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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ggcatgcaatcaatgtccacgtcacatacgcgcaggcacagaactgaatgagcatatatttctcgtgattactgtcatctcaaggttctattatatccagGTTTTTCAAAGAAGGCTTCCACCTGAAGCAGTGGACCTTGTTAGCAGGTTTCTACAATACTCACCAAATCTACGGTGCACTGCT

Basic information

species Zea mays
transcript GRMZM2G138676_T04
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G138676_T01 (Zea mays), 3'ss of exon 10
lower sequence: LOC_Os03g62500.1 (Oryza sativa), 3'ss of exon 10
ggcatgcaatcaatgtccacgtcacatacgcg--caggcacagaactgaatgagcatatatttctcgtgattactgtcatctcaaggttctattat--atccagGTTTTTCAAAGAAGGCTTCCACCTGAAGCAGTGGACCTTGTTAGCAGGTTTCTACAATACTCACCAAATCTACGGTGCACTGCT
    ||  | |||||||||  | |  |  | |  ||     | || | ||  |  |  |  |    ||  ||  ||| |    || ||| | || |  | ||||||||| |||| |||||||||||||||||||||||||||||| ||||||||||| ||||||||||||||||| |||||||| |||
---gtgtgagcaatgtccatattatgtgtgtgttcaattggaaaattaaacaa-tactttctcactgttctttttgtaactcaaaagttttgttttttacccagGTTTTCCAAAAAAGGCTTCCACCTGAAGCAGTGGACCTTGTAAGCAGGTTTCTGCAATACTCACCAAATCTTCGGTGCACCGCT
















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|76292959|gb|DV032527.1|DV032527
EST:     ACTATACGGAGTTCAAGTTCCCACAAATTAAAGCTCATCCGTGGCACAAG                         GTTTTTCAAAGAAGGCTTCCACCTGAAGCAGTGGACCTTGTTAGCAGGTTT
genomic: ACTATACGGAGTTCAAGTTCCCACAAATTAAAGCTCATCCGTGGCACAAGgtaattaata ... ttatatccagGTTTTTCAAAGAAGGCTTCCACCTGAAGCAGTGGACCTTGTTAGCAGGTTT
EST: gi|31355062|gb|CD439419.1|CD439419
EST:     ACTATACGGAGTTCAAGTTCCCACAAATTAAAGCTCATCCGTGGCACAAG                         GTTTTTCAAAGAAGGCTTCCACCTGAAGCAGTGGACCTTGTTAGCAGGTTT
genomic: ACTATACGGAGTTCAAGTTCCCACAAATTAAAGCTCATCCGTGGCACAAGgtaattaata ... ttatatccagGTTTTTCAAAGAAGGCTTCCACCTGAAGCAGTGGACCTTGTTAGCAGGTTT
EST: gi|38229772|gb|CF920085.1|CF920085
EST:     ACTACACGGAGTTCAAGTTCCCACAAATTAAAGCTCATCCGTGGCACAAG                         GTTTTTCAAAGAAGGCTTCCACCTGAAGCAGTGGACCTTGTTAGCAGGTTT
genomic: ACTATACGGAGTTCAAGTTCCCACAAATTAAAGCTCATCCGTGGCACAAGgtaattaata ... ttatatccagGTTTTTCAAAGAAGGCTTCCACCTGAAGCAGTGGACCTTGTTAGCAGGTTT
EST: gi|71322556|gb|DR797955.1|DR797955
EST:     ACTATACGGAGTTCAAGTTCCCACAAATTAAAGCTCATCCGTGGCACAAG                         GTTTTTCAAAGAAGGCTTCCACCTGAAGCAGTGGACCTCGTTAGCAGGTTT
genomic: ACTATACGGAGTTCAAGTTCCCACAAATTAAAGCTCATCCGTGGCACAAGgtaattaata ... ttatatccagGTTTTTCAAAGAAGGCTTCCACCTGAAGCAGTGGACCTTGTTAGCAGGTTT
EST: gi|71312506|gb|DR792786.1|DR792786
EST:     ACTATACGGAGTTCAAGTTCCCACAAATTAAAGCTCATCCGTGGCACAAG                         GTTTTTCAAAGAAGGCTTCCACCTGAAGCAGTGGACCTTGTTAGCAGGTTT
genomic: ACTATACGGAGTTCAAGTTCCCACAAATTAAAGCTCATCCGTGGCACAAGgtaattaata ... ttatatccagGTTTTTCAAAGAAGGCTTCCACCTGAAGCAGTGGACCTTGTTAGCAGGTTT
EST: gi|32834795|gb|CD974473.1|CD974473
EST:     ACTATACGGAGTTCAAGTTCCCACAAATTAAAGCTCATCCGTGGCACAAG                         GTTTTTCAAAGAAGGCTTCCACCTGAAGCAGTGGACCTTGTTAGCAGGTTT
genomic: ACTATACGGAGTTCAAGTTCCCACAAATTAAAGCTCATCCGTGGCACAAGgtaattaata ... ttatatccagGTTTTTCAAAGAAGGCTTCCACCTGAAGCAGTGGACCTTGTTAGCAGGTTT
EST: gi|32928721|gb|CF033533.1|CF033533
EST:     ACTATACGGAGTTCAAGTTCCCACAAATTAAAGCTCATCCGTGGCACAAG                         GTTTTTCAAAGAAGGCTTCCACCTGAAGCAGTGGACCTTGTTAGCAGGTTT
genomic: ACTATACGGAGTTCAAGTTCCCACAAATTAAAGCTCATCCGTGGCACAAGgtaattaata ... ttatatccagGTTTTTCAAAGAAGGCTTCCACCTGAAGCAGTGGACCTTGTTAGCAGGTTT
EST: gi|76292960|gb|DV032528.1|DV032528
EST:     ACTATACGGAGTTCAAGTTCCCACAAATTAAAGCTCATCCGTGGCACAAG                         GTTTTTCAAAGAAGGCTTCCACCTGAAGCAGTGGACCTTGTTAGCAGGTTT
genomic: ACTATACGGAGTTCAAGTTCCCACAAATTAAAGCTCATCCGTGGCACAAGgtaattaata ... ttatatccagGTTTTTCAAAGAAGGCTTCCACCTGAAGCAGTGGACCTTGTTAGCAGGTTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gaatgagcatatatttctcgtgattactgtcatctcaaggttctattatatccagGTTTTTCAAAGAAGGCTTCCACCTGAAGCAGTGGACCTTGTTAGCAGGTTTCTACAATACTCACCAAATCTACGGTGCACTGCT
                                        ttctatt  CT-rich tract
                                        ttctattatat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ggcatgcaatcaatgtccacgtcacatacgcgcaggcacagaactgaatgagcatatatttctcgtgattactgtcatctcaaggttctattatatccagGTTTTTCAAAGAAGGCTTCCACCTGAAGCAGTGGACCTTGTTAGCAGGTTTCTACAATACTCACCAAATCTACGGTGCACTGCT

ggcatgc
- - - - - - - - - - - cacatac
- - - - - - - - - - - - - - - -gcaggca
- - - - - - - - - - - - - - - - - - - - - -ctgaatg