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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaagctcatttgctctgttagaggcgaccccgataccaaatcactgacctgctgacactccacctcaacgcttctgtacctgtagGTCAAGAGGCCGCAAGCCAAAGCATACTTTGCAAAAGAGATCTCAGACATGTATGCACGGTTGCTAGAGACAGAGTTAGCTAGGTCGAAGTTGTAACTTG

Basic information

species Zea mays
transcript GRMZM2G059381_T01
intron # 22
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|60399365|gb|DN232179.1|DN232179
EST:     TTGCTGAGCCGTTCACATTGGATAATGGCCTTCTCACCCCAACATTCAAG                         GTCAAGAGGCCGCAAGCCAAAGCATACTTTGCAAAAGAGATCTCAGACATG
genomic: TTGCTGAGCCGTTCACATTGGATAATGGCCTTCTCACCCCAACATTCAAGgtaaagctca ... gtacctgtagGTCAAGAGGCCGCAAGCCAAAGCATACTTTGCAAAAGAGATCTCAGACATG
EST: gi|60395514|gb|DN228384.1|DN228384
EST:     TTGCTGAGCCATTCTCATTGGACAATGGCCTTCTCACCCCAACATTCAAG                         GTCAAGAGGCCGCAAGCCAAAGCATACTTTGCAAAAGAAATCTCAGACATG
genomic: TTGCTGAGCCGTTCACATTGGATAATGGCCTTCTCACCCCAACATTCAAGgtaaagctca ... gtacctgtagGTCAAGAGGCCGCAAGCCAAAGCATACTTTGCAAAAGAGATCTCAGACATG
EST: gi|93283329|gb|EB675593.1|EB675593
EST:     TTGCTGAGCCGTTCACATTGGATAATGGCCTTCTCACCCCAACATTCAAG                         GTCAAGAGGCCGCAAGCCAAAGCATACTTTGCAAAAGAGATCTCAGACATG
genomic: TTGCTGAGCCGTTCACATTGGATAATGGCCTTCTCACCCCAACATTCAAGgtaaagctca ... gtacctgtagGTCAAGAGGCCGCAAGCCAAAGCATACTTTGCAAAAGAGATCTCAGACATG

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), 37 (downstream exon)
Score: 60

CTGAGAGGTTTCGAGTTTGCTAAAGCGGTTACTCTTGTTGCTGAGCCGTTCACATTGGATAATGGCCTTCTCACCCCAACATTCAAGgtaaagctca ... gtacctgtagGTCAAGAGGCCGCAAGCCAAAGCATACTTTGCAAAAGAGATCTCAGACATGTATGCACGGTTGCTAGAGACAGAGTTAGCTAGGTCGAAGTTGTAACTTG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 122

CTGAGAGGTTTCGAGTTTGCTAAAGCGGTTACTCTTGTTGCTGAGCCGTTCACATTGGATAATGGCCTTCTCACCCCAACATTCAAGgtaaagctca ... gtacctgtagGTCAAGAGGCCGCAAGCCAAAGCATACTTTGCAAAAGAGATCTCAGACATGTATGCACGGTTGCTAGAGACAGAGTTAGCTAGGTCGAAGTTGTAACTTG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 42

CTGAGAGGTTTCGAGTTTGCTAAAGCGGTTACTCTTGTTGCTGAGCCGTTCACATTGGATAATGGCCTTCTCACCCCAACATTCAAGgtaaagctca ... gtacctgtagGTCAAGAGGCCGCAAGCCAAAGCATACTTTGCAAAAGAGATCTCAGACATGTATGCACGGTTGCTAGAGACAGAGTTAGCTAGGTCGAAGTTGTAACTTG


Block sizes: 47 (upstream exon), 43 (downstream exon)
Score: 102

CTGAGAGGTTTCGAGTTTGCTAAAGCGGTTACTCTTGTTGCTGAGCCGTTCACATTGGATAATGGCCTTCTCACCCCAACATTCAAGgtaaagctca ... gtacctgtagGTCAAGAGGCCGCAAGCCAAAGCATACTTTGCAAAAGAGATCTCAGACATGTATGCACGGTTGCTAGAGACAGAGTTAGCTAGGTCGAAGTTGTAACTTG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cgataccaaatcactgacctgctgacactccacctcaacgcttctgtacctgtagGTCAAGAGGCCGCAAGCCAAAGCATACTTTGCAAAAGAGATCTCAGACATGTATGCACGGTTGCTAGAGACAGAGTTAGCTAGGTCGAAGTTGTAACTTG
                   tgctgac  putative branch site (score: 102)
                                        cttctgt  putative PPT