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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGAGCACGATGGGCAAGGGCATGATGTTCGTCAACGGCCAGGGCATCGGCCGCTACTGGATCTCCTACAAGCACGCCCTCGGCCGGCCATCGCAGCAGCTgtaagctctaaagctcttatagcaattcttagtttttatccactatatttatatatgctgatatgcacgcgcgtgcag

Basic information

species Zea mays
transcript GRMZM2G175779_T01
intron # 13
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|87154652|gb|DY399441.1|DY399441
EST:     CGCTACTGGATCTCCTACAAGCACGCCCTCGGCCGGCCATCGCAGCAGCT                         TTACCACGTGCCCCGGTCCTTCCTGCGGCAGAAGGACAACATGCTGGTGCT
genomic: CGCTACTGGATCTCCTACAAGCACGCCCTCGGCCGGCCATCGCAGCAGCTgtaagctcta ... gcgcgtgcagTTACCACGTGCCCCGGTCCTTCCTGCGGCAGAAGGACAACATGCTGGTGCT
EST: gi|14311435|gb|BG901190.1|BG901190
EST:     GCACGCCCTCGGCCGGCCATCGCAGCAGCT                         TTACCACGTGCCCCGGTCCTTCCTGCGGCAGAAGGACAACATGCTGGTGCT
genomic: GCACGCCCTCGGCCGGCCATCGCAGCAGCTgtaagctcta ... gcgcgtgcagTTACCACGTGCCCCGGTCCTTCCTGCGGCAGAAGGACAACATGCTGGTGCT
EST: gi|76908487|gb|DV162965.1|DV162965
EST:     CGCTACTGGATCTCCTACAAGCACGCCCTCGGCCGGCCATCGCAGCAGCT                         TTACCACGTGCCCCGGTCCTTCCTGCGGCAGAAGGACAACATGCTGGTGCT
genomic: CGCTACTGGATCTCCTACAAGCACGCCCTCGGCCGGCCATCGCAGCAGCTgtaagctcta ... gcgcgtgcagTTACCACGTGCCCCGGTCCTTCCTGCGGCAGAAGGACAACATGCTGGTGCT
EST: gi|21390502|gb|BQ528551.1|BQ528551
EST:     CGCTACTGGATCTCCTACAAGCACGCCCTCGGCCGGCCATCGCAGCAGCT                         TTACCACGTGCCCCGGTCCTTCCTGCGGCAGAAGGACAACATGCTGGTGCT
genomic: CGCTACTGGATCTCCTACAAGCACGCCCTCGGCCGGCCATCGCAGCAGCTgtaagctcta ... gcgcgtgcagTTACCACGTGCCCCGGTCCTTCCTGCGGCAGAAGGACAACATGCTGGTGCT
EST: gi|78080985|gb|DV509397.1|DV509397
EST:     CGCTACTGGATCTCCTACAAGCACGCCCTCGGCCGGCCATCGCAGCAGCT                         TTACCACGTGCCCCGGTCCTTCCTGCGGCAGAAGGACAACATGCTGGTGCT
genomic: CGCTACTGGATCTCCTACAAGCACGCCCTCGGCCGGCCATCGCAGCAGCTgtaagctcta ... gcgcgtgcagTTACCACGTGCCCCGGTCCTTCCTGCGGCAGAAGGACAACATGCTGGTGCT
EST: gi|89761736|gb|DY689632.1|DY689632
EST:     CGCTACTGGATCTCCTACAAGCACGCCCTCGGCCGGCCATCGCAGCAGCT                         TTACCACGTGCCCCGGTCCTTCCTGCGGCAGAAGGACAACATGCTGGTGCT
genomic: CGCTACTGGATCTCCTACAAGCACGCCCTCGGCCGGCCATCGCAGCAGCTgtaagctcta ... gcgcgtgcagTTACCACGTGCCCCGGTCCTTCCTGCGGCAGAAGGACAACATGCTGGTGCT
EST: gi|87155117|gb|DY399906.1|DY399906
EST:     CGCTACTGGATCTCCTACAAGCACGCCCTCGGCCGGCCATCGCAGCAGCT                         TTACCACGTGCCCCGGTCCTTCCTGCGGCAGAAGGACAACATGCTGGTGCT
genomic: CGCTACTGGATCTCCTACAAGCACGCCCTCGGCCGGCCATCGCAGCAGCTgtaagctcta ... gcgcgtgcagTTACCACGTGCCCCGGTCCTTCCTGCGGCAGAAGGACAACATGCTGGTGCT
EST: gi|76281439|gb|DV021007.1|DV021007
EST:     CGCTACTGGATCTCCTACAAGCACGCCCTCGGCCGGCCATCGCAGCAGCT                         TTACCACGTGCCCCGGTCCTTCCTGCGGCAGAAGGACAACATGCTGGTGCT
genomic: CGCTACTGGATCTCCTACAAGCACGCCCTCGGCCGGCCATCGCAGCAGCTgtaagctcta ... gcgcgtgcagTTACCACGTGCCCCGGTCCTTCCTGCGGCAGAAGGACAACATGCTGGTGCT
EST: gi|26455203|gb|CA826786.1|CA826786
EST:     CGCTACTGGATTTTCTACAAGCACGCCCTCGGCCGGCCATCGCAGCAGCT                         TTACCACGTGCCCCGGTCCTTCCTGCGGCAGAAGGACAACATGCTGGTGCT
genomic: CGCTACTGGATCTCCTACAAGCACGCCCTCGGCCGGCCATCGCAGCAGCTgtaagctcta ... gcgcgtgcagTTACCACGTGCCCCGGTCCTTCCTGCGGCAGAAGGACAACATGCTGGTGCT
EST: gi|21330726|gb|BQ486107.1|BQ486107
EST:     CGCTACTGGATCTCCTACAAGCACGCCCTCGGCCGGCCATCGCAGCAGCT                         TTACCACGTGCCCCGGTCCTTCCTGCGGCAGAAGGACAACATGCTGGTGCT
genomic: CGCTACTGGATCTCCTACAAGCACGCCCTCGGCCGGCCATCGCAGCAGCTgtaagctcta ... gcgcgtgcagTTACCACGTGCCCCGGTCCTTCCTGCGGCAGAAGGACAACATGCTGGTGCT
EST: gi|21330841|gb|BQ486222.1|BQ486222
EST:     CGCTACTGGATCTCCTACAAGCACGCCCTCGGCCGGCCATCGCAGCAGCT                         TTACCACGTGCCCCGGTCCTTCCTGCGGCAGAAGGACAACATGCTGGTGCT
genomic: CGCTACTGGATCTCCTACAAGCACGCCCTCGGCCGGCCATCGCAGCAGCTgtaagctcta ... gcgcgtgcagTTACCACGTGCCCCGGTCCTTCCTGCGGCAGAAGGACAACATGCTGGTGCT
EST: gi|21330729|gb|BQ486110.1|BQ486110
EST:     CGCTACTGGATCTCCTACAAGCACGCCCTCGGCCGGCCATCGCAGCAGCT                         TTACCACGTGCCCCGGTCCTTCCTGCGGCAGAAGGACAACATGCTGGTGCT
genomic: CGCTACTGGATCTCCTACAAGCACGCCCTCGGCCGGCCATCGCAGCAGCTgtaagctcta ... gcgcgtgcagTTACCACGTGCCCCGGTCCTTCCTGCGGCAGAAGGACAACATGCTGGTGCT
EST: gi|71756906|gb|DR954843.1|DR954843
EST:     CGCTACTGGATTTCCTACAAGCACGCCCTCGGCCGGCCATCGCAGCAGCT                         TTACCACGTGCCCCGGTCCTTCCTGCGGCAGAAGGACAACATGCTGGTGCT
genomic: CGCTACTGGATCTCCTACAAGCACGCCCTCGGCCGGCCATCGCAGCAGCTgtaagctcta ... gcgcgtgcagTTACCACGTGCCCCGGTCCTTCCTGCGGCAGAAGGACAACATGCTGGTGCT
EST: gi|21390197|gb|BQ528246.1|BQ528246
EST:     CGCTACTGGATCTCCTACAAGCACGCCCTCGGCCGGCCATCGCAGCAGCT                         TTACCACGTGCCCCGGTCCTTCCTGCGGCAGAAGGACAACATGCTGGTGCT
genomic: CGCTACTGGATCTCCTACAAGCACGCCCTCGGCCGGCCATCGCAGCAGCTgtaagctcta ... gcgcgtgcagTTACCACGTGCCCCGGTCCTTCCTGCGGCAGAAGGACAACATGCTGGTGCT
EST: gi|76280915|gb|DV020483.1|DV020483
EST:     CGCTACTGGATCTCCTACAAGCACGCCCTCGGCCGGCCATCGCAGCAGCT                         TTACCACGTGCCCCGGTCCTTCCTGCGGCAGAAGGACAACATGCTGGTGCT
genomic: CGCTACTGGATCTCCTACAAGCACGCCCTCGGCCGGCCATCGCAGCAGCTgtaagctcta ... gcgcgtgcagTTACCACGTGCCCCGGTCCTTCCTGCGGCAGAAGGACAACATGCTGGTGCT

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 1 RNA-Seqlibrary.


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 73

TGAGCACGATGGGCAAGGGCATGATGTTCGTCAACGGCCAGGGCATCGGCCGCTACTGGATCTCCTACAAGCACGCCCTCGGCCGGCCATCGCAGCAGCTgtaagctcta ... gcgcgtgcagTTACCACGTGCCCCGGTCCTTCCTGCGGCAGAAGGACAACATGCTGGTGCTGTTCGAGGAGGAGTTCGGGCGGCCGGACGCGATCATGATCCTGACGGTG




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGAGCACGATGGGCAAGGGCATGATGTTCGTCAACGGCCAGGGCATCGGCCGCTACTGGATCTCCTACAAGCACGCCCTCGGCCGGCCATCGCAGCAGCTgtaagctctaaagctcttatagcaattcttagtttttatccactatatttatatatgctgatatgcacgcgcgtgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGCT