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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CAAACCCTTGCCTTTCGTGTCTGTTCATATTTCTCGTGGCTTGGTTATTCTGAAGGGTAAAACTTGCACAAGGCAGCTTTGATATTACAACAATGGATAGgtaacttttatattgactggctatttaggttgcttttatcttataacacttcttagttctacagattctctattttagattatttttgccttatcgcatgccttcgcag

Basic information

species Zea mays
transcript GRMZM2G178822_T01
intron # 5
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|211443458|gb|FL042456.1|FL042456
EST:     TGAAGGGTAAAACTTGCACAAGGCAGCTTTGATATTACAACAATGGATAG                         ATTCAAGTTGATTAAGGAAGTTGGCGATGGGACTTTTGGGAGTGTATGGCG
genomic: TGAAGGGTAAAACTTGCACAAGGCAGCTTTGATATTACAACAATGGATAGgtaactttta ... gccttcgcagATTCAAGTTGATTAAGGAAGTTGGCGATGGGACTTTTGGGAGTGTATGGCG
EST: gi|211443465|gb|FL042463.1|FL042463
EST:     TGAAGGGTAAAACTTGCACAAGGCAGCTTTGATATTACAACAATGGATAG                         ATTCAAGTTGATTAAGGAAGTTGGCGATGGGACTTTTGGGAGTGTATGGCG
genomic: TGAAGGGTAAAACTTGCACAAGGCAGCTTTGATATTACAACAATGGATAGgtaactttta ... gccttcgcagATTCAAGTTGATTAAGGAAGTTGGCGATGGGACTTTTGGGAGTGTATGGCG
EST: gi|211443464|gb|FL042462.1|FL042462
EST:     TGAAGGGTAAAACTTGCACAAGGCAGCTTTGATATTACAACAATGGATAG                         ATTCAAGTTGATTAAGGAAGTTGGCGATGGGACTTTTGGGAGTGTATGGCG
genomic: TGAAGGGTAAAACTTGCACAAGGCAGCTTTGATATTACAACAATGGATAGgtaactttta ... gccttcgcagATTCAAGTTGATTAAGGAAGTTGGCGATGGGACTTTTGGGAGTGTATGGCG
EST: gi|211441336|gb|FL042450.1|FL042450
EST:     TGAAGGGTAAAACTTGCACAAGGCAGCTTTGATATTACAACAATGGATAG                         ATTCAAGTTGATTAAGGAAGTTGGCGATGGGACTTTTGGGAGTGTATGGCG
genomic: TGAAGGGTAAAACTTGCACAAGGCAGCTTTGATATTACAACAATGGATAGgtaactttta ... gccttcgcagATTCAAGTTGATTAAGGAAGTTGGCGATGGGACTTTTGGGAGTGTATGGCG
EST: gi|211443461|gb|FL042459.1|FL042459
EST:     TGAAGGGTAAAACTTGCACAAGGCAGCTTTGATATTACAACAATGGATAG                         ATTCAAGTTGATTAAGGAAGTTGGCGATGGGACTTTTGGGAGTGTATGGCG
genomic: TGAAGGGTAAAACTTGCACAAGGCAGCTTTGATATTACAACAATGGATAGgtaactttta ... gccttcgcagATTCAAGTTGATTAAGGAAGTTGGCGATGGGACTTTTGGGAGTGTATGGCG
EST: gi|211443466|gb|FL042464.1|FL042464
EST:     TGAAGGGTAAAACTTGCACAAGGCAGCTTTGATATTACAACAATGGATAG                         ATTCAAGTTGATTAAGGAAGTTGGCGATGGGACTTTTGGGAGTGTATGGCG
genomic: TGAAGGGTAAAACTTGCACAAGGCAGCTTTGATATTACAACAATGGATAGgtaactttta ... gccttcgcagATTCAAGTTGATTAAGGAAGTTGGCGATGGGACTTTTGGGAGTGTATGGCG
EST: gi|211443460|gb|FL042458.1|FL042458
EST:     TGAAGGGTAAAACTTGCACAAGGCAGCTTTGATATTACAACAATGGATAG                         ATTCAAGTTGATTAAGGAAGTTGGCGATGGGACTTTTGGGAGTGTATGGCG
genomic: TGAAGGGTAAAACTTGCACAAGGCAGCTTTGATATTACAACAATGGATAGgtaactttta ... gccttcgcagATTCAAGTTGATTAAGGAAGTTGGCGATGGGACTTTTGGGAGTGTATGGCG
EST: gi|211443457|gb|FL042455.1|FL042455
EST:     TGAAGGGTAAAACTTGCACAAGGCAGCTTTGATATTACAACAATGGATAG                         ATTCAAGTTGATTAAGGAAGTTGGCGANGGGACTTTTGGGAGTGTATGGCG
genomic: TGAAGGGTAAAACTTGCACAAGGCAGCTTTGATATTACAACAATGGATAGgtaactttta ... gccttcgcagATTCAAGTTGATTAAGGAAGTTGGCGATGGGACTTTTGGGAGTGTATGGCG
EST: gi|211441339|gb|FL042453.1|FL042453
EST:     TGAAGGGTAAAACTTGCACNAGGCAGCTTTGATATTACAACAATGGATAG                         ATTCAAGTTGATTAAGGAAGTTGGCGATGGGACTTTTGGGAGTGTATGGCG
genomic: TGAAGGGTAAAACTTGCACAAGGCAGCTTTGATATTACAACAATGGATAGgtaactttta ... gccttcgcagATTCAAGTTGATTAAGGAAGTTGGCGATGGGACTTTTGGGAGTGTATGGCG
EST: gi|113748605|gb|DW871977.1|DW871977
EST:     TGAAGGGTAAAACTTGCACAAGGCAGCTTTGATATTACAACAATGGATAG                         ATTCAAGTTGATTAAGGAAGTTGGCGATGGGACTTTTGGGAGTGTATGG
genomic: TGAAGGGTAAAACTTGCACAAGGCAGCTTTGATATTACAACAATGGATAGgtaactttta ... gccttcgcagATTCAAGTTGATTAAGGAAGTTGGCGATGGGACTTTTGGGAGTGTATGG
EST: gi|211443463|gb|FL042461.1|FL042461
EST:     TGAAGGGTAAAACTTGCACAAGGCAGCTTTGATATTACAACAATGGATAG                         ATTCAAGTTGATTAAGGAAGTTGGCGATGGGACTTTTGGGAGTGTATGGCG
genomic: TGAAGGGTAAAACTTGCACAAGGCAGCTTTGATATTACAACAATGGATAGgtaactttta ... gccttcgcagATTCAAGTTGATTAAGGAAGTTGGCGATGGGACTTTTGGGAGTGTATGGCG

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: 385

CAAACCCTTGCCTTTCGTGTCTGTTCATATTTCTCGTGGCTTGGTTATTCTGAAGGGTAAAACTTGCACAAGGCAGCTTTGATATTACAACAATGGATAGgtaactttta ... gccttcgcagATTCAAGTTGATTAAGGAAGTTGGCGATGGGACTTTTGGGAGTGTATGGCGTGCTATGAATAAACAGAATGGCGAAGTT


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 195

CAAACCCTTGCCTTTCGTGTCTGTTCATATTTCTCGTGGCTTGGTTATTCTGAAGGGTAAAACTTGCACAAGGCAGCTTTGATATTACAACAATGGATAGgtaactttta ... gccttcgcagATTCAAGTTGATTAAGGAAGTTGGCGATGGGACTTTTGGGAGTGTATGGCGTGCTATGAATAAACAGAATGGCGAAGTT


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 124

CAAACCCTTGCCTTTCGTGTCTGTTCATATTTCTCGTGGCTTGGTTATTCTGAAGGGTAAAACTTGCACAAGGCAGCTTTGATATTACAACAATGGATAGgtaactttta ... gccttcgcagATTCAAGTTGATTAAGGAAGTTGGCGATGGGACTTTTGGGAGTGTATGGCGTGCTATGAATAAACAGAATGGCGAAGTT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 338

CAAACCCTTGCCTTTCGTGTCTGTTCATATTTCTCGTGGCTTGGTTATTCTGAAGGGTAAAACTTGCACAAGGCAGCTTTGATATTACAACAATGGATAGgtaactttta ... gccttcgcagATTCAAGTTGATTAAGGAAGTTGGCGATGGGACTTTTGGGAGTGTATGGCGTGCTATGAATAAACAGAATGGCGAAGTT


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CAAACCCTTGCCTTTCGTGTCTGTTCATATTTCTCGTGGCTTGGTTATTCTGAAGGGTAAAACTTGCACAAGGCAGCTTTGATATTACAACAATGGATAGgtaacttttatattgactggctatttaggttgcttttatcttataacacttcttagttctacagattctctattttagattatttttgccttatcgcatgccttcgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGCT