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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AAATACAGATTGGGAAGACAGTCTGGAAAAGAGTTAACGGAGCAATCAAAAGATGgtaagttacatgtaagtactgatgatattttaaacttccatgctacaccttttccatcccatgtgttattcatttattaacattcttaggtcatactcca...

Basic information

species Zea mays
transcript GRMZM2G113742_T02
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G113742_T02 (Zea mays), 5'ss of exon 3
lower sequence: LOC_Os08g25799.1 (Oryza sativa), 5'ss of exon 3
AAATACAGATTGGGAAGACAGTCTGGAAAAGAGTTAACGGAGCAATCAAAAGATGgtaagttacatgtaagtactga--tgatattttaaacttccatgctacaccttttccatcccatgtgttattcatttattaacattcttaggtcatactcca
||||||||||| ||||  || ||||| |||||| |  | |||||||||||||| |||||||||||   |  |  |||  ||| |   | |           ||| | |  |  |    |   |   | ||    | ||      |    | |  |  
AAATACAGATTAGGAAAGCAATCTGGCAAAGAGATGGCAGAGCAATCAAAAGACGgtaagttacagaaacatgttgatatgagaagctgaggcaagtgagcacaacctcactgttaatttcatgcatgatcatctgacccaaaaaaaaaaaaagc--
















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|78087009|gb|DV515402.1|DV515402
EST:     CTGGAAAAGAGTTAACGGAGCAATCAAAAGATG                         CTTCTTACCTTATGGAAGCTCAAAGTGGAACAACTTTGTCTCCTAGAGGTT
genomic: CTGGAAAAGAGTTAACGGAGCAATCAAAAGATGgtaagttaca ... acaattgcagCTTCTTACCTTATGGAAGCTCAAAGTGGAACAACTTTGTCTCCTAGAGGTT
EST: gi|211222683|gb|FL110211.1|FL110211
EST:     CAGATTGGGAAGACAGTCTGGAAAAGAGTTAACGGAGCAATCAAAAGATG                         CTTCTTACCTTATGGAAGCTCAAAGTGGAACAACTTTGTCTCCTAGAGGTT
genomic: CAGATTGGGAAGACAGTCTGGAAAAGAGTTAACGGAGCAATCAAAAGATGgtaagttaca ... acaattgcagCTTCTTACCTTATGGAAGCTCAAAGTGGAACAACTTTGTCTCCTAGAGGTT
EST: gi|60341005|gb|DN207978.1|DN207978
EST:     CAGATTGGGAAGACAGTCTGGAAAAGAGTTAACGGAGCAATCAAAAGATG                         CTTCTTACCTTATGGAAGCTCAAAGTGGAACAACTTTGTCTCCTAGAGGTT
genomic: CAGATTGGGAAGACAGTCTGGAAAAGAGTTAACGGAGCAATCAAAAGATGgtaagttaca ... acaattgcagCTTCTTACCTTATGGAAGCTCAAAGTGGAACAACTTTGTCTCCTAGAGGTT
EST: gi|211222687|gb|FL110215.1|FL110215
EST:     CAGATTGGGAAGACAGTCTGGAAAAGAGTTAACGGAGCAATCAAAAGATG                         CTTCTTACCTTATGGAAGCTCAAAGTGGAACAACTTTGTCTCCTAGAGGTT
genomic: CAGATTGGGAAGACAGTCTGGAAAAGAGTTAACGGAGCAATCAAAAGATGgtaagttaca ... acaattgcagCTTCTTACCTTATGGAAGCTCAAAGTGGAACAACTTTGTCTCCTAGAGGTT
EST: gi|211222685|gb|FL110213.1|FL110213
EST:     CAGATTGGGAAGACAGTCTGGAAAAGAGTTAACGGAGCAATCAAAAGATG                         CTTCTTACCTTATGGAAGCTCAAAGTGGAACAACTTTGTCTCCTAGAGGTT
genomic: CAGATTGGGAAGACAGTCTGGAAAAGAGTTAACGGAGCAATCAAAAGATGgtaagttaca ... acaattgcagCTTCTTACCTTATGGAAGCTCAAAGTGGAACAACTTTGTCTCCTAGAGGTT
EST: gi|67026619|gb|CO455368.1|CO455368
EST:     CAGATTGGGACGACAGTCTGGAAAAGAGTTAACGGAGCAATCAAAAGATG                         CTTCTTACCTTATGGAAGCTCAAAGTGGAACAACTTTGTCTCCTAGAGGTT
genomic: CAGATTGGGAAGACAGTCTGGAAAAGAGTTAACGGAGCAATCAAAAGATGgtaagttaca ... acaattgcagCTTCTTACCTTATGGAAGCTCAAAGTGGAACAACTTTGTCTCCTAGAGGTT
EST: gi|101389909|gb|EB816885.1|EB816885
EST:     CAGATTGGGAAGACAGTCTGGAAAAGAGTTAACGGAGCAATCAAAAGATG                         CTTCTTACCTTATGGAAGCTCAAAGTGGAACAACTTTGTCTCTTAGAGGTT
genomic: CAGATTGGGAAGACAGTCTGGAAAAGAGTTAACGGAGCAATCAAAAGATGgtaagttaca ... acaattgcagCTTCTTACCTTATGGAAGCTCAAAGTGGAACAACTTTGTCTCCTAGAGGTT
EST: gi|78120958|gb|DV539342.1|DV539342
EST:     CAGATGGGGAAGACAGTCTGGAAAAGAGTTAACGGAGCAATCAAAAGATG                         CTTCTTACCTTATGGAAGCTCAAAGTGGAACAACTTTGTCTCCTAGAGGTT
genomic: CAGATTGGGAAGACAGTCTGGAAAAGAGTTAACGGAGCAATCAAAAGATGgtaagttaca ... acaattgcagCTTCTTACCTTATGGAAGCTCAAAGTGGAACAACTTTGTCTCCTAGAGGTT
EST: gi|60341894|gb|DN208867.1|DN208867
EST:     CAGATGGGGAAGACAGTCTGGAAAAGAGTTAACGGAGCAATCAAAAGATG                         CTTCTTACCTTATGGAAGCTCAAAGTGGAACAACTTTGTCTCCTAGAGGTT
genomic: CAGATTGGGAAGACAGTCTGGAAAAGAGTTAACGGAGCAATCAAAAGATGgtaagttaca ... acaattgcagCTTCTTACCTTATGGAAGCTCAAAGTGGAACAACTTTGTCTCCTAGAGGTT
EST: gi|60400474|gb|DN233281.1|DN233281
EST:     CAGATTGGGAAGACAGTCTGGAAAAGAGTTAACGGAGCAATCAAAAGATG                         CTTCTTACCTTATGGAAGCTCAAAGTGGAACAACTTTGTCTCCTAGAGGTT
genomic: CAGATTGGGAAGACAGTCTGGAAAAGAGTTAACGGAGCAATCAAAAGATGgtaagttaca ... acaattgcagCTTCTTACCTTATGGAAGCTCAAAGTGGAACAACTTTGTCTCCTAGAGGTT
EST: gi|76916798|gb|DV166558.1|DV166558
EST:     CAGATTGGGAAGACAGTCTGGAAAAGAGTTAACGGAGCAATCAAAAGATG                         CTTCTTACCTTATGGAAGCTCAAAGTGGAACAACTTTGTCTCCTAGAGGTT
genomic: CAGATTGGGAAGACAGTCTGGAAAAGAGTTAACGGAGCAATCAAAAGATGgtaagttaca ... acaattgcagCTTCTTACCTTATGGAAGCTCAAAGTGGAACAACTTTGTCTCCTAGAGGTT

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: 48 (upstream exon), 45 (downstream exon)
Score: 117

AAATACAGATTGGGAAGACAGTCTGGAAAAGAGTTAACGGAGCAATCAAAAGATGgtaagttaca ... acaattgcagCTTCTTACCTTATGGAAGCTCAAAGTGGAACAACTTTGTCTCCTAGAGGTTCTACTCCAGATGTGAAAGA


Block sizes: 49 (upstream exon), 43 (downstream exon)
Score: 32

AAATACAGATTGGGAAGACAGTCTGGAAAAGAGTTAACGGAGCAATCAAAAGATGgtaagttaca ... acaattgcagCTTCTTACCTTATGGAAGCTCAAAGTGGAACAACTTTGTCTCCTAGAGGTTCTACTCCAGATGTGAAAGA


Block sizes: 44 (upstream exon), 47 (downstream exon)
Score: 64

AAATACAGATTGGGAAGACAGTCTGGAAAAGAGTTAACGGAGCAATCAAAAGATGgtaagttaca ... acaattgcagCTTCTTACCTTATGGAAGCTCAAAGTGGAACAACTTTGTCTCCTAGAGGTTCTACTCCAGATGTGAAAGA


Block sizes: 49 (upstream exon), 45 (downstream exon)
Score: 68

AAATACAGATTGGGAAGACAGTCTGGAAAAGAGTTAACGGAGCAATCAAAAGATGgtaagttaca ... acaattgcagCTTCTTACCTTATGGAAGCTCAAAGTGGAACAACTTTGTCTCCTAGAGGTTCTACTCCAGATGTGAAAGA


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AAATACAGATTGGGAAGACAGTCTGGAAAAGAGTTAACGGAGCAATCAAAAGATGgtaagttacatgtaagtactgatgatattttaaacttccatgctacaccttttccatcccatgtgttattcatttattaacattcttaggtcatactcca

- - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - GGAGCA
- - - - - - - - - - - - - - - - - - - - - - - -  AAGATG