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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...atggtccgcatttttttttctaattcccctgacttgttgagaggttttaaatgaaattgttggttcctcttgggtcatatatttcccttgatattttcagTTCTTGAAGTCGGTGATGGTGTTTTTGAGGTGCTGTCTACATCAGGTGACACTCACCTTGGTGGTGATGACTTTGACAAG

Basic information

species Zea mays
transcript GRMZM2G111475_T02
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G111475_T02 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os05g23740.1 (Oryza sativa), 3'ss of exon 2
--------atggtccgcatttttttttctaattcccctgacttgttgagaggttttaaatgaaattgttggttcctcttgggtcatatatttcccttgatattttcagTTCTTGAAGTCGGTGATGGTGTTTTTGAGGTGCTGTCTACATCAGGTGACACTCACCTTGGTGGTGATGACTTTGACAAG
         |||| ||  | |    |  |||||    | ||   ||   |  | |||||||| | | |  | ||||         |||||||    ||||  |||||||||||||||| |||||||||||||||||||||||||||||||| ||||||||||||||||||||||||||||||||||||
acttcattttggttcgtctgtcaaatgttaattaaattaacacttttc-atctcttaaatgagaat-tcagctcctaac------tatattttgggtgatgatttcagTTCTTGAAGTTGGTGATGGTGTTTTTGAGGTGCTGTCTACATCTGGTGACACTCACCTTGGTGGTGATGACTTTGACAAG
















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|211464629|gb|FK976060.1|FK976060
EST:     TGAAACAATTCTGGTTTTTGACCTCGGAGGTGGCACATTTGACGTTTCAG                         TTCTTGAAGTCGGTGATGGTGTTTTTGAGGTGCTGTCTACATCAGGTGACA
genomic: TGAAACAATTCTGGTTTTTGACCTCGGAGGTGGCACATTTGACGTTTCAGgtatctgtcc ... atattttcagTTCTTGAAGTCGGTGATGGTGTTTTTGAGGTGCTGTCTACATCAGGTGACA
EST: gi|22133613|gb|BQ833805.1|BQ833805
EST:     TGAAACAATTCTGGTTTTTGACCTCGGAGGTGGCACATTTGACGTTTCAG                         TTCTTGAAGTCGGTGATGGTGTTTTTGAGGTGCTGTCTACATCAGGTGACA
genomic: TGAAACAATTCTGGTTTTTGACCTCGGAGGTGGCACATTTGACGTTTCAGgtatctgtcc ... atattttcagTTCTTGAAGTCGGTGATGGTGTTTTTGAGGTGCTGTCTACATCAGGTGACA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttaaatgaaattgttggttcctcttgggtcatatatttcccttgatattttcagTTCTTGAAGTCGGTGATGGTGTTTTTGAGGTGCTGTCTACATCAGGTGACACTCACCTTGGTGGTGATGACTTTGACAAG
                                        ccttgat  putative branch site (score: 5)
                                              tattttc  CT-rich tract
                             tcatatattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
atggtccgcatttttttttctaattcccctgacttgttgagaggttttaaatgaaattgttggttcctcttgggtcatatatttcccttgatattttcagTTCTTGAAGTCGGTGATGGTGTTTTTGAGGTGCTGTCTACATCAGGTGACACTCACCTTGGTGGTGATGACTTTGACAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG