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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tcattcagcttcgtcagcaccactatcttctcgtggcacacatttatgaactacctttttttatgttttactaatttcttgggtgtcaaattgctcccagGTGGTTGCTGGTGCATTGCTTGGGTGTACAATAGCCACAGCAGGACAATTATTCCTTTGAACTACGAAGGTGCGGCAGAAATGTTGTAGCATTTGTATCG

Basic information

species Zea mays
transcript GRMZM2G091435_T01
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|166495279|gb|EG160874.1|EG160874
EST:     GAAC-TTTAGGCCATACACCAACCCAG                         GTGGTTGCTGGTGCATTGCTTGGGTGTACAATAGCCACAGCAGGACAATTA
genomic: GAACTTTTAGGCCATACACCAACTCAGgtttgttcac ... ttgctcccagGTGGTTGCTGGTGCATTGCTTGGGTGTACAATAGCCACAGCAGGACAATTA
EST: gi|166629047|gb|EG261260.1|EG261260
EST:     GAGAACTTTTAGGCCATACACCAACCCAG                         GTGGTTGCTGGTGCATTGCTTGGGTGTACAATAGCCACAGCAGGACAATTA
genomic: GAGAACTTTTAGGCCATACACCAACTCAGgtttgttcac ... ttgctcccagGTGGTTGCTGGTGCATTGCTTGGGTGTACAATAGCCACAGCAGGACAATTA
EST: gi|32923268|gb|CF028080.1|CF028080
EST:     TGTCTGAGACAAGACCACTGCGAGAACTTTTAGGCCATACACCAACCCAG                         GTGGTTGCTGGTGCATTGCTTGGGTGTA
genomic: TGTCTGAGACAAGACCACTGCGAGAACTTTTAGGCCATACACCAACTCAGgtttgttcac ... ttgctcccagGTGGTTGCTGGTGCATTGCTTGGGTGTA
EST: gi|8401376|gb|BE057010.1|BE057010
EST:     TGTCTGAGACAAGACCACTGCGAGAACTTTTAGGCCATACACCAACCCAG                         GTGGTTGCTGGTGCATTGCTTGGGTGTACAATAGCCACAGCAGGACAATTA
genomic: TGTCTGAGACAAGACCACTGCGAGAACTTTTAGGCCATACACCAACTCAGgtttgttcac ... ttgctcccagGTGGTTGCTGGTGCATTGCTTGGGTGTACAATAGCCACAGCAGGACAATTA
EST: gi|149074454|gb|EE162849.2|EE162849
EST:     TGTTTGAGACAAGACCACTGCGAGAACTTTTAGGCCATACACCAACTCAG                         GTGGTTGCTGGTGCATTGCTTGGGTGTACAATAGCCACAGCAGGACAATTA
genomic: TGTCTGAGACAAGACCACTGCGAGAACTTTTAGGCCATACACCAACTCAGgtttgttcac ... ttgctcccagGTGGTTGCTGGTGCATTGCTTGGGTGTACAATAGCCACAGCAGGACAATTA
EST: gi|166636873|gb|EG172033.1|EG172033
EST:     AACTTTTAGGCCATACACCAACCCAG                         GTGGTTGCTGGTGCATTGCTTGGGTGTACAATAGCCACAGCAGGACAATTA
genomic: AACTTTTAGGCCATACACCAACTCAGgtttgttcac ... ttgctcccagGTGGTTGCTGGTGCATTGCTTGGGTGTACAATAGCCACAGCAGGACAATTA
EST: gi|166566343|gb|EG175732.1|EG175732
EST:     GAACTTTTAGGCCATACACCAACCCAG                         GTGGTTGCTGGTGCATTGCTTGGGTGTACAATAGCCACAGCAGGACAATTA
genomic: GAACTTTTAGGCCATACACCAACTCAGgtttgttcac ... ttgctcccagGTGGTTGCTGGTGCATTGCTTGGGTGTACAATAGCCACAGCAGGACAATTA
EST: gi|91871453|gb|EB401428.1|EB401428
EST:     TGTTTGAGACAAGACCACTGCGAGAACTTTTAGGCCATACACCAACTCAG                         GTGGTTGGTGGTGCATTGCTTGGGTGTACAATAGCCACAGCAGGACAATTA
genomic: TGTCTGAGACAAGACCACTGCGAGAACTTTTAGGCCATACACCAACTCAGgtttgttcac ... ttgctcccagGTGGTTGCTGGTGCATTGCTTGGGTGTACAATAGCCACAGCAGGACAATTA

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), 47 (downstream exon)
Score: 12

GTATTGAATCAAATAGTTTGTGAACTTCCTTCTGAACACCCCTTGTCTGAGACAAGACCACTGCGAGAACTTTTAGGCCATACACCAACTCAGgtttgttcac ... ttgctcccagGTGGTTGCTGGTGCATTGCTTGGGTGTACAATAGCCACAGCAGGACAATTATTCCTTTGAACTACGAAGGTGCGGCAGAAATGTTGTAGCATTTGTATCG


Block sizes: 47 (upstream exon), 47 (downstream exon)
Score: 51

GTATTGAATCAAATAGTTTGTGAACTTCCTTCTGAACACCCCTTGTCTGAGACAAGACCACTGCGAGAACTTTTAGGCCATACACCAACTCAGgtttgttcac ... ttgctcccagGTGGTTGCTGGTGCATTGCTTGGGTGTACAATAGCCACAGCAGGACAATTATTCCTTTGAACTACGAAGGTGCGGCAGAAATGTTGTAGCATTTGTATCG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 128

GTATTGAATCAAATAGTTTGTGAACTTCCTTCTGAACACCCCTTGTCTGAGACAAGACCACTGCGAGAACTTTTAGGCCATACACCAACTCAGgtttgttcac ... ttgctcccagGTGGTTGCTGGTGCATTGCTTGGGTGTACAATAGCCACAGCAGGACAATTATTCCTTTGAACTACGAAGGTGCGGCAGAAATGTTGTAGCATTTGTATCG


Block sizes: 47 (upstream exon), 47 (downstream exon)
Score: 39

GTATTGAATCAAATAGTTTGTGAACTTCCTTCTGAACACCCCTTGTCTGAGACAAGACCACTGCGAGAACTTTTAGGCCATACACCAACTCAGgtttgttcac ... ttgctcccagGTGGTTGCTGGTGCATTGCTTGGGTGTACAATAGCCACAGCAGGACAATTATTCCTTTGAACTACGAAGGTGCGGCAGAAATGTTGTAGCATTTGTATCG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atgaactacctttttttatgttttactaatttcttgggtgtcaaattgctcccagGTGGTTGCTGGTGCATTGCTTGGGTGTACAATAGCCACAGCAGGACAATTATTCCTTTGAACTACGAAGGTGCGGCAGAAATGTTGTAGCATTTGTATCG
                       tactaat  putative branch site (score: 39)
                                             ttgctccc  putative PPT
          tttttttatgttttac  TA-rich tract