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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ctgtttatctagaactggcacaaccgagaaggcaggcaggcatagctgctaatatacatgtctttctcatacttatcaccagtgaaatgtttatttgcagACAATGGGTTGGTGAGGCAAAAAAAGGTCCATTTCATGTTCTTTAGCGTGATATCACCATTTCGTGGATGGTAGACTTTTCTGGTGGAAAATTTGCACAG

Basic information

species Zea mays
transcript GRMZM2G010146_T01
intron # 4
splice site 3'
intron type U2

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|14243987|gb|BG841705.2|BG841705
EST:     CAACAAACATCTCGATCAATACGTGAGAACAATAATTTGATGTCATTGAG                         ACAATGGGTTGGTGAGGCNNNNNNNGGTCCATTTCATGTTCTTTAGCGTGA
genomic: CAACAAACATCTCGATCAATACGTGAGAACAATAATTTGATGTCATTGAGgtaatttcta ... ttatttgcagACAATGGGTTGGTGAGGCAAAAAAAGGTCCATTTCATGTTCTTTAGCGTGA
EST: gi|211038848|gb|FL245344.1|FL245344
EST:     CAACAAACATCTCGATCAATACGTGAGAACAATAATTTGATGTCATTGAG                         ACAATGGGTTGGTGAGGCNNNNNNNGGTCCATTTCATGTTCTTTAGCGTGA
genomic: CAACAAACATCTCGATCAATACGTGAGAACAATAATTTGATGTCATTGAGgtaatttcta ... ttatttgcagACAATGGGTTGGTGAGGCAAAAAAAGGTCCATTTCATGTTCTTTAGCGTGA
EST: gi|32859647|gb|CD999328.1|CD999328
EST:     CAACAAACATCTCGATCAATACGTGAGAACAATAATTTGATGTCATTGAG                         ACAATGGGTTGGTGAGGCNNNNNNNGGTCCATTTCATGTTCTTTAGCGTGA
genomic: CAACAAACATCTCGATCAATACGTGAGAACAATAATTTGATGTCATTGAGgtaatttcta ... ttatttgcagACAATGGGTTGGTGAGGCAAAAAAAGGTCCATTTCATGTTCTTTAGCGTGA
EST: gi|211038853|gb|FL245349.1|FL245349
EST:     CAACAAACATCTCGATCAATACGTGAGAACAATAATTTGATGTCATTGAG                         ACAATGGGTTGGTGAGGCNNNNNNNGGTCCATTTCATGTTCTTTAGCGTGA
genomic: CAACAAACATCTCGATCAATACGTGAGAACAATAATTTGATGTCATTGAGgtaatttcta ... ttatttgcagACAATGGGTTGGTGAGGCAAAAAAAGGTCCATTTCATGTTCTTTAGCGTGA
EST: gi|76292671|gb|DV032239.1|DV032239
EST:     CAACAAACATCTCGATCAATACGTGAGAACAATAATTTGATGTCATTGAG                         ACAATGGGTTGGTGAGGCAAAAAA-GGTCCATTTCATGTTCTTTAGCGTGA
genomic: CAACAAACATCTCGATCAATACGTGAGAACAATAATTTGATGTCATTGAGgtaatttcta ... ttatttgcagACAATGGGTTGGTGAGGCAAAAAAAGGTCCATTTCATGTTCTTTAGCGTGA
EST: gi|211513208|gb|FL479766.1|FL479766
EST:     ACAAACATCTCGATCAATACGTGAGAACAATAATTTGATGTCATTGAG                         ACAATGGGTTGGTGAGGCNNNNNNNGGTCCATTTCATGTTCTTTAGCGTGA
genomic: ACAAACATCTCGATCAATACGTGAGAACAATAATTTGATGTCATTGAGgtaatttcta ... ttatttgcagACAATGGGTTGGTGAGGCAAAAAAAGGTCCATTTCATGTTCTTTAGCGTGA
EST: gi|71302502|gb|DR787369.1|DR787369
EST:     CAACAAACATCTCGATCAATACGTGAGAACAATAATTTGATGTCATTGAG                         ACAATGGGTTGGTGAGGCNNNNNNNGGTCCATTTCATGTTCTTTAGCGTGA
genomic: CAACAAACATCTCGATCAATACGTGAGAACAATAATTTGATGTCATTGAGgtaatttcta ... ttatttgcagACAATGGGTTGGTGAGGCAAAAAAAGGTCCATTTCATGTTCTTTAGCGTGA
EST: gi|76930391|gb|DV172363.1|DV172363
EST:     CAACAAACATCTCGATCAATACGTGAGAACAATAATTTGATGTCATTGAG                         ACAATGGGTTGGTGAGGCNNNNNNNGGTCCATTTCATGTTCTTTAGCGTGA
genomic: CAACAAACATCTCGATCAATACGTGAGAACAATAATTTGATGTCATTGAGgtaatttcta ... ttatttgcagACAATGGGTTGGTGAGGCAAAAAAAGGTCCATTTCATGTTCTTTAGCGTGA
EST: gi|76930392|gb|DV172364.1|DV172364
EST:     CAACAAACATCTCGATCAATACGTGAGAACAATAATTTGATGTCATTGAG                         ACAATGGGTTGGTGAGGCNNNNNNNGGTCCATTTCATGTTCTTTAGCGTGA
genomic: CAACAAACATCTCGATCAATACGTGAGAACAATAATTTGATGTCATTGAGgtaatttcta ... ttatttgcagACAATGGGTTGGTGAGGCAAAAAAAGGTCCATTTCATGTTCTTTAGCGTGA
EST: gi|211038850|gb|FL245346.1|FL245346
EST:     CAACAAACATCTCGATCAATACGTGAGAACAATAATTTGATGTCATTGAG                         ACAATGGGTTGGTGAGGCNNNNNNNGGTCCATTTCATGTTCTTTAGCGTGA
genomic: CAACAAACATCTCGATCAATACGTGAGAACAATAATTTGATGTCATTGAGgtaatttcta ... ttatttgcagACAATGGGTTGGTGAGGCAAAAAAAGGTCCATTTCATGTTCTTTAGCGTGA
EST: gi|78118287|gb|DV536673.1|DV536673
EST:     CAACAAACATCTCGATCAATACGTGAGAACAATAATTTGATGTCATTGAG                         ACAATGGGTTGGTGAGGCNNNNNNNGGTCCATTTCATGTTCTTTAGCGTGA
genomic: CAACAAACATCTCGATCAATACGTGAGAACAATAATTTGATGTCATTGAGgtaatttcta ... ttatttgcagACAATGGGTTGGTGAGGCAAAAAAAGGTCCATTTCATGTTCTTTAGCGTGA
EST: gi|32859646|gb|CD999327.1|CD999327
EST:     CAACAAACATCTCGATCAATACGTGAGAACAATAATTTGATGTCATTGAG                         ACAATGGGTTGGTGAGGCNNNNNNNGGTCCATTTCATGTTCTTTAGCGTGA
genomic: CAACAAACATCTCGATCAATACGTGAGAACAATAATTTGATGTCATTGAGgtaatttcta ... ttatttgcagACAATGGGTTGGTGAGGCAAAAAAAGGTCCATTTCATGTTCTTTAGCGTGA
EST: gi|148944695|gb|EC889832.2|EC889832
EST:     CAACAAACATCTCGATCAATACGTGAGAACAATAATTTGATGTCATTGAG                         ACAATGGGTTGGTGAGGC
genomic: CAACAAACATCTCGATCAATACGTGAGAACAATAATTTGATGTCATTGAGgtaatttcta ... ttatttgcagACAATGGGTTGGTGAGGC
EST: gi|71302504|gb|DR787370.1|DR787370
EST:     CAACAAACATCTCGATCAATACGTGAGAACAATAATTTGATGTCATTGAG                         ACAATGGGTTG
genomic: CAACAAACATCTCGATCAATACGTGAGAACAATAATTTGATGTCATTGAGgtaatttcta ... ttatttgcagACAATGGGTTG
EST: gi|71436488|gb|DR817538.1|DR817538
EST:     CAACAAACATCTCGATCAATACGTGAGAACAATAATTTGATGTCATTGAG                         ACAATGGGTTGGTGAGGCNNNNNNNGGTCCATTTCATGTTCTTTAGCGTGA
genomic: CAACAAACATCTCGATCAATACGTGAGAACAATAATTTGATGTCATTGAGgtaatttcta ... ttatttgcagACAATGGGTTGGTGAGGCAAAAAAAGGTCCATTTCATGTTCTTTAGCGTGA
EST: gi|71316462|gb|DR794908.1|DR794908
EST:     CAACAAACATCTCGATCAATACGTGAGAACAATAATTTGATGTCATTGAG                         ACAATGGGTTGGTGAGGCNNNNNNNGGTCCATTTCATGTTCTTTAGCGTGA
genomic: CAACAAACATCTCGATCAATACGTGAGAACAATAATTTGATGTCATTGAGgtaatttcta ... ttatttgcagACAATGGGTTGGTGAGGCAAAAAAAGGTCCATTTCATGTTCTTTAGCGTGA
EST: gi|148930227|gb|EC872669.2|EC872669
EST:     CAACAAACATCTCGATCAATACGTGAGAACAATAATTTGATGTCATTGAG                         ACAATGGGTTGGTGAGGCNNNNNNNGGTCCATTTCATGTTCTTTAGCGTGA
genomic: CAACAAACATCTCGATCAATACGTGAGAACAATAATTTGATGTCATTGAGgtaatttcta ... ttatttgcagACAATGGGTTGGTGAGGCAAAAAAAGGTCCATTTCATGTTCTTTAGCGTGA
EST: gi|101393644|gb|EB818754.1|EB818754
EST:     CAACAAACATCTCGATCAATACGTGAGAACAATAATTTGATGTCATTGAG                         ACAATGGGTTGGTGAGGC
genomic: CAACAAACATCTCGATCAATACGTGAGAACAATAATTTGATGTCATTGAGgtaatttcta ... ttatttgcagACAATGGGTTGGTGAGGC
EST: gi|211038851|gb|FL245347.1|FL245347
EST:     CAACAAACATCTCGATCAATACGTGAGAACAATAATTTGATGTCATTGAG                         ACAATGGGTTGGTGAGGCNNNNNNNGGTCCATTTCATGTTCTTTAGCGTGA
genomic: CAACAAACATCTCGATCAATACGTGAGAACAATAATTTGATGTCATTGAGgtaatttcta ... ttatttgcagACAATGGGTTGGTGAGGCAAAAAAAGGTCCATTTCATGTTCTTTAGCGTGA
EST: gi|76918988|gb|DV167546.1|DV167546
EST:     CAACAAACATCTCGATCAATACGTGAGAACAATAATTTGATGTCATTGAG                         ACAATGGGTTGGTGAGGCNNNNNNNGGTCCATTTCATGTTCTTTAGCGTGA
genomic: CAACAAACATCTCGATCAATACGTGAGAACAATAATTTGATGTCATTGAGgtaatttcta ... ttatttgcagACAATGGGTTGGTGAGGCAAAAAAAGGTCCATTTCATGTTCTTTAGCGTGA
EST: gi|211038847|gb|FL245343.1|FL245343
EST:     CAACAAACATCTCGATCAATACGTGAGAACAATAATTTGATGTCATTGAG                         ACAATGGGTTGGTGAGGCNNNNNNNGGTCCATTTCATGTTCTTTAGCGTGA
genomic: CAACAAACATCTCGATCAATACGTGAGAACAATAATTTGATGTCATTGAGgtaatttcta ... ttatttgcagACAATGGGTTGGTGAGGCAAAAAAAGGTCCATTTCATGTTCTTTAGCGTGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctgctaatatacatgtctttctcatacttatcaccagtgaaatgtttatttgcagACAATGGGTTGGTGAGGCAAAAAAAGGTCCATTTCATGTTCTTTAGCGTGATATCACCATTTCGTGGATGGTAGACTTTTCTGGTGGAAAATTTGCACAG
 tgctaat  putative branch site (score: 2)
                                            tttattt  putative PPT
                                     tgaaatgtttattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ctgtttatctagaactggcacaaccgagaaggcaggcaggcatagctgctaatatacatgtctttctcatacttatcaccagtgaaatgtttatttgcagACAATGGGTTGGTGAGGCAAAAAAAGGTCCATTTCATGTTCTTTAGCGTGATATCACCATTTCGTGGATGGTAGACTTTTCTGGTGGAAAATTTGCACAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA