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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagatatgaaaaggaatgattcaacgtatggtgagttgagtttaattgctgactgacactgacacattccgctgttccattagGTCTTCCGGCAGAAATTACACAAAACATTCAAGAACATCAAGGTTGTCTCCAACAGGATGGTGTTTAATGAAGAAGGCCGCCTCATAGCATTTAAAG

Basic information

species Zea mays
transcript GRMZM2G157310_T02
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G157310_T02 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os03g44660.1 (Oryza sativa), 3'ss of exon 5
gtaagatatgaaaaggaatgattcaacgtatggtgagttgag-tttaattgctgactgacactgacacattccgctgttccattagGTCTTCCGGCAGAAATTACACAAAACATTCAAGAACATCAAGGTTGTCTCCAACAGGATGGTGTTTAATGAAGAAGGCCGCCTCATAGCATTTAAAG
        | |  |  |   | ||  | |||| |||| |||| |||  |||| |||||||||  ||    |  |    ||   |||||||||||||||||| | |||| | ||||||||||||| |||||||| |||||||||||||| || ||||||||||| || ||  |  |||||||||
-------gtaagtactacaaagtcctcatatgatgagatgagctttggttgcagactgacac--acctgctttg----tcttctagGTCTTCCGGCAGAAACTCCACAGATCATTCAAGAACATTAAGGTTGTGTCCAACAGGATGGTCTTCAATGAAGAAGGTCGTCTTGTTTCATTTAAAG
















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|101386461|gb|EB815247.1|EB815247
EST:     AGATTCCAGTGCTGGTATTTTCTGCAGGACTTGCAGACATAATTGAAGAG                         GTCTTCCGGCAGAAATTACACAAAACATTCAAGAACATCAAGGTTGTCTCC
genomic: AGATTCCAGTGCTGGTATTTTCTGCAGGACTTGCAGACATAATTGAAGAGgtaagatatg ... gttccattagGTCTTCCGGCAGAAATTACACAAAACATTCAAGAACATCAAGGTTGTCTCC
EST: gi|149013204|gb|EE042840.2|EE042840
EST:     CCAGTGCTGGTATTTTCTGCAGGACTTGCAGACATAATTGAAGAG                         GTCTTCCGGCAGAAATTACACAAAACATTCAAGAACATCAAGGTTGTCTCC
genomic: CCAGTGCTGGTATTTTCTGCAGGACTTGCAGACATAATTGAAGAGgtaagatatg ... gttccattagGTCTTCCGGCAGAAATTACACAAAACATTCAAGAACATCAAGGTTGTCTCC
EST: gi|76293679|gb|DV033247.1|DV033247
EST:     AGATTCCAGTGCTGGTATTTTCTGCAGGACTTGCAGACATAATTGAAGAG                         GTCTTCCGGCAGAAATTACACAAAACATTCAAGAACATCAAGGTTGTCTCC
genomic: AGATTCCAGTGCTGGTATTTTCTGCAGGACTTGCAGACATAATTGAAGAGgtaagatatg ... gttccattagGTCTTCCGGCAGAAATTACACAAAACATTCAAGAACATCAAGGTTGTCTCC
EST: gi|101385767|gb|EB814932.1|EB814932
EST:     AGATTCCAGTGCTGGTATTTTCTGCAGGACTTGCAGACATAATTGAAGAG                         GTCTTCCGGCAGAAATTACACAAAACATTCAAGAACATCAAGGTTGTCTCC
genomic: AGATTCCAGTGCTGGTATTTTCTGCAGGACTTGCAGACATAATTGAAGAGgtaagatatg ... gttccattagGTCTTCCGGCAGAAATTACACAAAACATTCAAGAACATCAAGGTTGTCTCC
EST: gi|74242168|gb|DT650082.1|DT650082
EST:     AGATTCCAGTGCTGGTATTTTCTGCAGGACTTGCAGACATAATTGAAGAG                         GTCTTCCGGCAGAAATTACACAAAACATTCAAGAACATCAAGGTTGTCTCC
genomic: AGATTCCAGTGCTGGTATTTTCTGCAGGACTTGCAGACATAATTGAAGAGgtaagatatg ... gttccattagGTCTTCCGGCAGAAATTACACAAAACATTCAAGAACATCAAGGTTGTCTCC
EST: gi|78092209|gb|DV520583.1|DV520583
EST:     AGATTCCAGTGCTGGTATTTTCTGCAGGACTTGCAGACATAATTGAAGAG                         GTCTTCCGGCAGAAATTACACAAAACATTCAAGAACATCAAGGTTGTCTCC
genomic: AGATTCCAGTGCTGGTATTTTCTGCAGGACTTGCAGACATAATTGAAGAGgtaagatatg ... gttccattagGTCTTCCGGCAGAAATTACACAAAACATTCAAGAACATCAAGGTTGTCTCC
EST: gi|71774185|gb|DR972065.1|DR972065
EST:     AGATTCCAGTGCTGGTATTTTCTGCAGGACTNGCAGACATAATTGAAGAG                         GTCTTCCGGCAGAAATTACACAAAACATTCAAGAACATCAAGGTTGTCTCC
genomic: AGATTCCAGTGCTGGTATTTTCTGCAGGACTTGCAGACATAATTGAAGAGgtaagatatg ... gttccattagGTCTTCCGGCAGAAATTACACAAAACATTCAAGAACATCAAGGTTGTCTCC
EST: gi|91877197|gb|EB407154.1|EB407154
EST:     AGATTCCAGTGCTGGTATTTTCTGCAGGACTTGCAGACATAATTGAAGAG                         GTCTTCCGGCAGAAATTACACAAAACATTCAAGAACATCAAGGTTGTCTCC
genomic: AGATTCCAGTGCTGGTATTTTCTGCAGGACTTGCAGACATAATTGAAGAGgtaagatatg ... gttccattagGTCTTCCGGCAGAAATTACACAAAACATTCAAGAACATCAAGGTTGTCTCC
EST: gi|91050984|gb|EB161402.1|EB161402
EST:     AGATTCCAGTGCTGGTATTTTCTGCAGGACTTGCAGACATAATTGAAGAA                         GTCTTCCGGAAGAAATTACACAAAA
genomic: AGATTCCAGTGCTGGTATTTTCTGCAGGACTTGCAGACATAATTGAAGAGgtaagatatg ... gttccattagGTCTTCCGGCAGAAATTACACAAAA
EST: gi|149009394|gb|EE153935.2|EE153935
EST:     AGATTCCAGTGCTGGTATTTTCTGCAGGACTTGCAGACATAATTGAAGAG                         GTCTTCCGGCAGAAATTACACAAAACATTCAAGAACATCAAGGTTGTCTCC
genomic: AGATTCCAGTGCTGGTATTTTCTGCAGGACTTGCAGACATAATTGAAGAGgtaagatatg ... gttccattagGTCTTCCGGCAGAAATTACACAAAACATTCAAGAACATCAAGGTTGTCTCC
EST: gi|211118716|gb|FL311656.1|FL311656
EST:     AGATTCCAGTGCTGGTATTTTCTGCAGGACTTGCAGACATAATTGAAGAG                         GTCTTCCGGCAGAAACTACACAAAACATTCAAGAACATCAAGGTTGTCTCC
genomic: AGATTCCAGTGCTGGTATTTTCTGCAGGACTTGCAGACATAATTGAAGAGgtaagatatg ... gttccattagGTCTTCCGGCAGAAATTACACAAAACATTCAAGAACATCAAGGTTGTCTCC
EST: gi|31354764|gb|CD439121.1|CD439121
EST:     AGATTCCAGTGCTGGTATTTTCTGCAGGACTTGCAGACATAATTGAAGAG                         GTCTTCCGGCAGAAACTACACAAAACATTCAAGAACATCAAGGTTGTCTCC
genomic: AGATTCCAGTGCTGGTATTTTCTGCAGGACTTGCAGACATAATTGAAGAGgtaagatatg ... gttccattagGTCTTCCGGCAGAAATTACACAAAACATTCAAGAACATCAAGGTTGTCTCC
EST: gi|78092208|gb|DV520582.1|DV520582
EST:     CAGACATAATTGAAGAG                         GTCTTCCGGCAGAAATTACACAAAACATTCAAGAACATCAAGGTTGTCTCC
genomic: CAGACATAATTGAAGAGgtaagatatg ... gttccattagGTCTTCCGGCAGAAATTACACAAAACATTCAAGAACATCAAGGTTGTCTCC
EST: gi|71438827|gb|DR819877.1|DR819877
EST:     AGATTCCAGTGCTGGTATTTTCTGCAGGACTTGCAGACATAATTGAAGAG                         GTCTTCCGGCAGAAATTACACAAAACATTCAAGAACATCAAGGTTGTCTCC
genomic: AGATTCCAGTGCTGGTATTTTCTGCAGGACTTGCAGACATAATTGAAGAGgtaagatatg ... gttccattagGTCTTCCGGCAGAAATTACACAAAACATTCAAGAACATCAAGGTTGTCTCC
EST: gi|37400710|gb|CF637712.1|CF637712
EST:     AGATTCCAGTGCTGGTATTTTCTGCAGGACTTGCAGACATAATTGAAGAG                         GTCTTCCGGCAGAAACTACACAAAACATTCAAGAACATCAAGGTTGTCTCC
genomic: AGATTCCAGTGCTGGTATTTTCTGCAGGACTTGCAGACATAATTGAAGAGgtaagatatg ... gttccattagGTCTTCCGGCAGAAATTACACAAAACATTCAAGAACATCAAGGTTGTCTCC
EST: gi|50333544|gb|CO528670.1|CO528670
EST:     AGATTCCAGTGCTGGTATTTTCTGCAGGACTTGCAGACATAATTGAAGAG                         GTCTTCCGGCAGAAATTACACAAAACATTCAAGAACATCAAGGTTGTCTCC
genomic: AGATTCCAGTGCTGGTATTTTCTGCAGGACTTGCAGACATAATTGAAGAGgtaagatatg ... gttccattagGTCTTCCGGCAGAAATTACACAAAACATTCAAGAACATCAAGGTTGTCTCC
EST: gi|88749393|gb|DY533534.1|DY533534
EST:     AGATTCCAGTGCTGGTATTTTCTGCAGGACTTGCAGACATAATTGAAGAG                         GTCTTCCGGCAGAAATTACACAAAACATTCAAGAACATCAAGGTTGTCTCC
genomic: AGATTCCAGTGCTGGTATTTTCTGCAGGACTTGCAGACATAATTGAAGAGgtaagatatg ... gttccattagGTCTTCCGGCAGAAATTACACAAAACATTCAAGAACATCAAGGTTGTCTCC
EST: gi|71449422|gb|DR830472.1|DR830472
EST:     AGATTCCAGTGCTGGTATTTTCTGCAGGACTTGCAGACATAATTGAAGAG                         GTCTTCCGGCAGAAATTACACAAAACATTCAAGAACATCAAGGTTGTCTCC
genomic: AGATTCCAGTGCTGGTATTTTCTGCAGGACTTGCAGACATAATTGAAGAGgtaagatatg ... gttccattagGTCTTCCGGCAGAAATTACACAAAACATTCAAGAACATCAAGGTTGTCTCC

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: 149

GAGAGAGAGATTCCAGTGCTGGTATTTTCTGCAGGACTTGCAGACATAATTGAAGAGgtaagatatg ... gttccattagGTCTTCCGGCAGAAATTACACAAAACATTCAAGAACATCAAGGTTGTCTCCAACAGGATGGTGTTTAATGAAGAAGGCCGCCTCATAGCATTTAAAG


Block sizes: 43 (upstream exon), 49 (downstream exon)
Score: 92

GAGAGAGAGATTCCAGTGCTGGTATTTTCTGCAGGACTTGCAGACATAATTGAAGAGgtaagatatg ... gttccattagGTCTTCCGGCAGAAATTACACAAAACATTCAAGAACATCAAGGTTGTCTCCAACAGGATGGTGTTTAATGAAGAAGGCCGCCTCATAGCATTTAAAG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 86

GAGAGAGAGATTCCAGTGCTGGTATTTTCTGCAGGACTTGCAGACATAATTGAAGAGgtaagatatg ... gttccattagGTCTTCCGGCAGAAATTACACAAAACATTCAAGAACATCAAGGTTGTCTCCAACAGGATGGTGTTTAATGAAGAAGGCCGCCTCATAGCATTTAAAG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 115

GAGAGAGAGATTCCAGTGCTGGTATTTTCTGCAGGACTTGCAGACATAATTGAAGAGgtaagatatg ... gttccattagGTCTTCCGGCAGAAATTACACAAAACATTCAAGAACATCAAGGTTGTCTCCAACAGGATGGTGTTTAATGAAGAAGGCCGCCTCATAGCATTTAAAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tggtgagttgagtttaattgctgactgacactgacacattccgctgttccattagGTCTTCCGGCAGAAATTACACAAAACATTCAAGAACATCAAGGTTGTCTCCAACAGGATGGTGTTTAATGAAGAAGGCCGCCTCATAGCATTTAAAG
                            cactgac  putative branch site (score: 115)
                                           ctgttcc  putative PPT
          agtttaatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagatatgaaaaggaatgattcaacgtatggtgagttgagtttaattgctgactgacactgacacattccgctgttccattagGTCTTCCGGCAGAAATTACACAAAACATTCAAGAACATCAAGGTTGTCTCCAACAGGATGGTGTTTAATGAAGAAGGCCGCCTCATAGCATTTAAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG