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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaggtcagttttacaaataattgtttcaccctcagatccaatctttttttccttttgccttacattttgatatctcgtacagGTAAATTGGAAAACTGATTTAAGTATTCATTGTGGTGCTGTTGTGACTATGGGGTAACACCGTAACAGTGCAGCATATAGGATAGTAATAGATTGTCTGC

Basic information

species Zea mays
transcript GRMZM2G108364_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|6526816|gb|AW216085.1|AW216085
EST:     CCAAACAATAAGGTCTTAGGAGAGAATGGCCTCATGTTGGTCATAGCATG                         GTAAATTGGAAAACTGATTTAAGTATTCATTGTGGTGCTGTTGTGACTATG
genomic: CCAAACAATAAGGTCTTAGGAGAGAATGGCCTCATGTTGGTCATAGCATGgtaaggtcag ... tctcgtacagGTAAATTGGAAAACTGATTTAAGTATTCATTGTGGTGCTGTTGTGACTATG
EST: gi|211391902|gb|FL468029.1|FL468029
EST:     TTAGGAGAGAATGGCCTCATGTTGGTCATAGCATG                         GTAAATTGGAAAACTKATTTAAGTATTCATTGTGGYTGCTGTTGTGACTAT
genomic: TTAGGAGAGAATGGCCTCATGTTGGTCATAGCATGgtaaggtcag ... tctcgtacagGTAAATTGGAAAACTGATTTAAGTATTCATTGTGG-TGCTGTTGTGACTAT
EST: gi|86468836|gb|DY235206.1|DY235206
EST:     CCAAACAATAAGGTCTTAGGAGAGAATGGCCTCATGTTGGTCATAGCATG                         GTAAATTGGAAAACTGATTTAAGTATTCATTGTGGTGCTGTTGTGACTATG
genomic: CCAAACAATAAGGTCTTAGGAGAGAATGGCCTCATGTTGGTCATAGCATGgtaaggtcag ... tctcgtacagGTAAATTGGAAAACTGATTTAAGTATTCATTGTGGTGCTGTTGTGACTATG
EST: gi|6827711|gb|AW331354.1|AW331354
EST:     AAGGTCTTAGGAGAGAATGGCCTCATGTTGGTCATAGCATG                         GTAAATTGGAAAACTGATTTAAGTATTCATTGTGGTGCTGTTGTGACTATG
genomic: AAGGTCTTAGGAGAGAATGGCCTCATGTTGGTCATAGCATGgtaaggtcag ... tctcgtacagGTAAATTGGAAAACTGATTTAAGTATTCATTGTGGTGCTGTTGTGACTATG
EST: gi|76921088|gb|DV168449.1|DV168449
EST:     CCAAACAATAAGGTCTTAGGAGAGAATGGCCTCATGTTGGTCATAGCATGGTAAG                     
genomic: CCAAACAATAAGGTCTTAGGAGAGAATGGCCTCATGTTGGTCATAGCA---T--Ggtaaggtcag ... tctcgt
EST: gi|12972747|gb|BG268136.1|BG268136
EST:     CCAAACAATAAGGTCTTAGGAGAGAATGGCCTCATGTTGGTCATAGCATG                         GTAAATTGGAAAACTGATTTAAGTATTCATTGTGGTGCTGTTGTGACTATG
genomic: CCAAACAATAAGGTCTTAGGAGAGAATGGCCTCATGTTGGTCATAGCATGgtaaggtcag ... tctcgtacagGTAAATTGGAAAACTGATTTAAGTATTCATTGTGGTGCTGTTGTGACTATG
EST: gi|149072983|gb|EE161244.2|EE161244
EST:     CCAAACAATAAGGTCTTAGGAGAGAATGGCCTCATGTTGGTCATAGCATG                         GTAAATTGGAAAACTGATTTAAGTATTCATTGTGGTGCTGTTGTGACTATG
genomic: CCAAACAATAAGGTCTTAGGAGAGAATGGCCTCATGTTGGTCATAGCATGgtaaggtcag ... tctcgtacagGTAAATTGGAAAACTGATTTAAGTATTCATTGTGGTGCTGTTGTGACTATG
EST: gi|89106086|gb|DY576303.1|DY576303
EST:     CCAAACAATAAGGTCTTAGGAGAGAATGGCCTCATGTTGGTCATAGCATG                         GTAAATTGGAAAACTGATTTAAGTATTCATTGTGGTGCTGTTGTGACTATG
genomic: CCAAACAATAAGGTCTTAGGAGAGAATGGCCTCATGTTGGTCATAGCATGgtaaggtcag ... tctcgtacagGTAAATTGGAAAACTGATTTAAGTATTCATTGTGGTGCTGTTGTGACTATG

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), 43 (downstream exon)
Score: 26

AAGAATTTTAAATGCTGTTGATGCGAGCTGGAACTCATCAACACTATGAACCAAACAATAAGGTCTTAGGAGAGAATGGCCTCATGTTGGTCATAGCATGgtaaggtcag ... tctcgtacagGTAAATTGGAAAACTGATTTAAGTATTCATTGTGGTGCTGTTGTGACTATGGGGTAACACCGTAACAGTGCAGCATATAGGATAGTAATAGATTGTCTGC


Block sizes: 41 (upstream exon), 45 (downstream exon)
Score: 13

AAGAATTTTAAATGCTGTTGATGCGAGCTGGAACTCATCAACACTATGAACCAAACAATAAGGTCTTAGGAGAGAATGGCCTCATGTTGGTCATAGCATGgtaaggtcag ... tctcgtacagGTAAATTGGAAAACTGATTTAAGTATTCATTGTGGTGCTGTTGTGACTATGGGGTAACACCGTAACAGTGCAGCATATAGGATAGTAATAGATTGTCTGC


Block sizes: 48 (upstream exon), 47 (downstream exon)
Score: 29

AAGAATTTTAAATGCTGTTGATGCGAGCTGGAACTCATCAACACTATGAACCAAACAATAAGGTCTTAGGAGAGAATGGCCTCATGTTGGTCATAGCATGgtaaggtcag ... tctcgtacagGTAAATTGGAAAACTGATTTAAGTATTCATTGTGGTGCTGTTGTGACTATGGGGTAACACCGTAACAGTGCAGCATATAGGATAGTAATAGATTGTCTGC


Block sizes: 43 (upstream exon), 43 (downstream exon)
Score: 11

AAGAATTTTAAATGCTGTTGATGCGAGCTGGAACTCATCAACACTATGAACCAAACAATAAGGTCTTAGGAGAGAATGGCCTCATGTTGGTCATAGCATGgtaaggtcag ... tctcgtacagGTAAATTGGAAAACTGATTTAAGTATTCATTGTGGTGCTGTTGTGACTATGGGGTAACACCGTAACAGTGCAGCATATAGGATAGTAATAGATTGTCTGC




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

accctcagatccaatctttttttccttttgccttacattttgatatctcgtacagGTAAATTGGAAAACTGATTTAAGTATTCATTGTGGTGCTGTTGTGACTATGGGGTAACACCGTAACAGTGCAGCATATAGGATAGTAATAGATTGTCTGC
                                ttacattttgatat  TA-rich tract