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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtccctcaaatctactcaaatgcaccgctccgctctttaatttgcatctcaaaacgcatggcactaactttcagaggggaattaccttctctcttttttttaataatgcagGTCACTGGAAAAGCCCTCGTTTTGGACGAGATCATCAACTACGTGCAGTCCTTGCAGAACCAAGTCGAG

Basic information

species Zea mays
transcript GRMZM2G178182_T02
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G178182_T02 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os09g33580.1 (Oryza sativa), 3'ss of exon 3
------------------gtccctcaaatctactcaaatgcaccgctccgctctttaatt-tgcatctcaaaacgcatggcactaactttcagaggggaattaccttctctcttttttttaataatgcagGTCACTGGAAAAGCCCTCGTTTTGGACGAGATCATCAACTACGTGCAGTCCTTGCAGAACCAAGTCGAG
                    |   | || ||| |   ||   | |   |  | |||  || |  || | || | |  ||  |||| |||| | || | ||  |  |  | | | |          || ||||||||||||| || ||| ||||||| |||||||||||||| ||||||||||| ||||||||||| |||
gttagatcactagttaactactaactaaactagtggtatttgcagtgacaatttttttttgtatatgttaatatgtttgatactatctttgaaagtgaaaaaaaatcatttatct---------gtgtagGTCACTGGAAAGGCTCTCATTTTGGATGAGATCATCAACTATGTGCAGTCCTTACAGAACCAAGTTGAG
















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|71767729|gb|DR965666.1|DR965666
EST:     TCAGCGAGAGGATGAGGGTGCTGCAGGCCCTGGTCCCTGGCTGTGATAAG                         GTCACTGGAAAAGCCCTCGTTTTGGACGAGATCATCAACTACGTGCAGTCC
genomic: TCAGCGAGAGGATGAGGGTGCTGCAGGCCCTGGTCCCTGGCTGTGATAAGgtccctcaaa ... aataatgcagGTCACTGGAAAAGCCCTCGTTTTGGACGAGATCATCAACTACGTGCAGTCC
EST: gi|88756498|gb|DY540639.1|DY540639
EST:     TCAGCGAGAGGATGAGGGTGCTGCAGGCCCTGGTCCCTGGCTGTGATAAA                         GTCACTGGAAAAGCCCTCGTTTTGGACGAGATCATCAACTACGTGCAGTCC
genomic: TCAGCGAGAGGATGAGGGTGCTGCAGGCCCTGGTCCCTGGCTGTGATAAGgtccctcaaa ... aataatgcagGTCACTGGAAAAGCCCTCGTTTTGGACGAGATCATCAACTACGTGCAGTCC
EST: gi|78113320|gb|DV531712.1|DV531712
EST:     TCAGCGAGAGGATGAGGGTGCTGCAGGCCCTGGTCCCTGGCTGTGATAAG                         GTCACTGGAAAAGCCCTCGTTTTGGACGAGATCATCAACTACGTGCAGTCC
genomic: TCAGCGAGAGGATGAGGGTGCTGCAGGCCCTGGTCCCTGGCTGTGATAAGgtccctcaaa ... aataatgcagGTCACTGGAAAAGCCCTCGTTTTGGACGAGATCATCAACTACGTGCAGTCC
EST: gi|93013083|gb|EB638603.1|EB638603
EST:     TCAGCGAGAGGATGAGGGTGCTGCAGGCCCTGGTCCCTGGCTGTGATAAG                         GTCACTGGAAAAGCCCTCGTTTTGGACGAGATCATCAACTACGTGCAGTCC
genomic: TCAGCGAGAGGATGAGGGTGCTGCAGGCCCTGGTCCCTGGCTGTGATAAGgtccctcaaa ... aataatgcagGTCACTGGAAAAGCCCTCGTTTTGGACGAGATCATCAACTACGTGCAGTCC
EST: gi|78113319|gb|DV531711.1|DV531711
EST:     TCCCTGGCTGTGATAAG                         GTCACTGGAAAAGCCCTCGTTTTGGACGAGATCATCAACTACGTGCAGTCC
genomic: TCCCTGGCTGTGATAAGgtccctcaaa ... aataatgcagGTCACTGGAAAAGCCCTCGTTTTGGACGAGATCATCAACTACGTGCAGTCC
EST: gi|76914768|gb|DV165681.1|DV165681
EST:     TCAGCGAGAGGATGAGGGTGCTGCAGGCCCTGGTCCCTGGCTGTGATAAG                         GTCACTGGAAAAGCCCTCGTTTTGGACGAGATCATCAACTACGTGCAGTCC
genomic: TCAGCGAGAGGATGAGGGTGCTGCAGGCCCTGGTCCCTGGCTGTGATAAGgtccctcaaa ... aataatgcagGTCACTGGAAAAGCCCTCGTTTTGGACGAGATCATCAACTACGTGCAGTCC
EST: gi|76280841|gb|DV020409.1|DV020409
EST:     TCAGCGAGAGGATGAGGGTGCTGCAGGCCCTGGTCCCTGGCTGTGATAAG                         GTCACTGGAAAAGCCCTCGTTTTGGACGAGATCATCAACTACGTGCAGTCC
genomic: TCAGCGAGAGGATGAGGGTGCTGCAGGCCCTGGTCCCTGGCTGTGATAAGgtccctcaaa ... aataatgcagGTCACTGGAAAAGCCCTCGTTTTGGACGAGATCATCAACTACGTGCAGTCC
EST: gi|50330951|gb|CO526077.1|CO526077
EST:     TCAGCGAGAGGATGAGGGTGCTGCAGGCCCTGGTCCCTGGCTGTGATAAG                         GTCACTGGAAAAGCCCTCGTTTTGGACGAGATCATCAACTACGTGCAGTCC
genomic: TCAGCGAGAGGATGAGGGTGCTGCAGGCCCTGGTCCCTGGCTGTGATAAGgtccctcaaa ... aataatgcagGTCACTGGAAAAGCCCTCGTTTTGGACGAGATCATCAACTACGTGCAGTCC
EST: gi|71439158|gb|DR820208.1|DR820208
EST:     TCAGCGAGAGGATGAGGGTGCTGCAGGCCCTGGTCCCTGGCTGTGATAAG                         GTCACTGGAAAAGCCCTCGTTTTGGACGAGATCATCAACTACGTGCAGTCC
genomic: TCAGCGAGAGGATGAGGGTGCTGCAGGCCCTGGTCCCTGGCTGTGATAAGgtccctcaaa ... aataatgcagGTCACTGGAAAAGCCCTCGTTTTGGACGAGATCATCAACTACGTGCAGTCC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

catggcactaactttcagaggggaattaccttctctcttttttttaataatgcagGTCACTGGAAAAGCCCTCGTTTTGGACGAGATCATCAACTACGTGCAGTCCTTGCAGAACCAAGTCGAG
                         ttaccttctctctttt  CT-rich tract
                              ttctctctttttttta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtccctcaaatctactcaaatgcaccgctccgctctttaatttgcatctcaaaacgcatggcactaactttcagaggggaattaccttctctcttttttttaataatgcagGTCACTGGAAAAGCCCTCGTTTTGGACGAGATCATCAACTACGTGCAGTCCTTGCAGAACCAAGTCGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGATCA