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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatattcttttcgtctgcagaaacatacatgcatctcagttttggattattacttctgaccaggctaacttttccacttgaataacagGAACCCGCTTTACCTGTTTGCCATATTTGTGATTTATCTCGTTGGAAAAGCCATTTGGGTGCAATCAGAAATCGGCAGGGAATTCCAACACGGATTT

Basic information

species Zea mays
transcript GRMZM5G873287_T01
intron # 3
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|113702244|gb|EE679748.1|EE679748
EST:     GGCTATTCTTGGATTCAACGAGTTCATGACATTACTGAG                         GAACCCGCTTTACCTGTTTGCCATATTTGTGATTTATCTCGTTGGAAAAGC
genomic: GGCTATTCTTGGATTCAACGAGTTCATGACATTACTGAGgtatattctt ... tgaataacagGAACCCGCTTTACCTGTTTGCCATATTTGTGATTTATCTCGTTGGAAAAGC
EST: gi|78179393|gb|DV549766.1|DV549766
EST:     CTTGCTGCAATGGCTATCCTTGGATTCAACGAGTTCATGACATTACTGAG                         GAACCCGCTTTACCTGTTTGCCATATTTGTGATGTATCTCATTGGAAAAGC
genomic: CTTGCTGCAATGGCTATTCTTGGATTCAACGAGTTCATGACATTACTGAGgtatattctt ... tgaataacagGAACCCGCTTTACCTGTTTGCCATATTTGTGATTTATCTCGTTGGAAAAGC
EST: gi|29130328|gb|CB381032.1|CB381032
EST:     CTTGCTGCAATGGCTATTCTTGGATTCAACGAGNTCATGACATTACTGAG                         GAACCCGCTTTACCT
genomic: CTTGCTGCAATGGCTATTCTTGGATTCAACGAGTTCATGACATTACTGAGgtatattctt ... tgaataacagGAACCCGCTTTACCT
EST: gi|6859862|gb|AW355856.1|AW355856
EST:     CTTGCTGCAATGGCTATCCTTGGATTCAACGAGTTCATGACATTACTGAG                         GAACCCGCTTTACCTGTTTGCCATATTTGTGATGTATCTCATTGGAAAAGC
genomic: CTTGCTGCAATGGCTATTCTTGGATTCAACGAGTTCATGACATTACTGAGgtatattctt ... tgaataacagGAACCCGCTTTACCTGTTTGCCATATTTGTGATTTATCTCGTTGGAAAAGC
EST: gi|60397891|gb|DN230707.1|DN230707
EST:     CTTGCTGCAATGGCTATCCTTGGATTCAACGAGTTCATGACATTACTGAG                         GAACCCACTTTACCTGTTTGCCATATTTGTGATGTATCTCATTGGAAAAGC
genomic: CTTGCTGCAATGGCTATTCTTGGATTCAACGAGTTCATGACATTACTGAGgtatattctt ... tgaataacagGAACCCGCTTTACCTGTTTGCCATATTTGTGATTTATCTCGTTGGAAAAGC

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: 49 (upstream exon), 49 (downstream exon)
Score: 308

GAAGCAAATAAGAGGAACAACAACTGGCTACCACCTCCATGGGCACTTGCTGCAATGGCTATTCTTGGATTCAACGAGTTCATGACATTACTGAGgtatattctt ... tgaataacagGAACCCGCTTTACCTGTTTGCCATATTTGTGATTTATCTCGTTGGAAAAGCCATTTGGGTGCAATCAGAAATCGGCAGGGAATTCCAACACGGATTT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 456

GAAGCAAATAAGAGGAACAACAACTGGCTACCACCTCCATGGGCACTTGCTGCAATGGCTATTCTTGGATTCAACGAGTTCATGACATTACTGAGgtatattctt ... tgaataacagGAACCCGCTTTACCTGTTTGCCATATTTGTGATTTATCTCGTTGGAAAAGCCATTTGGGTGCAATCAGAAATCGGCAGGGAATTCCAACACGGATTT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 477

GAAGCAAATAAGAGGAACAACAACTGGCTACCACCTCCATGGGCACTTGCTGCAATGGCTATTCTTGGATTCAACGAGTTCATGACATTACTGAGgtatattctt ... tgaataacagGAACCCGCTTTACCTGTTTGCCATATTTGTGATTTATCTCGTTGGAAAAGCCATTTGGGTGCAATCAGAAATCGGCAGGGAATTCCAACACGGATTT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 399

GAAGCAAATAAGAGGAACAACAACTGGCTACCACCTCCATGGGCACTTGCTGCAATGGCTATTCTTGGATTCAACGAGTTCATGACATTACTGAGgtatattctt ... tgaataacagGAACCCGCTTTACCTGTTTGCCATATTTGTGATTTATCTCGTTGGAAAAGCCATTTGGGTGCAATCAGAAATCGGCAGGGAATTCCAACACGGATTT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tctcagttttggattattacttctgaccaggctaacttttccacttgaataacagGAACCCGCTTTACCTGTTTGCCATATTTGTGATTTATCTCGTTGGAAAAGCCATTTGGGTGCAATCAGAAATCGGCAGGGAATTCCAACACGGATTT
                             ggctaac  putative branch site (score: 399)
                                   cttttccactt  CT-rich tract
            attattactt  TA-rich tract