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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgaaacagttatattttgtgcttagagtttcatgcattttattccggtaaaatcacttggttgcgaaatttcttgacaataatcaattgcaaaataatagGGAGAAGAAATCATTGCTATAGTTCCTTGGGATGAATGGTGGGCCATGGCTCTCAAGGATGAATCAAATCCTCAGATAGCCCTGCTTCCTTTGCACCCTG

Basic information

species Zea mays
transcript GRMZM2G031824_T01
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G031824_T01 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os09g22440.1 (Oryza sativa), 3'ss of exon 3
tgaaacagttatattttgtgcttagagtttcatgcattttattccggta-aaatcacttg--gttgcgaaattt-cttgacaataatcaattgcaaa-----ataatagGGAGAAGAAATCATTGCTATAGTTCCTTGGGATGAATGGTGGGCCATGGCTCTCAAGGATGAATCAAATCCTCAGATAGCCCTGCTTCCTTTGCACCCTG
             ||     ||||    ||||| ||||||||||| ||  | | || | |   ||| | | ||| |||||  ||| ||  || ||||     |||||||||||||||||| |||| ||||||||||||||||||||||||||| ||||| |||||||||   |||||||||||||||||||| || ||  | || ||||
-----tgccccccttcaaaactta----ttcattcattttattcctgtgcataacattcgcatttgtgtatttttcttgatgatactctgttacaaattacaataatagGGAGAAGAAATTATTGTTATAGTTCCTTGGGATGAATGGTGGGCAATGGCACTCAAGGATTCGTCAAATCCTCAGATAGCCCTTCTACCACTACATCCTG
















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|32842172|gb|CD981853.1|CD981853
EST:     ACGAGAAGGGTGATCTTTGGGTTGCAGAGTCAGGCTATGAAAACGAGAAG                         GGAGAAGAAATCATTGCTATAGTTCCTTGGGATGAATGGTGGGCCATGGCT
genomic: ACGAGAAGGGTGATCTTTGGGTTGCAGAGTCAGGCTATGAAAACGAGAAGgtaattcata ... aaaataatagGGAGAAGAAATCATTGCTATAGTTCCTTGGGATGAATGGTGGGCCATGGCT
EST: gi|32925672|gb|CF030484.1|CF030484
EST:     ACGAGAAGGGTGATCTTTGGGTTGCAGAGTCAGGCTATGAAAACGAGAAG                         GGAGGAGAAATCATTGCTATAGTTCCTTGGGATGAATGGTGGGCCATGGCT
genomic: ACGAGAAGGGTGATCTTTGGGTTGCAGAGTCAGGCTATGAAAACGAGAAGgtaattcata ... aaaataatagGGAGAAGAAATCATTGCTATAGTTCCTTGGGATGAATGGTGGGCCATGGCT
EST: gi|32850032|gb|CD989713.1|CD989713
EST:     ACGAGAAGGGTGATCTTTGGGTTGCAGAGTCAGGCTATGAAAACGAGAAG                         GGAGAAGAAATCATTGCTATAGTTCCTTGGGATGAATGGTGGGCCATGGCT
genomic: ACGAGAAGGGTGATCTTTGGGTTGCAGAGTCAGGCTATGAAAACGAGAAGgtaattcata ... aaaataatagGGAGAAGAAATCATTGCTATAGTTCCTTGGGATGAATGGTGGGCCATGGCT
EST: gi|32841464|gb|CD981145.1|CD981145
EST:     ACGAGAAGGGTGATCTTTGGGTTGCAGAGTCAGGCTATGAAAACGAGAAG                         GGAGAAGAAATCATTGCTATAGTTCCTTGGGATGAATGGTGGGCCATGGCT
genomic: ACGAGAAGGGTGATCTTTGGGTTGCAGAGTCAGGCTATGAAAACGAGAAGgtaattcata ... aaaataatagGGAGAAGAAATCATTGCTATAGTTCCTTGGGATGAATGGTGGGCCATGGCT
EST: gi|32924871|gb|CF029683.1|CF029683
EST:     ACGAGAAGGGTGATCTTTGGGTTGCAGAGTCAGGCTATGAAAACGAGAAG                         GGAGAAGAAATCATTGCTATAGTTCCTTGGGATGAATGGTGGGCCATGGCT
genomic: ACGAGAAGGGTGATCTTTGGGTTGCAGAGTCAGGCTATGAAAACGAGAAGgtaattcata ... aaaataatagGGAGAAGAAATCATTGCTATAGTTCCTTGGGATGAATGGTGGGCCATGGCT
EST: gi|32924893|gb|CF029705.1|CF029705
EST:     ACGAGAAGGGTGATCTTTGGGTTGCAGAGTCAGGCTATGAAAACGAGAAG                         GGAGAAGAAATCATTGCTATAGTTCCTTGGGATGAATGGTGGGCCATGGCT
genomic: ACGAGAAGGGTGATCTTTGGGTTGCAGAGTCAGGCTATGAAAACGAGAAGgtaattcata ... aaaataatagGGAGAAGAAATCATTGCTATAGTTCCTTGGGATGAATGGTGGGCCATGGCT
EST: gi|32841167|gb|CD980848.1|CD980848
EST:     ACGAGAAGGGTGATCTTTGGGTTGCAGAGTCAGGCTATGAAAACGAGAAG                         GGAGAAGAAATCATTGCTATAGTTCCTTGGGATGAATGGTGGGCCATGGCT
genomic: ACGAGAAGGGTGATCTTTGGGTTGCAGAGTCAGGCTATGAAAACGAGAAGgtaattcata ... aaaataatagGGAGAAGAAATCATTGCTATAGTTCCTTGGGATGAATGGTGGGCCATGGCT
EST: gi|32925223|gb|CF030035.1|CF030035
EST:     ACGAGAAGGGTGATCTTTGGGTTGCAGAGTCAGGCTATGAAAACGAGAAG                         GGAGAAGAAATCATTGCTATAGTTCCTTGGGATGAATGGTGGGCCATGGCT
genomic: ACGAGAAGGGTGATCTTTGGGTTGCAGAGTCAGGCTATGAAAACGAGAAGgtaattcata ... aaaataatagGGAGAAGAAATCATTGCTATAGTTCCTTGGGATGAATGGTGGGCCATGGCT
EST: gi|32841238|gb|CD980919.1|CD980919
EST:     ACGAGAAGGGTGATCTTTGG-TTGCAGAGTCAGGCTATGAAAACGAGAAG                         GGAGAAGAAATCATTGCTATAGTTCCTTGGGATGAATGGTGGGCCATGGCT
genomic: ACGAGAAGGGTGATCTTTGGGTTGCAGAGTCAGGCTATGAAAACGAGAAGgtaattcata ... aaaataatagGGAGAAGAAATCATTGCTATAGTTCCTTGGGATGAATGGTGGGCCATGGCT
EST: gi|32842171|gb|CD981852.1|CD981852
EST:     ACGAGAAGGGTGATCTTTGGGTTGCAGAGTCAGGCTATGAAAACGAGAAG                         GGAGAAGAAATCATTGCTATAGTTCCTTGGGATGAATGGTGGGCCATGGCT
genomic: ACGAGAAGGGTGATCTTTGGGTTGCAGAGTCAGGCTATGAAAACGAGAAGgtaattcata ... aaaataatagGGAGAAGAAATCATTGCTATAGTTCCTTGGGATGAATGGTGGGCCATGGCT
EST: gi|32921666|gb|CF026478.1|CF026478
EST:     ACGAGAAGGGTGATCTTTGGGTTGCAGAGTCAGGCTATGAAAACGAGAAG                         GGAGAAGAAATCATTGCTATAGTTCCTTGGGATGAATGGTGGGCCATGGCT
genomic: ACGAGAAGGGTGATCTTTGGGTTGCAGAGTCAGGCTATGAAAACGAGAAGgtaattcata ... aaaataatagGGAGAAGAAATCATTGCTATAGTTCCTTGGGATGAATGGTGGGCCATGGCT
EST: gi|32924738|gb|CF029550.1|CF029550
EST:     ACGAGAAGGGTGATCTTTGGGTTGCAGAGTCAGGCTATGAAAACGAGAAG                         GGAGAAGAAATCATTGCTATAGTTCCTTGGGATGAATGGTGGGCCATGGCT
genomic: ACGAGAAGGGTGATCTTTGGGTTGCAGAGTCAGGCTATGAAAACGAGAAGgtaattcata ... aaaataatagGGAGAAGAAATCATTGCTATAGTTCCTTGGGATGAATGGTGGGCCATGGCT
EST: gi|91875426|gb|EB405383.1|EB405383
EST:     ACGAGAAGGGTGATCTTTGGGGTGCAGAGTCAGGCTATGAAAACGAGAGG                         GGAGAAGAAAT
genomic: ACGAGAAGGGTGATCTTTGGGTTGCAGAGTCAGGCTATGAAAACGAGAAGgtaattcata ... aaaataatagGGAGAAGAAAT
EST: gi|32841288|gb|CD980969.1|CD980969
EST:     ACGAGAAGGGTGATCTTTGGGTTGCAGAGTCAGGCTATGAAAACGAGAAG                         GGAGAAGAAATCATTGCTATAGTTCCTTGGGATGAATGGTGGGCCATGGCT
genomic: ACGAGAAGGGTGATCTTTGGGTTGCAGAGTCAGGCTATGAAAACGAGAAGgtaattcata ... aaaataatagGGAGAAGAAATCATTGCTATAGTTCCTTGGGATGAATGGTGGGCCATGGCT
EST: gi|32925872|gb|CF030684.1|CF030684
EST:     ACGAGAAGGGTGATCTTTGGGTTGCAGAGTCAGGCTATGAAAACGAGAAG                         GGAGAAGAAATCATTGCTATAGTTCCTTGGGATGAATGGTGGGCCATGGCT
genomic: ACGAGAAGGGTGATCTTTGGGTTGCAGAGTCAGGCTATGAAAACGAGAAGgtaattcata ... aaaataatagGGAGAAGAAATCATTGCTATAGTTCCTTGGGATGAATGGTGGGCCATGGCT
EST: gi|32924755|gb|CF029567.1|CF029567
EST:     ACGAGAAGGGTGATCTTTGGGTTGCAGAGTCAGGCTATGAAAACGAGAAG                         GGAGAAGAAATCATTGCTATAGTTCCTTGGGATGAATGGTGGGCCATGGCT
genomic: ACGAGAAGGGTGATCTTTGGGTTGCAGAGTCAGGCTATGAAAACGAGAAGgtaattcata ... aaaataatagGGAGAAGAAATCATTGCTATAGTTCCTTGGGATGAATGGTGGGCCATGGCT
EST: gi|32840853|gb|CD980534.1|CD980534
EST:     ACGAGAAGGGTGATCTTTGGGTTGCAGAGTCAGGCTATGAAAACGAGAAG                         GGAGAAGAAATCATTGCTATAGTTCCTTGGGATGAATGGTGGGCCATGGCT
genomic: ACGAGAAGGGTGATCTTTGGGTTGCAGAGTCAGGCTATGAAAACGAGAAGgtaattcata ... aaaataatagGGAGAAGAAATCATTGCTATAGTTCCTTGGGATGAATGGTGGGCCATGGCT
EST: gi|32840051|gb|CD979732.1|CD979732
EST:     ACGAGAAGGGTGATCTTTGGGTTGCAGAGTCAGGCTATGAAAACGAGAAG                         GGAGAAGAAATCATTGCTATAGTTCCTTGGGATGAATGGTGGGCCATGGCT
genomic: ACGAGAAGGGTGATCTTTGGGTTGCAGAGTCAGGCTATGAAAACGAGAAGgtaattcata ... aaaataatagGGAGAAGAAATCATTGCTATAGTTCCTTGGGATGAATGGTGGGCCATGGCT
EST: gi|32925065|gb|CF029877.1|CF029877
EST:     ACGAGAAGGGTGATCTTTGGGTTGCAGAGTCAGGCTATGAAAACGAGAAG                         GGAGAAGAAATCATTGCTATAGTTCCTTGGGATGAATGGTGGGCCATGGCT
genomic: ACGAGAAGGGTGATCTTTGGGTTGCAGAGTCAGGCTATGAAAACGAGAAGgtaattcata ... aaaataatagGGAGAAGAAATCATTGCTATAGTTCCTTGGGATGAATGGTGGGCCATGGCT
EST: gi|32922055|gb|CF026867.1|CF026867
EST:     CAGAGTCAGGCTATGAAAACGAGAAG                         GGAGAAGAAATCATTGCTATAGTTCCTTGGGATGAATGGTGGGCCATGGCT
genomic: CAGAGTCAGGCTATGAAAACGAGAAGgtaattcata ... aaaataatagGGAGAAGAAATCATTGCTATAGTTCCTTGGGATGAATGGTGGGCCATGGCT
EST: gi|32920261|gb|CF025073.1|CF025073
EST:     ACGAGAAGGGTGATCTTTGGGTTGCAGAGTCAGGCTATGAAAACGAGAAG                         GGAGAAGAAATCATTGCTATAGTTCCTTGGGATGAATGGTGGGCCATGGCT
genomic: ACGAGAAGGGTGATCTTTGGGTTGCAGAGTCAGGCTATGAAAACGAGAAGgtaattcata ... aaaataatagGGAGAAGAAATCATTGCTATAGTTCCTTGGGATGAATGGTGGGCCATGGCT
EST: gi|32841249|gb|CD980930.1|CD980930
EST:     ACGAGAAGGGTGATCTTTGGGTTGCAGAGTCAGGCTATGAAAACGAGAAG                         GGAGAAGAAATCATTGCTATAGTTCCTTGGGATGAATGGTGGGCCATGGCT
genomic: ACGAGAAGGGTGATCTTTGGGTTGCAGAGTCAGGCTATGAAAACGAGAAGgtaattcata ... aaaataatagGGAGAAGAAATCATTGCTATAGTTCCTTGGGATGAATGGTGGGCCATGGCT
EST: gi|32840052|gb|CD979733.1|CD979733
EST:     ACGAGAAGGGTGATCTTTGGGTTGCAGAGTCAGGCTATGAAAACGAGAAG                         GGAGAAGAAATCATTGCTATAGTTCCTTGGGATGAATGGTGGGCCATGGCT
genomic: ACGAGAAGGGTGATCTTTGGGTTGCAGAGTCAGGCTATGAAAACGAGAAGgtaattcata ... aaaataatagGGAGAAGAAATCATTGCTATAGTTCCTTGGGATGAATGGTGGGCCATGGCT
EST: gi|32841608|gb|CD981289.1|CD981289
EST:     CGAGAAGGGTGATCTTTGGGTTGCAGAGTCAGGCTATGAAAACGAGAAG                         GGAGAAGAAATCATTGCTATAGTTCCTTGGGATGAATGGTGGGCCATGGCT
genomic: CGAGAAGGGTGATCTTTGGGTTGCAGAGTCAGGCTATGAAAACGAGAAGgtaattcata ... aaaataatagGGAGAAGAAATCATTGCTATAGTTCCTTGGGATGAATGGTGGGCCATGGCT

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: 321

GAAATGGGTGACTGGTGCATTTGCTGGGCATACCTCGGTTTGCTTAAAAGACGAGAAGGGTGATCTTTGGGTTGCAGAGTCAGGCTATGAAAACGAGAAGgtaattcata ... aaaataatagGGAGAAGAAATCATTGCTATAGTTCCTTGGGATGAATGGTGGGCCATGGCTCTCAAGGATGAATCAAATCCTCAGATAGCCCTGCTTCCTTTGCACCCTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 458

GAAATGGGTGACTGGTGCATTTGCTGGGCATACCTCGGTTTGCTTAAAAGACGAGAAGGGTGATCTTTGGGTTGCAGAGTCAGGCTATGAAAACGAGAAGgtaattcata ... aaaataatagGGAGAAGAAATCATTGCTATAGTTCCTTGGGATGAATGGTGGGCCATGGCTCTCAAGGATGAATCAAATCCTCAGATAGCCCTGCTTCCTTTGCACCCTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 592

GAAATGGGTGACTGGTGCATTTGCTGGGCATACCTCGGTTTGCTTAAAAGACGAGAAGGGTGATCTTTGGGTTGCAGAGTCAGGCTATGAAAACGAGAAGgtaattcata ... aaaataatagGGAGAAGAAATCATTGCTATAGTTCCTTGGGATGAATGGTGGGCCATGGCTCTCAAGGATGAATCAAATCCTCAGATAGCCCTGCTTCCTTTGCACCCTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 596

GAAATGGGTGACTGGTGCATTTGCTGGGCATACCTCGGTTTGCTTAAAAGACGAGAAGGGTGATCTTTGGGTTGCAGAGTCAGGCTATGAAAACGAGAAGgtaattcata ... aaaataatagGGAGAAGAAATCATTGCTATAGTTCCTTGGGATGAATGGTGGGCCATGGCTCTCAAGGATGAATCAAATCCTCAGATAGCCCTGCTTCCTTTGCACCCTG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ggtaaaatcacttggttgcgaaatttcttgacaataatcaattgcaaaataatagGGAGAAGAAATCATTGCTATAGTTCCTTGGGATGAATGGTGGGCCATGGCTCTCAAGGATGAATCAAATCCTCAGATAGCCCTGCTTCCTTTGCACCCTG
                         tcttgac  putative branch site (score: 596)
                                aataatcaattgcaaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgaaacagttatattttgtgcttagagtttcatgcattttattccggtaaaatcacttggttgcgaaatttcttgacaataatcaattgcaaaataatagGGAGAAGAAATCATTGCTATAGTTCCTTGGGATGAATGGTGGGCCATGGCTCTCAAGGATGAATCAAATCCTCAGATAGCCCTGCTTCCTTTGCACCCTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGATG
- - - - - - - - tgtgctt
- - - - - - - - - - - - - - ttcatgc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - -tggttgc