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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aagaacgctggtttctgtatgctttgtttgtttagaccagtatgtagctctcttcagtctccacttttgaagattttatgtattttgcatctattgccagCTTACTGGAACAATGATAAGGAAGAAACTCAAAAGTGCGATTCAGTTGATATATCTATTGCTGTTGCTACAGAGAAG

Basic information

species Zea mays
transcript GRMZM2G082664_T01
intron # 13
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G082664_T01 (Zea mays), 3'ss of exon 13
lower sequence: LOC_Os06g30460.4 (Oryza sativa), 3'ss of exon 11
--aagaacgctggtttctgtatgc-tttgtttgtttagaccagtatgtagctctcttcagtctccacttttgaagatt-ttatgtattttgcatctattgccagCTTACTGGAACAATGATAAGGAAGAAACTCAAAAGTGCGATTCAGTTGATATATCTATTGCTGTTGCTACAGAGAAG
  |  |||      |||  | | |   |  | |||||   ||   |    || | ||  ||||      | |   ||  ||||   |||  |||  ||| ||||| |||||||||||||| |||||| || | || ||||| | |||||||||||||||||| || |||||||||||||||
ggactaactgaatattcaatttacacatagtggtttaagtcaactt----ctttgtttggtctaatggatagctcatcattattcttttctcatgaatttccagCATACTGGAACAATGACAAGGAACAAGCCCAGAAGTGTGTTTCAGTTGATATATCTATCGCAGTTGCTACAGAGAAG
















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|61119124|gb|DN560085.1|DN560085
EST:     CATCATAAAGGCTGTGGCAATTGCGTTGCGGAACGTCCCTGAAGCAAATG                         CTTACTGGAACAATGATAAGGAAGAAACTCAAAAGTGCGATTCAGTTGATA
genomic: CATCATAAAGGCTGTGGCAATTGCGTTGCGGAACGTCCCTGAAGCAAATGgtaatttcaa ... ctattgccagCTTACTGGAACAATGATAAGGAAGAAACTCAAAAGTGCGATTCAGTTGATA
EST: gi|60347222|gb|DN214195.1|DN214195
EST:     CATCATAAAGGCTGTGGCAATTGCCTTGCGGAACGTCCCTGAAGCAAATG                         CTTACTGGAACAATGATAAGGAAGAAACCCAAAAGTGTGATTCAGTTGATA
genomic: CATCATAAAGGCTGTGGCAATTGCGTTGCGGAACGTCCCTGAAGCAAATGgtaatttcaa ... ctattgccagCTTACTGGAACAATGATAAGGAAGAAACTCAAAAGTGCGATTCAGTTGATA
EST: gi|50331519|gb|CO526645.1|CO526645
EST:     CATCATAAAGGCTGTGGCAATTGCGTTGCGGAACGTCCCTGAAGCAAATG                         CTTACTGGAACAATGATAAGGAAGAAACTCAAAAGTGCGATTCAGTTGATA
genomic: CATCATAAAGGCTGTGGCAATTGCGTTGCGGAACGTCCCTGAAGCAAATGgtaatttcaa ... ctattgccagCTTACTGGAACAATGATAAGGAAGAAACTCAAAAGTGCGATTCAGTTGATA
EST: gi|37398003|gb|CF636310.1|CF636310
EST:     TCCCTGAAGCAAATG                         CTTACTGGTACAATGATAAGGAAGAAACTCAAAAGTGCGATTCAGTTGATA
genomic: TCCCTGAAGCAAATGgtaatttcaa ... ctattgccagCTTACTGGAACAATGATAAGGAAGAAACTCAAAAGTGCGATTCAGTTGATA
EST: gi|40337298|gb|CK371368.1|CK371368
EST:     GCGTTGCGGAACGTCCCTGAAGCAAATG                         CTTACTGGTACAATGATAAGGAAGAAACTCAAAAGTGCGATTCAGTTGATA
genomic: GCGTTGCGGAACGTCCCTGAAGCAAATGgtaatttcaa ... ctattgccagCTTACTGGAACAATGATAAGGAAGAAACTCAAAAGTGCGATTCAGTTGATA
EST: gi|50331482|gb|CO526608.1|CO526608
EST:     CATCATAAAGGCTGTGGCAATTGCGTTGCGGAACGTCCCTGAAGCAAATG                         CTTACTGGAACAATGATAAGGAAGAAACTCAAAAGTGCGATTCAGTTGATA
genomic: CATCATAAAGGCTGTGGCAATTGCGTTGCGGAACGTCCCTGAAGCAAATGgtaatttcaa ... ctattgccagCTTACTGGAACAATGATAAGGAAGAAACTCAAAAGTGCGATTCAGTTGATA

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), 49 (downstream exon)
Score: 129

AGCTACATGGCATTAAAGTTTCAGTAAATGACATCATCATAAAGGCTGTGGCAATTGCGTTGCGGAACGTCCCTGAAGCAAATGgtaatttcaa ... ctattgccagCTTACTGGAACAATGATAAGGAAGAAACTCAAAAGTGCGATTCAGTTGATATATCTATTGCTGTTGCTACAGAGAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 176

AGCTACATGGCATTAAAGTTTCAGTAAATGACATCATCATAAAGGCTGTGGCAATTGCGTTGCGGAACGTCCCTGAAGCAAATGgtaatttcaa ... ctattgccagCTTACTGGAACAATGATAAGGAAGAAACTCAAAAGTGCGATTCAGTTGATATATCTATTGCTGTTGCTACAGAGAAG


Block sizes: 47 (upstream exon), 48 (downstream exon)
Score: 149

AGCTACATGGCATTAAAGTTTCAGTAAATGACATCATCATAAAGGCTGTGGCAATTGCGTTGCGGAACGTCCCTGAAGCAAATGgtaatttcaa ... ctattgccagCTTACTGGAACAATGATAAGGAAGAAACTCAAAAGTGCGATTCAGTTGATATATCTATTGCTGTTGCTACAGAGAAG


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 173

AGCTACATGGCATTAAAGTTTCAGTAAATGACATCATCATAAAGGCTGTGGCAATTGCGTTGCGGAACGTCCCTGAAGCAAATGgtaatttcaa ... ctattgccagCTTACTGGAACAATGATAAGGAAGAAACTCAAAAGTGCGATTCAGTTGATATATCTATTGCTGTTGCTACAGAGAAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agctctcttcagtctccacttttgaagattttatgtattttgcatctattgccagCTTACTGGAACAATGATAAGGAAGAAACTCAAAAGTGCGATTCAGTTGATATATCTATTGCTGTTGCTACAGAGAAG
                   ttttgaagattttatg  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aagaacgctggtttctgtatgctttgtttgtttagaccagtatgtagctctcttcagtctccacttttgaagattttatgtattttgcatctattgccagCTTACTGGAACAATGATAAGGAAGAAACTCAAAAGTGCGATTCAGTTGATATATCTATTGCTGTTGCTACAGAGAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGTT
- - - gctggtt
- - - - - - - -tgtatgc
- - - - - - - - - - - - tgtttgt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ttttgca