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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aaggctttcgggcatggttgtccgtattctctcataccgttgtcatagtttctgctgtaactttcaacattattattgacaactgaagtacttgcatcagGACTGGGATCGTCAAAATCCAACTCAAATTGTAACAGAGATGTGTGGTTTTGTTACCATTCTTTCGGGGACGTTTCTTCTCCACAAGACAAAAGACATGG

Basic information

species Zea mays
transcript GRMZM2G110398_T02
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G110398_T01 (Zea mays), 3'ss of exon 7
lower sequence: LOC_Os01g65986.1 (Oryza sativa), 3'ss of exon 7
-aaggctttcgggcatggttgtccgtattctctcataccgttgtcatagtttctgctgtaactttcaacattattattgacaactgaagtacttgcat-cagGACTGGGATCGTCAAAATCCAACTCAAATTGTAACAGAGATGTGTGGTTTTGTTACCATTCTTTCGGGGACGTTTCTTCTCCACAAGACAAAAGACATGG
     || ||       ||| | | | |        |    ||   |  ||  ||    ||  |  |    | || | || |||| |  ||||||||| ||||||||||||||||||||||||||||||||||| |||||||||||||||||||||||||| ||||| |||||||||||||| |||||||| ||||| ||||
gtccactgtcctat-cagttatacatgtagcggtggaaacctgctgtgcttagtga-acaagctcaagttgtgttgtggataactaatatacttgcatgcagGACTGGGATCGTCAAAATCCAACTCAAATTGTGACAGAGATGTGTGGTTTTGTTACCATCCTTTCTGGGACGTTTCTTCTTCACAAGACGAAAGATATGG
















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|148966487|gb|EE017504.2|EE017504
EST:     ATACAATGTTCACGTCACTAACCATTTTGGCTAGCGTGATAATGTTCAAG                         GACTGGGATCGTCAAAATCCAACTCAAATTGTAACAGAGATGTGTGGTTTT
genomic: ATACAATGTTCACGTCACTAACCATTTTGGCTAGCGTGATAATGTTCAAGgtaacatttg ... cttgcatcagGACTGGGATCGTCAAAATCCAACTCAAATTGTAACAGAGATGTGTGGTTTT
EST: gi|60342405|gb|DN209378.1|DN209378
EST:     ATACAATGTTCACGTCACTAACCATTTTGGCTAGCGTGATAATGTTCAAG                         GACTGGGATCGTCAAAATCCAACTCAAATTGTAACAGAGATGTGTGGTTTT
genomic: ATACAATGTTCACGTCACTAACCATTTTGGCTAGCGTGATAATGTTCAAGgtaacatttg ... cttgcatcagGACTGGGATCGTCAAAATCCAACTCAAATTGTAACAGAGATGTGTGGTTTT
EST: gi|71759889|gb|DR957826.1|DR957826
EST:     ATACAATGTTCACGTCACTAACCATTTTGGCTAGCGTGATAATGTTCAAG                         GACTGGGATCGTCAAAATCCAACTCAAATTGTAACAGAGATGTGTGGTTTT
genomic: ATACAATGTTCACGTCACTAACCATTTTGGCTAGCGTGATAATGTTCAAGgtaacatttg ... cttgcatcagGACTGGGATCGTCAAAATCCAACTCAAATTGTAACAGAGATGTGTGGTTTT
EST: gi|71442597|gb|DR823647.1|DR823647
EST:     ATACAATGTTCACGTCACTAACCATTTTGGCTAGCGTGATAATGTTCAAG                         GACTGGGATCGTCAAAATCCAACTCAAATTGTAACAGAGATGTGTGGTTTT
genomic: ATACAATGTTCACGTCACTAACCATTTTGGCTAGCGTGATAATGTTCAAGgtaacatttg ... cttgcatcagGACTGGGATCGTCAAAATCCAACTCAAATTGTAACAGAGATGTGTGGTTTT
EST: gi|37381314|gb|CF627534.1|CF627534
EST:     TACAATGTTCACGTCACTAACCATTTTGGCTAGCGTGATAATGTTCAAG                         GACTGGGATCGTCAAAATCCAACTCAAATTGTAACAGAGATGTGTGGTTTT
genomic: TACAATGTTCACGTCACTAACCATTTTGGCTAGCGTGATAATGTTCAAGgtaacatttg ... cttgcatcagGACTGGGATCGTCAAAATCCAACTCAAATTGTAACAGAGATGTGTGGTTTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tagtttctgctgtaactttcaacattattattgacaactgaagtacttgcatcagGACTGGGATCGTCAAAATCCAACTCAAATTGTAACAGAGATGTGTGGTTTTGTTACCATTCTTTCGGGGACGTTTCTTCTCCACAAGACAAAAGACATGG
                            tattgac  putative branch site (score: 2)
                tttcaacattattatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aaggctttcgggcatggttgtccgtattctctcataccgttgtcatagtttctgctgtaactttcaacattattattgacaactgaagtacttgcatcagGACTGGGATCGTCAAAATCCAACTCAAATTGTAACAGAGATGTGTGGTTTTGTTACCATTCTTTCGGGGACGTTTCTTCTCCACAAGACAAAAGACATGG

- - - - -gggcatg
- - - - - - - - - - - - - - - - cataccg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aactgaa