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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagctaaatgtttgtacatggaatactaaactgtttaacaattttcttactctttctcttttaccagTGAAGAGTTCAATTCTGGATTTGGTTCTCATACCCCAATGCTTCTTGGTCAAGCAAAAGTTATTCGCTACTATCCATATTACCAAAG

Basic information

species Zea mays
transcript GRMZM5G881605_T01
intron # 2
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|32838015|gb|CD977693.1|CD977693
EST:     AGACAAATTTCTGAACCTTGTGATCCAGTTGTTTGGGTCAATAAGCTAAG                         TGAAGAGTTCAATTCTGGATTTGGTTCTCATACCCCAATGCTTCTTGGTCA
genomic: AGACAAATTTCTGAACCTTGTGATCCAGTTGTTTGGGTCAATAAGCTAAGgtgagctaaa ... cttttaccagTGAAGAGTTCAATTCTGGATTTGGTTCTCATACCCCAATGCTTCTTGGTCA
EST: gi|32838156|gb|CD977834.1|CD977834
EST:     AGACAAATTTCTGAACCTTGTGATCCAGTTGTTTGGGTCAATAAGCTAAG                         TGAAGAGTTCAATTCTGGATTTGGTTCTCATACCCCAATGCTTCTTGGTCA
genomic: AGACAAATTTCTGAACCTTGTGATCCAGTTGTTTGGGTCAATAAGCTAAGgtgagctaaa ... cttttaccagTGAAGAGTTCAATTCTGGATTTGGTTCTCATACCCCAATGCTTCTTGGTCA
EST: gi|32836966|gb|CD976644.1|CD976644
EST:     AGACAAATTTCTGAACCTTGTGATCCAGGTGGTTGGGTCAATAAGCTAAG                         TGAAGAGTTCAATTCTGGATTTGGTTCTCATACCCCAATGCTTCTTGGTCA
genomic: AGACAAATTTCTGAACCTTGTGATCCAGTTGTTTGGGTCAATAAGCTAAGgtgagctaaa ... cttttaccagTGAAGAGTTCAATTCTGGATTTGGTTCTCATACCCCAATGCTTCTTGGTCA
EST: gi|60352092|gb|DN219065.1|DN219065
EST:     AGACAAATTTCTGAACCTTGTGATCCAGTTGTTTGGGTCAATAAGCTAAG                         TGAAGAGTTCAATTCTGGATTTGGTTCTCATACCCCAATGCTTCTTGGTCA
genomic: AGACAAATTTCTGAACCTTGTGATCCAGTTGTTTGGGTCAATAAGCTAAGgtgagctaaa ... cttttaccagTGAAGAGTTCAATTCTGGATTTGGTTCTCATACCCCAATGCTTCTTGGTCA
EST: gi|32915069|gb|CF019881.1|CF019881
EST:     AGACAAATTTCTGAACCTTGTGATCCAGTTGTTTGGGTCAATAAGCTAAG                         TGAAGAGTTCAATTCTGGATTTGGTTCTCATACCCCAATGCTTCTTGGTCA
genomic: AGACAAATTTCTGAACCTTGTGATCCAGTTGTTTGGGTCAATAAGCTAAGgtgagctaaa ... cttttaccagTGAAGAGTTCAATTCTGGATTTGGTTCTCATACCCCAATGCTTCTTGGTCA
EST: gi|32837534|gb|CD977212.1|CD977212
EST:     AGACAAATTTCTGAACCTTGTGATCCAGTTGTTTGGGTCAATAAGCTAAG                         TGAAGAGTTCAATTCTGGATTTGGTTCTCATACCCCAATGCTTCTTGGTCA
genomic: AGACAAATTTCTGAACCTTGTGATCCAGTTGTTTGGGTCAATAAGCTAAGgtgagctaaa ... cttttaccagTGAAGAGTTCAATTCTGGATTTGGTTCTCATACCCCAATGCTTCTTGGTCA
EST: gi|32838849|gb|CD978530.1|CD978530
EST:     AGACAAATTTCTGAACCTTGTGATCCAGTTGTTTGGGTCAATAAGCTAAG                         TGAAGAGTTCAATTCTGGATTTGGTTCTCATACCCCAATGCTTCTTGGTCA
genomic: AGACAAATTTCTGAACCTTGTGATCCAGTTGTTTGGGTCAATAAGCTAAGgtgagctaaa ... cttttaccagTGAAGAGTTCAATTCTGGATTTGGTTCTCATACCCCAATGCTTCTTGGTCA
EST: gi|60338386|gb|DN205359.1|DN205359
EST:     ACCTTGTGATCCAGTTGTTTGGGTCAATAAGCTAAG                         TGAAGAGTTCAATTCTGGATTTGGTTCTCATACCCCAATGCTTCTTGGTCA
genomic: ACCTTGTGATCCAGTTGTTTGGGTCAATAAGCTAAGgtgagctaaa ... cttttaccagTGAAGAGTTCAATTCTGGATTTGGTTCTCATACCCCAATGCTTCTTGGTCA
EST: gi|60344687|gb|DN211660.1|DN211660
EST:     ACCTTGTGATCCAGTTGTTTGGGTCAATAAGCTAAG                         TGAAGAGTTCAATTCTGGATTTGGTTCTCATACCCCAATGCTTCTTGGTCA
genomic: ACCTTGTGATCCAGTTGTTTGGGTCAATAAGCTAAGgtgagctaaa ... cttttaccagTGAAGAGTTCAATTCTGGATTTGGTTCTCATACCCCAATGCTTCTTGGTCA
EST: gi|60340174|gb|DN207147.1|DN207147
EST:     AGACAAATTTCTGAACCTTGTGATCCAGTTGTTTGGGTCAATAAGCTAAG                         TGAAGAGTTCAATTCTGGATTTGGTTCTCATACCCCAATGCTTCTTGGTCA
genomic: AGACAAATTTCTGAACCTTGTGATCCAGTTGTTTGGGTCAATAAGCTAAGgtgagctaaa ... cttttaccagTGAAGAGTTCAATTCTGGATTTGGTTCTCATACCCCAATGCTTCTTGGTCA

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: 47 (upstream exon), 49 (downstream exon)
Score: 100

CCGGGATCTCTCTTTCCTGGCAGGATGTCTATAACATTGCTGTTAAGTGGAGACAAATTTCTGAACCTTGTGATCCAGTTGTTTGGGTCAATAAGCTAAGgtgagctaaa ... cttttaccagTGAAGAGTTCAATTCTGGATTTGGTTCTCATACCCCAATGCTTCTTGGTCAAGCAAAAGTTATTCGCTACTATCCATATTACCAAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 93

CCGGGATCTCTCTTTCCTGGCAGGATGTCTATAACATTGCTGTTAAGTGGAGACAAATTTCTGAACCTTGTGATCCAGTTGTTTGGGTCAATAAGCTAAGgtgagctaaa ... cttttaccagTGAAGAGTTCAATTCTGGATTTGGTTCTCATACCCCAATGCTTCTTGGTCAAGCAAAAGTTATTCGCTACTATCCATATTACCAAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 117

CCGGGATCTCTCTTTCCTGGCAGGATGTCTATAACATTGCTGTTAAGTGGAGACAAATTTCTGAACCTTGTGATCCAGTTGTTTGGGTCAATAAGCTAAGgtgagctaaa ... cttttaccagTGAAGAGTTCAATTCTGGATTTGGTTCTCATACCCCAATGCTTCTTGGTCAAGCAAAAGTTATTCGCTACTATCCATATTACCAAAG


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 82

CCGGGATCTCTCTTTCCTGGCAGGATGTCTATAACATTGCTGTTAAGTGGAGACAAATTTCTGAACCTTGTGATCCAGTTGTTTGGGTCAATAAGCTAAGgtgagctaaa ... cttttaccagTGAAGAGTTCAATTCTGGATTTGGTTCTCATACCCCAATGCTTCTTGGTCAAGCAAAAGTTATTCGCTACTATCCATATTACCAAAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgtacatggaatactaaactgtttaacaattttcttactctttctcttttaccagTGAAGAGTTCAATTCTGGATTTGGTTCTCATACCCCAATGCTTCTTGGTCAAGCAAAAGTTATTCGCTACTATCCATATTACCAAAG
                          caattttcttactctt  CT-rich tract
                     tttaacaattttctta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagctaaatgtttgtacatggaatactaaactgtttaacaattttcttactctttctcttttaccagTGAAGAGTTCAATTCTGGATTTGGTTCTCATACCCCAATGCTTCTTGGTCAAGCAAAAGTTATTCGCTACTATCCATATTACCAAAG

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