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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgattcttcagtgcttggactgctgcagtaactactttgttaagtcatatagtatctttttttttcccactgaaacgcaacatttggattacagTATTTATTGGAAAGGCGAAGATGACGTGGCAGTTGCTGGTCTGGGAGGTGAATCAGAGGTCCATCCTTACGTCTCATTCACCATAAACTTTGTTTGAGCA

Basic information

species Zea mays
transcript GRMZM2G177912_T01
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|148969237|gb|EE019991.2|EE019991
EST:     GAGAAGAAAGTGAGGAGCATTTTAGAGGACCTTTGCGGCAATGTCCATAG                         TATTTATTGGAAAGGCGAAGATGACGTGGCAGTTGCTGGTTTGGGAGGTGA
genomic: GAGAAGAAAGTGAGGAGCATCTTAGAGGACCTTTGCGGCAATGTCCATAGgtgattcttc ... tggattacagTATTTATTGGAAAGGCGAAGATGACGTGGCAGTTGCTGGTCTGGGAGGTGA
EST: gi|76288289|gb|DV027857.1|DV027857
EST:     GAGAAGAAAGTGAGGAGCATCTTAGAGGACCTTTGCGGCAATGTCCATAG                         TATTTATTGGAAAGGCGAAGATGACGTGGCAGTTGCTGGTCTGGGAGGTGA
genomic: GAGAAGAAAGTGAGGAGCATCTTAGAGGACCTTTGCGGCAATGTCCATAGgtgattcttc ... tggattacagTATTTATTGGAAAGGCGAAGATGACGTGGCAGTTGCTGGTCTGGGAGGTGA
EST: gi|211233368|gb|FL465080.1|FL465080
EST:     GAGAAGAAAGTAAGGAGCATCTTAGAGGACCTTTGCGGCAATGTCCATAG                         TATTTATTGGAAAGGCGAAGATGACGTGGCAGTTGCTGGTCTGGAAGGTGA
genomic: GAGAAGAAAGTGAGGAGCATCTTAGAGGACCTTTGCGGCAATGTCCATAGgtgattcttc ... tggattacagTATTTATTGGAAAGGCGAAGATGACGTGGCAGTTGCTGGTCTGGGAGGTGA
EST: gi|60338311|gb|DN205284.1|DN205284
EST:     GAGAAGAAAGTGAGGAGCATCTTAGAGGACCTTTGCGGCAATGTCCATAG                         TATTTATTGGAAAGGCGAAGATGACGTGGCAGTTGCTGGTCTGGGAGGTGA
genomic: GAGAAGAAAGTGAGGAGCATCTTAGAGGACCTTTGCGGCAATGTCCATAGgtgattcttc ... tggattacagTATTTATTGGAAAGGCGAAGATGACGTGGCAGTTGCTGGTCTGGGAGGTGA
EST: gi|60340364|gb|DN207337.1|DN207337
EST:     GAGAAGAAAGTGAGGAGCATCTTAGAGGACCTTTGCGGCAATGTCCATAG                         TATTTATTGGAAAGGCGAAGATGACGTGGCAGTTGCTGGTCTGGGAGGTGA
genomic: GAGAAGAAAGTGAGGAGCATCTTAGAGGACCTTTGCGGCAATGTCCATAGgtgattcttc ... tggattacagTATTTATTGGAAAGGCGAAGATGACGTGGCAGTTGCTGGTCTGGGAGGTGA
EST: gi|37397643|gb|CF636126.1|CF636126
EST:     GAGAAGAAAGTGAGGAGCATCTTAGAGGACCTTTGCGGCAATGTCCATAG                         TATTTATTGGAAAGGCGAAGATGACGTGGCAGTTGCTGGTCTGGGAGGTGA
genomic: GAGAAGAAAGTGAGGAGCATCTTAGAGGACCTTTGCGGCAATGTCCATAGgtgattcttc ... tggattacagTATTTATTGGAAAGGCGAAGATGACGTGGCAGTTGCTGGTCTGGGAGGTGA
EST: gi|211430021|gb|FL445207.1|FL445207
EST:     GAGAAGAAAGTAAGGAGCATCTTAGAGGACCTTTGCGGCAATGTCCATAG                         TATTTATTGGAAAGGCGAAGATGACGTGGCAGTTGCTGGTCTGGGAGGTGA
genomic: GAGAAGAAAGTGAGGAGCATCTTAGAGGACCTTTGCGGCAATGTCCATAGgtgattcttc ... tggattacagTATTTATTGGAAAGGCGAAGATGACGTGGCAGTTGCTGGTCTGGGAGGTGA
EST: gi|71327561|gb|DR800389.1|DR800389
EST:     GAGAAGAAAGTGAGGAGCATCTTAGAGGACCTTTGCGGCAATGTCCATAG                         TATTTATTGGAAAGGCGAAGATGACGTGGCAGTTGCTGGTCTGGGAGGTGA
genomic: GAGAAGAAAGTGAGGAGCATCTTAGAGGACCTTTGCGGCAATGTCCATAGgtgattcttc ... tggattacagTATTTATTGGAAAGGCGAAGATGACGTGGCAGTTGCTGGTCTGGGAGGTGA
EST: gi|40337132|gb|CK371202.1|CK371202
EST:     GAGAAGAAAGTGAGGAGCATCTTAGAGGACCTTTGCGGCAATGTCCATAG                         TATTTATTGGAAAGGCGAAGATGACGTGGCAGTTGCTGGTCTGGGAGGTGA
genomic: GAGAAGAAAGTGAGGAGCATCTTAGAGGACCTTTGCGGCAATGTCCATAGgtgattcttc ... tggattacagTATTTATTGGAAAGGCGAAGATGACGTGGCAGTTGCTGGTCTGGGAGGTGA
EST: gi|78120130|gb|DV538514.1|DV538514
EST:     GAGAAGAAAGTGAGGAGCATCTTAGAGGACCTTTGCGGCAATGTCCATAG                         TATTTATTGGAAAGGCGAAGATGACGTGGCAGTTGCTGGTCTGGGAGGTGA
genomic: GAGAAGAAAGTGAGGAGCATCTTAGAGGACCTTTGCGGCAATGTCCATAGgtgattcttc ... tggattacagTATTTATTGGAAAGGCGAAGATGACGTGGCAGTTGCTGGTCTGGGAGGTGA

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), 47 (downstream exon)
Score: 110

TCTGCCGTTCTTGCTCCGTCTACAAAGGGCGAGAAGAAAGTGAGGAGCATCTTAGAGGACCTTTGCGGCAATGTCCATAGgtgattcttc ... tggattacagTATTTATTGGAAAGGCGAAGATGACGTGGCAGTTGCTGGTCTGGGAGGTGAATCAGAGGTCCATCCTTACGTCTCATTCACCATAAACTTTGTTTGAGCA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 178

TCTGCCGTTCTTGCTCCGTCTACAAAGGGCGAGAAGAAAGTGAGGAGCATCTTAGAGGACCTTTGCGGCAATGTCCATAGgtgattcttc ... tggattacagTATTTATTGGAAAGGCGAAGATGACGTGGCAGTTGCTGGTCTGGGAGGTGAATCAGAGGTCCATCCTTACGTCTCATTCACCATAAACTTTGTTTGAGCA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 205

TCTGCCGTTCTTGCTCCGTCTACAAAGGGCGAGAAGAAAGTGAGGAGCATCTTAGAGGACCTTTGCGGCAATGTCCATAGgtgattcttc ... tggattacagTATTTATTGGAAAGGCGAAGATGACGTGGCAGTTGCTGGTCTGGGAGGTGAATCAGAGGTCCATCCTTACGTCTCATTCACCATAAACTTTGTTTGAGCA


Block sizes: 48 (upstream exon), 45 (downstream exon)
Score: 105

TCTGCCGTTCTTGCTCCGTCTACAAAGGGCGAGAAGAAAGTGAGGAGCATCTTAGAGGACCTTTGCGGCAATGTCCATAGgtgattcttc ... tggattacagTATTTATTGGAAAGGCGAAGATGACGTGGCAGTTGCTGGTCTGGGAGGTGAATCAGAGGTCCATCCTTACGTCTCATTCACCATAAACTTTGTTTGAGCA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttaagtcatatagtatctttttttttcccactgaaacgcaacatttggattacagTATTTATTGGAAAGGCGAAGATGACGTGGCAGTTGCTGGTCTGGGAGGTGAATCAGAGGTCCATCCTTACGTCTCATTCACCATAAACTTTGTTTGAGCA
     tcatatagtatctttt  TA-rich tract