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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ACAGATGGCTGCGGGGGGCGGGCGGTGCTTGCTCGCCTTGGCGCTCGCCGCCGCTTGGATCTCCGGCGCGGTGGTCGCCGCCTCATCGTCGGGTGAGCAGgtacgtaaggggtggatgggcgctcctggttcacgccaattttactcgtgcgcagtttttgtgcggaaattatgatctttcgttgattcggatttgctag...

Basic information

species Zea mays
transcript GRMZM2G167728_T02
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|148944392|gb|EC889499.2|EC889499
EST:     CCGCTTGGATCTCCGGCGCGGTGGTCGCCGCCTCATCGTCGGGTGAGCAG                         GAAGGCGGAAGCCGCACACCCGTCAAATGCATGCCCTGCTCTAGAACGTAC
genomic: CCGCTTGGATCTCCGGCGCGGTGGTCGCCGCCTCATCGTCGGGTGAGCAGgtacgtaagg ... cattgcgcagGAAGGCGGAAGCCGCACACCCGTCAAATGCATGCCCTGCTCTAGAACGTAC
EST: gi|76293671|gb|DV033239.1|DV033239
EST:     CCGCTTGGATCTCCGGCGCGGTGGTCGCCGCCTCATCGTCGGGTGAGCAG                         GAAGGCGGAAGCCGCACACCCGTCAAATGCATGCCCTGCTCTAGAACGTAC
genomic: CCGCTTGGATCTCCGGCGCGGTGGTCGCCGCCTCATCGTCGGGTGAGCAGgtacgtaagg ... cattgcgcagGAAGGCGGAAGCCGCACACCCGTCAAATGCATGCCCTGCTCTAGAACGTAC
EST: gi|211020371|gb|FL072946.1|FL072946
EST:     CCGCTTGGATCTCCGGCGCGGTGGTCGCCGCCTCATCGTCGGGTGAGCAG                         GAAGGCGGAAGCCGCACACCCGTCAAATGCATGCCCTGCTCTAGAACGTAC
genomic: CCGCTTGGATCTCCGGCGCGGTGGTCGCCGCCTCATCGTCGGGTGAGCAGgtacgtaagg ... cattgcgcagGAAGGCGGAAGCCGCACACCCGTCAAATGCATGCCCTGCTCTAGAACGTAC
EST: gi|76933654|gb|DV173532.1|DV173532
EST:     CCGCTTGGATCTCCGGCGCGGTGGTCGCCGCCTCATCGTCGGGTGAGCAG                         GAAGGCGGAAGCCGCACACCCGTCAAATGCATGCCCTGCTCTAGAACGTAC
genomic: CCGCTTGGATCTCCGGCGCGGTGGTCGCCGCCTCATCGTCGGGTGAGCAGgtacgtaagg ... cattgcgcagGAAGGCGGAAGCCGCACACCCGTCAAATGCATGCCCTGCTCTAGAACGTAC
EST: gi|9794782|gb|BE553090.1|BE553090
EST:     CCGCTTGTATTTCTGGCGCGGTGGTCGCCGCCTCATCGTCGGGTGAGCAG                         GAAGGCGGAAGCCGCAAACCCGTCAAATGCATGCCCTGCTCTAGAACGTAC
genomic: CCGCTTGGATCTCCGGCGCGGTGGTCGCCGCCTCATCGTCGGGTGAGCAGgtacgtaagg ... cattgcgcagGAAGGCGGAAGCCGCACACCCGTCAAATGCATGCCCTGCTCTAGAACGTAC
EST: gi|50332944|gb|CO528070.1|CO528070
EST:     CCGCTTGGATCTCCGGCGCGGTGGTCGCCGCCTCATCGTCGGGTGAGCAG                         GAAGGCGGAAGCCGCACACCCGTCAAATGCATGCCCTGCTCTAGAACGTAC
genomic: CCGCTTGGATCTCCGGCGCGGTGGTCGCCGCCTCATCGTCGGGTGAGCAGgtacgtaagg ... cattgcgcagGAAGGCGGAAGCCGCACACCCGTCAAATGCATGCCCTGCTCTAGAACGTAC
EST: gi|76017740|gb|DT944910.1|DT944910
EST:     CCGCTTGGATCTCCGGCGCGGTGGTCGCCGCCTCATCGTCGGGTGAGCAG                         GAAGGCGGAAGCCGCACACCCGTCAAATGCATGCCCTGCTCTAGAACGTAC
genomic: CCGCTTGGATCTCCGGCGCGGTGGTCGCCGCCTCATCGTCGGGTGAGCAGgtacgtaagg ... cattgcgcagGAAGGCGGAAGCCGCACACCCGTCAAATGCATGCCCTGCTCTAGAACGTAC

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: 46 (upstream exon), 47 (downstream exon)
Score: 14

ACAGATGGCTGCGGGGGGCGGGCGGTGCTTGCTCGCCTTGGCGCTCGCCGCCGCTTGGATCTCCGGCGCGGTGGTCGCCGCCTCATCGTCGGGTGAGCAGgtacgtaagg ... cattgcgcagGAAGGCGGAAGCCGCACACCCGTCAAATGCATGCCCTGCTCTAGAACGTACATTGGTGGTGCACATCTGGACACCTTGACGGGCCAGCTTGCTCAGCGTC


Block sizes: 42 (upstream exon), 40 (downstream exon)
Score: 4

ACAGATGGCTGCGGGGGGCGGGCGGTGCTTGCTCGCCTTGGCGCTCGCCGCCGCTTGGATCTCCGGCGCGGTGGTCGCCGCCTCATCGTCGGGTGAGCAGgtacgtaagg ... cattgcgcagGAAGGCGGAAGCCGCACACCCGTCAAATGCATGCCCTGCTCTAGAACGTACATTGGTGGTGCACATCTGGACACCTTGACGGGCCAGCTTGCTCAGCGTC


Block sizes: 42 (upstream exon), 45 (downstream exon)
Score: 9

ACAGATGGCTGCGGGGGGCGGGCGGTGCTTGCTCGCCTTGGCGCTCGCCGCCGCTTGGATCTCCGGCGCGGTGGTCGCCGCCTCATCGTCGGGTGAGCAGgtacgtaagg ... cattgcgcagGAAGGCGGAAGCCGCACACCCGTCAAATGCATGCCCTGCTCTAGAACGTACATTGGTGGTGCACATCTGGACACCTTGACGGGCCAGCTTGCTCAGCGTC


Block sizes: 24 (upstream exon), 44 (downstream exon)
Score: 6

ACAGATGGCTGCGGGGGGCGGGCGGTGCTTGCTCGCCTTGGCGCTCGCCGCCGCTTGGATCTCCGGCGCGGTGGTCGCCGCCTCATCGTCGGGTGAGCAGgtacgtaagg ... cattgcgcagGAAGGCGGAAGCCGCACACCCGTCAAATGCATGCCCTGCTCTAGAACGTACATTGGTGGTGCACATCTGGACACCTTGACGGGCCAGCTTGCTCAGCGTC


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ACAGATGGCTGCGGGGGGCGGGCGGTGCTTGCTCGCCTTGGCGCTCGCCGCCGCTTGGATCTCCGGCGCGGTGGTCGCCGCCTCATCGTCGGGTGAGCAGgtacgtaaggggtggatgggcgctcctggttcacgccaattttactcgtgcgcagtttttgtgcggaaattatgatctttcgttgattcggatttgctag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCAG