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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ataacaacctattcaaatttggttcactagaaatttcgtgaaccaaacagcaccttaacagtaactttggttgtttcctatcactatttgctggtggcagTGTGGCAGTATTTGCATCATGGGCACGACACTTTGTCTTGACAAACGAAGAACCTACAGAGAAAAG

Basic information

species Zea mays
transcript GRMZM5G840928_T02
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G840928_T02 (Zea mays), 3'ss of exon 8
lower sequence: LOC_Os11g17610.1 (Oryza sativa), 3'ss of exon 8
ataacaacctattcaaatttggttcactagaaatttcgtgaaccaaacagcaccttaacagtaactttggttgtttcctatcactatt--------tgctggtggcagTGTGGCAGTATTTGCATCATGGGCACGACACTTTGTCTTGACAAACGAAGAACCTACAGAGAAAAG
            ||||| ||    || ||| | ||     ||            | |||  | | ||| | || || ||  |  |||         || |||||| ||||| ||||||||||||||||||||||| |||||| || |||| || ||  | ||||||||||| ||
------ggtagctcaaaattctggcattagtacttcaa--aagtgtgtttttattcaacgttcatttttgctggtttcttaccttatccggtttactgttggtggtagTGTTGCAGTATTTGCATCATGGGCACGTCACTTTCTCCTGACGAATGAGTACCCTACAGAGAAGAG
















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|76016157|gb|DT943327.1|DT943327
EST:     TTT-GTTCCCCAAGACGGTGTGGTGGTCAAGG-GACATCCTTTCTGGAAG                         TGTGGCAGTATTTGCATCATGGGCACGACACTTTGTCTTGACAAACGAAGA
genomic: TTTGGTTCCCCAAGACGGTGTGGTGGTCAAGGTGACATCCTTTCTGGAAGgtctgttatg ... ctggtggcagTGTGGCAGTATTTGCATCATGGGCACGACACTTTGTCTTGACAAACGAAGA
EST: gi|211044162|gb|FL460073.1|FL460073
EST:     TTTGGTTCCCCAAGACGGTGTGGTGGTCAAGGTGACATCCTTTCTGGAAG                         TGTGGCAGTATTTGCATCATGGGCACGACACTTTGTCTTGACAAACGAAGA
genomic: TTTGGTTCCCCAAGACGGTGTGGTGGTCAAGGTGACATCCTTTCTGGAAGgtctgttatg ... ctggtggcagTGTGGCAGTATTTGCATCATGGGCACGACACTTTGTCTTGACAAACGAAGA
EST: gi|94474415|gb|EB703373.1|EB703373
EST:     TTTGGTTCCCCAAGACGGTGTGGTGGTCAAGGTGACATCCTTTCTGGAAG                         TGTGGCAGTATTTGCATCATGGGCACGACACTTTGTCTTGACAAACGAAGA
genomic: TTTGGTTCCCCAAGACGGTGTGGTGGTCAAGGTGACATCCTTTCTGGAAGgtctgttatg ... ctggtggcagTGTGGCAGTATTTGCATCATGGGCACGACACTTTGTCTTGACAAACGAAGA
EST: gi|211044163|gb|FL460074.1|FL460074
EST:     GGTGTGGTGGTCAAGGTGACATCCTTTCTGGAAG                         TGTGGCAGTATTTGCATCATGGGCACGACACTTTGTCTTGACAAACGAAGA
genomic: GGTGTGGTGGTCAAGGTGACATCCTTTCTGGAAGgtctgttatg ... ctggtggcagTGTGGCAGTATTTGCATCATGGGCACGACACTTTGTCTTGACAAACGAAGA
EST: gi|32933908|gb|CF038720.1|CF038720
EST:     TTTGGTTCCCCAAGACGGTGTGGTGGTCAAGGTGACATCCTTTCTGGAAG                         TGTGGCAGTATTTGCATCATGGGCACGACACTTTGGCTCGACAAACGAAGA
genomic: TTTGGTTCCCCAAGACGGTGTGGTGGTCAAGGTGACATCCTTTCTGGAAGgtctgttatg ... ctggtggcagTGTGGCAGTATTTGCATCATGGGCACGACACTTTGTCTTGACAAACGAAGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aacagcaccttaacagtaactttggttgtttcctatcactatttgctggtggcagTGTGGCAGTATTTGCATCATGGGCACGACACTTTGTCTTGACAAACGAAGAACCTACAGAGAAAAG
             cagtaac  putative branch site (score: 2)
                taacttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ataacaacctattcaaatttggttcactagaaatttcgtgaaccaaacagcaccttaacagtaactttggttgtttcctatcactatttgctggtggcagTGTGGCAGTATTTGCATCATGGGCACGACACTTTGTCTTGACAAACGAAGAACCTACAGAGAAAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAC