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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagtacttgctgttctaattttagtttcttgaagttgtgcgttttcaacactgtttgtcttatgtatcttgaattattgatacagGAACTATTTGATTTCATTGCTGCTGCATTGGCTAAATTTGTCGGTACTGAAGGTGAAGATTTCCAACTCCCAGAGGGTAGGCAGAGAGAACTTGGTTTCA

Basic information

species Zea mays
transcript GRMZM2G058745_T02
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G058745_T02 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os05g44760.1 (Oryza sativa), 3'ss of exon 2
gtgagtacttgctgttctaattttagtttcttgaagttgtgcgttttcaacactgtttgtcttatgtatcttg-aattattgatacagGAACTATTTGATTTCATTGCTGCTGCATTGGCTAAATTTGTCGGTACTGAAGGTGAAGATTTCCAACTCCCAGAGGGTAGGCAGAGAGAACTTGGTTTCA
|| || | |||||| |  | ||| | ||||||| || ||| | ||        || ||||||||||||| ||   | |||| || |||||||| |||||||| |||||| |||||||| | |||||||| | |||||||||||| |||||||| |||||||| || || |||||||| || || ||||
gtaagcatttgctgcttgattttaaatttcttggagctgtacattcca-----tgcttgtcttatgtattttctgactattaatgcagGAACTGTTTGATTTTATTGCTTCTGCATTGTCAAAATTTGTTGATACTGAAGGTGATGATTTCCACCTCCCAGAAGGGAGACAGAGAGAGCTGGGCTTCA

upper sequence: GRMZM2G058745_T02 (Zea mays), 3'ss of exon 2
lower sequence: Vv11s0016g03070.t01 (Vitis vinifera), 3'ss of exon 2
gtgagtacttgctgttctaattttagtttcttgaagttgtgcgttttcaacactgtttgtcttatgta-tct-tgaattat--tgata-cagGAACTATTTGATTTCATTGCTGCTGCATTGGCTAAATTTGTCGGTACTGAAGGTGAAGATTTCCAACTCCCAGAGGGTAGGCAGAGAGAACTTGGTTTCA
    ||   || | ||| |   ||       ||   || |||  |||  |     ||  |  | || | ||| ||||| ||  ||||  ||||   ||||||||| ||||||||| ||| | ||||||||||| | |||||||||||||| | | ||  |  |    ||||| || || ||||| ||||| |
----gtgagtgttattcaagcattcaaagaatgtt-ttatgctgtttagatttgtttcatgctctgaagtctgtgaatgatggtgatttcagGCTTTATTTGATTACATTGCTGCAGCACTTGCTAAATTTGTTGCTACTGAAGGTGAAGGTCTTCATGTTTCTCCTGGTAGACAAAGGGAACTGGGTTTTA
















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|148951791|gb|EC897551.2|EC897551
EST:     AGTATGAGGAGGTTTCCATTCCACCACATTTGATGGTCGGGACTTCCATG                         GAACTATTTGATTTCATTGCTGCTGCATTGGCTAAATTTGTCGGTACTGAA
genomic: AGTATGAGGAGGTTTCCATTCCACCACATTTGATGGTCGGGACTTCCATGgtgagtactt ... attgatacagGAACTATTTGATTTCATTGCTGCTGCATTGGCTAAATTTGTCGGTACTGAA
EST: gi|149104506|gb|EE289955.2|EE289955
EST:     AGTATGAGGAGGTTTCCATTCCACCACATTTGATGGTCGGGACTTCCATG                         GAACTATTTGATTTCATTGCTGCTGCATTGGCTAAATTTGTCGGTACTGAA
genomic: AGTATGAGGAGGTTTCCATTCCACCACATTTGATGGTCGGGACTTCCATGgtgagtactt ... attgatacagGAACTATTTGATTTCATTGCTGCTGCATTGGCTAAATTTGTCGGTACTGAA
EST: gi|148968085|gb|EE019415.2|EE019415
EST:     AGTATGAGGAGGTTTCCATTCCCCCACATTTGATGGTCGGGACTTCCATG                         GAACTATTTGATTTCATTGCTGCTGCATTGGCTAAATTTGTCGGTACTGAA
genomic: AGTATGAGGAGGTTTCCATTCCACCACATTTGATGGTCGGGACTTCCATGgtgagtactt ... attgatacagGAACTATTTGATTTCATTGCTGCTGCATTGGCTAAATTTGTCGGTACTGAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gaagttgtgcgttttcaacactgtttgtcttatgtatcttgaattattgatacagGAACTATTTGATTTCATTGCTGCTGCATTGGCTAAATTTGTCGGTACTGAAGGTGAAGATTTCCAACTCCCAGAGGGTAGGCAGAGAGAACTTGGTTTCA
                                            tattgat  putative branch site (score: 3)
                                  tatcttgaattatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagtacttgctgttctaattttagtttcttgaagttgtgcgttttcaacactgtttgtcttatgtatcttgaattattgatacagGAACTATTTGATTTCATTGCTGCTGCATTGGCTAAATTTGTCGGTACTGAAGGTGAAGATTTCCAACTCCCAGAGGGTAGGCAGAGAGAACTTGGTTTCA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA