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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacatgtgatgaactttgtcatttttagaatattaactgaaagccatattaaccaatttatttgtgcagGAAGCATTGTTGAAGAATATCAAGCTGGACTTAAAGAAGCTTGAAAACAAAGTTAGGTTTATCCGCTGTGTTGTTGATAATGAAATTATAGTTAACAACA

Basic information

species Zea mays
transcript GRMZM2G021270_T01
intron # 16
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|211354438|gb|FK991815.1|FK991815
EST:     TACTTGAGGAATTCTTTCAATTAAGGNTTGAATTCTATTGTAAGAGAAAG                         GNAGCATTGTTGAAGAATATCAAGCTGGACTTAAAGAAGCTTGAAAACNAA
genomic: TACTTGAGGAATTCTTTCAATTAAGGCTTGAATTCTATTGTAAGAGAAAGgtacatgtga ... atttgtgcagGAAGCATTGTTGAAGAATATCAAGCTGGACTTAAAGAAGCTTGAAAACAAA
EST: gi|211354445|gb|FK991822.1|FK991822
EST:     TACTTGAGGAATTCTTTCAATTAAGGCTTGAATTCTATTGTAAGAGAAAG                         GAAGCATTGTTGAAGAATATCAAGCTGGACTTAAAGAAGCTTGAAAACAAA
genomic: TACTTGAGGAATTCTTTCAATTAAGGCTTGAATTCTATTGTAAGAGAAAGgtacatgtga ... atttgtgcagGAAGCATTGTTGAAGAATATCAAGCTGGACTTAAAGAAGCTTGAAAACAAA
EST: gi|86465874|gb|DY232247.1|DY232247
EST:     TACTTGAGGAATTCTTTCAATTAAGGCTTGAATTCTATTGTAAGAGAAAG                         GAAGCATTGTTGAAGAATATCAAGCTGGACTTAAAGAAGCTTGAAAACAAA
genomic: TACTTGAGGAATTCTTTCAATTAAGGCTTGAATTCTATTGTAAGAGAAAGgtacatgtga ... atttgtgcagGAAGCATTGTTGAAGAATATCAAGCTGGACTTAAAGAAGCTTGAAAACAAA
EST: gi|211354440|gb|FK991817.1|FK991817
EST:     TACTTGAGGAATTCTTTCAATTAAGGCTTGAATTCTATTGTAAGAGAAAG                         GAAGCATTGTTGAAGAATATCAAGCTGGACTTAAAGAAGCTTGAAAACAAA
genomic: TACTTGAGGAATTCTTTCAATTAAGGCTTGAATTCTATTGTAAGAGAAAGgtacatgtga ... atttgtgcagGAAGCATTGTTGAAGAATATCAAGCTGGACTTAAAGAAGCTTGAAAACAAA
EST: gi|211354441|gb|FK991818.1|FK991818
EST:     TACTTGAGGAATTCTTTCAATTAAGGCTTGAATTCTATTGTAAGAGAAAG                         GAAGCATTGTTGAAGAATATCAAGCTGGACTTAAAGAAGCTTGAAAACAAA
genomic: TACTTGAGGAATTCTTTCAATTAAGGCTTGAATTCTATTGTAAGAGAAAGgtacatgtga ... atttgtgcagGAAGCATTGTTGAAGAATATCAAGCTGGACTTAAAGAAGCTTGAAAACAAA
EST: gi|32930202|gb|CF035014.1|CF035014
EST:     TACTTGAGGAATTCTTTCAATTAAGGCTTGAATTCTATTGTAAGAGAAAG                         GAAGCATTGTTGAAGAATATCAAGCTGGACTTAAAGAAGCTTGAAAACAAA
genomic: TACTTGAGGAATTCTTTCAATTAAGGCTTGAATTCTATTGTAAGAGAAAGgtacatgtga ... atttgtgcagGAAGCATTGTTGAAGAATATCAAGCTGGACTTAAAGAAGCTTGAAAACAAA
EST: gi|22935395|gb|BU571670.1|BU571670
EST:     GAATTCTATTGTAAGAGAAAG                         GAAGCATTGTTGAAGAATATCAAGCTGGACTTAAAGAAGCTTGAAAACAAA
genomic: GAATTCTATTGTAAGAGAAAGgtacatgtga ... atttgtgcagGAAGCATTGTTGAAGAATATCAAGCTGGACTTAAAGAAGCTTGAAAACAAA
EST: gi|211354443|gb|FK991820.1|FK991820
EST:     TACTTGAGGAATTCTTTCAATTAAGGCTTGAATTCTATTGTAAGAGAAAG                         GAAGCATTGTTGAAGAATATCAAGCTGGACTTAAAGAAGCTTGAAAACAAA
genomic: TACTTGAGGAATTCTTTCAATTAAGGCTTGAATTCTATTGTAAGAGAAAGgtacatgtga ... atttgtgcagGAAGCATTGTTGAAGAATATCAAGCTGGACTTAAAGAAGCTTGAAAACAAA
EST: gi|211354442|gb|FK991819.1|FK991819
EST:     TACTTGAGGAATTCTTTCAATTAAGGCTTGAATTCTATTGTAAGAGAAAG                         GAAGCATTGTTGAAGAATATCAAGCTGGACTTAAAGAAGCTTGAAAACAAA
genomic: TACTTGAGGAATTCTTTCAATTAAGGCTTGAATTCTATTGTAAGAGAAAGgtacatgtga ... atttgtgcagGAAGCATTGTTGAAGAATATCAAGCTGGACTTAAAGAAGCTTGAAAACAAA
EST: gi|87157557|gb|DY402346.1|DY402346
EST:     TACTTGAGGAATTCTTTCAATTAAGGCTTGAATTCTATTGTAAGAGAAAG                         GAAGCATTGTTGAAGAATATCAAGCTGGACTTAAAGAAGCTTGAAAACAAA
genomic: TACTTGAGGAATTCTTTCAATTAAGGCTTGAATTCTATTGTAAGAGAAAGgtacatgtga ... atttgtgcagGAAGCATTGTTGAAGAATATCAAGCTGGACTTAAAGAAGCTTGAAAACAAA

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), 49 (downstream exon)
Score: 181

TACTTGAGGAATTCTTTCAATTAAGGCTTGAATTCTATTGTAAGAGAAAGgtacatgtga ... atttgtgcagGAAGCATTGTTGAAGAATATCAAGCTGGACTTAAAGAAGCTTGAAAACAAAGTTAGGTTTATCCGCTGTGTTGTTGATAATGAAATTATAGTTAACAACA


Block sizes: 47 (upstream exon), 41 (downstream exon)
Score: 12

TACTTGAGGAATTCTTTCAATTAAGGCTTGAATTCTATTGTAAGAGAAAGgtacatgtga ... atttgtgcagGAAGCATTGTTGAAGAATATCAAGCTGGACTTAAAGAAGCTTGAAAACAAAGTTAGGTTTATCCGCTGTGTTGTTGATAATGAAATTATAGTTAACAACA


Block sizes: 42 (upstream exon), 48 (downstream exon)
Score: 16

TACTTGAGGAATTCTTTCAATTAAGGCTTGAATTCTATTGTAAGAGAAAGgtacatgtga ... atttgtgcagGAAGCATTGTTGAAGAATATCAAGCTGGACTTAAAGAAGCTTGAAAACAAAGTTAGGTTTATCCGCTGTGTTGTTGATAATGAAATTATAGTTAACAACA


Block sizes: 41 (upstream exon), 41 (downstream exon)
Score: 9

TACTTGAGGAATTCTTTCAATTAAGGCTTGAATTCTATTGTAAGAGAAAGgtacatgtga ... atttgtgcagGAAGCATTGTTGAAGAATATCAAGCTGGACTTAAAGAAGCTTGAAAACAAAGTTAGGTTTATCCGCTGTGTTGTTGATAATGAAATTATAGTTAACAACA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttgtcatttttagaatattaactgaaagccatattaaccaatttatttgtgcagGAAGCATTGTTGAAGAATATCAAGCTGGACTTAAAGAAGCTTGAAAACAAAGTTAGGTTTATCCGCTGTGTTGTTGATAATGAAATTATAGTTAACAACA
                                tattaac  putative branch site (score: 9)
                                          tttattt  putative PPT
      atttttagaatattaa  TA-rich tract