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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGGCCCTTTGAAATGCCGAAAGAGAGCCGTTCCCTGTTGCCGAAAGCCCGAAACTAGggcctgtttggttcgtggctaactgcgccacactttgcctaaggttaggcgttcgaattgaagaactaaccttaggcagaaaagttagacaaagtgtggcaagttaggcagtgaaccaaacaagcccctag

Basic information

species Zea mays
transcript GRMZM2G102021_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|211105117|gb|FL057783.1|FL057783
EST:     TTGAAATGCCGAAAGAGAGCCGTTCCCTGTTGCCGAAAGCCCGAAACTAG                         TCTTCCCTCCTG
genomic: TTGAAATGCCGAAAGAGAGCCGTTCCCTGTTGCCGAAAGCCCGAAACTAGggcctgtttg ... aagcccctagTCTTCCCTCCTG
EST: gi|211177671|gb|FL258730.1|FL258730
EST:     GAAAGCCCGAAACTAG                         TCTTCCCTCCTGCTGGCGGCGTGCGGAGGGCCGGAGGCCGGGTCGACAAGA
genomic: GAAAGCCCGAAACTAGggcctgtttg ... aagcccctagTCTTCCCTCCTGCTGGCGGCGTGCGGAGGGCCGGAGGCCGGGTCGACAAGA
EST: gi|211177678|gb|FL258737.1|FL258737
EST:     GAAAGCCCGAAACTAG                         TCTTCCCTCCTGCTGGCGGCGTGCGGAGGGCCGGAGGCCGGGTCGACAAGA
genomic: GAAAGCCCGAAACTAGggcctgtttg ... aagcccctagTCTTCCCTCCTGCTGGCGGCGTGCGGAGGGCCGGAGGCCGGGTCGACAAGA
EST: gi|211177676|gb|FL258735.1|FL258735
EST:     GAAAGCCCGAAACTAG                         TCTTCCCTCCTGCTGGCGGCGTGCGGAGGGCCGGAGGCCGGGTCGACAAGA
genomic: GAAAGCCCGAAACTAGggcctgtttg ... aagcccctagTCTTCCCTCCTGCTGGCGGCGTGCGGAGGGCCGGAGGCCGGGTCGACAAGA
EST: gi|22546043|gb|BU098364.1|BU098364
EST:     CCCGAAACTAG                         TCTTCCCTCCTGCTGGCGGCGTGCGGAGGGCCGGAGGCCGGGTCGACAAGA
genomic: CCCGAAACTAGggcctgtttg ... aagcccctagTCTTCCCTCCTGCTGGCGGCGTGCGGAGGGCCGGAGGCCGGGTCGACAAGA
EST: gi|87155707|gb|DY400496.1|DY400496
EST:     GCCGTTCCCTGTTGCCGAAAGCCCGAAACTAG                         TCTTCCCTCCTGCTGGCGGCGTGCGGAGGGCCGGAGGCCGGGTCGACAAGA
genomic: GCCGTTCCCTGTTGCCGAAAGCCCGAAACTAGggcctgtttg ... aagcccctagTCTTCCCTCCTGCTGGCGGCGTGCGGAGGGCCGGAGGCCGGGTCGACAAGA
EST: gi|211105119|gb|FL057785.1|FL057785
EST:     GCCGAAAGCCCGAAACTAG                         TCTTCCCTCCTGCTGGCGGCGTGCGGAGGGCCGGAGGCCGGGTCGACAAGA
genomic: GCCGAAAGCCCGAAACTAGggcctgtttg ... aagcccctagTCTTCCCTCCTGCTGGCGGCGTGCGGAGGGCCGGAGGCCGGGTCGACAAGA
EST: gi|211287766|gb|FL258743.1|FL258743
EST:     AAAGCCCGAAACTAG                         TCTTCCCTCCTGCTGGCGGCGTGCGGAGGGCCGG
genomic: AAAGCCCGAAACTAGggcctgtttg ... aagcccctagTCTTCCCTCCTGCTGGCGGCGTGCGGAGGGCCGG
EST: gi|22818908|gb|BU498998.1|BU498998
EST:     GCCGTTCCCTGTTGCCGAAAGCCTGAAACTAG                         TCTTCCCTCCTGCTGGCGGCGTGCGGAGGGCCGGAGGCCGGGTCGACAAGA
genomic: GCCGTTCCCTGTTGCCGAAAGCCCGAAACTAGggcctgtttg ... aagcccctagTCTTCCCTCCTGCTGGCGGCGTGCGGAGGGCCGGAGGCCGGGTCGACAAGA
EST: gi|87156122|gb|DY400911.1|DY400911
EST:     CCCGAAACTAG                         TCTTCCCTCCTGCTGGCGGCGTGCGGAGGGCCGGAGGCCGGGTCGACAAGA
genomic: CCCGAAACTAGggcctgtttg ... aagcccctagTCTTCCCTCCTGCTGGCGGCGTGCGGAGGGCCGGAGGCCGGGTCGACAAGA

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: 43 (upstream exon), 49 (downstream exon)
Score: 108

AGGCCCTTTGAAATGCCGAAAGAGAGCCGTTCCCTGTTGCCGAAAGCCCGAAACTAGggcctgtttg ... aagcccctagTCTTCCCTCCTGCTGGCGGCGTGCGGAGGGCCGGAGGCCGGGTCGACAAGAGGAGATGACGTTGGCGGCGGGGCTGGGTTACGCCCTGATCGCGCTGGGC


Block sizes: 41 (upstream exon), 49 (downstream exon)
Score: 51

AGGCCCTTTGAAATGCCGAAAGAGAGCCGTTCCCTGTTGCCGAAAGCCCGAAACTAGggcctgtttg ... aagcccctagTCTTCCCTCCTGCTGGCGGCGTGCGGAGGGCCGGAGGCCGGGTCGACAAGAGGAGATGACGTTGGCGGCGGGGCTGGGTTACGCCCTGATCGCGCTGGGC


Block sizes: 42 (upstream exon), 49 (downstream exon)
Score: 40

AGGCCCTTTGAAATGCCGAAAGAGAGCCGTTCCCTGTTGCCGAAAGCCCGAAACTAGggcctgtttg ... aagcccctagTCTTCCCTCCTGCTGGCGGCGTGCGGAGGGCCGGAGGCCGGGTCGACAAGAGGAGATGACGTTGGCGGCGGGGCTGGGTTACGCCCTGATCGCGCTGGGC


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 64

AGGCCCTTTGAAATGCCGAAAGAGAGCCGTTCCCTGTTGCCGAAAGCCCGAAACTAGggcctgtttg ... aagcccctagTCTTCCCTCCTGCTGGCGGCGTGCGGAGGGCCGGAGGCCGGGTCGACAAGAGGAGATGACGTTGGCGGCGGGGCTGGGTTACGCCCTGATCGCGCTGGGC


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AGGCCCTTTGAAATGCCGAAAGAGAGCCGTTCCCTGTTGCCGAAAGCCCGAAACTAGggcctgtttggttcgtggctaactgcgccacactttgcctaaggttaggcgttcgaattgaagaactaaccttaggcagaaaagttagacaaagtgtggcaagttaggcagtgaaccaaacaagcccctag

- - - - - - - - -  AAGAGA