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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgaagtgatgacatgctattagtcaacagtctattgtgatagctggtgttggggaactgggctgcttgatgctaactctcttctgttaatttggaggatttgtagATATCAAAGCACGCACCAAGGGTCACCCTGTCGGTTGAAACAGAAGGTCACACACATGGTTACTGCTGTACAGAGGCTGGATCTGTCTGGGTTGCAGACT

Basic information

species Zea mays
transcript GRMZM2G133959_T03
intron # 11
splice site 3'
intron type U2

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|211416883|gb|FL440253.1|FL440253
EST:     TTTTGTTCGGTGTGGATGATCACTGGGGCCCACTATCTCACTTAGAAGAG                         ATATCAAAGCACGCACCAAGGGTCACCCTGTCGGTTGAAACAGAAGGTCAC
genomic: TTTTGTTCGGTGTGGATGATCACTGGGGCCCACTATCTCACTTAGAAGAGgtgaagtgat ... ggatttgtagATATCAAAGCACGCACCAAGGGTCACCCTGTCGGTTGAAACAGAAGGTCAC
EST: gi|12058307|gb|BF729165.2|BF729165
EST:     TTTTGTTCGGTGTGGATGATCACTGGGGCCCACTATCTCACTTAGAAGAG                         ATATCAAAGCACGCACCAAGGGTCACCCTGTCGGTTGAAACAGAAGATAAA
genomic: TTTTGTTCGGTGTGGATGATCACTGGGGCCCACTATCTCACTTAGAAGAGgtgaagtgat ... ggatttgtagATATCAAAGCACGCACCAAGGGTCACCCTGTCGGTTGAAACAGAAGGTCAC
EST: gi|71445212|gb|DR826262.1|DR826262
EST:     TTTTGTTCGGTGTGGATGATCACTGGGGCCCCCTATCTCACTTAGAAGAG                         ATATCAAAGCACGCCCCAAGGGTCACCCTGTCGGTTGAAACAGAAGGTCAC
genomic: TTTTGTTCGGTGTGGATGATCACTGGGGCCCACTATCTCACTTAGAAGAGgtgaagtgat ... ggatttgtagATATCAAAGCACGCACCAAGGGTCACCCTGTCGGTTGAAACAGAAGGTCAC
EST: gi|113842859|gb|DW969810.1|DW969810
EST:     TCTCACTTAGAAGAG                         ATATCAAAGCACGCACCAAGGGTCACCCTGTCGGTTGAAACAGAAGGTCAC
genomic: TCTCACTTAGAAGAGgtgaagtgat ... ggatttgtagATATCAAAGCACGCACCAAGGGTCACCCTGTCGGTTGAAACAGAAGGTCAC
EST: gi|78179633|gb|DV550006.1|DV550006
EST:     TTTTGTTCGGTGTGGATGATCACTGGGGCCCACTATCTCACTTAGAAGAG                         ATATCAAAGCACGCACCAAGGGTCACCCTGTCGGTTGAAACAGAAGGTCAC
genomic: TTTTGTTCGGTGTGGATGATCACTGGGGCCCACTATCTCACTTAGAAGAGgtgaagtgat ... ggatttgtagATATCAAAGCACGCACCAAGGGTCACCCTGTCGGTTGAAACAGAAGGTCAC
EST: gi|8383032|gb|BE055915.1|BE055915
EST:     TTTTGTTCGGTGTGGATGATCACTGGGGCCCACTATCTCACTTAGAAGAG                         ATATCAAAGCACGCACCAAGGGTCACCCTGTCGGTTGAAACAGAAGGTCAC
genomic: TTTTGTTCGGTGTGGATGATCACTGGGGCCCACTATCTCACTTAGAAGAGgtgaagtgat ... ggatttgtagATATCAAAGCACGCACCAAGGGTCACCCTGTCGGTTGAAACAGAAGGTCAC
EST: gi|78080386|gb|DV508798.1|DV508798
EST:     TTTTGTTCGGTGTGGATGATCACTGGGGCCCCCTATCTCACTTAGAAGAG                         ATATCAAAGCACGCACCAAGGGTCACCCTGTCGGTTGAAACAGAAGGTCAC
genomic: TTTTGTTCGGTGTGGATGATCACTGGGGCCCACTATCTCACTTAGAAGAGgtgaagtgat ... ggatttgtagATATCAAAGCACGCACCAAGGGTCACCCTGTCGGTTGAAACAGAAGGTCAC
EST: gi|76290046|gb|DV029614.1|DV029614
EST:     TTTTGTTCGGTGTGGATGATCACTGGGGCCCACTATCTCACTTAGAAGAG                         ATATCAAAGCACGCCCCAAGGGTCACCCTGTCGGTTGAAACAGAAGGTCAC
genomic: TTTTGTTCGGTGTGGATGATCACTGGGGCCCACTATCTCACTTAGAAGAGgtgaagtgat ... ggatttgtagATATCAAAGCACGCACCAAGGGTCACCCTGTCGGTTGAAACAGAAGGTCAC
EST: gi|71431548|gb|DR812598.1|DR812598
EST:     TTTTGTTCGGTGTGGATGATCACTGGGGCCCACTATCTCACTTAGAAGAG                         ATATCAAAGCACGCACCAAGGGTCACCCTGTCGGTTGAAACAGAAGGTCAC
genomic: TTTTGTTCGGTGTGGATGATCACTGGGGCCCACTATCTCACTTAGAAGAGgtgaagtgat ... ggatttgtagATATCAAAGCACGCACCAAGGGTCACCCTGTCGGTTGAAACAGAAGGTCAC
EST: gi|9954002|gb|BE640600.1|BE640600
EST:     TTTTGTTCGGTGTGGATGATCACTGGGGCCCACTATCTCACTTAGAAGAG                         ATATCAAAGCACGCACCAAGGGTCACCCTGTCGGTTGAACCAGAAGGTCAC
genomic: TTTTGTTCGGTGTGGATGATCACTGGGGCCCACTATCTCACTTAGAAGAGgtgaagtgat ... ggatttgtagATATCAAAGCACGCACCAAGGGTCACCCTGTCGGTTGAAACAGAAGGTCAC

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: 41 (upstream exon), 49 (downstream exon)
Score: 24

TGAAGAACCAGACTGGACTTTCATCAGAGCACAAGAGGACAAAATGGCCTTTTTGTTCGGTGTGGATGATCACTGGGGCCCACTATCTCACTTAGAAGAGgtgaagtgat ... ggatttgtagATATCAAAGCACGCACCAAGGGTCACCCTGTCGGTTGAAACAGAAGGTCACACACATGGTTACTGCTGTACAGAGGCTGGATCTGTCTGGGTTGCAGACT


Block sizes: 42 (upstream exon), 48 (downstream exon)
Score: 13

TGAAGAACCAGACTGGACTTTCATCAGAGCACAAGAGGACAAAATGGCCTTTTTGTTCGGTGTGGATGATCACTGGGGCCCACTATCTCACTTAGAAGAGgtgaagtgat ... ggatttgtagATATCAAAGCACGCACCAAGGGTCACCCTGTCGGTTGAAACAGAAGGTCACACACATGGTTACTGCTGTACAGAGGCTGGATCTGTCTGGGTTGCAGACT


Block sizes: 41 (upstream exon), 45 (downstream exon)
Score: 20

TGAAGAACCAGACTGGACTTTCATCAGAGCACAAGAGGACAAAATGGCCTTTTTGTTCGGTGTGGATGATCACTGGGGCCCACTATCTCACTTAGAAGAGgtgaagtgat ... ggatttgtagATATCAAAGCACGCACCAAGGGTCACCCTGTCGGTTGAAACAGAAGGTCACACACATGGTTACTGCTGTACAGAGGCTGGATCTGTCTGGGTTGCAGACT


Block sizes: 49 (upstream exon), 36 (downstream exon)
Score: 16

TGAAGAACCAGACTGGACTTTCATCAGAGCACAAGAGGACAAAATGGCCTTTTTGTTCGGTGTGGATGATCACTGGGGCCCACTATCTCACTTAGAAGAGgtgaagtgat ... ggatttgtagATATCAAAGCACGCACCAAGGGTCACCCTGTCGGTTGAAACAGAAGGTCACACACATGGTTACTGCTGTACAGAGGCTGGATCTGTCTGGGTTGCAGACT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ggggaactgggctgcttgatgctaactctcttctgttaatttggaggatttgtagATATCAAAGCACGCACCAAGGGTCACCCTGTCGGTTGAAACAGAAGGTCACACACATGGTTACTGCTGTACAGAGGCTGGATCTGTCTGGGTTGCAGACT
                                 tgttaattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgaagtgatgacatgctattagtcaacagtctattgtgatagctggtgttggggaactgggctgcttgatgctaactctcttctgttaatttggaggatttgtagATATCAAAGCACGCACCAAGGGTCACCCTGTCGGTTGAAACAGAAGGTCACACACATGGTTACTGCTGTACAGAGGCTGGATCTGTCTGGGTTGCAGACT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGGA