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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacttatatttttaccaacaatatgcataaatcatgattattgcactgctaactcagtctcgtgaatgaaactgcagTTTCATAATCCCAGGCCTTGGGGATGCTGGAGATCGCAGCTATGGAACATGACTCCGGCCCTTCGGTGATGGCCATCGTTAGGAATTTCAGCAAAACCCA

Basic information

species Zea mays
transcript GRMZM5G816432_T01
intron # 9
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|211541384|gb|FL468171.1|FL468171
EST:     GATTTGTGTGTATACAGGAGCCATGGATCAAATTGTAAACGAGAAAGG                         TTTCATAATCCCAGGCCTTGGGGATGCTGGAGATCGCAGCTATGGAACATG
genomic: GATTTGTGTGTATACAGGAGCCATGGATCAAATTGTAAACGAGAAAGGgtacttatat ... gaaactgcagTTTCATAATCCCAGGCCTTGGGGATGCTGGAGATCGCAGCTATGGAACATG
EST: gi|31406396|gb|CD485128.1|CD485128
EST:     GATTTGTGTGTATACAGGAGCCATGGATCAAATTGTAAACGAGAAAGG                         TTTCATAATCCCAGGCCTTGGGGATGCTGGAGATCGCAGCTATGGAACATG
genomic: GATTTGTGTGTATACAGGAGCCATGGATCAAATTGTAAACGAGAAAGGgtacttatat ... gaaactgcagTTTCATAATCCCAGGCCTTGGGGATGCTGGAGATCGCAGCTATGGAACATG
EST: gi|50335539|gb|CO530665.1|CO530665
EST:     CCATGGATCAAATTGTAAACGAGAAAGG                         TTTCATAATCCCAGGCCTTGGGGATGCTGGAGATCGCAGCTATGGAACATG
genomic: CCATGGATCAAATTGTAAACGAGAAAGGgtacttatat ... gaaactgcagTTTCATAATCCCAGGCCTTGGGGATGCTGGAGATCGCAGCTATGGAACATG
EST: gi|5713652|gb|AI943644.1|AI943644
EST:     GATTTGTGTGTATACAGGAGCCATGGATCAAATTGTAAACGAGAAAGG                         TTTCATAATCCCAGGCCTTGGGGATGCTGGAGATCGCAGCTATGGAACATG
genomic: GATTTGTGTGTATACAGGAGCCATGGATCAAATTGTAAACGAGAAAGGgtacttatat ... gaaactgcagTTTCATAATCCCAGGCCTTGGGGATGCTGGAGATCGCAGCTATGGAACATG
EST: gi|50335538|gb|CO530664.1|CO530664
EST:     AGGATTTGTGTGTATACAGGAGCCATGGATCAAATTGTAAACGAGAAAGG                         TTTCATAATCCCAGGCCTTGGGGATGCTGGAGATCGCAGCTATGGAACATG
genomic: AGGATTTGTGTGTATACAGGAGCCATGGATCAAATTGTAAACGAGAAAGGgtacttatat ... gaaactgcagTTTCATAATCCCAGGCCTTGGGGATGCTGGAGATCGCAGCTATGGAACATG
EST: gi|211468297|gb|FL467296.1|FL467296
EST:     GATTTGTGTGTATACAGGAGCCATGGATCAAATTGTAAACGAGAAAGG                         TTTCATAATCCCAGGCCTTGGGGATGCTGGAGATCGCAGCTATGGAACATG
genomic: GATTTGTGTGTATACAGGAGCCATGGATCAAATTGTAAACGAGAAAGGgtacttatat ... gaaactgcagTTTCATAATCCCAGGCCTTGGGGATGCTGGAGATCGCAGCTATGGAACATG
EST: gi|211394252|gb|FL456747.1|FL456747
EST:     GATTTGTGTGTATACAGGAGCCATGGATCAAATTGTAAACGAGAAAGG                         TTTCATAATCCCAGGCCTTGGGGATGCTGGAGATCGCAGCTATGGAACATG
genomic: GATTTGTGTGTATACAGGAGCCATGGATCAAATTGTAAACGAGAAAGGgtacttatat ... gaaactgcagTTTCATAATCCCAGGCCTTGGGGATGCTGGAGATCGCAGCTATGGAACATG
EST: gi|78025784|gb|DV494171.1|DV494171
EST:     GATTTGTGTGTATACAGGAGCCATGGATCAAATTGTAAACGAGAAAGG                         TTTCATAATCCCAGGCCTTGGGGATGTTGGAGATCGCAGCTATGGAACATG
genomic: GATTTGTGTGTATACAGGAGCCATGGATCAAATTGTAAACGAGAAAGGgtacttatat ... gaaactgcagTTTCATAATCCCAGGCCTTGGGGATGCTGGAGATCGCAGCTATGGAACATG

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), 44 (downstream exon)
Score: 47

GATTTGTGTGTATACAGGAGCCATGGATCAAATTGTAAACGAGAAAGGgtacttatat ... gaaactgcagTTTCATAATCCCAGGCCTTGGGGATGCTGGAGATCGCAGCTATGGAACATGACTCCGGCCCTTCGGTGATGGCCATCGTTAGGAATTTCAGCAAAACCCA


Block sizes: 47 (upstream exon), 48 (downstream exon)
Score: 38

GATTTGTGTGTATACAGGAGCCATGGATCAAATTGTAAACGAGAAAGGgtacttatat ... gaaactgcagTTTCATAATCCCAGGCCTTGGGGATGCTGGAGATCGCAGCTATGGAACATGACTCCGGCCCTTCGGTGATGGCCATCGTTAGGAATTTCAGCAAAACCCA


Block sizes: 48 (upstream exon), 48 (downstream exon)
Score: 57

GATTTGTGTGTATACAGGAGCCATGGATCAAATTGTAAACGAGAAAGGgtacttatat ... gaaactgcagTTTCATAATCCCAGGCCTTGGGGATGCTGGAGATCGCAGCTATGGAACATGACTCCGGCCCTTCGGTGATGGCCATCGTTAGGAATTTCAGCAAAACCCA


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 119

GATTTGTGTGTATACAGGAGCCATGGATCAAATTGTAAACGAGAAAGGgtacttatat ... gaaactgcagTTTCATAATCCCAGGCCTTGGGGATGCTGGAGATCGCAGCTATGGAACATGACTCCGGCCCTTCGGTGATGGCCATCGTTAGGAATTTCAGCAAAACCCA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atgcataaatcatgattattgcactgctaactcagtctcgtgaatgaaactgcagTTTCATAATCCCAGGCCTTGGGGATGCTGGAGATCGCAGCTATGGAACATGACTCCGGCCCTTCGGTGATGGCCATCGTTAGGAATTTCAGCAAAACCCA
                        tgctaac  putative branch site (score: 119)
     taaatcatgattatt  TA-rich tract