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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgtcattttcatagtactgatctgatgtttgctggtaacttgtgaaatttttgcatttttataattttctttattgtgtgttacttgttccatactccagGCACTCTCCAGAAGGATCCACTATGGGAAGTTTGTGGCAGAGGCCAAGTTTCAAGAGTCCCCTGAAGCTTACACGCCAGCCATAATAGCCCAAGTCTGCT

Basic information

species Zea mays
transcript GRMZM2G124365_T03
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G124365_T03 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os01g55870.1 (Oryza sativa), 3'ss of exon 4
tgtcattttcatagtactgatctgatgtttgctggtaacttgtgaaatttttgcatttttataat-----------tttctttattgtgtgttacttgttccatactccagGCACTCTCCAGAAGGATCCACTATGGGAAGTTTGTGGCAGAGGCCAAGTTTCAAGAGTCCCCTGAAGCTTACACGCCAGCCATAATAGCCCAAGTCTGCT
           |||||||   ||| ||||  ||||| ||| ||| ||||   ||||||||||| |            |    | || |   || | ||||| ||  ||||||| ||||||| ||| || |||||||| ||||||||||||||||| |||||||||||||| ||||||||||||| ||| || |||||||| ||        
----------ttagtactatactgttgttcactggtgactcgtgcaattag-gcatttttatattgggaaattatgctcacctgttcttgttttcctgttctatcatccagGCGCTCTCCAAAAGAATTCACTATGGTAAGTTTGTGGCAGAGGCTAAGTTTCAAGAGTCTCCTGAAGCTTACATGCCTGCGATAATAGCACAG-------
















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|148996150|gb|EE035419.2|EE035419
EST:     GTGATGGTAATGCTGGATCCAGTGCTCTTTGTGACACAACCTGCTTGCAG                         GCACTCTCCAGAAGGATCCACTATGGGAAGTTTGTGGCAGAGGCCAAGTTT
genomic: GTGATGGTAATGCTGGATCCAGTGCTCTTTGTGACACAACCTGCTTGCAGgtacagctga ... catactccagGCACTCTCCAGAAGGATCCACTATGGGAAGTTTGTGGCAGAGGCCAAGTTT
EST: gi|71304463|gb|DR788345.1|DR788345
EST:     GTGATGGTAATGCTGGATCCAGTGCTCTTTGTGACACAACCTGCTTGCAG                         GCACTCTCCAGAAGGATCCACT
genomic: GTGATGGTAATGCTGGATCCAGTGCTCTTTGTGACACAACCTGCTTGCAGgtacagctga ... catactccagGCACTCTCCAGAAGGATCCACT
EST: gi|32842669|gb|CD982350.1|CD982350
EST:     GTGATGGTAATGCTGGATCCAGTGCTCTTTGTGACACAACCTGCTTGCAG                         GCACTCTCCAGAAGGATCCACT
genomic: GTGATGGTAATGCTGGATCCAGTGCTCTTTGTGACACAACCTGCTTGCAGgtacagctga ... catactccagGCACTCTCCAGAAGGATCCACT
EST: gi|67040651|gb|CO466906.1|CO466906
EST:     GTGATGGTAATGCTGGATCCAGTGCTCTTTGTGA-ACAACCTGCTTGCAG                         GCACTCTCCAGAAGGATCCACTATGGGAAAGTT-GTGGCAGAGGCCAAGTT
genomic: GTGATGGTAATGCTGGATCCAGTGCTCTTTGTGACACAACCTGCTTGCAGgtacagctga ... catactccagGCACTCTCCAGAAGGATCCACTATGGGAA-GTTTGTGGCAGAGGCCAAGTT
EST: gi|89763811|gb|DY690849.1|DY690849
EST:     GTGATGGTAATGCTGGATCCAGTGCTCTTTGTGACACAACCTGCTTGCAG                         GCACTCTCCAGAAGGATCCACTATGGGAAGTTTGTGGCAGAAGGCCA-GTT
genomic: GTGATGGTAATGCTGGATCCAGTGCTCTTTGTGACACAACCTGCTTGCAGgtacagctga ... catactccagGCACTCTCCAGAAGGATCCACTATGGGAAGTTTGTGGCAGA-GGCCAAGTT
EST: gi|211304787|gb|FL143336.1|FL143336
EST:     GTGATGGNAATGCTGGATCCAGTGCTGTTTGNGACACAACCTGNTTGCAG                         GCACTCTGCACAAGGATCCACTATGGGAAGTTTGTGGC
genomic: GTGATGGTAATGCTGGATCCAGTGCTCTTTGTGACACAACCTGCTTGCAGgtacagctga ... catactccagGCACTCTCCAGAAGGATCCACTATGGGAAGTTTGTGGC
EST: gi|32842790|gb|CD982471.1|CD982471
EST:     GTGATGGTAATGCTGGATCCAGTGCTCTTTGTGACACAACCTGCTTGCAG                         GCACTCTCCAGAAGGATCCACTATGGGAAGTTTGTGGCAGAGGCCAAGTTT
genomic: GTGATGGTAATGCTGGATCCAGTGCTCTTTGTGACACAACCTGCTTGCAGgtacagctga ... catactccagGCACTCTCCAGAAGGATCCACTATGGGAAGTTTGTGGCAGAGGCCAAGTTT
EST: gi|67041520|gb|CO467775.1|CO467775
EST:     GTGATGGTAATGCTGGATCCAGTGCTCTTTGTGACACAACCTGCTTGCAG                         GCACTCTCCACAAAGATCCACTATGGGAAGTTTGTGGCAGAGGCCAAGTTT
genomic: GTGATGGTAATGCTGGATCCAGTGCTCTTTGTGACACAACCTGCTTGCAGgtacagctga ... catactccagGCACTCTCCAGAAGGATCCACTATGGGAAGTTTGTGGCAGAGGCCAAGTTT
EST: gi|149077332|gb|EE166011.2|EE166011
EST:     GTGATGGTAATGCTGGATCCAGTGCTCTTTGTGACACAACCTGCTTGCAG                         GCACTCTCCAGAAGGATCCACTATGGGAAGTTTGTGGCAGAGGCCAAGTTT
genomic: GTGATGGTAATGCTGGATCCAGTGCTCTTTGTGACACAACCTGCTTGCAGgtacagctga ... catactccagGCACTCTCCAGAAGGATCCACTATGGGAAGTTTGTGGCAGAGGCCAAGTTT
EST: gi|148931381|gb|EC874300.2|EC874300
EST:     GTGATGGTAATGCTGGATCCAGTGCTCTTTGTGACACAACCTGCTTGCAG                         GCACTCTCCAGAAGGATCCACTATGGGAAGTTTGTGGCAGAGGCCAAGTTT
genomic: GTGATGGTAATGCTGGATCCAGTGCTCTTTGTGACACAACCTGCTTGCAGgtacagctga ... catactccagGCACTCTCCAGAAGGATCCACTATGGGAAGTTTGTGGCAGAGGCCAAGTTT
EST: gi|67040128|gb|CO466383.1|CO466383
EST:     GTGATGGTAATGCTGGATCCAGTGCTCTTTGTGACACAACCTGCTTGCAN                         GCACTCTCCAGAAGGATCCACTATGGGAAGTTTGTGGGCAGAGGCCA-GTT
genomic: GTGATGGTAATGCTGGATCCAGTGCTCTTTGTGACACAACCTGCTTGCAGgtacagctga ... catactccagGCACTCTCCAGAAGGATCCACTATGGGAAGTTTGTGG-CAGAGGCCAAGTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aatttttgcatttttataattttctttattgtgtgttacttgttccatactccagGCACTCTCCAGAAGGATCCACTATGGGAAGTTTGTGGCAGAGGCCAAGTTTCAAGAGTCCCCTGAAGCTTACACGCCAGCCATAATAGCCCAAGTCTGCT
                                      cttgttcc  CT-rich tract
         atttttataattttct  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgtcattttcatagtactgatctgatgtttgctggtaacttgtgaaatttttgcatttttataattttctttattgtgtgttacttgttccatactccagGCACTCTCCAGAAGGATCCACTATGGGAAGTTTGTGGCAGAGGCCAAGTTTCAAGAGTCCCCTGAAGCTTACACGCCAGCCATAATAGCCCAAGTCTGCT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC