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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttagtcttacttatcagttatcacatactaacgtgtataggcaaagcatgtcaacgcatagatgtaatttgatcttctgtagttgaccatgatgcgtcgtaacaattgcagGATCTGGAATGGGGGCAGCAGCTGTGTTCGAGCTATGTTCGGCCCGGCTGGAGGTATCGACCATCACTCGTCACTGTAACCCGATGGTGATCGACGACCG

Basic information

species Zea mays
transcript GRMZM2G143790_T01
intron # 4
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|78082844|gb|DV511237.1|DV511237
EST:     GAAGTGCCGGGGCAGAGACTGCAGATTTGGTGTTGTCCCCATGTGTATCG                         GATCTGGAATGGGGGCAGCAGCCGTGTTCGAGCTATGTTCGGCCCGGCCGG
genomic: GAAGTGCCGGGGCAGAGACTGCAGATTTGGTGTTGTCACCATGTGTATCGgttagtctta ... acaattgcagGATCTGGAATGGGGGCAGCAGCTGTGTTCGAGCTATGTTCGGCCCGGCTGG




















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), 48 (downstream exon)
Score: 326

GTGCCCGGTGCGTGGCTACTCTTCTAAATGAAATGAAGTGCCGGGGCAGAGACTGCAGATTTGGTGTTGTCACCATGTGTATCGgttagtctta ... acaattgcagGATCTGGAATGGGGGCAGCAGCTGTGTTCGAGCTATGTTCGGCCCGGCTGGAGGTATCGACCATCACTCGTCACTGTAACCCGATGGTGATCGACGACCG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 824

GTGCCCGGTGCGTGGCTACTCTTCTAAATGAAATGAAGTGCCGGGGCAGAGACTGCAGATTTGGTGTTGTCACCATGTGTATCGgttagtctta ... acaattgcagGATCTGGAATGGGGGCAGCAGCTGTGTTCGAGCTATGTTCGGCCCGGCTGGAGGTATCGACCATCACTCGTCACTGTAACCCGATGGTGATCGACGACCG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 823

GTGCCCGGTGCGTGGCTACTCTTCTAAATGAAATGAAGTGCCGGGGCAGAGACTGCAGATTTGGTGTTGTCACCATGTGTATCGgttagtctta ... acaattgcagGATCTGGAATGGGGGCAGCAGCTGTGTTCGAGCTATGTTCGGCCCGGCTGGAGGTATCGACCATCACTCGTCACTGTAACCCGATGGTGATCGACGACCG


Block sizes: 47 (upstream exon), 48 (downstream exon)
Score: 760

GTGCCCGGTGCGTGGCTACTCTTCTAAATGAAATGAAGTGCCGGGGCAGAGACTGCAGATTTGGTGTTGTCACCATGTGTATCGgttagtctta ... acaattgcagGATCTGGAATGGGGGCAGCAGCTGTGTTCGAGCTATGTTCGGCCCGGCTGGAGGTATCGACCATCACTCGTCACTGTAACCCGATGGTGATCGACGACCG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

catagatgtaatttgatcttctgtagttgaccatgatgcgtcgtaacaattgcagGATCTGGAATGGGGGCAGCAGCTGTGTTCGAGCTATGTTCGGCCCGGCTGGAGGTATCGACCATCACTCGTCACTGTAACCCGATGGTGATCGACGACCG
                                        tcgtaac  putative branch site (score: 760)
     atgtaattt  TA-rich tract