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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATCGCCAACAAAGAACAATTTGAATAGCAACAATAGCATCAAAGATATTTCTCAAGAGCACAAGAAATTAGCAAATGGATTCAACCTTTTCCAGAAGGAGgtaatgacggaacttctcttggtgtattatttctttcaggttgtaatacatattatgtgaaaagcaaatttcacttgttgggaaaatgtccagacatttt...

Basic information

species Zea mays
transcript GRMZM2G179421_T01
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G179421_T02 (Zea mays), 5'ss of exon 2
lower sequence: LOC_Os10g21940.1 (Oryza sativa), 5'ss of exon 9
ATCGCCAACAAAGAACAATTTGAATAGCAACAATAGCATCAAAGATATTTCTCAAGAGCACAAGAAATTAGCAAATGGATTCAACCTTTTCCAGAAGGAGgtaatgacggaacttctcttggtgtattatttctttcaggttgtaatacatattatgtgaaaagcaaatttcacttgttgggaaaatgtccagacatttt-------
  |  |   | ||||  ||| || | | || | |  |||  | ||||||||    ||||| | ||||||||||  ||  || || | ||||||  |||||||| ||    |||||||||||||||||||||||||  |      | | |||    | | | |||    |||       |||  | ||  |  |  |  |        
GCCATCTTTAGAGAATCATTCGACTGGTAAAACTTCCATTGAGGATATTTCAATGGAGCATAGGAAATTAGCAGTTGACTTGAATCATTTCCATCAGGAGgta-tgtgaaaacttctcttggtgtattatttcttcaaacacaaattgcat----tcttacaagtt--tttagacgactggatatatccctgggtacctgctgaaaa
















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|22545689|gb|BU098048.1|BU098048
EST:     CTCAAGAGCACAAGAAATTAGCAAATGGATTCAACCTTTTCCAGAAGGAG                         CTGGAAAGACTGAAAGATGAGAATCTGTCTCCTCTTCTTCCCCTAGACGTC
genomic: CTCAAGAGCACAAGAAATTAGCAAATGGATTCAACCTTTTCCAGAAGGAGgtaatgacgg ... ttgtgtgcagCTGGAAAGACTGAAAGATGAGAATCTGTCTCCTCTTCTTCCCCTAGACGTC
EST: gi|211190020|gb|FL186110.1|FL186110
EST:     CAAGAGCACAAGAAATTAGCAAATGGATTCAACCTTTTCCAGAAGGAG                         CTGGAAAGACTGAAAGATGAGAATCTGTCTCCTCTTCTTCCCCTAGACGTC
genomic: CAAGAGCACAAGAAATTAGCAAATGGATTCAACCTTTTCCAGAAGGAGgtaatgacgg ... ttgtgtgcagCTGGAAAGACTGAAAGATGAGAATCTGTCTCCTCTTCTTCCCCTAGACGTC
EST: gi|6101978|gb|AW126448.1|AW126448
EST:     CTCAAGAGCACAAGAAATTAGCAAATGGATTCAACCTTTTCCAGAAGGAG                         CTGGAAAGACTGAAAGATGAGAATCTGTCTCCTCTTCTTCCCCTAGACGTC
genomic: CTCAAGAGCACAAGAAATTAGCAAATGGATTCAACCTTTTCCAGAAGGAGgtaatgacgg ... ttgtgtgcagCTGGAAAGACTGAAAGATGAGAATCTGTCTCCTCTTCTTCCCCTAGACGTC
EST: gi|32945711|gb|CF050530.1|CF050530
EST:     AGAAATTAGCAAATGGATTCAACCTTTTCCAGAAGGAG                         CTGGAAAGACTGAAAGATGAGAATCTGTCTCCTCTTCTTCCCCTAGACGTC
genomic: AGAAATTAGCAAATGGATTCAACCTTTTCCAGAAGGAGgtaatgacgg ... ttgtgtgcagCTGGAAAGACTGAAAGATGAGAATCTGTCTCCTCTTCTTCCCCTAGACGTC
EST: gi|60343676|gb|DN210649.1|DN210649
EST:     CTCAAGAGCACAAGAAATTAGCAAATGGATTCAACCTTTTCCAGAAGGAG                         CTGGAAAGACTGAAAGATGAGAATCTGTCTCCTCTTCTTCCCCTAGACGTC
genomic: CTCAAGAGCACAAGAAATTAGCAAATGGATTCAACCTTTTCCAGAAGGAGgtaatgacgg ... ttgtgtgcagCTGGAAAGACTGAAAGATGAGAATCTGTCTCCTCTTCTTCCCCTAGACGTC
EST: gi|211190018|gb|FL186108.1|FL186108
EST:     CTCAAGAGCACAAGAAATTAGCAAATGGATTCAACCTTTTCCAGAAGGAG                         CTGGAAAGACTGAAAGATGAGAATCTGTCTCCTCTTCTTCCCCTAGACGTC
genomic: CTCAAGAGCACAAGAAATTAGCAAATGGATTCAACCTTTTCCAGAAGGAGgtaatgacgg ... ttgtgtgcagCTGGAAAGACTGAAAGATGAGAATCTGTCTCCTCTTCTTCCCCTAGACGTC

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), 48 (downstream exon)
Score: 259

ATCGCCAACAAAGAACAATTTGAATAGCAACAATAGCATCAAAGATATTTCTCAAGAGCACAAGAAATTAGCAAATGGATTCAACCTTTTCCAGAAGGAGgtaatgacgg ... ttgtgtgcagCTGGAAAGACTGAAAGATGAGAATCTGTCTCCTCTTCTTCCCCTAGACGTCAATCTAACTGACCCATCACTCAGTGGTTTGGAAAGGACATTGTCACAAC


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 120

ATCGCCAACAAAGAACAATTTGAATAGCAACAATAGCATCAAAGATATTTCTCAAGAGCACAAGAAATTAGCAAATGGATTCAACCTTTTCCAGAAGGAGgtaatgacgg ... ttgtgtgcagCTGGAAAGACTGAAAGATGAGAATCTGTCTCCTCTTCTTCCCCTAGACGTCAATCTAACTGACCCATCACTCAGTGGTTTGGAAAGGACATTGTCACAAC


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 176

ATCGCCAACAAAGAACAATTTGAATAGCAACAATAGCATCAAAGATATTTCTCAAGAGCACAAGAAATTAGCAAATGGATTCAACCTTTTCCAGAAGGAGgtaatgacgg ... ttgtgtgcagCTGGAAAGACTGAAAGATGAGAATCTGTCTCCTCTTCTTCCCCTAGACGTCAATCTAACTGACCCATCACTCAGTGGTTTGGAAAGGACATTGTCACAAC


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 160

ATCGCCAACAAAGAACAATTTGAATAGCAACAATAGCATCAAAGATATTTCTCAAGAGCACAAGAAATTAGCAAATGGATTCAACCTTTTCCAGAAGGAGgtaatgacgg ... ttgtgtgcagCTGGAAAGACTGAAAGATGAGAATCTGTCTCCTCTTCTTCCCCTAGACGTCAATCTAACTGACCCATCACTCAGTGGTTTGGAAAGGACATTGTCACAAC


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ATCGCCAACAAAGAACAATTTGAATAGCAACAATAGCATCAAAGATATTTCTCAAGAGCACAAGAAATTAGCAAATGGATTCAACCTTTTCCAGAAGGAGgtaatgacggaacttctcttggtgtattatttctttcaggttgtaatacatattatgtgaaaagcaaatttcacttgttgggaaaatgtccagacatttt

- - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aaaagcaa