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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...atcatccgcctagctagcacaagccatccgcgacagtgttagtgctaccgtcgaccgcacgccgctcaacccgcgcgcgcgctgttgtctgttgtctcagATCAGCTTTGCAGCTAAGGACAGCGAATTCTCGGACTGGGACGGCGACATACTCGCGGTCGCCGTGACGGACAAGGACGTGCAGGTGCAGCCCCACGTCT

Basic information

species Zea mays
transcript GRMZM2G043893_T02
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|89247434|gb|DY619220.1|DY619220
EST:     CCGCCACTCTCGGCCTGACCTGGCCCAACGCCGCCGTCGAACTG-C-C--                         -TCAGCTTTGCAGCTAAGGACAGCGAATTCTCGGACTGGGACGGCGACATA
genomic: CCGCCACTCTCGGCCTGACCTGGCCCAACGCCGCCGTCGAACTGCCTCAGgtgcgccgcc ... gttgtctcagATCAGCTTTGCAGCTAAGGACAGCGAATTCTCGGACTGGGACGGCGACATA
EST: gi|101393109|gb|EB818485.1|EB818485
EST:     CCGCCACTCTCGGCCTGACCTGGCCCAACGCCGCCGTCGAACTGCCTCAG                         ATCAGCTTTGCAGCTAAGGACAGCGAATTCTCGGACTGGGACGGCGACATA
genomic: CCGCCACTCTCGGCCTGACCTGGCCCAACGCCGCCGTCGAACTGCCTCAGgtgcgccgcc ... gttgtctcagATCAGCTTTGCAGCTAAGGACAGCGAATTCTCGGACTGGGACGGCGACATA
EST: gi|148991872|gb|EE033466.2|EE033466
EST:     CCGCCACTCTCGGCCTGACCTGGCCCAACGCCGCCGTCGAACTG-C-C--                         -TCAGCTTTGCAGCTAAGGACAGCGAATTCTCGGACTGGGACGGCGACATA
genomic: CCGCCACTCTCGGCCTGACCTGGCCCAACGCCGCCGTCGAACTGCCTCAGgtgcgccgcc ... gttgtctcagATCAGCTTTGCAGCTAAGGACAGCGAATTCTCGGACTGGGACGGCGACATA
EST: gi|76913696|gb|DV165228.1|DV165228
EST:     CCGCCACTCTCGGCCTGACCTGGCCCAACGCCGCCGTCGAACTGCCTCAG                         ATCAGCTTTGCAGCTAAGGACAGCGAATTCTCGGACTGGGACGGCGACATA
genomic: CCGCCACTCTCGGCCTGACCTGGCCCAACGCCGCCGTCGAACTGCCTCAGgtgcgccgcc ... gttgtctcagATCAGCTTTGCAGCTAAGGACAGCGAATTCTCGGACTGGGACGGCGACATA
EST: gi|149001042|gb|EE038291.2|EE038291
EST:     CCGCCACTCTCGGCCTGACCTGGCCCAACGCCGCCGTCGAACTGCCTCAG                         ATCAGCTTTGCAGCTAAGGACAGCGAATTCTCGGACTGGGACGGCGACATA
genomic: CCGCCACTCTCGGCCTGACCTGGCCCAACGCCGCCGTCGAACTGCCTCAGgtgcgccgcc ... gttgtctcagATCAGCTTTGCAGCTAAGGACAGCGAATTCTCGGACTGGGACGGCGACATA
EST: gi|74236862|gb|DT644776.1|DT644776
EST:     CCGCCACTCTCGGCCTGACCTGGCCCAACGCCGCCGTCGAACTG-C-C--                         -TCAGCTTTGCAGCTAAGGACAGCGAATTCTCGGACTGGGACGGCGACATA
genomic: CCGCCACTCTCGGCCTGACCTGGCCCAACGCCGCCGTCGAACTGCCTCAGgtgcgccgcc ... gttgtctcagATCAGCTTTGCAGCTAAGGACAGCGAATTCTCGGACTGGGACGGCGACATA
EST: gi|148958193|gb|EC904398.2|EC904398
EST:     CCGCCACTCTCGGCCTGACCTGGCCCAACGCCGCCGTCGAACTGCCTCAG                         ATCAGCTTTGCAGCTAAGGACAGCGAATTCTCGGACTGGGACGGCGACATA
genomic: CCGCCACTCTCGGCCTGACCTGGCCCAACGCCGCCGTCGAACTGCCTCAGgtgcgccgcc ... gttgtctcagATCAGCTTTGCAGCTAAGGACAGCGAATTCTCGGACTGGGACGGCGACATA
EST: gi|71436982|gb|DR818032.1|DR818032
EST:     CCGCCACTCTCGGCCTGACCTGGCCCAACGCCGCCGTCGAACTGCCTCAG                         ATCAGCTTTGCAGCTAAGGACAGCGAATTCTCGGACTGGGACGGCGACATA
genomic: CCGCCACTCTCGGCCTGACCTGGCCCAACGCCGCCGTCGAACTGCCTCAGgtgcgccgcc ... gttgtctcagATCAGCTTTGCAGCTAAGGACAGCGAATTCTCGGACTGGGACGGCGACATA
EST: gi|71774295|gb|DR972173.1|DR972173
EST:     CCGCCACTCTCGGCCTGACCTGGCCCAACGCCGCCGTCGAACTGCCTCAG                         ATCAGCTTTGCAGCTAAGGACAGCGAATTCTCGGACTGGGACGGCGACATA
genomic: CCGCCACTCTCGGCCTGACCTGGCCCAACGCCGCCGTCGAACTGCCTCAGgtgcgccgcc ... gttgtctcagATCAGCTTTGCAGCTAAGGACAGCGAATTCTCGGACTGGGACGGCGACATA
EST: gi|71318210|gb|DR795867.1|DR795867
EST:     CCGCCACTCTCGGCCTGACCTGGCCCAACGCCGCCGTCGAACTGCCTCAG                         ATCAGCTTTGCAGCTAAGGACAGCGAATTCTCGGACTGGGACGGCGACATA
genomic: CCGCCACTCTCGGCCTGACCTGGCCCAACGCCGCCGTCGAACTGCCTCAGgtgcgccgcc ... gttgtctcagATCAGCTTTGCAGCTAAGGACAGCGAATTCTCGGACTGGGACGGCGACATA

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 3 RNA-Seq libraries.


Block sizes: 49 (upstream exon), 45 (downstream exon)
Score: 51

GCCGGCACATTTCCTGTTGTCTCCGATGGGTGACGCCGCTACTGCCGCCGCCGCCACTCTCGGCCTGACCTGGCCCAACGCCGCCGTCGAACTGCCTCAGgtgcgccgcc ... gttgtctcagATCAGCTTTGCAGCTAAGGACAGCGAATTCTCGGACTGGGACGGCGACATACTCGCGGTCGCCGTGACGGACAAGGACGTGCAGGTGCAGCCCCACGTCT


Block sizes: 48 (upstream exon), 45 (downstream exon)
Score: 33

GCCGGCACATTTCCTGTTGTCTCCGATGGGTGACGCCGCTACTGCCGCCGCCGCCACTCTCGGCCTGACCTGGCCCAACGCCGCCGTCGAACTGCCTCAGgtgcgccgcc ... gttgtctcagATCAGCTTTGCAGCTAAGGACAGCGAATTCTCGGACTGGGACGGCGACATACTCGCGGTCGCCGTGACGGACAAGGACGTGCAGGTGCAGCCCCACGTCT


Block sizes: 25 (upstream exon), 25 (downstream exon)
Score: 2

GCCGGCACATTTCCTGTTGTCTCCGATGGGTGACGCCGCTACTGCCGCCGCCGCCACTCTCGGCCTGACCTGGCCCAACGCCGCCGTCGAACTGCCTCAGgtgcgccgcc ... gttgtctcagATCAGCTTTGCAGCTAAGGACAGCGAATTCTCGGACTGGGACGGCGACATACTCGCGGTCGCCGTGACGGACAAGGACGTGCAGGTGCAGCCCCACGTCT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

taccgtcgaccgcacgccgctcaacccgcgcgcgcgctgttgtctgttgtctcagATCAGCTTTGCAGCTAAGGACAGCGAATTCTCGGACTGGGACGGCGACATACTCGCGGTCGCCGTGACGGACAAGGACGTGCAGGTGCAGCCCCACGTCT
                                              ttgtctc  CT-rich tract