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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaggcttcagtttcttgttaactttataactcttgtattttctgaatgaactgagattaaggacttatgacaatgcttgtgatcttccattgcttactccagGACCTCTGTTAGCCATATGGATTTTCCAGAAATTGTGGAGGGAGGGATCAAGCAGATGTTAGAATTACTTGGTGATGACAATGCACCATTTGAT

Basic information

species Zea mays
transcript GRMZM2G144362_T02
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G144362_T02 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os06g41390.4 (Oryza sativa), 3'ss of exon 3
-------------------------------------gtaaggcttc-agtttcttgttaactttataactcttg--tattttctgaatgaactgagattaaggacttatgacaatgcttgtgatcttccattgcttactccagGACCTCTGTTAGCCATATGGATTTTCCAGAAATTGTGGAGGGAGGGATCAAGCAGATGTTAGAATTACTTGGTGATGACAATGCACCATTTGAT
                                     |||||||||   |||||||||  | ||||  ||||||   ||| || |  || |  |||             ||| |   |||       | | |  || | | |||||||||  ||||||| ||||| || ||| ||||||||||||||||| |||| ||||||||||||||||||||||||||||||||||| ||||||
gtaagtgaaaaaggaagtgagcatttaagctgaacctgtaaggcttttggtttcttgtgtaatttagtactcttatttatcttttccatcacttga-------------tgatacctctttctggtattcttaactaatttcagGACCTCCATTAGCCACATGGACTTCCCAAAAATTGTGGAGGGAGGGCTCAAACAGATGTTAGAATTACTTGGTGATGACAATGCACCGTTTGAT

upper sequence: GRMZM2G144362_T02 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os06g41390.3 (Oryza sativa), 3'ss of exon 3
gtaaggcttc-agtttcttgttaactttataactcttgt--attttctgaatgaactgagattaaggacttatgacaatgcttgtgatcttccattgcttactccagGACCTCTGTTAGCCATATGGATTTTCCAGAAATTGTGGAGGGAGGGATCAAGCAGATGTTAGAATTACTTGGTGATGACAATGCACCATTTGAT
|||||||||   |||||||||  | ||||  |||||| |  || || |  || |  |||             ||| |   |||       | | |  || | | |||||||||  ||||||| ||||| || ||| ||||||||||||||||| |||| ||||||||||||||||||||||||||||||||||| ||||||
gtaaggcttttggtttcttgtgtaatttagtactcttatttatcttttccatcacttga-------------tgatacctctttctggtattcttaactaatttcagGACCTCCATTAGCCACATGGACTTCCCAAAAATTGTGGAGGGAGGGCTCAAACAGATGTTAGAATTACTTGGTGATGACAATGCACCGTTTGAT
















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|32798502|gb|CD950738.1|CD950738
EST:     CAACAAGACTGGAATGTAAGTGAAAAAGAAGTGAGCATTTATCTGATCCT                         GACCTCTGTTAGCCATATGGATTTTCCAGAAATTGTGGAGGGAGGGATCAA
genomic: CAACAAGACTGGAATGTAAGTGAAAAAGAAGTGAGCATTTATCTGATCCTgtaaggcttc ... cttactccagGACCTCTGTTAGCCATATGGATTTTCCAGAAATTGTGGAGGGAGGGATCAA
EST: gi|86468333|gb|DY234703.1|DY234703
EST:     CAACAAGACTGGAATGTAAGTGAAAAAGAAGTGAGCATTTATCTGATCCT                         GACCTCTGTTACCCATATGGATTTT
genomic: CAACAAGACTGGAATGTAAGTGAAAAAGAAGTGAGCATTTATCTGATCCTgtaaggcttc ... cttactccagGACCTCTGTTAGCCATATGGATTTT
EST: gi|93281088|gb|EB673352.1|EB673352
EST:     CAACAAGACTGGAATGTAAGTGAAAAAGAAGTGAGCATTTATCTGATCCT                         GACCTCTGTTAGCCATATGGATTTTCCAGAAATTGTGGAGGGAGGGATCAA
genomic: CAACAAGACTGGAATGTAAGTGAAAAAGAAGTGAGCATTTATCTGATCCTgtaaggcttc ... cttactccagGACCTCTGTTAGCCATATGGATTTTCCAGAAATTGTGGAGGGAGGGATCAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gaactgagattaaggacttatgacaatgcttgtgatcttccattgcttactccagGACCTCTGTTAGCCATATGGATTTTCCAGAAATTGTGGAGGGAGGGATCAAGCAGATGTTAGAATTACTTGGTGATGACAATGCACCATTTGAT
                                           tgcttac  putative branch site (score: 2)
                                             cttactcc  CT-rich tract
      agattaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaaggcttcagtttcttgttaactttataactcttgtattttctgaatgaactgagattaaggacttatgacaatgcttgtgatcttccattgcttactccagGACCTCTGTTAGCCATATGGATTTTCCAGAAATTGTGGAGGGAGGGATCAAGCAGATGTTAGAATTACTTGGTGATGACAATGCACCATTTGAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGATG