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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TTTAAACCCTGACGCCACCTTGTGCTGTTCAAGGAGTGAATACTGAACAGTCCAGTCAGTCGTCTCTACCTCATACGCCTGACGAATCTTGATTCTTGAGgtgagcctgcctctctcgtctccctcttcccctcgatgcttcttgctcctcctgcagctgtaaccctagatctgtgggggttttttttgggtggtgggtg...

Basic information

species Zea mays
transcript GRMZM2G082346_T01
intron # 1
splice site 5'
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|211110939|gb|FL028255.1|FL028255
EST:     TCCAGTCAGTCGTCTCTACCTCATACGCCTGACGAATCTTGATTCTTGAG                         CTTGATTGGGTGTCATCTCTTTTAGCTGCAACTGCAGCTGGCTGTGATCAT
genomic: TCCAGTCAGTCGTCTCTACCTCATACGCCTGACGAATCTTGATTCTTGAGgtgagcctgc ... tatgctccagCTTGATTGGGTGTCATCTCTTTTAGCTGCAACTGCAGCTGGCTGTGATCAT
EST: gi|211110940|gb|FL028256.1|FL028256
EST:     TCCAGGCAGTCGTCTCTACCTCATCCGCCTGACGAATCTTGGTTCTTGAG                         CTTGATTGGGTGTCATCTCTTTTAGCTGCAACTGCAGCTGGCTGTGATCAT
genomic: TCCAGTCAGTCGTCTCTACCTCATACGCCTGACGAATCTTGATTCTTGAGgtgagcctgc ... tatgctccagCTTGATTGGGTGTCATCTCTTTTAGCTGCAACTGCAGCTGGCTGTGATCAT
EST: gi|211135733|gb|FL282459.1|FL282459
EST:     TCCAGTCAGTCGTCTCTACCTCATACGCCTGACGAATCTTGATTCTTGAG                         CTTGATTGGGTGTCATCTCTTTTAGCTGCAACTGCAGCTGGCTGTGATCAT
genomic: TCCAGTCAGTCGTCTCTACCTCATACGCCTGACGAATCTTGATTCTTGAGgtgagcctgc ... tatgctccagCTTGATTGGGTGTCATCTCTTTTAGCTGCAACTGCAGCTGGCTGTGATCAT
EST: gi|88751889|gb|DY536030.1|DY536030
EST:     CGCCTGACGAATCTTGATTCTTGAG                         CTTGATTGGGTGTCATCTCTTTTAGCTGCAGCTGCAGCTGGCTGTGATCAT
genomic: CGCCTGACGAATCTTGATTCTTGAGgtgagcctgc ... tatgctccagCTTGATTGGGTGTCATCTCTTTTAGCTGCAACTGCAGCTGGCTGTGATCAT
EST: gi|74243445|gb|DT651359.1|DT651359
EST:     TCCAGTCAGTCGTCTCTACCTCATACGCCTGACGAATCTTGATTCTTGAG                         CTTGATTGGGTGTCATCTCTTTTAGCTGCAACTGCAGCTGGCTGTGATCAT
genomic: TCCAGTCAGTCGTCTCTACCTCATACGCCTGACGAATCTTGATTCTTGAGgtgagcctgc ... tatgctccagCTTGATTGGGTGTCATCTCTTTTAGCTGCAACTGCAGCTGGCTGTGATCAT
EST: gi|211135735|gb|FL282461.1|FL282461
EST:     TCCAGTCAGTCGTCTCTACCTCATACGCCTGACGAATCTTGATTCTTGAG                         CTTGATTGGGTGTCATCTCTTTTAGCTGCAACTGCA
genomic: TCCAGTCAGTCGTCTCTACCTCATACGCCTGACGAATCTTGATTCTTGAGgtgagcctgc ... tatgctccagCTTGATTGGGTGTCATCTCTTTTAGCTGCAACTGCA
EST: gi|13126610|gb|BG317180.1|BG317180
EST:     CCAG-CAGTCGTCTCTACCTCATACGCCTGACGAATCTTGATTCTTGAG                         CTTGATTGGGTGTCATCTCTTTTAGCTGCAACTGCAGCTGGCTGTGATCAT
genomic: CCAGTCAGTCGTCTCTACCTCATACGCCTGACGAATCTTGATTCTTGAGgtgagcctgc ... tatgctccagCTTGATTGGGTGTCATCTCTTTTAGCTGCAACTGCAGCTGGCTGTGATCAT
EST: gi|91056519|gb|EB166937.1|EB166937
EST:     GCCTGACGAATCTTGATTCTTGAG                         CTTGATTGGGTGTCATCTCTTTTAGCTGCAACTGCAGCTGGCTGTGATCAT
genomic: GCCTGACGAATCTTGATTCTTGAGgtgagcctgc ... tatgctccagCTTGATTGGGTGTCATCTCTTTTAGCTGCAACTGCAGCTGGCTGTGATCAT

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), 49 (downstream exon)
Score: 85

TTTAAACCCTGACGCCACCTTGTGCTGTTCAAGGAGTGAATACTGAACAGTCCAGTCAGTCGTCTCTACCTCATACGCCTGACGAATCTTGATTCTTGAGgtgagcctgc ... tatgctccagCTTGATTGGGTGTCATCTCTTTTAGCTGCAACTGCAGCTGGCTGTGATCATGGCATCGCTGAGTGCTGACCTCTTTTACGACATACTCAAGCGTCTCGAT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 27

TTTAAACCCTGACGCCACCTTGTGCTGTTCAAGGAGTGAATACTGAACAGTCCAGTCAGTCGTCTCTACCTCATACGCCTGACGAATCTTGATTCTTGAGgtgagcctgc ... tatgctccagCTTGATTGGGTGTCATCTCTTTTAGCTGCAACTGCAGCTGGCTGTGATCATGGCATCGCTGAGTGCTGACCTCTTTTACGACATACTCAAGCGTCTCGAT


Block sizes: 39 (upstream exon), 49 (downstream exon)
Score: 21

TTTAAACCCTGACGCCACCTTGTGCTGTTCAAGGAGTGAATACTGAACAGTCCAGTCAGTCGTCTCTACCTCATACGCCTGACGAATCTTGATTCTTGAGgtgagcctgc ... tatgctccagCTTGATTGGGTGTCATCTCTTTTAGCTGCAACTGCAGCTGGCTGTGATCATGGCATCGCTGAGTGCTGACCTCTTTTACGACATACTCAAGCGTCTCGAT


Block sizes: 49 (upstream exon), 46 (downstream exon)
Score: 22

TTTAAACCCTGACGCCACCTTGTGCTGTTCAAGGAGTGAATACTGAACAGTCCAGTCAGTCGTCTCTACCTCATACGCCTGACGAATCTTGATTCTTGAGgtgagcctgc ... tatgctccagCTTGATTGGGTGTCATCTCTTTTAGCTGCAACTGCAGCTGGCTGTGATCATGGCATCGCTGAGTGCTGACCTCTTTTACGACATACTCAAGCGTCTCGAT


Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TTTAAACCCTGACGCCACCTTGTGCTGTTCAAGGAGTGAATACTGAACAGTCCAGTCAGTCGTCTCTACCTCATACGCCTGACGAATCTTGATTCTTGAGgtgagcctgcctctctcgtctccctcttcccctcgatgcttcttgctcctcctgcagctgtaaccctagatctgtgggggttttttttgggtggtgggtg

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -cctctctc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - cctcttcc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ctcctcct