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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagatgagatcactcagcagttcatctactgcgctgcgcatttccctttcgtctcctgatttttgatgaaaggtgaaccgtgtcgtctgtgctgccatctaattcctatttccatctctttctttttttttccttcttaaactctagCCAATGTTGAGGTTACTCTGCGCATAGTATGCCAACCACAAGCACTTTTCCGGATCAGGCCGGTCAACCGATGCTCTGCCACGATTGCTG

Basic information

species Zea mays
transcript GRMZM2G157034_T02
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|148969156|gb|EE019897.2|EE019897
EST:     AGACGAGGAGCTCTCTGTCCACCTGGGTGCTTACATGCGGCAGAAGAACG                         CCAATGTTGAGGTTACTCTGCGCATAGTATGCCAACCACAAGCACTTTTCC
genomic: AGACGAGGAGCTCTCTGTCTACCTGGGTGCTTACATGCGGCAGAAGAACGgtgagatgag ... taaactctagCCAATGTTGAGGTTACTCTGCGCATAGTATGCCAACCACAAGCACTTTTCC
EST: gi|149042078|gb|EE047056.2|EE047056
EST:     AGACGAGGAGCTCTCTGTCCACCTGGGTGCTTACATGCGGCAGAAGAACG                         CCAATGTTGAGGTTACTCTGCGCATAGTATGCCAACCACAAGCACTTTTCC
genomic: AGACGAGGAGCTCTCTGTCTACCTGGGTGCTTACATGCGGCAGAAGAACGgtgagatgag ... taaactctagCCAATGTTGAGGTTACTCTGCGCATAGTATGCCAACCACAAGCACTTTTCC
EST: gi|148939524|gb|EC884116.2|EC884116
EST:     AGACGAGGAGCTCTCTGTCCACCTGGGTGCTTACATGCGGCAGAAGAACG                         CCAATGTTGAGGTTACTCTGCGCATAGTATGCCAACCACAAGCACTTTTCC
genomic: AGACGAGGAGCTCTCTGTCTACCTGGGTGCTTACATGCGGCAGAAGAACGgtgagatgag ... taaactctagCCAATGTTGAGGTTACTCTGCGCATAGTATGCCAACCACAAGCACTTTTCC

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: 128

GAGGAGAAGTTGCCCTATGCATTCTACGTTGGAGACGAGGAGCTCTCTGTCTACCTGGGTGCTTACATGCGGCAGAAGAACGgtgagatgag ... taaactctagCCAATGTTGAGGTTACTCTGCGCATAGTATGCCAACCACAAGCACTTTTCCGGATCAGGCCGGTCAACCGATGCTCTGCCACGATTGCTG


Block sizes: 47 (upstream exon), 48 (downstream exon)
Score: 104

GAGGAGAAGTTGCCCTATGCATTCTACGTTGGAGACGAGGAGCTCTCTGTCTACCTGGGTGCTTACATGCGGCAGAAGAACGgtgagatgag ... taaactctagCCAATGTTGAGGTTACTCTGCGCATAGTATGCCAACCACAAGCACTTTTCCGGATCAGGCCGGTCAACCGATGCTCTGCCACGATTGCTG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 68

GAGGAGAAGTTGCCCTATGCATTCTACGTTGGAGACGAGGAGCTCTCTGTCTACCTGGGTGCTTACATGCGGCAGAAGAACGgtgagatgag ... taaactctagCCAATGTTGAGGTTACTCTGCGCATAGTATGCCAACCACAAGCACTTTTCCGGATCAGGCCGGTCAACCGATGCTCTGCCACGATTGCTG


Block sizes: 44 (upstream exon), 49 (downstream exon)
Score: 70

GAGGAGAAGTTGCCCTATGCATTCTACGTTGGAGACGAGGAGCTCTCTGTCTACCTGGGTGCTTACATGCGGCAGAAGAACGgtgagatgag ... taaactctagCCAATGTTGAGGTTACTCTGCGCATAGTATGCCAACCACAAGCACTTTTCCGGATCAGGCCGGTCAACCGATGCTCTGCCACGATTGCTG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgccatctaattcctatttccatctctttctttttttttccttcttaaactctagCCAATGTTGAGGTTACTCTGCGCATAGTATGCCAACCACAAGCACTTTTCCGGATCAGGCCGGTCAACCGATGCTCTGCCACGATTGCTG
    atctaat  putative branch site (score: 70)
       taattcctatttccat  CT-rich tract
                        tctttcttttttttt  TA-rich tract