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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CACCACTGAGTTATGGGTAGAGAAATTCTATAAGAAGGTAACCAATCTACCGGAGCCTTTTCCCCATGATCTTGTTGAGAAGTTAGAAGAATACCTGGATgtaagtattatataccatacattgcataagtgtactttcatgatgaaataatgcatatatatgttctgattttccttcatctatggtgccccttgtag

Basic information

species Zea mays
transcript GRMZM2G135968_T01
intron # 14
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|8577449|gb|BE130086.1|BE130086
EST:     CGGAGCCTTTTCCCCATGATCTTGTTGAGAAGTTAGAAGAATACCTGGAT                         AAACTTGAAGGGCAACTCGTGGACTTGTCTTCCTTATTGTATGACCACCGG
genomic: CGGAGCCTTTTCCCCATGATCTTGTTGAGAAGTTAGAAGAATACCTGGATgtaagtatta ... ccccttgtagAAACTTGAAGGGCAACTCGTGGACTTGTCTTCCTTATTGTATGACCACCGG
EST: gi|5525523|gb|AI861416.1|AI861416
EST:     CGGAGCCTTTTCCCCATGATCTTGTTGAGAAGTTAGAAGAATACCTGGAT                         AAACTTGAAGGGCAACTCGTGGACTTGTCTTCCTTATTGTATGACCACCGG
genomic: CGGAGCCTTTTCCCCATGATCTTGTTGAGAAGTTAGAAGAATACCTGGATgtaagtatta ... ccccttgtagAAACTTGAAGGGCAACTCGTGGACTTGTCTTCCTTATTGTATGACCACCGG
EST: gi|37376379|gb|CF624708.1|CF624708
EST:     CGGAGCCTTTTCCCCATGATCTTGTTGAGAAGTTAGAAGAATACCTGGAT                         AAACTTGAAGGGCAACTCGTGGACTTGTCTTCCTTATTGTATGACCACCGG
genomic: CGGAGCCTTTTCCCCATGATCTTGTTGAGAAGTTAGAAGAATACCTGGATgtaagtatta ... ccccttgtagAAACTTGAAGGGCAACTCGTGGACTTGTCTTCCTTATTGTATGACCACCGG
EST: gi|60343412|gb|DN210385.1|DN210385
EST:     CGGAGCCTTTTCCCCATGATCTTGTTGAGAAGTTAGAAGAATACCTGGAT                         AAACTTGAAGGGCAACTCGTGGACTTGTCTTCCTTATTGTATGACCACCGG
genomic: CGGAGCCTTTTCCCCATGATCTTGTTGAGAAGTTAGAAGAATACCTGGATgtaagtatta ... ccccttgtagAAACTTGAAGGGCAACTCGTGGACTTGTCTTCCTTATTGTATGACCACCGG
EST: gi|5713983|gb|AI943968.1|AI943968
EST:     CGGAGCCTTTTCCCCATGATCTTGTTGAGAAGTTAGAAGAATACCTGGAT                         AAACTTGAAGGGCAACTCGTGGACTTGTCTTCCTTATTGTATGACCACCGG
genomic: CGGAGCCTTTTCCCCATGATCTTGTTGAGAAGTTAGAAGAATACCTGGATgtaagtatta ... ccccttgtagAAACTTGAAGGGCAACTCGTGGACTTGTCTTCCTTATTGTATGACCACCGG
EST: gi|60398231|gb|DN231047.1|DN231047
EST:     CGGAGCCTTTTCCCCATGATCTTGTTGAGAAGTTAGAAGAATACCTGGAT                         AAACTTGAAGGGCAACTCGTGGACTTGTCTTCCTTATTGTATGACCACCGG
genomic: CGGAGCCTTTTCCCCATGATCTTGTTGAGAAGTTAGAAGAATACCTGGATgtaagtatta ... ccccttgtagAAACTTGAAGGGCAACTCGTGGACTTGTCTTCCTTATTGTATGACCACCGG
EST: gi|60397588|gb|DN230404.1|DN230404
EST:     CGGAGCCTTTTCCCCATGATCTTGTTGAGAAGTTAGAAGAATACCTGGAT                         AAACTTGAAGGGCAACTCGTGGACTTGTCTTCCTTATTGTATGACCACCGG
genomic: CGGAGCCTTTTCCCCATGATCTTGTTGAGAAGTTAGAAGAATACCTGGATgtaagtatta ... ccccttgtagAAACTTGAAGGGCAACTCGTGGACTTGTCTTCCTTATTGTATGACCACCGG
EST: gi|31357399|gb|CD441756.1|CD441756
EST:     CGGAGCCTTTTCCCCATGATCTTGTTGAGAAGTTAGAAGAATACCTGGAT                         AAACTTGAAGGGCAACTCGTGGACTTGTCTTCCTTATTGTATGACCACCGG
genomic: CGGAGCCTTTTCCCCATGATCTTGTTGAGAAGTTAGAAGAATACCTGGATgtaagtatta ... ccccttgtagAAACTTGAAGGGCAACTCGTGGACTTGTCTTCCTTATTGTATGACCACCGG

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: 48 (upstream exon), 47 (downstream exon)
Score: 110

CACCACTGAGTTATGGGTAGAGAAATTCTATAAGAAGGTAACCAATCTACCGGAGCCTTTTCCCCATGATCTTGTTGAGAAGTTAGAAGAATACCTGGATgtaagtatta ... ccccttgtagAAACTTGAAGGGCAACTCGTGGACTTGTCTTCCTTATTGTATGACCACCGGCTGGTCGATGCATATCAAAACAGTACCGATATCCTGCAAAGCACTATTT


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

CACCACTGAGTTATGGGTAGAGAAATTCTATAAGAAGGTAACCAATCTACCGGAGCCTTTTCCCCATGATCTTGTTGAGAAGTTAGAAGAATACCTGGATgtaagtatta ... ccccttgtagAAACTTGAAGGGCAACTCGTGGACTTGTCTTCCTTATTGTATGACCACCGGCTGGTCGATGCATATCAAAACAGTACCGATATCCTGCAAAGCACTATTT


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 212

CACCACTGAGTTATGGGTAGAGAAATTCTATAAGAAGGTAACCAATCTACCGGAGCCTTTTCCCCATGATCTTGTTGAGAAGTTAGAAGAATACCTGGATgtaagtatta ... ccccttgtagAAACTTGAAGGGCAACTCGTGGACTTGTCTTCCTTATTGTATGACCACCGGCTGGTCGATGCATATCAAAACAGTACCGATATCCTGCAAAGCACTATTT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 194

CACCACTGAGTTATGGGTAGAGAAATTCTATAAGAAGGTAACCAATCTACCGGAGCCTTTTCCCCATGATCTTGTTGAGAAGTTAGAAGAATACCTGGATgtaagtatta ... ccccttgtagAAACTTGAAGGGCAACTCGTGGACTTGTCTTCCTTATTGTATGACCACCGGCTGGTCGATGCATATCAAAACAGTACCGATATCCTGCAAAGCACTATTT


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CACCACTGAGTTATGGGTAGAGAAATTCTATAAGAAGGTAACCAATCTACCGGAGCCTTTTCCCCATGATCTTGTTGAGAAGTTAGAAGAATACCTGGATgtaagtattatataccatacattgcataagtgtactttcatgatgaaataatgcatatatatgttctgattttccttcatctatggtgccccttgtag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGT