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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CATGCAGTCTTTTTCTGTCTCAGTCTTTTGACTCCAGCGTTTGGTCGAGCCACATTTTATACTGAAAGGTGCTCAAAGCTGCCATTTTTCCTTACGTCAGgcaagtgtattttcccacattattccctgatatgtctcattaccttggaagggaataggcattaattctaactggaacaacgatttgtaaatacacgtttcttcctagttctatttgatgcagtttggtgttctgaatttgtttgtcacgataacccttatccctgtatgctatttcag

Basic information

species Zea mays
transcript GRMZM2G102021_T01
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G102021_T01 (Zea mays), 5'ss of exon 5
lower sequence: LOC_Os02g17280.1 (Oryza sativa), 5'ss of exon 4
CATGCAGTCTTTTTCTGTCTCAGTCTTTTGACTCCAGCGTTTGGTCGAGCCACATTTTATACTGAAAGGTGCTCAAAGCTGCCATTTTTCCTTACGTCAGgcaagtgtattttcccacattattccctgatatgtctcattaccttggaa-gggaataggcattaattctaactggaacaacgatttgtaaatacacgtttcttcctagttctatttgatgcagtttggtgttctgaatttgtttgtcacgataacccttatccctgtatgctatttcag
||||| ||||||||||| ||||| ||||| |||||||| || ||  |||| |||||||||  ||||| |||||||| | ||||||||||||||  |||||| ||||  ||  |  | | ||| || || ||| |  |      || |||| |  || | || ||  |||||| ||||     | |    || |  |   |                                                                                
CATGCCGTCTTTTTCTGCCTCAGCCTTTTAACTCCAGCATTCGGCAGAGCTACATTTTATGTTGAAAAGTGCTCAAGGATGCCATTTTTCCTTGTGTCAGgtaagt-catagtttctccttactctctaatacgaattgggctctaggaatgaaaagaagccttccttctaattggattggtggtaaacaattttataata-------------------------------------------------------------------------------
















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|211287765|gb|FL258742.1|FL258742
EST:     CACATTTTATACTGAAAGGTGCTCAAAGCTGCCATTTTTCCTTACGTCAG                         CCCTTATTGCACTTGGATTCTTGGTCATCCATACATTCTCAATGATTATTG
genomic: CACATTTTATACTGAAAGGTGCTCAAAGCTGCCATTTTTCCTTACGTCAGgcaagtgtat ... gctatttcagCCCTTATTGCACTTGGATTCTTGGTCATCCATACATTCTCAATGATTATTG
EST: gi|33285553|gb|CF075348.1|CF075348
EST:     CACATTTTATACTGAAAGGTGCTCAAAGCTGCCATTTTTCCTTGCGTCAG                         CCCTTATTGCACTTGGATTCTTGGTCATCCATACATTCTCAATGATTATTG
genomic: CACATTTTATACTGAAAGGTGCTCAAAGCTGCCATTTTTCCTTACGTCAGgcaagtgtat ... gctatttcagCCCTTATTGCACTTGGATTCTTGGTCATCCATACATTCTCAATGATTATTG
EST: gi|86468508|gb|DY234878.1|DY234878
EST:     CACATTTTATACTGAAAGGTGCTCAAAGCTGCCATTTTTCCTTACGTCAG                         CCCTTATTGCACTTGGATTCTTGGTCATCCATACATTCTCAATGATTATTG
genomic: CACATTTTATACTGAAAGGTGCTCAAAGCTGCCATTTTTCCTTACGTCAGgcaagtgtat ... gctatttcagCCCTTATTGCACTTGGATTCTTGGTCATCCATACATTCTCAATGATTATTG
EST: gi|211072382|gb|FL433877.1|FL433877
EST:     CACATTTTATACTGAAAGGTGCTCAAAGCTGCCATTTTTCCTTACGTCAG                         CCCTTATTGCACTTGGATTCTTGGTCATCCATACATTCTCAATGATTATTG
genomic: CACATTTTATACTGAAAGGTGCTCAAAGCTGCCATTTTTCCTTACGTCAGgcaagtgtat ... gctatttcagCCCTTATTGCACTTGGATTCTTGGTCATCCATACATTCTCAATGATTATTG
EST: gi|211105116|gb|FL057782.1|FL057782
EST:     CACATTTTATACTGAAAGGTGCTCAAAGCTGCCATTTTTCCTTACGTCAG                         CCCTTATTGCACTTGGATTCTTGGTCATCCATACATTCTCAATGATTATTG
genomic: CACATTTTATACTGAAAGGTGCTCAAAGCTGCCATTTTTCCTTACGTCAGgcaagtgtat ... gctatttcagCCCTTATTGCACTTGGATTCTTGGTCATCCATACATTCTCAATGATTATTG
EST: gi|22546043|gb|BU098364.1|BU098364
EST:     CACATTTTATACTGAAAGGTGCTCAAAGCTGCCATTTTTCCTTGCGTCAG                         CCCTTATTGCACTTGGATTCTTGGTCATCCATACATTCTCAATGATTATTG
genomic: CACATTTTATACTGAAAGGTGCTCAAAGCTGCCATTTTTCCTTACGTCAGgcaagtgtat ... gctatttcagCCCTTATTGCACTTGGATTCTTGGTCATCCATACATTCTCAATGATTATTG
EST: gi|149048871|gb|EE048372.2|EE048372
EST:     CACATTTTATACTGAAAGGTGCTCAAAGCTGCCATTTTTCCTTACGTCAG                         CCCTTATTGCACTTGGATTCTTGGTCATCCATACATTCTCAATGATTATTG
genomic: CACATTTTATACTGAAAGGTGCTCAAAGCTGCCATTTTTCCTTACGTCAGgcaagtgtat ... gctatttcagCCCTTATTGCACTTGGATTCTTGGTCATCCATACATTCTCAATGATTATTG
EST: gi|87155707|gb|DY400496.1|DY400496
EST:     CACATTTTATACTGAAAGGTGCTCAAAGCTGCCATTTTTCCTTGCGTCAG                         CCCTTATTGCACTTGGATTCTTGGTCATCCATACATTCTCAATGATTATTG
genomic: CACATTTTATACTGAAAGGTGCTCAAAGCTGCCATTTTTCCTTACGTCAGgcaagtgtat ... gctatttcagCCCTTATTGCACTTGGATTCTTGGTCATCCATACATTCTCAATGATTATTG
EST: gi|148946111|gb|EC891405.2|EC891405
EST:     CACATTTTATACTGAAAGGTGCTCAAAGCTGCCATTTTTCCTTACGTCAG                         CCCTTATTGCACTTGGATTCTTGGTCATCCATACATTCTCAATGATTATTG
genomic: CACATTTTATACTGAAAGGTGCTCAAAGCTGCCATTTTTCCTTACGTCAGgcaagtgtat ... gctatttcagCCCTTATTGCACTTGGATTCTTGGTCATCCATACATTCTCAATGATTATTG
EST: gi|91876597|gb|EB406554.1|EB406554
EST:     CACATTTTATACTGAAAGGTGCTCAAAGCTGCCATTTTTCCTTACGTCAG                         CCCTTATTGCACTTGGATTCTTGGTCATCCATACATTCTCAATGATTATTG
genomic: CACATTTTATACTGAAAGGTGCTCAAAGCTGCCATTTTTCCTTACGTCAGgcaagtgtat ... gctatttcagCCCTTATTGCACTTGGATTCTTGGTCATCCATACATTCTCAATGATTATTG
EST: gi|113703076|gb|EE680580.1|EE680580
EST:     CACATTTTATACTGAAAGGTGCTCAAAGCTGCCATTTTTCCTTGCGTCAG                         CCCTTATTGCACTTGGATTCTTGGTCATCCATACATTCTCAATGATTATTG
genomic: CACATTTTATACTGAAAGGTGCTCAAAGCTGCCATTTTTCCTTACGTCAGgcaagtgtat ... gctatttcagCCCTTATTGCACTTGGATTCTTGGTCATCCATACATTCTCAATGATTATTG
EST: gi|37395770|gb|CF635168.1|CF635168
EST:     CACATTTTATACTGAAAGGTGCTCAAAGCTGCCATTTTTCCTTGCGTCAG                         CCCTTATTGCACTTGGATTCTTGGTCATCCATACATTCTCAATGATTATTG
genomic: CACATTTTATACTGAAAGGTGCTCAAAGCTGCCATTTTTCCTTACGTCAGgcaagtgtat ... gctatttcagCCCTTATTGCACTTGGATTCTTGGTCATCCATACATTCTCAATGATTATTG
EST: gi|33091816|gb|CF051810.1|CF051810
EST:     CACATTTTATACTGAAAGGTGCTCAAAGCTGCCATTTTTCCTTGCGTCAG                         CCCTTATTGCACTTGGATTCTTGGTCATCCATACATTCTCAATGATTATTG
genomic: CACATTTTATACTGAAAGGTGCTCAAAGCTGCCATTTTTCCTTACGTCAGgcaagtgtat ... gctatttcagCCCTTATTGCACTTGGATTCTTGGTCATCCATACATTCTCAATGATTATTG
EST: gi|87156122|gb|DY400911.1|DY400911
EST:     CACATTTTATACTGAAAGGTGCTCAAAGCTGCCATTTTTCCTTGCGTCAG                         CCCTTATTGCACTTGGATTCTTGGTCATCCATACATTCTCAATGATTATTG
genomic: CACATTTTATACTGAAAGGTGCTCAAAGCTGCCATTTTTCCTTACGTCAGgcaagtgtat ... gctatttcagCCCTTATTGCACTTGGATTCTTGGTCATCCATACATTCTCAATGATTATTG
EST: gi|26559868|gb|CA832103.1|CA832103
EST:     CACATTTTATACTGAAAGGTGCTCAAAGCTGCCATTTTTCCTTGCGTCAG                         CCCTTATTGCACTTGGATTCTTGGTCATCCATACATTCTCAAT
genomic: CACATTTTATACTGAAAGGTGCTCAAAGCTGCCATTTTTCCTTACGTCAGgcaagtgtat ... gctatttcagCCCTTATTGCACTTGGATTCTTGGTCATCCATACATTCTCAAT
EST: gi|211503758|gb|FL479708.1|FL479708
EST:     CACATTTTATACTGAAAGGTGCTCAAAGCTGCCATTTTTCCTTGCGTCAG                         CCCTTATTGCACTTGGATTCTTGGTCATCCATACATTCTCAATGATTATTG
genomic: CACATTTTATACTGAAAGGTGCTCAAAGCTGCCATTTTTCCTTACGTCAGgcaagtgtat ... gctatttcagCCCTTATTGCACTTGGATTCTTGGTCATCCATACATTCTCAATGATTATTG
EST: gi|40336955|gb|CK371025.1|CK371025
EST:     CACATTTTATACTGAAAGGTGCTCAAAGCTGCCATTTTTCCTTGCGTCAG                         CCCTTATTGCACTTGGATTCTTGGTCATCCATACATTCTCAATGATTATTG
genomic: CACATTTTATACTGAAAGGTGCTCAAAGCTGCCATTTTTCCTTACGTCAGgcaagtgtat ... gctatttcagCCCTTATTGCACTTGGATTCTTGGTCATCCATACATTCTCAATGATTATTG
EST: gi|148946112|gb|EC891406.2|EC891406
EST:     CACATTTTATACTGAAAGGTGCTCAAAGCTGCCATTTTTCCTTACGTCAG                         CCCTTATTGCACTTGGATTCTTGGTCATCCATACATTCTCAATGATTATTG
genomic: CACATTTTATACTGAAAGGTGCTCAAAGCTGCCATTTTTCCTTACGTCAGgcaagtgtat ... gctatttcagCCCTTATTGCACTTGGATTCTTGGTCATCCATACATTCTCAATGATTATTG

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: 151

CATGCAGTCTTTTTCTGTCTCAGTCTTTTGACTCCAGCGTTTGGTCGAGCCACATTTTATACTGAAAGGTGCTCAAAGCTGCCATTTTTCCTTACGTCAGgcaagtgtat ... gctatttcagCCCTTATTGCACTTGGATTCTTGGTCATCCATACATTCTCAATGATTATTGCTTTTAATGCATATGACGAGGGAAAGAAAAGTGATCAAGTCTTTGTTCC


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 55

CATGCAGTCTTTTTCTGTCTCAGTCTTTTGACTCCAGCGTTTGGTCGAGCCACATTTTATACTGAAAGGTGCTCAAAGCTGCCATTTTTCCTTACGTCAGgcaagtgtat ... gctatttcagCCCTTATTGCACTTGGATTCTTGGTCATCCATACATTCTCAATGATTATTGCTTTTAATGCATATGACGAGGGAAAGAAAAGTGATCAAGTCTTTGTTCC


Block sizes: 49 (upstream exon), 45 (downstream exon)
Score: 89

CATGCAGTCTTTTTCTGTCTCAGTCTTTTGACTCCAGCGTTTGGTCGAGCCACATTTTATACTGAAAGGTGCTCAAAGCTGCCATTTTTCCTTACGTCAGgcaagtgtat ... gctatttcagCCCTTATTGCACTTGGATTCTTGGTCATCCATACATTCTCAATGATTATTGCTTTTAATGCATATGACGAGGGAAAGAAAAGTGATCAAGTCTTTGTTCC


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 63

CATGCAGTCTTTTTCTGTCTCAGTCTTTTGACTCCAGCGTTTGGTCGAGCCACATTTTATACTGAAAGGTGCTCAAAGCTGCCATTTTTCCTTACGTCAGgcaagtgtat ... gctatttcagCCCTTATTGCACTTGGATTCTTGGTCATCCATACATTCTCAATGATTATTGCTTTTAATGCATATGACGAGGGAAAGAAAAGTGATCAAGTCTTTGTTCC


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CATGCAGTCTTTTTCTGTCTCAGTCTTTTGACTCCAGCGTTTGGTCGAGCCACATTTTATACTGAAAGGTGCTCAAAGCTGCCATTTTTCCTTACGTCAGgcaagtgtattttcccacattattccctgatatgtctcattaccttggaagggaataggcattaattctaactggaacaacgatttgtaaatacacgtttcttcctagttctatttgatgcagtttggtgttctgaatttgtttgtcacgataacccttatccctgtatgctatttcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC