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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagaacattgacttcagtgccacaaaacttccgttttttttagaaaaaaactagtactttactagttctgaaatatttgtgagctgtgacttgctgaatgatcagatcctgacactgtttcagTGGAGTTCGTGTCGTGGCAAAATGGCGGGGGCATCCTGCACCGGGCGGCCTCCGTTGACCCCACTGCTGTGGTGGAGGCTGGAGCGGTTGTGCACTCTGG

Basic information

species Zea mays
transcript GRMZM5G803610_T02
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G803610_T02 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os07g04200.1 (Oryza sativa), 3'ss of exon 1
gtaagaacattgacttcagtgccacaaaacttccgttttttttagaaaaaaactagtactttactagttctgaaatatttgtgagctgtgacttgctgaatgat--cagatcctgacactgtttcagTGGAGTTCGTGTCGTGGCAAAATGGCGGGGGCATCCTGCACCGGGCGGCCTCCGTTGACCCCACTGCTGTGGTGGAGGCTGGAGCGGTTGTGCACTCTGG
                  ||  ||   |||||   || |  |   | | |  ||  | |  |  |  |  |||  ||  |  |    |   |||  || ||| |  ||||| | |    || ||| | |||||||||  ||||||| || ||||||||| || ||||| |||| || |||||||||||||| || ||||||||||| ||                  
------------------gtagcaatcaacttatattctcct---atatatgct--tcccgtcttgatcttgagttagcttagcttagcttcttcttggatgtttccagATGCGGCGGTTGCTTCGGGGGAGTTCGTCCCGTGGCACAACGGCGGGGGCGTCTTGCACAGGGCCGCGTCCGTTGACCCCACCGCGGTGGTGGAGGCCGG------------------
















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|211168538|gb|FK982826.1|FK982826
EST:     CGCCTGTCACTTTGCGCGGTCTTTGGGCGGCGTCTCTTCTGCTTGCAGCA                         TGGAGTTCGTGTCGTGGCAAAATGGCGGGGGCATCCTGCACCGGGCGGCCT
genomic: CGCCTGTCACTTTGCGCGGTCTTTGGGCGGCGTCTCTTCTGCTTGCAGCAgtaagaacat ... actgtttcagTGGAGTTCGTGTCGTGGCAAAATGGCGGGGGCATCCTGCACCGGGCGGCCT
EST: gi|33467350|gb|CF244399.1|CF244399
EST:     CGCCTGTCACTTTGCGCGGTCTTTGGGCGGCGTCTCTTCTGCTTGCAGCA                         TGGAGTTCGTGTCGTGGCAAAATGGCGGGGGCATCCTGCACCGGGCGGCCT
genomic: CGCCTGTCACTTTGCGCGGTCTTTGGGCGGCGTCTCTTCTGCTTGCAGCAgtaagaacat ... actgtttcagTGGAGTTCGTGTCGTGGCAAAATGGCGGGGGCATCCTGCACCGGGCGGCCT
EST: gi|78107382|gb|DV525800.1|DV525800
EST:     CGCCTGTCACTTTGCGCGGTCTTTGGGCGGCGTCTCTTCTGCTTGCAGCA                         TGGAGTTCGTGTCGTGGCAAAATGGCGGGGGCATCCTGCACCGGGCGGCCT
genomic: CGCCTGTCACTTTGCGCGGTCTTTGGGCGGCGTCTCTTCTGCTTGCAGCAgtaagaacat ... actgtttcagTGGAGTTCGTGTCGTGGCAAAATGGCGGGGGCATCCTGCACCGGGCGGCCT
EST: gi|211168536|gb|FK982824.1|FK982824
EST:     CGCCTGTCACTTTGCGCGGTCTTTGGGCGGCGTCTCTTCTGCTTGCAGCA                         TGGAGTTCGTGTCGTGGCAAAATGGCGGGGGCATCCTGCACCGGGCGGCCT
genomic: CGCCTGTCACTTTGCGCGGTCTTTGGGCGGCGTCTCTTCTGCTTGCAGCAgtaagaacat ... actgtttcagTGGAGTTCGTGTCGTGGCAAAATGGCGGGGGCATCCTGCACCGGGCGGCCT
EST: gi|211168540|gb|FK982828.1|FK982828
EST:     CGCCTGTCACTTTGCGCGGTCTTTGGGCGGCGTCTCTTCTGCTTGCAGCA                         TGGAGTTCGTGTCGTGGCAAAATGGCGGGGGCATCCTGCACCGGGCGGCCT
genomic: CGCCTGTCACTTTGCGCGGTCTTTGGGCGGCGTCTCTTCTGCTTGCAGCAgtaagaacat ... actgtttcagTGGAGTTCGTGTCGTGGCAAAATGGCGGGGGCATCCTGCACCGGGCGGCCT
EST: gi|211170210|gb|FK982830.1|FK982830
EST:     CGCCTGTCACTTTGCGCGGTCTTTGGGCGGCGTCTCTTCTGCTTGCAGCA                         TGGAGTTCGTGTCGTGGCAAAATGGCGGGGGCATCCTGCACCGGGCGGCCT
genomic: CGCCTGTCACTTTGCGCGGTCTTTGGGCGGCGTCTCTTCTGCTTGCAGCAgtaagaacat ... actgtttcagTGGAGTTCGTGTCGTGGCAAAATGGCGGGGGCATCCTGCACCGGGCGGCCT
EST: gi|211168537|gb|FK982825.1|FK982825
EST:     CGCCTGTCACTTTGCGCGGTCTTTGGGCGGCGTCTCTTCTGCTTGCAGCA                         TGGAGTTCGTGTCGTGGCAAAATGGCGGGGGCATCCTGCACCGGGCGGCCT
genomic: CGCCTGTCACTTTGCGCGGTCTTTGGGCGGCGTCTCTTCTGCTTGCAGCAgtaagaacat ... actgtttcagTGGAGTTCGTGTCGTGGCAAAATGGCGGGGGCATCCTGCACCGGGCGGCCT
EST: gi|211168535|gb|FK982823.1|FK982823
EST:     CGCCTGTCACTTTGCGCGGTCTTTGGGCGGCGTCTCTTCTGCTTGCAGCA                         TGGAGTTCGTGTCGTGGCAAAATGGCGGGGGCATCCTGCACCGGGCGGCCT
genomic: CGCCTGTCACTTTGCGCGGTCTTTGGGCGGCGTCTCTTCTGCTTGCAGCAgtaagaacat ... actgtttcagTGGAGTTCGTGTCGTGGCAAAATGGCGGGGGCATCCTGCACCGGGCGGCCT
EST: gi|74232550|gb|DT640464.1|DT640464
EST:     CGCCTGTCACTTTGCGCGGTCTTTGGGCGGCGTCTCTTCTGCTTGCAGCA                         TGGAGTTCGTGTCGTGGCAAAATGGCGGGGGCATCCTGCACCGGGCGGCCT
genomic: CGCCTGTCACTTTGCGCGGTCTTTGGGCGGCGTCTCTTCTGCTTGCAGCAgtaagaacat ... actgtttcagTGGAGTTCGTGTCGTGGCAAAATGGCGGGGGCATCCTGCACCGGGCGGCCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgaaatatttgtgagctgtgacttgctgaatgatcagatcctgacactgtttcagTGGAGTTCGTGTCGTGGCAAAATGGCGGGGGCATCCTGCACCGGGCGGCCTCCGTTGACCCCACTGCTGTGGTGGAGGCTGGAGCGGTTGTGCACTCTGG
                                      tcctgac  putative branch site (score: 2)
                                              ctgtttc  CT-rich tract
     tatttgt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagaacattgacttcagtgccacaaaacttccgttttttttagaaaaaaactagtactttactagttctgaaatatttgtgagctgtgacttgctgaatgatcagatcctgacactgtttcagTGGAGTTCGTGTCGTGGCAAAATGGCGGGGGCATCCTGCACCGGGCGGCCTCCGTTGACCCCACTGCTGTGGTGGAGGCTGGAGCGGTTGTGCACTCTGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA