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 5'  3'   		2  
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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGCGCTGGGTCAACTACCTCCACCCTGGCCTCAAGCGTGGGCGCATGTCTCCCCATGAAGAGCGACTCATCCTAGAGCTGCACGCTCGGTGGGGAAACAGgtctgattaccaaaagataataaaaaaggacggtttttctctctctctctaaaatttgttgacatgttcaataacttgtcctaaacag

Basic information

species Zea mays
transcript GRMZM2G130149_T06
intron # 2
splice site 5'
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|113702347|gb|EE679851.1|EE679851
EST:     CCCCATGAAGAGCGACTCATCCTAGAGCTGCACGCTCGGTGGGGAAACAG                         GTGGTCCAGGATAGCACGCCGCTTGCCAGGGCGCACTGACAATGAGATCAA
genomic: CCCCATGAAGAGCGACTCATCCTAGAGCTGCACGCTCGGTGGGGAAACAGgtctgattac ... tcctaaacagGTGGTCCAGGATAGCACGCCGCTTGCCAGGGCGCACTGACAATGAGATCAA
EST: gi|78543921|gb|DV621419.1|DV621419
EST:     TAGAGCTGCACGCTCGGTGGGGAAACAG                         GTGGTCCAGGATAGCACGCCGCTTGCCAGGGCGCACTGACAATGAGATCAA
genomic: TAGAGCTGCACGCTCGGTGGGGAAACAGgtctgattac ... tcctaaacagGTGGTCCAGGATAGCACGCCGCTTGCCAGGGCGCACTGACAATGAGATCAA
EST: gi|94475219|gb|EB704177.1|EB704177
EST:     CTCCATGAAGAGCGACTCATCCTAGAGCTGCACGCTCGGTGGGGAAACAG                         GTGGTCCAGGATAGCACGCCGCTTGCCAGGGCGCACTGACAATGAGATCAA
genomic: CCCCATGAAGAGCGACTCATCCTAGAGCTGCACGCTCGGTGGGGAAACAGgtctgattac ... tcctaaacagGTGGTCCAGGATAGCACGCCGCTTGCCAGGGCGCACTGACAATGAGATCAA
EST: gi|67026346|gb|CO455095.1|CO455095
EST:     CCCCATGAAGAGCGACTCATCCTAGAGCTGCACGCTCGGTGGGGAAACAG                         GTGGTCCAGGATAGCACGCCGCTTGCCAGGGCGCACTGACAATGAGATCAA
genomic: CCCCATGAAGAGCGACTCATCCTAGAGCTGCACGCTCGGTGGGGAAACAGgtctgattac ... tcctaaacagGTGGTCCAGGATAGCACGCCGCTTGCCAGGGCGCACTGACAATGAGATCAA
EST: gi|78104874|gb|DV523292.1|DV523292
EST:     CCCCATGAAGAGCGACTCATCCTAGAGCTGCACGCTCGGTGGGGAAACAG                         GTGGTCCAGGATAGCACGCCGCTTGCCAGGGCGCACTGACAATGAGATCAA
genomic: CCCCATGAAGAGCGACTCATCCTAGAGCTGCACGCTCGGTGGGGAAACAGgtctgattac ... tcctaaacagGTGGTCCAGGATAGCACGCCGCTTGCCAGGGCGCACTGACAATGAGATCAA
EST: gi|32851249|gb|CD990930.1|CD990930
EST:     CCCCATGAAGAGCGACTCATCCTAGAGCTGCACGCTCGGTGGGGAAACAG                         GTGGTCCAGGATAGCACGCCGCTTGCCAGGGCGCACTGACAATGAGATCAA
genomic: CCCCATGAAGAGCGACTCATCCTAGAGCTGCACGCTCGGTGGGGAAACAGgtctgattac ... tcctaaacagGTGGTCCAGGATAGCACGCCGCTTGCCAGGGCGCACTGACAATGAGATCAA
EST: gi|76911847|gb|DV164463.1|DV164463
EST:     CCCCATGAAGAGCGACTCATCCTAGAGCTGCACGCTCGGTGGGGAAACAG                         GTGGTCCAGGATAGCACGCCGCTTGCCAGGGCGCACTGACAATGAGATCAA
genomic: CCCCATGAAGAGCGACTCATCCTAGAGCTGCACGCTCGGTGGGGAAACAGgtctgattac ... tcctaaacagGTGGTCCAGGATAGCACGCCGCTTGCCAGGGCGCACTGACAATGAGATCAA
EST: gi|67012428|gb|CO441177.1|CO441177
EST:     CCCCATGAAGAGCGACTCATCCTAGAGCTGCACGCTCGGTGGGGAAACAG                         GTGGTCCAGGATAGCACGCCGCTTGCCAGGGCGCACTGACAATGAGATCAA
genomic: CCCCATGAAGAGCGACTCATCCTAGAGCTGCACGCTCGGTGGGGAAACAGgtctgattac ... tcctaaacagGTGGTCCAGGATAGCACGCCGCTTGCCAGGGCGCACTGACAATGAGATCAA
EST: gi|23357664|gb|BU645313.1|BU645313
EST:     CCCCATGAAGAGCGACTCATCCTAGAGCTGCACGCTCGGTGGGGAAACAG                         GTGGTCCAGGATAGCACGCCGCTTGCCAGGGCGCACTGACAATGAGATCAA
genomic: CCCCATGAAGAGCGACTCATCCTAGAGCTGCACGCTCGGTGGGGAAACAGgtctgattac ... tcctaaacagGTGGTCCAGGATAGCACGCCGCTTGCCAGGGCGCACTGACAATGAGATCAA
EST: gi|20811250|gb|BQ295728.1|BQ295728
EST:     CCCCATGAAGAGCGACTCATCCTAGAGCTGCACGCTCGGTGGGGAAACAG                         GTGGTCCAGGATAGCACGCCGCTTGCCAGGGCGCACTGACAATGAGATCAA
genomic: CCCCATGAAGAGCGACTCATCCTAGAGCTGCACGCTCGGTGGGGAAACAGgtctgattac ... tcctaaacagGTGGTCCAGGATAGCACGCCGCTTGCCAGGGCGCACTGACAATGAGATCAA
EST: gi|71308212|gb|DR790338.1|DR790338
EST:     CCCCATGAAGAGCGACTCATCCTAGAGCTGCACGCTCGGTGGGGAAACAG                         GTGGTCCAGGATAGCACGCCGCTTGCCAGGGCGCACTGACAATGAGATCAA
genomic: CCCCATGAAGAGCGACTCATCCTAGAGCTGCACGCTCGGTGGGGAAACAGgtctgattac ... tcctaaacagGTGGTCCAGGATAGCACGCCGCTTGCCAGGGCGCACTGACAATGAGATCAA
EST: gi|22473234|gb|BU037714.1|BU037714
EST:     CCCCATGAAGAGCGACTCATCCTAGAGCTGCACGCTCGGTGGGGAAACAG                         GTGGTCCAGGATAGCACGCCGCTTGCCAGGGCGCACTGACAATGAGATCAA
genomic: CCCCATGAAGAGCGACTCATCCTAGAGCTGCACGCTCGGTGGGGAAACAGgtctgattac ... tcctaaacagGTGGTCCAGGATAGCACGCCGCTTGCCAGGGCGCACTGACAATGAGATCAA
EST: gi|71315567|gb|DR794388.1|DR794388
EST:     CACGCTCGGTGGGGAAACAG                         GTGGTCCAGGATAGCACGCCGCTTGCCAGGGCGCACTGACAATGAGATCAA
genomic: CACGCTCGGTGGGGAAACAGgtctgattac ... tcctaaacagGTGGTCCAGGATAGCACGCCGCTTGCCAGGGCGCACTGACAATGAGATCAA
EST: gi|26457517|gb|CA829100.1|CA829100
EST:     CCCCATGAAGAGCGACTCATCCTAGAGCTGCACGCTCGGTGGGGAAACAG                         GTGGTCCAGGATAGCACGCCGCTTGCCAGGGCGCACTGACAATGAGATCAA
genomic: CCCCATGAAGAGCGACTCATCCTAGAGCTGCACGCTCGGTGGGGAAACAGgtctgattac ... tcctaaacagGTGGTCCAGGATAGCACGCCGCTTGCCAGGGCGCACTGACAATGAGATCAA

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: 82

TGCGCTGGGTCAACTACCTCCACCCTGGCCTCAAGCGTGGGCGCATGTCTCCCCATGAAGAGCGACTCATCCTAGAGCTGCACGCTCGGTGGGGAAACAGgtctgattac ... tcctaaacagGTGGTCCAGGATAGCACGCCGCTTGCCAGGGCGCACTGACAATGAGATCAAGAACTACTGGAGGACACACATGAGAAAGAAGGCACAGGAGAGGAAGAGG


Block sizes: 47 (upstream exon), 48 (downstream exon)
Score: 14

TGCGCTGGGTCAACTACCTCCACCCTGGCCTCAAGCGTGGGCGCATGTCTCCCCATGAAGAGCGACTCATCCTAGAGCTGCACGCTCGGTGGGGAAACAGgtctgattac ... tcctaaacagGTGGTCCAGGATAGCACGCCGCTTGCCAGGGCGCACTGACAATGAGATCAAGAACTACTGGAGGACACACATGAGAAAGAAGGCACAGGAGAGGAAGAGG


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 62

TGCGCTGGGTCAACTACCTCCACCCTGGCCTCAAGCGTGGGCGCATGTCTCCCCATGAAGAGCGACTCATCCTAGAGCTGCACGCTCGGTGGGGAAACAGgtctgattac ... tcctaaacagGTGGTCCAGGATAGCACGCCGCTTGCCAGGGCGCACTGACAATGAGATCAAGAACTACTGGAGGACACACATGAGAAAGAAGGCACAGGAGAGGAAGAGG


Block sizes: 42 (upstream exon), 49 (downstream exon)
Score: 30

TGCGCTGGGTCAACTACCTCCACCCTGGCCTCAAGCGTGGGCGCATGTCTCCCCATGAAGAGCGACTCATCCTAGAGCTGCACGCTCGGTGGGGAAACAGgtctgattac ... tcctaaacagGTGGTCCAGGATAGCACGCCGCTTGCCAGGGCGCACTGACAATGAGATCAAGAACTACTGGAGGACACACATGAGAAAGAAGGCACAGGAGAGGAAGAGG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGCGCTGGGTCAACTACCTCCACCCTGGCCTCAAGCGTGGGCGCATGTCTCCCCATGAAGAGCGACTCATCCTAGAGCTGCACGCTCGGTGGGGAAACAGgtctgattaccaaaagataataaaaaaggacggtttttctctctctctctaaaatttgttgacatgttcaataacttgtcctaaacag

- - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGC