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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...atagacacagtctaacaactcatactaccatcattggcttccatatttgtttttaaacagaataaatgtatcacactaaaggaattaactaaacttgcagAGGCTGTGGCAGATGCTAACAAAGCAATTGGTCTTGATCCTACAATGCATAAAGCCTACTACCGGAAAGG

Basic information

species Zea mays
transcript GRMZM2G149704_T02
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G149704_T02 (Zea mays), 3'ss of exon 1
lower sequence: GLYMA16G29450.2 (Glycine max), 3'ss of exon 1
atagacacagtctaacaactcatactaccatcattggcttccatatttgtttttaaacagaataaatgtatcacactaaaggaattaactaaactt---gcagAGGCTGTGGCAGATGCTAACAAAGCAATTGGTCTTGATCCTACAATGCATAAAGCCTACTACCGGAAAGG
|| |      | |      ||||     | |  | | | |     | |  | ||  ||  ||| | |  ||      ||   ||||  ||    ||   ||||||||||| || |||||||||||||||||||   |  || || |  | |  ||||| || |  ||||||||
atggtgtttattttgtg-ttcatggcgtcct-gtagacatgtggttgtaatgttttact-aattactaaattttgggaactaaattttcttgcttttgtgcagAGGCTGTTGCTGATGCTAACAAAGCAATTGAATTGAATTCTTCTCTACCAAAAGCATATTTGCGGAAAGG

upper sequence: GRMZM2G149704_T02 (Zea mays), 3'ss of exon 1
lower sequence: GLYMA09G23980.1 (Glycine max), 3'ss of exon 1
--atagacacagtctaacaactcatactaccatcattggcttccatatttgtttttaaacagaata--aatgtatcacactaaaggaattaactaaacttgcagAGGCTGTGGCAGATGCTAACAAAGCAATTGGTCTTGATCCTACAATGCATAAAGCCTACTACCGGAAAGG
  || |      | |   |  ||||    || |    | | |     | |  | ||  ||  | ||  ||| |     |||||     ||   |     ||||||||||||||| |||||||||||||||||||   |  ||||| |  | |  ||||| || |  ||||||||
atatggtgtttattttgta-ttcatggcgccct-gcagacatgtggttgtaatgtttgactaattactaattttgggaactaattttcttgctt--ttgtgcagAGGCTGTGGCTGATGCTAACAAAGCAATTGAATTGAATCCTTCTCTACCAAAAGCATATTTGCGGAAAGG

upper sequence: GRMZM2G149704_T02 (Zea mays), 3'ss of exon 1
lower sequence: AT4G23570.3 (Arabidopsis thaliana), 3'ss of exon 1
atagacacag-tctaacaactcatactac-catcattggctt----ccatatttgtttttaaacagaataaatgtatcacactaaaggaattaactaaacttgcagAGGCTGTGGCAGATGCTAACAAAGCAATTGGTCTTGATCCTACAATGCATAAAGCCTACTACCGGAAAGG
 ||      | | ||| ||   || ||   |||  || || |     ||||    |||   |   | ||||   | |    || |    |||  || ||   |||||||| ||||||||||| |||||||||||||   | |||||| || ||   ||||| |||    | |||||
ctatttcttgctttaagaaagtattctctgcatttttagcgtagtatcatagaactttactagttggataag-attttggtctcatttgatt--ctcaatgagCAGAGGCCGTGGCAGATGCGAACAAAGCAATTGAGTTGGATCCTTCATTGACCAAAGCTTACCTAAGAAAAGG

upper sequence: GRMZM2G149704_T02 (Zea mays), 3'ss of exon 1
lower sequence: AT4G23570.1 (Arabidopsis thaliana), 3'ss of exon 2
atagacacagtctaacaactcatactac-catcattggctt----ccatatttgtttttaaacagaataaatgtatcacactaaaggaattaactaaacttgcagAGGCTGTGGCAGATGCTAACAAAGCAATTGGTCTTGATCCTACAATGCATAAAGCCTACTACCGGAAAGG
     |    | ||| ||   || ||   |||  || || |     ||||    |||   |   | ||||   | |    || |    |||  || ||   |||||||| ||||||||||| |||||||||||||   | |||||| || ||   ||||| |||    | |||||
--tttcttgctttaagaaagtattctctgcatttttagcgtagtatcatagaactttactagttggataag-attttggtctcatttgatt--ctcaatgagcagAGGCCGTGGCAGATGCGAACAAAGCAATTGAGTTGGATCCTTCATTGACCAAAGCTTACCTAAGAAAAGG

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|211045632|gb|FL292671.1|FL292671
EST:     TCTCTACGCCGACCGCGCCCAGGCGCACATCAAGCTCGGCAACTACACTG                         AGGCTGTGGCAGATGCTAACAAAGCAATTGGTCTTGATCCTACAATGCATA
genomic: TCTCTACGCCGACCGCGCCCAGGCGCACATCAAGCTCGGCAACTACACTGgtgcgggcag ... aaacttgcagAGGCTGTGGCAGATGCTAACAAAGCAATTGGTCTTGATCCTACAATGCATA
EST: gi|211042678|gb|FL292667.1|FL292667
EST:     TCTCTACGCCGACCGCGCCCAGGCGCACATCAAGCTCGGCAACTACACTG                         AGGCTGTGGCAGATGCTAACAAAGCAATTGGTCTTGATCCTACAATGCATA
genomic: TCTCTACGCCGACCGCGCCCAGGCGCACATCAAGCTCGGCAACTACACTGgtgcgggcag ... aaacttgcagAGGCTGTGGCAGATGCTAACAAAGCAATTGGTCTTGATCCTACAATGCATA
EST: gi|78080588|gb|DV509000.1|DV509000
EST:     TCTCTACGCCGACCGCGCCCAGGCGCACATCAAGCTCGGCAACTACACTG                         AGGCTGTGGCAGATGCTAACAAAGCAATTGGTCTTGATCCTACAATGCATA
genomic: TCTCTACGCCGACCGCGCCCAGGCGCACATCAAGCTCGGCAACTACACTGgtgcgggcag ... aaacttgcagAGGCTGTGGCAGATGCTAACAAAGCAATTGGTCTTGATCCTACAATGCATA
EST: gi|211045637|gb|FL292676.1|FL292676
EST:     TCTCTACGCCGACCGCGCCCAGGCGCACATCAAGCTCGGCAACTACACTG                         AGGCTGTGGCAGATGCTAACAAAGCAATTGGTCTTGATCCTACAATGCATA
genomic: TCTCTACGCCGACCGCGCCCAGGCGCACATCAAGCTCGGCAACTACACTGgtgcgggcag ... aaacttgcagAGGCTGTGGCAGATGCTAACAAAGCAATTGGTCTTGATCCTACAATGCATA
EST: gi|89757539|gb|DY687098.1|DY687098
EST:     TCTCTACGCCGACCGCGCCCAGGCGCACATCAAGCTCGGCAACTACACTG                         AGGCTGTGGCAGATGCTAACAAAGCAATTGGTCTTGATCCTACAATGCATA
genomic: TCTCTACGCCGACCGCGCCCAGGCGCACATCAAGCTCGGCAACTACACTGgtgcgggcag ... aaacttgcagAGGCTGTGGCAGATGCTAACAAAGCAATTGGTCTTGATCCTACAATGCATA
EST: gi|149076474|gb|EE165099.2|EE165099
EST:     TCTCTACGCCGACCGCGCCCAGGCGCACATCAAGCTCGGCAACTACACTG                         AGGCTGTGGCAGATGCTAACAAAGCAATTGGTCTTGATCCTACAATGCATA
genomic: TCTCTACGCCGACCGCGCCCAGGCGCACATCAAGCTCGGCAACTACACTGgtgcgggcag ... aaacttgcagAGGCTGTGGCAGATGCTAACAAAGCAATTGGTCTTGATCCTACAATGCATA
EST: gi|32801805|gb|CD954041.1|CD954041
EST:     TCTCTACGCCGACCGCGCCCAGGCGCACATCAAGCTCGGCAACTACACTG                         AGGCTGTGGCAGATGCTAACAAAGCAATTGGTCTTGATCCTACAATGCATA
genomic: TCTCTACGCCGACCGCGCCCAGGCGCACATCAAGCTCGGCAACTACACTGgtgcgggcag ... aaacttgcagAGGCTGTGGCAGATGCTAACAAAGCAATTGGTCTTGATCCTACAATGCATA
EST: gi|211042677|gb|FL292666.1|FL292666
EST:     TCTCTACGCCGACCGCGCCCAGGCGCACATCAAGCTCGGCAACTACACTG                         AGGCTGTGGCAGATGCTAACAAAGCAATTGGTCTTGATCCTACAATGCATA
genomic: TCTCTACGCCGACCGCGCCCAGGCGCACATCAAGCTCGGCAACTACACTGgtgcgggcag ... aaacttgcagAGGCTGTGGCAGATGCTAACAAAGCAATTGGTCTTGATCCTACAATGCATA
EST: gi|32791338|gb|CD943574.1|CD943574
EST:     TCTCTACGCCGACCGCGCCCAGGCGCACATCAAGCTCGGCAACTACACTG                         AGGCTGTGGCAGAAGCTAACAAAGCAATTGGTCTTGATCCTACAATGCATA
genomic: TCTCTACGCCGACCGCGCCCAGGCGCACATCAAGCTCGGCAACTACACTGgtgcgggcag ... aaacttgcagAGGCTGTGGCAGATGCTAACAAAGCAATTGGTCTTGATCCTACAATGCATA
EST: gi|29947233|gb|CB816549.1|CB816549
EST:     TCTCTACGCCGACCGCGCCCAGGCGCACATCAAGCTCGGCAACTACACTG                         AGGCTGTGGCAGATGCTAACAAAGCAATTGGTCTTGATCCTACAATGCATA
genomic: TCTCTACGCCGACCGCGCCCAGGCGCACATCAAGCTCGGCAACTACACTGgtgcgggcag ... aaacttgcagAGGCTGTGGCAGATGCTAACAAAGCAATTGGTCTTGATCCTACAATGCATA
EST: gi|149104781|gb|EE290244.2|EE290244
EST:     TCTCTACGCCGACCGCGCCCAGGCGCACATCAAGCTCGGCAACTACACTG                         AGGCTGTGGCAGATGCTAACAAAGCAATTGGTCTTGATCCTACAATGCATA
genomic: TCTCTACGCCGACCGCGCCCAGGCGCACATCAAGCTCGGCAACTACACTGgtgcgggcag ... aaacttgcagAGGCTGTGGCAGATGCTAACAAAGCAATTGGTCTTGATCCTACAATGCATA
EST: gi|211045633|gb|FL292672.1|FL292672
EST:     TCTCTACGCCGACCGCGCCCAGGCGCACATCAAGCTCGGCAACTACACTG                         AGGCTGTGGCAGAT
genomic: TCTCTACGCCGACCGCGCCCAGGCGCACATCAAGCTCGGCAACTACACTGgtgcgggcag ... aaacttgcagAGGCTGTGGCAGAT
EST: gi|211045636|gb|FL292675.1|FL292675
EST:     TCTCTACGCCGACCGCGCCCAGGCGCACATCAAGCTCGGCAACTACACTG                         AGGCTGTGGCAGATGCTAACAAAGCAATTGGTCTTGATCCTACAATGCATA
genomic: TCTCTACGCCGACCGCGCCCAGGCGCACATCAAGCTCGGCAACTACACTGgtgcgggcag ... aaacttgcagAGGCTGTGGCAGATGCTAACAAAGCAATTGGTCTTGATCCTACAATGCATA
EST: gi|211045634|gb|FL292673.1|FL292673
EST:     TCTCTACGCCGACCGCGCCCAGGCGCACATCAAGCTCGGCAACTACACTG                         AGGCTGTGGCAGATGCTAACAAAGCAATTGGTCTTGATCCTACAATGCATA
genomic: TCTCTACGCCGACCGCGCCCAGGCGCACATCAAGCTCGGCAACTACACTGgtgcgggcag ... aaacttgcagAGGCTGTGGCAGATGCTAACAAAGCAATTGGTCTTGATCCTACAATGCATA
EST: gi|148975634|gb|EE025764.2|EE025764
EST:     TCTCTACGCCGACCGCGCCCAGGCGCACATCAAGCTCGGCAACTACACTG                         AGGCTGTGGCAGATGCTAACAAAGCAATTGGTCTTGATCCTACAATGCATA
genomic: TCTCTACGCCGACCGCGCCCAGGCGCACATCAAGCTCGGCAACTACACTGgtgcgggcag ... aaacttgcagAGGCTGTGGCAGATGCTAACAAAGCAATTGGTCTTGATCCTACAATGCATA
EST: gi|211045630|gb|FL292669.1|FL292669
EST:     TCTCTACGCCGACCGCGCCCAGGCGCACATCAAGCTCGGCAACTACACTG                         AGGCTGTGGCAGATGCTAACAAAGCAATTGGTCTTGATCCTACAATGCATA
genomic: TCTCTACGCCGACCGCGCCCAGGCGCACATCAAGCTCGGCAACTACACTGgtgcgggcag ... aaacttgcagAGGCTGTGGCAGATGCTAACAAAGCAATTGGTCTTGATCCTACAATGCATA
EST: gi|31612314|gb|CD568936.1|CD568936
EST:     TCTCTACGCCGACCGCGCCCAGGCGCACATCAAGCTCGGCAACTACACTG                         AGGCTGTGGCAGATGCTAACAAAGCAATTGGTCTTGATCCTACAATGCATA
genomic: TCTCTACGCCGACCGCGCCCAGGCGCACATCAAGCTCGGCAACTACACTGgtgcgggcag ... aaacttgcagAGGCTGTGGCAGATGCTAACAAAGCAATTGGTCTTGATCCTACAATGCATA

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), 49 (downstream exon)
Score: 168

GCCGCCGAACTCTACACGCAGGCCATCGACGCCGGGCCCGCCACTGCCGATCTCTACGCCGACCGCGCCCAGGCGCACATCAAGCTCGGCAACTACACTGgtgcgggcag ... aaacttgcagAGGCTGTGGCAGATGCTAACAAAGCAATTGGTCTTGATCCTACAATGCATAAAGCCTACTACCGGAAAGG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 125

GCCGCCGAACTCTACACGCAGGCCATCGACGCCGGGCCCGCCACTGCCGATCTCTACGCCGACCGCGCCCAGGCGCACATCAAGCTCGGCAACTACACTGgtgcgggcag ... aaacttgcagAGGCTGTGGCAGATGCTAACAAAGCAATTGGTCTTGATCCTACAATGCATAAAGCCTACTACCGGAAAGG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 170

GCCGCCGAACTCTACACGCAGGCCATCGACGCCGGGCCCGCCACTGCCGATCTCTACGCCGACCGCGCCCAGGCGCACATCAAGCTCGGCAACTACACTGgtgcgggcag ... aaacttgcagAGGCTGTGGCAGATGCTAACAAAGCAATTGGTCTTGATCCTACAATGCATAAAGCCTACTACCGGAAAGG


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

GCCGCCGAACTCTACACGCAGGCCATCGACGCCGGGCCCGCCACTGCCGATCTCTACGCCGACCGCGCCCAGGCGCACATCAAGCTCGGCAACTACACTGgtgcgggcag ... aaacttgcagAGGCTGTGGCAGATGCTAACAAAGCAATTGGTCTTGATCCTACAATGCATAAAGCCTACTACCGGAAAGG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttgtttttaaacagaataaatgtatcacactaaaggaattaactaaacttgcagAGGCTGTGGCAGATGCTAACAAAGCAATTGGTCTTGATCCTACAATGCATAAAGCCTACTACCGGAAAGG
                                         aactaaa  putative branch site (score: 63)
     ttttaaacagaataaa  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
atagacacagtctaacaactcatactaccatcattggcttccatatttgtttttaaacagaataaatgtatcacactaaaggaattaactaaacttgcagAGGCTGTGGCAGATGCTAACAAAGCAATTGGTCTTGATCCTACAATGCATAAAGCCTACTACCGGAAAGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCAA
- agacaca
- - - - - - -aacaact
- - - - - - - - - - - - - - - - - - gcttcca
- - - - - - - - - - - - - - - - - - - - - - - - - - - aaacaga
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - acactaa