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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGCTTTCAAATCAAAATCCCGCTTTGAGCAGCTTGAATTTGCCCAAAACAAAAGGCAGAATGCATGGCAGCAGTTTCAAACCAAGGGGAAAGCCAAAAAGgtagcttcttggcccccacgtaatttttttttgctttcttaaaaatggctaggcactcttccattgagttggaattctgaatctcaaggtactacatatg...

Basic information

species Zea mays
transcript GRMZM2G005737_T01
intron # 7
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G005737_T01 (Zea mays), 5'ss of exon 7
lower sequence: LOC_Os08g01840.1 (Oryza sativa), 5'ss of exon 7
TGCTTTCAAATCAAAATCCCGCTTTGAGCAGCTTGAATTTGCCCAAAACAAAAGGCAGAATGCATGGCAGCAGTTTCAAAC---CAAGGGGAAAGCCAAAAAGgtagcttcttggcccccacg---taatttttttttgc---tttcttaaaaatggctaggcactcttccattgagttggaattctgaatctcaaggtactacatatg
    ||||| |||||| |||||||||||||||| |||||||| ||||| || ||||||||||||||||||||||| |||||   ||| ||||||||||||||||||   |||  ||| || |    ||| ||      ||   | | |   | | || |      |  |  ||  |  |  || |||           ||  |      
---ATTCAAGTCAAAAGCCCGCTTTGAGCAGCTAGAATTTGCACAAAATAAGAGGCAGAATGCATGGCAGCAGTTCCAAACGACCAAAGGGAAAGCCAAAAAGgtactgtctctgccaccccactctaacttggccaggcacctctttctgagaaggatgtaaggtgctatatatacctcaaaatctagcatgttgtctagaa------
















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|113701598|gb|EE679102.1|EE679102
EST:     AAAGGCAGAATGCATGGCAGCAGTTTCAAACCAAAGGGAAAGCCAAAAAG                         GTGGGGTTCTTCTCCGGTCGCAAGAAGGAGAGCATCTTCAAGTCACCGGAC
genomic: AAAGGCAGAATGCATGGCAGCAGTTTCAAACCAAGGGGAAAGCCAAAAAGgtagcttctt ... tgtttgccagGTGGGGTTCTTCTCCGGTCGCAAGAAGGAGAGCATCTTCAAGTCACCGGAC
EST: gi|60399699|gb|DN232509.1|DN232509
EST:     AAAGGCAGAATGCATGGCAGCAGTTTCAAACCAAGGGGAAAGCCAAAAAG                         ATGGGGTTCTTCTCCGGTCGCAAGAAGGAGAGCATCTTCAAGTCACCGGAC
genomic: AAAGGCAGAATGCATGGCAGCAGTTTCAAACCAAGGGGAAAGCCAAAAAGgtagcttctt ... tgtttgccagGTGGGGTTCTTCTCCGGTCGCAAGAAGGAGAGCATCTTCAAGTCACCGGAC
EST: gi|32935795|gb|CF040607.1|CF040607
EST:     AAAGGCAGAATGCATGGCAGCAGTTTCAAACCAAGGGGAAAGCCAAAAAG                         GTGGGGTTCTTCTCCGGTCGCAAGAAGGAGAGCATCTTCAAGTCACCGGAC
genomic: AAAGGCAGAATGCATGGCAGCAGTTTCAAACCAAGGGGAAAGCCAAAAAGgtagcttctt ... tgtttgccagGTGGGGTTCTTCTCCGGTCGCAAGAAGGAGAGCATCTTCAAGTCACCGGAC
EST: gi|86465810|gb|DY232183.1|DY232183
EST:     AAAGGCAGAATGCATGGCAGCAGTTTCAAACCAAGGGGAAAGCCAAAAAG                         GTGGGGNNNNNNNCCGGTCGCAAGAAGGAGAGCATCTTCAAGTCCCCGGAC
genomic: AAAGGCAGAATGCATGGCAGCAGTTTCAAACCAAGGGGAAAGCCAAAAAGgtagcttctt ... tgtttgccagGTGGGGTTCTTCTCCGGTCGCAAGAAGGAGAGCATCTTCAAGTCACCGGAC
EST: gi|37375691|gb|CF624300.1|CF624300
EST:     AAAGGCAGAATGCATGGCAGCAGTTTCAAACCAAAGGGAAAGCCAAAAAG                         GTGGGGTTCTTCTCCGGTCGCAAGAAGGAGAGCATCTTCAAGTCACCGGAC
genomic: AAAGGCAGAATGCATGGCAGCAGTTTCAAACCAAGGGGAAAGCCAAAAAGgtagcttctt ... tgtttgccagGTGGGGTTCTTCTCCGGTCGCAAGAAGGAGAGCATCTTCAAGTCACCGGAC
EST: gi|211238064|gb|FL481625.1|FL481625
EST:     AAAGGCAGAATGCATGGCAGCAGTTTCAAACCAAAGGGAAAGCCAAAAAG                         GTGGGGTTCTTCTCCGGTCGCAAGAAGGAGAGCATCTTCAAGTCACCGGAC
genomic: AAAGGCAGAATGCATGGCAGCAGTTTCAAACCAAGGGGAAAGCCAAAAAGgtagcttctt ... tgtttgccagGTGGGGTTCTTCTCCGGTCGCAAGAAGGAGAGCATCTTCAAGTCACCGGAC
EST: gi|44900308|gb|CK826853.1|CK826853
EST:     AAAGGCAGAATGCATGGCAGCAGTTTCAAACCAAAGGGAAAGCCAAAAAG                         GTGGGGT-CTTCTCCGGTCGCAAGAAGGAGAGCATCTTCAAGTCACCGGAC
genomic: AAAGGCAGAATGCATGGCAGCAGTTTCAAACCAAGGGGAAAGCCAAAAAGgtagcttctt ... tgtttgccagGTGGGGTTCTTCTCCGGTCGCAAGAAGGAGAGCATCTTCAAGTCACCGGAC
EST: gi|60398835|gb|DN231651.1|DN231651
EST:     AAAGGCAGAATGCATGGCAGCAGTTTCAAACCAAGGGGAAAGCCAAAAAG                         GTGGGGTTTTTCTCCGGTCGCAAGAAGGAGAGCATCTTCAAGTCACCGGAC
genomic: AAAGGCAGAATGCATGGCAGCAGTTTCAAACCAAGGGGAAAGCCAAAAAGgtagcttctt ... tgtttgccagGTGGGGTTCTTCTCCGGTCGCAAGAAGGAGAGCATCTTCAAGTCACCGGAC
EST: gi|211368455|gb|FL037565.1|FL037565
EST:     AAAGGCAGAATGCATGGCAGCAGTTTCAAACCAAAGGGAAAGCCAAAAAG                         GTGGGGTTCTTCTCCGGTCGCAAGAAGGAGAGCATCTTCAAGTCACCGGAC
genomic: AAAGGCAGAATGCATGGCAGCAGTTTCAAACCAAGGGGAAAGCCAAAAAGgtagcttctt ... tgtttgccagGTGGGGTTCTTCTCCGGTCGCAAGAAGGAGAGCATCTTCAAGTCACCGGAC
EST: gi|67018352|gb|CO447101.1|CO447101
EST:     AAAGGCAGAATGCATGGCAGCAGTTTCAAACCAAGGGGAAAGCCAAAAAG                         GTGGGGTTCTTCTCCGGTCGCAAGAAGGAGAGCATCTTCAAGTCACCGGAC
genomic: AAAGGCAGAATGCATGGCAGCAGTTTCAAACCAAGGGGAAAGCCAAAAAGgtagcttctt ... tgtttgccagGTGGGGTTCTTCTCCGGTCGCAAGAAGGAGAGCATCTTCAAGTCACCGGAC
EST: gi|78075367|gb|DV503801.1|DV503801
EST:     AAAGGCAGAATGCATGGCAGCAGTTTCAAACCAAGGGGAAAGCCAAAAAG                         GTGGGGTTCTTCTCCGG
genomic: AAAGGCAGAATGCATGGCAGCAGTTTCAAACCAAGGGGAAAGCCAAAAAGgtagcttctt ... tgtttgccagGTGGGGTTCTTCTCCGG
EST: gi|211154208|gb|FL453078.1|FL453078
EST:     AAAGGCAGAATGCATGGCAGCAGTTTCAAACCAAAGGGAAAGCCAAAAAG                         GTGGGGTTCTTCTCCGGTCGCAAGAAGGAGAGCATCTTCAAGTCACCGGAC
genomic: AAAGGCAGAATGCATGGCAGCAGTTTCAAACCAAGGGGAAAGCCAAAAAGgtagcttctt ... tgtttgccagGTGGGGTTCTTCTCCGGTCGCAAGAAGGAGAGCATCTTCAAGTCACCGGAC
EST: gi|211538727|gb|FL481468.1|FL481468
EST:     AAAGGCAGAATGCATGGCAGCAGTTTCAAACCAAAGGGAAAGCCAAAAAG                         GTGGGGTTCTTCTCCGGTCGCAAGAAGGAGAGCATCTTCAAGTCACCGGAC
genomic: AAAGGCAGAATGCATGGCAGCAGTTTCAAACCAAGGGGAAAGCCAAAAAGgtagcttctt ... tgtttgccagGTGGGGTTCTTCTCCGGTCGCAAGAAGGAGAGCATCTTCAAGTCACCGGAC
EST: gi|211477790|gb|FK995982.1|FK995982
EST:     AAAGGCAGAATGCATGGCAGCAGTTTCAAACCAAGGGGAAAGCCAAAAAG                         GTGGGGTTCTTCTCCGGTCGCAAGAAGGAGAGCATCTTCAAGTCACCGGAC
genomic: AAAGGCAGAATGCATGGCAGCAGTTTCAAACCAAGGGGAAAGCCAAAAAGgtagcttctt ... tgtttgccagGTGGGGTTCTTCTCCGGTCGCAAGAAGGAGAGCATCTTCAAGTCACCGGAC
EST: gi|60348776|gb|DN215749.1|DN215749
EST:     AAAGGCAGAATGCATGGCAGCAGTTTCAAACCAAGGGGAAAGCCAAAAAG                         GTGGGGTTCTTCTCCGGTCGCAAGAAGGAGAGCATCTTCAAGTCACCGGAC
genomic: AAAGGCAGAATGCATGGCAGCAGTTTCAAACCAAGGGGAAAGCCAAAAAGgtagcttctt ... tgtttgccagGTGGGGTTCTTCTCCGGTCGCAAGAAGGAGAGCATCTTCAAGTCACCGGAC
EST: gi|211477791|gb|FK995983.1|FK995983
EST:     AAAGGCAGAATGCATGGCAGCAGTTTCAAACCAAGGGGAAAGCCAAAAAG                         GTGGGGTTCTTCTCCGGTCGCAAGAAGGAGAGCATCTTCAAGTCACCGGAC
genomic: AAAGGCAGAATGCATGGCAGCAGTTTCAAACCAAGGGGAAAGCCAAAAAGgtagcttctt ... tgtttgccagGTGGGGTTCTTCTCCGGTCGCAAGAAGGAGAGCATCTTCAAGTCACCGGAC
EST: gi|24765200|gb|CA400359.1|CA400359
EST:     AAAGGCAGAATGCATGGCAGCAGTTTCAAACCAAGGGGAAAGCCAAAAAG                         GTGGGGTTCTTCTCCGGTCGCAAGAAGGAGAGCATCTTCAAGTCACCGGAC
genomic: AAAGGCAGAATGCATGGCAGCAGTTTCAAACCAAGGGGAAAGCCAAAAAGgtagcttctt ... tgtttgccagGTGGGGTTCTTCTCCGGTCGCAAGAAGGAGAGCATCTTCAAGTCACCGGAC
EST: gi|211147842|gb|FK968701.1|FK968701
EST:     AAAGGCAGAATGCATGGCAGCAGTTTCAAACCAAAGGGAAAGCCAAAAAG                         GTGGGGTTCTTCTCCGGTCGCAAGAAGGAGAGCATCTTCAAGTCACCGGAC
genomic: AAAGGCAGAATGCATGGCAGCAGTTTCAAACCAAGGGGAAAGCCAAAAAGgtagcttctt ... tgtttgccagGTGGGGTTCTTCTCCGGTCGCAAGAAGGAGAGCATCTTCAAGTCACCGGAC
EST: gi|60394898|gb|DN227767.1|DN227767
EST:     AAAGGCAGAATGCATGGCAGCAGTTTCAAACCAAGGGGAAAGCCAAAAAG                         GTGGGGTTCTTCTCCGGTCGCAAGAAGGAGAGCATCTTCAAGTCACCGGAC
genomic: AAAGGCAGAATGCATGGCAGCAGTTTCAAACCAAGGGGAAAGCCAAAAAGgtagcttctt ... tgtttgccagGTGGGGTTCTTCTCCGGTCGCAAGAAGGAGAGCATCTTCAAGTCACCGGAC
EST: gi|211253693|gb|FL475671.1|FL475671
EST:     AAAGGCAGAATGCATGGCAGCAGTTTCAAACCAAAGGGAAAGCCAAAAAG                         GTGGGGTTCTTCTCCGGTCGCAAGAAGGAGAGCATYTTCAAGTCACCGGAC
genomic: AAAGGCAGAATGCATGGCAGCAGTTTCAAACCAAGGGGAAAGCCAAAAAGgtagcttctt ... tgtttgccagGTGGGGTTCTTCTCCGGTCGCAAGAAGGAGAGCATCTTCAAGTCACCGGAC
EST: gi|113704163|gb|EE681667.1|EE681667
EST:     AAAGGCAGAATGCATGGCAGCAGTTTCAAACCAAAGGGAAAGCCAAAAAG                         GTGGGGTTCTTCTCCGGTCGCAAGAAGGAGAGCATTTTCAAGTCACCGGAC
genomic: AAAGGCAGAATGCATGGCAGCAGTTTCAAACCAAGGGGAAAGCCAAAAAGgtagcttctt ... tgtttgccagGTGGGGTTCTTCTCCGGTCGCAAGAAGGAGAGCATCTTCAAGTCACCGGAC

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), 47 (downstream exon)
Score: 204

TGCTTTCAAATCAAAATCCCGCTTTGAGCAGCTTGAATTTGCCCAAAACAAAAGGCAGAATGCATGGCAGCAGTTTCAAACCAAGGGGAAAGCCAAAAAGgtagcttctt ... tgtttgccagGTGGGGTTCTTCTCCGGTCGCAAGAAGGAGAGCATCTTCAAGTCACCGGACGACCACAGAGGTAAGGTGGGTGTCACTGGGAGTGGCAAGGGCCTGACCG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 164

TGCTTTCAAATCAAAATCCCGCTTTGAGCAGCTTGAATTTGCCCAAAACAAAAGGCAGAATGCATGGCAGCAGTTTCAAACCAAGGGGAAAGCCAAAAAGgtagcttctt ... tgtttgccagGTGGGGTTCTTCTCCGGTCGCAAGAAGGAGAGCATCTTCAAGTCACCGGACGACCACAGAGGTAAGGTGGGTGTCACTGGGAGTGGCAAGGGCCTGACCG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 217

TGCTTTCAAATCAAAATCCCGCTTTGAGCAGCTTGAATTTGCCCAAAACAAAAGGCAGAATGCATGGCAGCAGTTTCAAACCAAGGGGAAAGCCAAAAAGgtagcttctt ... tgtttgccagGTGGGGTTCTTCTCCGGTCGCAAGAAGGAGAGCATCTTCAAGTCACCGGACGACCACAGAGGTAAGGTGGGTGTCACTGGGAGTGGCAAGGGCCTGACCG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 156

TGCTTTCAAATCAAAATCCCGCTTTGAGCAGCTTGAATTTGCCCAAAACAAAAGGCAGAATGCATGGCAGCAGTTTCAAACCAAGGGGAAAGCCAAAAAGgtagcttctt ... tgtttgccagGTGGGGTTCTTCTCCGGTCGCAAGAAGGAGAGCATCTTCAAGTCACCGGACGACCACAGAGGTAAGGTGGGTGTCACTGGGAGTGGCAAGGGCCTGACCG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGCTTTCAAATCAAAATCCCGCTTTGAGCAGCTTGAATTTGCCCAAAACAAAAGGCAGAATGCATGGCAGCAGTTTCAAACCAAGGGGAAAGCCAAAAAGgtagcttcttggcccccacgtaatttttttttgctttcttaaaaatggctaggcactcttccattgagttggaattctgaatctcaaggtactacatatg

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - cccccac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aaaaatgg