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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tcgttttttgaacattggcatgcaactatcaacatttttgtgtatttattttctgtgcatgcttatttacctccatgtttcttgcataccaaaataacagGAGCGGTCTTCTGGGCGATCTCGTGGGTTTGGCTATGTAACATTCGCATCAGCCGACGATGCAAAGGTTGTAAAATAATGAAGATAACTTTTCATTTTCT

Basic information

species Zea mays
transcript GRMZM2G030902_T04
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G030902_T04 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os01g71770.1 (Oryza sativa), 3'ss of exon 3
-----tcgttttttgaacattggcatgcaactatcaacatttttgtgtatttattttctgtgcatgcttatttacctccatgtttcttgcataccaaaataacagGAGCGGTCTTCTGGGCGATCTCGTGGGTTTGGCTATGTAACATTCGCATCAGCCGACGATGCAAAGGTTGTAAAATAATGAAGATAACTTTTCATTTTCT
     |   || || |  | ||      |   |||||  | || |  |  ||   |  | ||  | || | | ||| | || ||||||| |    ||||| | ||||||| || ||||| ||||||||||||||||| |||||||| ||| ||||||| || ||||| |||                                  
ttaaataacttcttcagtactg-----tattcatcaatttattagcctgatttggtaatttgtgtactgactgaccactatctttcttgtacgttaaaattatagGAGCGTTCGTCTGGTCGATCTCGTGGGTTTGGTTATGTAACGTTCTCATCAGCTGATGATGCCAAG----------------------------------
















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|211347523|gb|FL007072.1|FL007072
EST:     AGAGTACATGGCCAAGTTTGGACCCCTAGATGATTGTGTCGTCATGGAAG                         GAGCGGTCTTCTGGG
genomic: AGAGTACATGGCCAAGTTTGGACCCCTAGATGATTGTGTCGTCATG-AAGgtttgccata ... aaaataacagGAGCGGTCTTCTGGG
EST: gi|31664299|gb|CD573024.1|CD573024
EST:     GAGAGTACATGGCCAAGTTTGGACCCCTAGATGATTGTGTCGTCATGAAG                         GAGCGGTCTTCTGGGCGATCTCGTGGGTTTGGCTATGTAACATTCGCATCA
genomic: GAGAGTACATGGCCAAGTTTGGACCCCTAGATGATTGTGTCGTCATGAAGgtttgccata ... aaaataacagGAGCGGTCTTCTGGGCGATCTCGTGGGTTTGGCTATGTAACATTCGCATCA
EST: gi|211345133|gb|FL007069.1|FL007069
EST:     GAGAGTACATGGCCAAGTTTGGACCCCTAGATGATTGTGTCGTCATGAAG                         GAGCGGTCTTCTGGGCGATCTCGTGGGTTTGGCTATGTAACATTCGCATCA
genomic: GAGAGTACATGGCCAAGTTTGGACCCCTAGATGATTGTGTCGTCATGAAGgtttgccata ... aaaataacagGAGCGGTCTTCTGGGCGATCTCGTGGGTTTGGCTATGTAACATTCGCATCA
EST: gi|211345131|gb|FL007067.1|FL007067
EST:     GAGAGTACATGGCCAAGTTTGGACCCCTAGATGATTGTGTCGTCATGAAG                         GAGCGGTCTTCTGGGCGATCTCGTGGGTTTGGCTATGTAACATTCGCATCA
genomic: GAGAGTACATGGCCAAGTTTGGACCCCTAGATGATTGTGTCGTCATGAAGgtttgccata ... aaaataacagGAGCGGTCTTCTGGGCGATCTCGTGGGTTTGGCTATGTAACATTCGCATCA
EST: gi|211345128|gb|FL007064.1|FL007064
EST:     GAGAGTACATGGCCAAGTTTGGACCCCTAGATGATTGTGTCGTCATGAAG                         GAGCGGTCTTCTGGGCGATCTCGTGGGTTTGGCTATGTAACATTCGCATCA
genomic: GAGAGTACATGGCCAAGTTTGGACCCCTAGATGATTGTGTCGTCATGAAGgtttgccata ... aaaataacagGAGCGGTCTTCTGGGCGATCTCGTGGGTTTGGCTATGTAACATTCGCATCA
EST: gi|211345132|gb|FL007068.1|FL007068
EST:     GAGAGTACATGGCCAAGTTTGGACCCCTAGATGATTGTGTCGTCATGAAG                         GAGCGGTCTTCTGGGCGATCTCGTGGGTTTGGCTATGTAACATTCGCATCA
genomic: GAGAGTACATGGCCAAGTTTGGACCCCTAGATGATTGTGTCGTCATGAAGgtttgccata ... aaaataacagGAGCGGTCTTCTGGGCGATCTCGTGGGTTTGGCTATGTAACATTCGCATCA
EST: gi|6564152|gb|AW231774.1|AW231774
EST:     GAGAGTACATGGCCAAGTTTGGACCCCTAGATGATTGTGTCGTCATGAAG                         GAGCGGTCTTCTGGGCGATCTCGTGGGTTTGGCTATGTAACATTCGCATCA
genomic: GAGAGTACATGGCCAAGTTTGGACCCCTAGATGATTGTGTCGTCATGAAGgtttgccata ... aaaataacagGAGCGGTCTTCTGGGCGATCTCGTGGGTTTGGCTATGTAACATTCGCATCA
EST: gi|211345130|gb|FL007066.1|FL007066
EST:     GAGAGTACATGGCCAAGTTTGGACCCCTAGATGATTGTGTCGTCATGAAG                         GAGCGGTCTTCTGGGCGATCTCGTGG
genomic: GAGAGTACATGGCCAAGTTTGGACCCCTAGATGATTGTGTCGTCATGAAGgtttgccata ... aaaataacagGAGCGGTCTTCTGGGCGATCTCGTGG
EST: gi|211345122|gb|FL007058.1|FL007058
EST:     GAGAGTACATGGCCAAGTTTGGACCCCTAGATGATTGTGTCGTCATGAAG                         GAGCGGTCTTCTGGGCGATCTC
genomic: GAGAGTACATGGCCAAGTTTGGACCCCTAGATGATTGTGTCGTCATGAAGgtttgccata ... aaaataacagGAGCGGTCTTCTGGGCGATCTC
EST: gi|211345125|gb|FL007061.1|FL007061
EST:     AGAGTACATGGCCAAGTTTGGACCCCTAGATGATTGTGTCGTCATTGAAG                         GAGCGGTCTTCTGGGCGATCTCGTGGGTTTGGCTATGTAACATTCGCATC
genomic: AGAGTACATGGCCAAGTTTGGACCCCTAGATGATTGTGTCGTCAT-GAAGgtttgccata ... aaaataacagGAGCGGTCTTCTGGGCGATCTCGTGGGTTTGGCTATGTAACATTCGCATC
EST: gi|211345127|gb|FL007063.1|FL007063
EST:     GAGAGTACATGGCCAAGTTTGGACCCCTAGATGATTGTGTCGTCATGAAG                         GAGCGGTCTTCT
genomic: GAGAGTACATGGCCAAGTTTGGACCCCTAGATGATTGTGTCGTCATGAAGgtttgccata ... aaaataacagGAGCGGTCTTCT
EST: gi|211345135|gb|FL007071.1|FL007071
EST:     GAGAGTACATGGCCAAGTTTGGACCCCTAGATGATTGTGTCGTCATGAAA                         GAGCGGTCTTCTGGGCGATCTCGTGGGTTTGGCTATGTAACATTCGCATCA
genomic: GAGAGTACATGGCCAAGTTTGGACCCCTAGATGATTGTGTCGTCATGAAGgtttgccata ... aaaataacagGAGCGGTCTTCTGGGCGATCTCGTGGGTTTGGCTATGTAACATTCGCATCA
EST: gi|211345129|gb|FL007065.1|FL007065
EST:     GAGAGTACATGGCCAAGTTTGGACCCCTAGATGATTGTGTCGTCATGAAG                         GAACGGCCTTCTGGGCGATCTCGTGGGCTTGGCTATGTACCTTTCGCATCA
genomic: GAGAGTACATGGCCAAGTTTGGACCCCTAGATGATTGTGTCGTCATGAAGgtttgccata ... aaaataacagGAGCGGTCTTCTGGGCGATCTCGTGGGTTTGGCTATGTAACATTCGCATCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttattttctgtgcatgcttatttacctccatgtttcttgcataccaaaataacagGAGCGGTCTTCTGGGCGATCTCGTGGGTTTGGCTATGTAACATTCGCATCAGCCGACGATGCAAAGGTTGTAAAATAATGAAGATAACTTTTCATTTTCT
                                             aaaataaca  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tcgttttttgaacattggcatgcaactatcaacatttttgtgtatttattttctgtgcatgcttatttacctccatgtttcttgcataccaaaataacagGAGCGGTCTTCTGGGCGATCTCGTGGGTTTGGCTATGTAACATTCGCATCAGCCGACGATGCAAAGGTTGTAAAATAATGAAGATAACTTTTCATTTTCT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - ggcatgc
- - - - - - - - - - - - - -atcaaca
- - - - - - - - - - - - - - - - - - - - tgtattt
- - - - - - - - - - - - - - - - - - - - - - - - ttttctg
- - - - - - - - - - - - - - - - - - - - - - - - - - - -tgcatgc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gcatacc