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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tcactgtcttctgctgaaaaagaaggaagttgtgagcttcttttttgtaaccttttgaagtataattaattgttgattatcgttatcttgattatttcagTATGCTGAGAAGGATTTCGTGCGGAAACATAACATGGATGGGATTCAACTTGCAGAACAGATGTGGGACAATGTAAGTTCGAACAACAAGAAGGGGGTGT

Basic information

species Zea mays
transcript GRMZM2G059225_T02
intron # 17
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G059225_T02 (Zea mays), 3'ss of exon 17
lower sequence: LOC_Os09g33600.1 (Oryza sativa), 3'ss of exon 17
tcactgtcttctgctgaaaaagaagga-----agttgtgagcttcttttttgtaaccttttgaagtataattaattgttgattatcgttatcttgattatttcagTATGCTGAGAAGGATTTCGTGCGGAAACATAACATGGATGGGATTCAACTTGCAGAACAGATGTGGGACAATGTAAGTTCGAACAACAAGAAGGGGGTGT
    |  ||||     || |||  ||      |  ||||  ||  |  |||| ||  |||  ||  ||   ||    ||||   | ||| | || | ||||||||||||| |||   ||||  ||||| || | ||| |||||||  |  |   | ||  ||||||||||||| ||||| ||||| ||||||||||||||||| |
----taccttcctaaaaataagtcggcctaccaagtgtgtactg-tcatttggaatatttgaaatgatttatagcatttgacagttgttttatttaatatttcagTATGCCGAGCGAGATTATGTGCGAAAGCTTAATATGGATGATAGCCTGGTAGCTCAACAGATGTGGGAAAATGTTAGTTCAAACAACAAGAAGGGGGTTT
















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|71772945|gb|DR970866.1|DR970866
EST:     CTAAACAATCTGATTCTATTGCAGTGAAGGAGAAATTTATTCATGCCAAG                         TATGCTGAGAAGGATTTCGTGCGGAAACATAACATGGATGGGATTCAACTT
genomic: CTAAACAATCTGATTCTATTGCAGTGAAGGAGAAATTTATTCATGCCAAGgtacttcctc ... attatttcagTATGCTGAGAAGGATTTCGTGCGGAAACATAACATGGATGGGATTCAACTT
EST: gi|31361423|gb|CD445780.1|CD445780
EST:     CTAAACAATCTGATTCTATTGCAGTGAAGGAGAAATTTATTCATGCCAAG                         TATGCTGAGAAGGATTTCGTGCGGAAACATAGCGTGGATGGGATTCAACTT
genomic: CTAAACAATCTGATTCTATTGCAGTGAAGGAGAAATTTATTCATGCCAAGgtacttcctc ... attatttcagTATGCTGAGAAGGATTTCGTGCGGAAACATAACATGGATGGGATTCAACTT
EST: gi|93016491|gb|EB642011.1|EB642011
EST:     CTAAACAATCTGATTCTATTGCAGTGAAGGAGAAATTTATTCATGCCAAG                         TATGCTGAGAAGGATTTCGTGCGGAAACATAACATGGATGGGATTCAACTT
genomic: CTAAACAATCTGATTCTATTGCAGTGAAGGAGAAATTTATTCATGCCAAGgtacttcctc ... attatttcagTATGCTGAGAAGGATTTCGTGCGGAAACATAACATGGATGGGATTCAACTT
EST: gi|5268408|gb|AI770372.1|AI770372
EST:     CTAAACAATCTGATTCTATTGCAGTGAAGGAGAAATTTATTCATGCCAAG                         TATGCTGAGAAGGATTTCGTGCGGAAACATAACATGGATGGGATTCAACTT
genomic: CTAAACAATCTGATTCTATTGCAGTGAAGGAGAAATTTATTCATGCCAAGgtacttcctc ... attatttcagTATGCTGAGAAGGATTTCGTGCGGAAACATAACATGGATGGGATTCAACTT
EST: gi|60338936|gb|DN205909.1|DN205909
EST:     CTAAACAATCTGATTCTATTGCAGTGAAGGAGAAATTTATTCATGCCAAG                         TATGCTGAGAAGGATTTCGTGCGGAAACATAACATGGATGGGATTCAACTT
genomic: CTAAACAATCTGATTCTATTGCAGTGAAGGAGAAATTTATTCATGCCAAGgtacttcctc ... attatttcagTATGCTGAGAAGGATTTCGTGCGGAAACATAACATGGATGGGATTCAACTT
EST: gi|60354506|gb|DN221479.1|DN221479
EST:     CTAAACAATCTGATTCTATTGCAGTGAAGGAGAAATTTATTCATGCCAAG                         TATGCTGAGAAGGATTTCGTGCGGAAACATAACATGGATGGGATTCAACTT
genomic: CTAAACAATCTGATTCTATTGCAGTGAAGGAGAAATTTATTCATGCCAAGgtacttcctc ... attatttcagTATGCTGAGAAGGATTTCGTGCGGAAACATAACATGGATGGGATTCAACTT
EST: gi|60337093|gb|DN204066.1|DN204066
EST:     CTAAACAATCTGATTCTATTGCAGTGAAGGAGAAATTTATTCATGCCAAG                         TATGCTGAGAAGGATTTCGTGCGGAAACATAACATGGATGGGATTCAACTT
genomic: CTAAACAATCTGATTCTATTGCAGTGAAGGAGAAATTTATTCATGCCAAGgtacttcctc ... attatttcagTATGCTGAGAAGGATTTCGTGCGGAAACATAACATGGATGGGATTCAACTT
EST: gi|60354512|gb|DN221485.1|DN221485
EST:     CTAAACAATCTGATTCTATTGCAGTGAAGGAGAAATTTATTCATGCCAAG                         TATGCTGAGAAGGATTTCGTGCGGAAACATAACATGGATGGGATTCAACTT
genomic: CTAAACAATCTGATTCTATTGCAGTGAAGGAGAAATTTATTCATGCCAAGgtacttcctc ... attatttcagTATGCTGAGAAGGATTTCGTGCGGAAACATAACATGGATGGGATTCAACTT
EST: gi|60395181|gb|DN228050.1|DN228050
EST:     CTAAACAATCTGATTCTATTGCAGTGAAGGAGAAATTTATTCATGCCAAG                         TATGCTGAGAAGGATTTCGTGCGGAAACATAACATGGATGGGATTCAACTT
genomic: CTAAACAATCTGATTCTATTGCAGTGAAGGAGAAATTTATTCATGCCAAGgtacttcctc ... attatttcagTATGCTGAGAAGGATTTCGTGCGGAAACATAACATGGATGGGATTCAACTT
EST: gi|50332291|gb|CO527417.1|CO527417
EST:     CTAAACAATCTGATTCTATTGCAGTGAAGGAGAAATTTATTCATGCCAAG                         TATGCTGAGAAGGATTTCGTGCGGAAACATAACATGGATGGGATTCAACTT
genomic: CTAAACAATCTGATTCTATTGCAGTGAAGGAGAAATTTATTCATGCCAAGgtacttcctc ... attatttcagTATGCTGAGAAGGATTTCGTGCGGAAACATAACATGGATGGGATTCAACTT

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: 223

GGCTGATGGATTAGAAAACATGTCGCATGGCTTTGCACCCAAGAAGCCTAAACAATCTGATTCTATTGCAGTGAAGGAGAAATTTATTCATGCCAAGgtacttcctc ... attatttcagTATGCTGAGAAGGATTTCGTGCGGAAACATAACATGGATGGGATTCAACTTGCAGAACAGATGTGGGACAATGTAAGTTCGAACAACAAGAAGGGGGTGT


Block sizes: 43 (upstream exon), 45 (downstream exon)
Score: 25

GGCTGATGGATTAGAAAACATGTCGCATGGCTTTGCACCCAAGAAGCCTAAACAATCTGATTCTATTGCAGTGAAGGAGAAATTTATTCATGCCAAGgtacttcctc ... attatttcagTATGCTGAGAAGGATTTCGTGCGGAAACATAACATGGATGGGATTCAACTTGCAGAACAGATGTGGGACAATGTAAGTTCGAACAACAAGAAGGGGGTGT


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

GGCTGATGGATTAGAAAACATGTCGCATGGCTTTGCACCCAAGAAGCCTAAACAATCTGATTCTATTGCAGTGAAGGAGAAATTTATTCATGCCAAGgtacttcctc ... attatttcagTATGCTGAGAAGGATTTCGTGCGGAAACATAACATGGATGGGATTCAACTTGCAGAACAGATGTGGGACAATGTAAGTTCGAACAACAAGAAGGGGGTGT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 110

GGCTGATGGATTAGAAAACATGTCGCATGGCTTTGCACCCAAGAAGCCTAAACAATCTGATTCTATTGCAGTGAAGGAGAAATTTATTCATGCCAAGgtacttcctc ... attatttcagTATGCTGAGAAGGATTTCGTGCGGAAACATAACATGGATGGGATTCAACTTGCAGAACAGATGTGGGACAATGTAAGTTCGAACAACAAGAAGGGGGTGT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgtaaccttttgaagtataattaattgttgattatcgttatcttgattatttcagTATGCTGAGAAGGATTTCGTGCGGAAACATAACATGGATGGGATTCAACTTGCAGAACAGATGTGGGACAATGTAAGTTCGAACAACAAGAAGGGGGTGT
                                              ttatttc  CT-rich tract
       ttttgaagtataatta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tcactgtcttctgctgaaaaagaaggaagttgtgagcttcttttttgtaaccttttgaagtataattaattgttgattatcgttatcttgattatttcagTATGCTGAGAAGGATTTCGTGCGGAAACATAACATGGATGGGATTCAACTTGCAGAACAGATGTGGGACAATGTAAGTTCGAACAACAAGAAGGGGGTGT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - -tctgctg
- - - - - - - - -aaaagaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgttgat