGTTGTAATTCGCAACAACAAGACTGGAAT


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

CGCGCCGGAGAGGCGGATCTCGGCAGGGCAGGAGGGGGCGCCGAAGCACGTCTACGTGTTCCAGCGGGAGTACGCCACGGTGGATCCGGCGCGCGTCGAGgtgcgtggag ... tgcgttatagTTAGTTGGCACAGATGAGGCTACTACATGCATTGGTGTTGTAATTCGCAACAACAAGACTGGAAT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

catatgtcatttaaaattgaataacacctgagttaatatgtcttttgcgttatagTTAGTTGGCACAGATGAGGCTACTACATGCATTGGTGTTGTAATTCGCAACAACAAGACTGGAAT
                                      tgtctttt  CT-rich tract
      tcatttaaaattgaat  TA-rich tract