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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...attcgcaatcaaagaaaaacgactaaaaaactgattatcgaataaataccgtttccgaccgttttcatcttacatgagctgtgtttttttttacctttagGTCATAACTGGAGTTATTCCCGATACTGTTGGCAAAAAGCTCATAGGCCTTGTGACTAGCAAAGAGGAAATTGCTGATCTACTAGCG

Basic information

species Zea mays
transcript GRMZM2G028535_T01
intron # 11
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|32931318|gb|CF036130.1|CF036130
EST:     TTTTGAAAGGAGGGAAAGAAGTTATGAGATCAAATGCAATATTACACAAG                         GTCATAACTGGAGTTATTCCCGATACTGTTGGCAAAAAGCTCATAGGCCTT
genomic: TTTTGAAAGGAGGGAAAGAAGTTATGAGATCAAATGCAATATTACACAAGgttgtacgga ... ttacctttagGTCATAACTGGAGTTATTCCCGATACTGTTGGCAAAAAGCTCATAGGCCTT
EST: gi|33094388|gb|CF054382.1|CF054382
EST:     TTTTGAAAGGAGGGAAAGAAGTTATGAGATCAAATGCAATATTACACAAG                         GTCATAACTGGAGTTATTCCCGATACTGTTGGCAAAAAGCTCATAGGCCTT
genomic: TTTTGAAAGGAGGGAAAGAAGTTATGAGATCAAATGCAATATTACACAAGgttgtacgga ... ttacctttagGTCATAACTGGAGTTATTCCCGATACTGTTGGCAAAAAGCTCATAGGCCTT
EST: gi|32931519|gb|CF036331.1|CF036331
EST:     TTTTGAAAGGAGGGAAAGAAGTTATGAGATCAAATGCAATATTACACAAG                         GTCATAACTGGAGTTATTCCCGATACTGTTGGCAAAAAGCTCATAGGCCTT
genomic: TTTTGAAAGGAGGGAAAGAAGTTATGAGATCAAATGCAATATTACACAAGgttgtacgga ... ttacctttagGTCATAACTGGAGTTATTCCCGATACTGTTGGCAAAAAGCTCATAGGCCTT
EST: gi|24934245|gb|CA452463.1|CA452463
EST:     TTTTGAAAGGAGGGAAAGAAGTTATGAGATCAAATGCAATATTACACAAG                         GTCATAACTGGAGTTATTCCCGATACTGTTGGCAAAAAGCTCATAGGCCTT
genomic: TTTTGAAAGGAGGGAAAGAAGTTATGAGATCAAATGCAATATTACACAAGgttgtacgga ... ttacctttagGTCATAACTGGAGTTATTCCCGATACTGTTGGCAAAAAGCTCATAGGCCTT
EST: gi|211307860|gb|FL092738.1|FL092738
EST:     TTTTGAAAGGAGGGAAAGAAGTTATGAGATCAAATGCAATATTACACAAG                         GTCATAACTGGAGTTATTCCCGATACTGTTGGCAAAAAGCTCATAGGCCTT
genomic: TTTTGAAAGGAGGGAAAGAAGTTATGAGATCAAATGCAATATTACACAAGgttgtacgga ... ttacctttagGTCATAACTGGAGTTATTCCCGATACTGTTGGCAAAAAGCTCATAGGCCTT
EST: gi|211307861|gb|FL092739.1|FL092739
EST:     CTTTGAAAGGAGGGAAAGAAGTTATGAGATCAAATGCAATATTACACAAG                         GTCATAACTGGAGTTATTCCCGATACTGTTGGCAAAAAGCTCATAGGCCTT
genomic: TTTTGAAAGGAGGGAAAGAAGTTATGAGATCAAATGCAATATTACACAAGgttgtacgga ... ttacctttagGTCATAACTGGAGTTATTCCCGATACTGTTGGCAAAAAGCTCATAGGCCTT
EST: gi|211307862|gb|FL092740.1|FL092740
EST:     TTTTGAAAGGAGGGAAAGAAGTTATGAGATCAAATGCAATATTACACAAG                         GTCATAACTGGAGTTATTCCCGATACTGTTGGCAAAAAGCTCATAGGCCTT
genomic: TTTTGAAAGGAGGGAAAGAAGTTATGAGATCAAATGCAATATTACACAAGgttgtacgga ... ttacctttagGTCATAACTGGAGTTATTCCCGATACTGTTGGCAAAAAGCTCATAGGCCTT
EST: gi|32932079|gb|CF036891.1|CF036891
EST:     TTTTGAAAGGAGGGAAAGAAGTTATGAGATCAAATGCAATATTACACAAG                         GTCATAACTGGAGTTATTCCCGATACTGTTGGCAAAAAGCTCATAGGCCTT
genomic: TTTTGAAAGGAGGGAAAGAAGTTATGAGATCAAATGCAATATTACACAAGgttgtacgga ... ttacctttagGTCATAACTGGAGTTATTCCCGATACTGTTGGCAAAAAGCTCATAGGCCTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ataccgtttccgaccgttttcatcttacatgagctgtgtttttttttacctttagGTCATAACTGGAGTTATTCCCGATACTGTTGGCAAAAAGCTCATAGGCCTTGTGACTAGCAAAGAGGAAATTGCTGATCTACTAGCG
                     atcttac  putative branch site (score: 3)
                                    tgtttttttttacctt  putative PPT
                                      tttttttttaccttta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
attcgcaatcaaagaaaaacgactaaaaaactgattatcgaataaataccgtttccgaccgttttcatcttacatgagctgtgtttttttttacctttagGTCATAACTGGAGTTATTCCCGATACTGTTGGCAAAAAGCTCATAGGCCTTGTGACTAGCAAAGAGGAAATTGCTGATCTACTAGCG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT