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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CGTGAATGTTAATTAAGATTAATACTTCCAATTATAATTTCAGGAGAGAGAGATTCCAGTGCTGGTATTTTCTGCAGGACTTGCAGACATAATTGAAGAGgtaagatatgaaaaggaatgattcaacgtatggtgagttgagtttaattgctgactgacactgacacattccgctgttccattag

Basic information

species Zea mays
transcript GRMZM2G157310_T01
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G157310_T01 (Zea mays), 5'ss of exon 1
lower sequence: LOC_Os03g44660.1 (Oryza sativa), 5'ss of exon 5
CGTGAATGTTAATTAAGATTAATACTTCCAATTATAATTTCAGGAGAGAGAGATTCCAGTGCTGGTATTTTCTGCAGGACTTGCAGACATAATTGAAGAGgtaagatatgaaaaggaatgattcaacgtatggtgagttgag-tttaattgctgactgacactgacacattccgctgttccattag
                                           |||||||| ||||||||  | ||||||||||| |||||||||||||||||||| ||||||||   |  ||||       ||  | |||| |||| |||| |||  |||| |||||||||  ||    |  |   ||| |    
-------------------------------------------GAGAGAGATATTCCAGTATTAGTATTTTCTGCTGGACTTGCAGACATAATTGAGGAGgtaagtactacaaag-------tcctcatatgatgagatgagctttggttgcagactgacac--acctgctttgtc-ttctag---
















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|149013204|gb|EE042840.2|EE042840
EST:     CCAGTGCTGGTATTTTCTGCAGGACTTGCAGACATAATTGAAGAG                         GTCTTCCGGCAGAAATTACACAAAACATTCAAGAACATCAAGGTTGTCTCC
genomic: CCAGTGCTGGTATTTTCTGCAGGACTTGCAGACATAATTGAAGAGgtaagatatg ... gttccattagGTCTTCCGGCAGAAATTACACAAAACATTCAAGAACATCAAGGTTGTCTCC
EST: gi|71774185|gb|DR972065.1|DR972065
EST:     AGATTCCAGTGCTGGTATTTTCTGCAGGACTNGCAGACATAATTGAAGAG                         GTCTTCCGGCAGAAATTACACAAAACATTCAAGAACATCAAGGTTGTCTCC
genomic: AGATTCCAGTGCTGGTATTTTCTGCAGGACTTGCAGACATAATTGAAGAGgtaagatatg ... gttccattagGTCTTCCGGCAGAAATTACACAAAACATTCAAGAACATCAAGGTTGTCTCC
EST: gi|149009394|gb|EE153935.2|EE153935
EST:     AGATTCCAGTGCTGGTATTTTCTGCAGGACTTGCAGACATAATTGAAGAG                         GTCTTCCGGCAGAAATTACACAAAACATTCAAGAACATCAAGGTTGTCTCC
genomic: AGATTCCAGTGCTGGTATTTTCTGCAGGACTTGCAGACATAATTGAAGAGgtaagatatg ... gttccattagGTCTTCCGGCAGAAATTACACAAAACATTCAAGAACATCAAGGTTGTCTCC
EST: gi|32832154|gb|CD971832.1|CD971832
EST:     AGATTCCAGTGCTGGTATTTTCTGCAGGACTTGCGGACATAATTGAAGAG                         GTCTTCCGGCAGAAACTACACAAAACATTCAAGAACATCAAGGTTGTCTCC
genomic: AGATTCCAGTGCTGGTATTTTCTGCAGGACTTGCAGACATAATTGAAGAGgtaagatatg ... gttccattagGTCTTCCGGCAGAAATTACACAAAACATTCAAGAACATCAAGGTTGTCTCC
EST: gi|37400710|gb|CF637712.1|CF637712
EST:     AGATTCCAGTGCTGGTATTTTCTGCAGGACTTGCAGACATAATTGAAGAG                         GTCTTCCGGCAGAAACTACACAAAACATTCAAGAACATCAAGGTTGTCTCC
genomic: AGATTCCAGTGCTGGTATTTTCTGCAGGACTTGCAGACATAATTGAAGAGgtaagatatg ... gttccattagGTCTTCCGGCAGAAATTACACAAAACATTCAAGAACATCAAGGTTGTCTCC
EST: gi|78092208|gb|DV520582.1|DV520582
EST:     CAGACATAATTGAAGAG                         GTCTTCCGGCAGAAATTACACAAAACATTCAAGAACATCAAGGTTGTCTCC
genomic: CAGACATAATTGAAGAGgtaagatatg ... gttccattagGTCTTCCGGCAGAAATTACACAAAACATTCAAGAACATCAAGGTTGTCTCC
EST: gi|88749393|gb|DY533534.1|DY533534
EST:     AGATTCCAGTGCTGGTATTTTCTGCAGGACTTGCAGACATAATTGAAGAG                         GTCTTCCGGCAGAAATTACACAAAACATTCAAGAACATCAAGGTTGTCTCC
genomic: AGATTCCAGTGCTGGTATTTTCTGCAGGACTTGCAGACATAATTGAAGAGgtaagatatg ... gttccattagGTCTTCCGGCAGAAATTACACAAAACATTCAAGAACATCAAGGTTGTCTCC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CGTGAATGTTAATTAAGATTAATACTTCCAATTATAATTTCAGGAGAGAGAGATTCCAGTGCTGGTATTTTCTGCAGGACTTGCAGACATAATTGAAGAGgtaagatatgaaaaggaatgattcaacgtatggtgagttgagtttaattgctgactgacactgacacattccgctgttccattag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA