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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagttgcctccggtccctccgtctcgtcaaatttgctacttgctagcagtgctctgtgtcttatagtatcggatggtggctattgaaactattctctctcgagtattatctaattacatgagctgtgattctttctccttttggaatctagATTGCTATTGCTACAACTACAACTTAGGCTATCTCCTCATATTCAAACACGTTGCAAAAGAGCGTAGACTACGTTGCAAAACAATGTTTTGGATGATCTG

Basic information

species Zea mays
transcript GRMZM2G133082_T04
intron # 1
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|33098562|gb|CF058522.1|CF058522
EST:     GCCGACGCCGGGATGGACGCCGTCCAGCGGCGGCTCATGTTTGAGGACGA                         ATTGCTATTGCTACAACTACAACTTAGGCTATCTCCTCATATTCAAACACG
genomic: GCCGACGCCGGGATGGACGCCGTCCAGCGGCGGCTCATGTTTGAGGACGAgtgagttgcc ... tggaatctagATTGCTATTGCTACAACTACAACTTAGGCTATCTCCTCATATTCAAACACG
EST: gi|50332608|gb|CO527734.1|CO527734
EST:     GCCGACGCCGGGATGGACGCCGTCCAGCGGCGGCTCATGTTTGAGGACGA                         ATTGCTATTGCTACAACTACAACTTAGGCTATCTCCTCATATTCAAACACG
genomic: GCCGACGCCGGGATGGACGCCGTCCAGCGGCGGCTCATGTTTGAGGACGAgtgagttgcc ... tggaatctagATTGCTATTGCTACAACTACAACTTAGGCTATCTCCTCATATTCAAACACG

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 2 RNA-Seq libraries.


Block sizes: 39 (upstream exon), 11 (downstream exon)
Score: 2

CCTCCGCAGGGGGCGCCGTGATGGGGAAGCCAGGCCCCGGGGTCGTTGACGCCGACGCCGGGATGGACGCCGTCCAGCGGCGGCTCATGTTTGAGGACGAgtgagttgcc ... tggaatctagATTGCTATTGCTACAACTACAACTTAGGCTATCTCCTCATATTCAAACACGTTGCAAAAGAGCGTAGACTACGTTGCAAAACAATGTTTTGGATGATCTG


Block sizes: 43 (upstream exon), 26 (downstream exon)
Score: 2

CCTCCGCAGGGGGCGCCGTGATGGGGAAGCCAGGCCCCGGGGTCGTTGACGCCGACGCCGGGATGGACGCCGTCCAGCGGCGGCTCATGTTTGAGGACGAgtgagttgcc ... tggaatctagATTGCTATTGCTACAACTACAACTTAGGCTATCTCCTCATATTCAAACACGTTGCAAAAGAGCGTAGACTACGTTGCAAAACAATGTTTTGGATGATCTG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tctcgagtattatctaattacatgagctgtgattctttctccttttggaatctagATTGCTATTGCTACAACTACAACTTAGGCTATCTCCTCATATTCAAACACGTTGCAAAAGAGCGTAGACTACGTTGCAAAACAATGTTTTGGATGATCTG
           atctaat  putative branch site (score: 2)
                             tgattctttctccttt  putative PPT
       tattatctaattacat  TA-rich tract