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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TTCCTTCCTCATCCAGTGTTCTGTCCTAGCGCCGCCGCCGCCCCAGCTCGCCTTGCGTGACTGAGAGCTCGTCGGCTTCCGTCCACGCGTGAAGCGAGAGgtgcgactcttctgtctccatccatccccccttaaacgtttcctgtttgcatggcttgattcatgtgtgagcgttctgaatcctctggtcttaggcgctt...

Basic information

species Zea mays
transcript GRMZM2G455828_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|211418582|gb|FL177387.1|FL177387
EST:     CCTTGCGTGACTGAGAGCTCGTCGGCTTCCGTCCACGCGTGAAGCGAGAG                         CATGGACACCCAGGTGAAGCTTGCTGTTGTGGTGAAGGTGA
genomic: CCTTGCGTGACTGAGAGCTCGTCGGCTTCCGTCCACGCGTGAAGCGAGAGgtgcgactct ... attaatgcagCATGGACACCCAGGTGAAGCTTGCTGTTGTGGTGAAGGTGA
EST: gi|61117799|gb|DN558760.1|DN558760
EST:     CCTAGCGTGACTGAGAGCTCGTCGGCTTCAGTCCACGCGTGAAGCGAGAG                         CATGGACACCCAGGTGAAGCTTGCTGTTGTGGTGAAGGTGATGGGCAGGAC
genomic: CCTTGCGTGACTGAGAGCTCGTCGGCTTCCGTCCACGCGTGAAGCGAGAGgtgcgactct ... attaatgcagCATGGACACCCAGGTGAAGCTTGCTGTTGTGGTGAAGGTGATGGGCAGGAC
EST: gi|211020066|gb|FL177492.1|FL177492
EST:     CCTTGCGTGACTGANAGCTCGTCGGCTTCCGTCCACGCGTGAAGCGAGAG                         CATGGACACCCAGGTGAAGCTTGCTGTTGTGGTGAAGGTGATGGGCAGGAC
genomic: CCTTGCGTGACTGAGAGCTCGTCGGCTTCCGTCCACGCGTGAAGCGAGAGgtgcgactct ... attaatgcagCATGGACACCCAGGTGAAGCTTGCTGTTGTGGTGAAGGTGATGGGCAGGAC
EST: gi|31910962|gb|CD651686.1|CD651686
EST:     CCTTGCGTGACTGAGAGCTCGTCGGCTTCCGTCCACGCGTGAAGCGAGAG                         CATGGACACCCAGGTGAAGCTTGCTGTTGTGGTGAAGGTGATGGGCAGGAC
genomic: CCTTGCGTGACTGAGAGCTCGTCGGCTTCCGTCCACGCGTGAAGCGAGAGgtgcgactct ... attaatgcagCATGGACACCCAGGTGAAGCTTGCTGTTGTGGTGAAGGTGATGGGCAGGAC
EST: gi|211405825|gb|FL177316.1|FL177316
EST:     CCTTGCGTGACTGAGAGCTCGTCGGCTTCCGTCCACGCGTGAASS-AGAG                         CATGGACACCCAGGTGAAGCTTGCTGTTGTGGTGAAGGTGATGGGCAGGAC
genomic: CCTTGCGTGACTGAGAGCTCGTCGGCTTCCGTCCACGCGTGAAGCGAGAGgtgcgactct ... attaatgcagCATGGACACCCAGGTGAAGCTTGCTGTTGTGGTGAAGGTGATGGGCAGGAC
EST: gi|5005545|gb|AI711607.1|AI711607
EST:     CCTTGCGTGACTGAAAGCTCGTCGGCTTCCGTCCACGCGAGAAGCGAGAG                         CATGGACACCCAGGTGAAGCTTGCTGTTGTGGTGAAGGTGATGGGCAGGAC
genomic: CCTTGCGTGACTGAGAGCTCGTCGGCTTCCGTCCACGCGTGAAGCGAGAGgtgcgactct ... attaatgcagCATGGACACCCAGGTGAAGCTTGCTGTTGTGGTGAAGGTGATGGGCAGGAC
EST: gi|31612100|gb|CD568722.1|CD568722
EST:     CCTTGCGTGACTGAGAGCTCGTCGGCTTCCGTCCACGCGTGAAGCGAGAG                         CATGGACACCCAGGTGAAGCTTGCTGTTGTGGTGAAGGTGATGGGCAGGAC
genomic: CCTTGCGTGACTGAGAGCTCGTCGGCTTCCGTCCACGCGTGAAGCGAGAGgtgcgactct ... attaatgcagCATGGACACCCAGGTGAAGCTTGCTGTTGTGGTGAAGGTGATGGGCAGGAC
EST: gi|211416039|gb|FL177376.1|FL177376
EST:     CCTTGCGTGACTGAGAGCTCGTCGGCTTCCGTCCACGCGTGAA--SAGAG                         CATGGACACCCAGGTGAAGCTTGCTGTTGTGGTGAAGGTGATGGGCAGGAC
genomic: CCTTGCGTGACTGAGAGCTCGTCGGCTTCCGTCCACGCGTGAAGCGAGAGgtgcgactct ... attaatgcagCATGGACACCCAGGTGAAGCTTGCTGTTGTGGTGAAGGTGATGGGCAGGAC
EST: gi|211020060|gb|FL177486.1|FL177486
EST:     CCTTGCGTGACTGAGAGCTCGTCGGCTTCCGTCCACGCGTGAAGCGAGAG                         CATGGACACCCAGGTGAAGCTTGCTGTTGTGGTGAAGGTGATGGGCAGGAC
genomic: CCTTGCGTGACTGAGAGCTCGTCGGCTTCCGTCCACGCGTGAAGCGAGAGgtgcgactct ... attaatgcagCATGGACACCCAGGTGAAGCTTGCTGTTGTGGTGAAGGTGATGGGCAGGAC
EST: gi|31998113|gb|CD661929.1|CD661929
EST:     CCTTGCGTGACTGAGAGCTCGTCGGCTTCCGTCCACGCGTGAAGCGAGAG                         CATGGACACCCAGGTGAAGCTTGCTGTTGTGGTGAAGGTGATGGGCAGGAC
genomic: CCTTGCGTGACTGAGAGCTCGTCGGCTTCCGTCCACGCGTGAAGCGAGAGgtgcgactct ... attaatgcagCATGGACACCCAGGTGAAGCTTGCTGTTGTGGTGAAGGTGATGGGCAGGAC
EST: gi|211413482|gb|FL177356.1|FL177356
EST:     CCTTGCGTGACTGAGAGCTCGTCGGCTTCCGTCCACGCGTGAAGCGAGAG                         CATGGACACCCAGGTGAAGCTTGCTGTT
genomic: CCTTGCGTGACTGAGAGCTCGTCGGCTTCCGTCCACGCGTGAAGCGAGAGgtgcgactct ... attaatgcagCATGGACACCCAGGTGAAGCTTGCTGTT
EST: gi|211416038|gb|FL177375.1|FL177375
EST:     CCTTGCGTGACTGAGAGCTCGTCGGCTTCCGTCCACGCGTGAASS-AGAG                         CATGGACACCCAGGTGAAGCTTGCTGTTGTGGTGAAGGTGATGGGCAGGAC
genomic: CCTTGCGTGACTGAGAGCTCGTCGGCTTCCGTCCACGCGTGAAGCGAGAGgtgcgactct ... attaatgcagCATGGACACCCAGGTGAAGCTTGCTGTTGTGGTGAAGGTGATGGGCAGGAC

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 2 RNA-Seq libraries.


Block sizes: 31 (upstream exon), 49 (downstream exon)
Score: 76

TTCCTTCCTCATCCAGTGTTCTGTCCTAGCGCCGCCGCCGCCCCAGCTCGCCTTGCGTGACTGAGAGCTCGTCGGCTTCCGTCCACGCGTGAAGCGAGAGgtgcgactct ... attaatgcagCATGGACACCCAGGTGAAGCTTGCTGTTGTGGTGAAGGTGATGGGCAGGACCGGCTCCAGGGGTCAGGTGACCCAGGTCAGAGTGAAGTTTTTGGATGAC


Block sizes: 18 (upstream exon), 49 (downstream exon)
Score: 47

TTCCTTCCTCATCCAGTGTTCTGTCCTAGCGCCGCCGCCGCCCCAGCTCGCCTTGCGTGACTGAGAGCTCGTCGGCTTCCGTCCACGCGTGAAGCGAGAGgtgcgactct ... attaatgcagCATGGACACCCAGGTGAAGCTTGCTGTTGTGGTGAAGGTGATGGGCAGGACCGGCTCCAGGGGTCAGGTGACCCAGGTCAGAGTGAAGTTTTTGGATGAC




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TTCCTTCCTCATCCAGTGTTCTGTCCTAGCGCCGCCGCCGCCCCAGCTCGCCTTGCGTGACTGAGAGCTCGTCGGCTTCCGTCCACGCGTGAAGCGAGAGgtgcgactcttctgtctccatccatccccccttaaacgtttcctgtttgcatggcttgattcatgtgtgagcgttctgaatcctctggtcttaggcgctt

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -cccccct