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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagtagagttcgttgaattgactttgtgttttagggaagcaaaaaaaaatccttacagattttctcacttatatagGGTGGTTTGACAATTAATTCATCACCGGAGGTACATCCAGGTTTAGGGGCTCAACAGAGTATTGACAG

Basic information

species Zea mays
transcript GRMZM2G003734_T01
intron # 20
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|67020761|gb|CO449510.1|CO449510
EST:     AAGAACTGTTGAAACTATTGCCAGGCCCACATCTGGATTTGAAAAGA                         GGTGGTTTGACAATTAATTCATCACCGGAGGTACATCCAGGTTTAGGGGCT
genomic: AAGAACTGTTGAAACTATTGCCAGGCCCACATCTGGATTTGAAAAGAgtgagtagag ... acttatatagGGTGGTTTGACAATTAATTCATCACCGGAGGTACATCCAGGTTTAGGGGCT
EST: gi|32828198|gb|CD967876.1|CD967876
EST:     TTGAAGAACTGTTGAAACTATTGCCAGGCCCACATCTGGATTTGAAAAGA                         GGTGGTTTGACAATTA
genomic: TTGAAGAACTGTTGAAACTATTGCCAGGCCCACATCTGGATTTGAAAAGAgtgagtagag ... acttatatagGGTGGTTTGACAATTA
EST: gi|60358866|gb|DN225839.1|DN225839
EST:     TTGAAGAACTGTTGAAACTATTGCCAGGCCCACATCTGGATTTGAAAAGA                         GGTGGTTTGACAATTAATTCATCACCGGAGGTACATCCAGGTTTAGGGGCT
genomic: TTGAAGAACTGTTGAAACTATTGCCAGGCCCACATCTGGATTTGAAAAGAgtgagtagag ... acttatatagGGTGGTTTGACAATTAATTCATCACCGGAGGTACATCCAGGTTTAGGGGCT
EST: gi|211528665|gb|FL445659.1|FL445659
EST:     TTGAAGAACTGTTGAAACTATTGCCAGGCCCACATCTGGATTTGAAAAGA                         GGTGGTTTGACAATTAATTCATCACCGGAGGTACATCCAGGTTTAGGGGCT
genomic: TTGAAGAACTGTTGAAACTATTGCCAGGCCCACATCTGGATTTGAAAAGAgtgagtagag ... acttatatagGGTGGTTTGACAATTAATTCATCACCGGAGGTACATCCAGGTTTAGGGGCT
EST: gi|37399448|gb|CF637052.1|CF637052
EST:     TTGAAGAACTGTTGAAACTATTGCCAGGCCCACATCTGGATTTGAAAAGA                         GGTGGTTTGACAATTAATTCATCACCGGAGGTACATCCAGGTTTAGGGGCT
genomic: TTGAAGAACTGTTGAAACTATTGCCAGGCCCACATCTGGATTTGAAAAGAgtgagtagag ... acttatatagGGTGGTTTGACAATTAATTCATCACCGGAGGTACATCCAGGTTTAGGGGCT
EST: gi|60347475|gb|DN214448.1|DN214448
EST:     TTGAAGAACTGTTGAAACTATTGCCAGGCCCACATCTGGATTTGAAAAGA                         GGTGGTTTGACAATTAATTCATCACCGGAGGTACATCCAGGTTTAGGGGCT
genomic: TTGAAGAACTGTTGAAACTATTGCCAGGCCCACATCTGGATTTGAAAAGAgtgagtagag ... acttatatagGGTGGTTTGACAATTAATTCATCACCGGAGGTACATCCAGGTTTAGGGGCT
EST: gi|60353462|gb|DN220435.1|DN220435
EST:     TTGAAGAACTGTTGAAACTATTGCCAGGCCCACATCTGGATTTGAAAAGA                         GGTGGTTTGACAATTAATTCATCACCGGAGGTACATCCAGGTTTAGGGGCT
genomic: TTGAAGAACTGTTGAAACTATTGCCAGGCCCACATCTGGATTTGAAAAGAgtgagtagag ... acttatatagGGTGGTTTGACAATTAATTCATCACCGGAGGTACATCCAGGTTTAGGGGCT
EST: gi|32805346|gb|CD957582.1|CD957582
EST:     TTGAAGAACTGTTGAAACTATTGCCAGGCCCACATCTGGATTTGAAAAGA                         GGTGGTTTGACAATTA
genomic: TTGAAGAACTGTTGAAACTATTGCCAGGCCCACATCTGGATTTGAAAAGAgtgagtagag ... acttatatagGGTGGTTTGACAATTA
EST: gi|71440283|gb|DR821333.1|DR821333
EST:     TTGAAGAACTGTTGAAACTATTGCCAGGCCCACATCTGGATTTGAAAAGA                         GGTGGTTTGACAATTAATTCATCACCGGAGGTACATCCAGGTTTAGGGGCT
genomic: TTGAAGAACTGTTGAAACTATTGCCAGGCCCACATCTGGATTTGAAAAGAgtgagtagag ... acttatatagGGTGGTTTGACAATTAATTCATCACCGGAGGTACATCCAGGTTTAGGGGCT
EST: gi|74241259|gb|DT649173.1|DT649173
EST:     TTGAAGAACTGTTGAAACTATTGCCAGGCCCACATCTGGATTTGAAAAGA                         GGTGGTTTGACAATTAATTCATCACCGGAGGTACATCCAGGTTTAGGGGCT
genomic: TTGAAGAACTGTTGAAACTATTGCCAGGCCCACATCTGGATTTGAAAAGAgtgagtagag ... acttatatagGGTGGTTTGACAATTAATTCATCACCGGAGGTACATCCAGGTTTAGGGGCT
EST: gi|76292770|gb|DV032338.1|DV032338
EST:     TTGAAGAACTGTTGAAACTATTGCCAGGCCCACATCTGGATTTGAAAAGA                         GGTGGTTTGACAATTAATTCATCACCGGAGGTACATCCAGGTTTAGGGGCT
genomic: TTGAAGAACTGTTGAAACTATTGCCAGGCCCACATCTGGATTTGAAAAGAgtgagtagag ... acttatatagGGTGGTTTGACAATTAATTCATCACCGGAGGTACATCCAGGTTTAGGGGCT
EST: gi|60401370|gb|DN234177.1|DN234177
EST:     TTGAAGAACTGTTGAAACTATTGCCAGGCCCACATCTGGATTTGAAAAGA                         GGTGGTTTGACAATTAATTCATCACCGGAGGTACATCCAGGTTTAGGGGCT
genomic: TTGAAGAACTGTTGAAACTATTGCCAGGCCCACATCTGGATTTGAAAAGAgtgagtagag ... acttatatagGGTGGTTTGACAATTAATTCATCACCGGAGGTACATCCAGGTTTAGGGGCT

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: 47 (upstream exon), 40 (downstream exon)
Score: 64

GCGGTCTATTGAAGAACTGTTGAAACTATTGCCAGGCCCACATCTGGATTTGAAAAGAgtgagtagag ... acttatatagGGTGGTTTGACAATTAATTCATCACCGGAGGTACATCCAGGTTTAGGGGCTCAACAGAGTATTGACAG


Block sizes: 47 (upstream exon), 40 (downstream exon)
Score: 56

GCGGTCTATTGAAGAACTGTTGAAACTATTGCCAGGCCCACATCTGGATTTGAAAAGAgtgagtagag ... acttatatagGGTGGTTTGACAATTAATTCATCACCGGAGGTACATCCAGGTTTAGGGGCTCAACAGAGTATTGACAG


Block sizes: 47 (upstream exon), 40 (downstream exon)
Score: 39

GCGGTCTATTGAAGAACTGTTGAAACTATTGCCAGGCCCACATCTGGATTTGAAAAGAgtgagtagag ... acttatatagGGTGGTTTGACAATTAATTCATCACCGGAGGTACATCCAGGTTTAGGGGCTCAACAGAGTATTGACAG


Block sizes: 47 (upstream exon), 40 (downstream exon)
Score: 51

GCGGTCTATTGAAGAACTGTTGAAACTATTGCCAGGCCCACATCTGGATTTGAAAAGAgtgagtagag ... acttatatagGGTGGTTTGACAATTAATTCATCACCGGAGGTACATCCAGGTTTAGGGGCTCAACAGAGTATTGACAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctttgtgttttagggaagcaaaaaaaaatccttacagattttctcacttatatagGGTGGTTTGACAATTAATTCATCACCGGAGGTACATCCAGGTTTAGGGGCTCAACAGAGTATTGACAG
                                        ttctcac  putative branch site (score: 51)
                                      ttttctcactt  CT-rich tract
                   aaaaaaaaatcctta  TA-rich tract