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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...agggggaaaataacgctcctgtgaatgtgtgcattaatttgtaacctgccgagctaatcaaagccgctgtcctcctcatctgcaatctggctacctccagATCCTATCCAAAGCCGCAGAGAACACGGTCATGGAGACGGTAGACCAGGACATCACCGACACGTGCAAGGACCTCGGCGAGGTCAAGAAGGTGTTCCAGC

Basic information

species Zea mays
transcript GRMZM2G463904_T01
intron # 25
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G463904_T03 (Zea mays), 3'ss of exon 26
lower sequence: LOC_Os02g53720.1 (Oryza sativa), 3'ss of exon 5
----agggggaaaataacgctcctgtgaatgtgtgcattaatttgtaacctgccgagctaatcaaagccgctgtcc-tcctcatctgcaatctggctacctccagATCCTATCCAAAGCCGCAGAGAACACGGTCATGGAGACGGTAGACCAGGACATCACCGACACGTGCAAGGACCTCGGCGAGGTCAAGAAGGTGTTCCAGC
      |     ||||  ||  |||| ||     |  || |    | | || ||  | |   ||     |||||   | |||||  |     ||  |  || ||||||||||||||||||||||| |||||||||||||||| ||| ||||  |||||| |||| |||||||| || || |||||||||||||||||||||||| 
ggtccagtacggaatagtgcaactgtaaacagtcgattttagcgatgaacttcctggtttg-catgaatgctgtttatgctcattggt----tgcttctctgcagATCCTATCCAAAGCCGCAGACAACACGGTCATGGAGATGGTCGACCCAGACATCGCCGATACGTGCAAAGATCTTGGCGAGGTCAAGAAGGTGTTCCAGT
















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|166416593|gb|EG304671.1|EG304671
EST:     TCGACGACGAGTGCAACCTTCACCACTTG                         ATCCTATCCAAAGCCGCAGAGAACACGGTCATGGAGACGGTCGACCAGGAC
genomic: TCGACGACGAGTGCAACCTTCACCACTTGgtaactattc ... ctacctccagATCCTATCCAAAGCCGCAGAGAACACGGTCATGGAGACGGTAGACCAGGAC
EST: gi|71758846|gb|DR956783.1|DR956783
EST:     TGCTTACCGGCAAAAAGCCTGTCGACGACGAGTGCAACCTTCACCACTTG                         ATCCTATCCAAAGCCGCAGAGAACACGGTCATGGAGACGGTAGACCAGGAC
genomic: TGCTTACCGGCAAAAAGCCTGTCGACGACGAGTGCAACCTTCACCACTTGgtaactattc ... ctacctccagATCCTATCCAAAGCCGCAGAGAACACGGTCATGGAGACGGTAGACCAGGAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctgccgagctaatcaaagccgctgtcctcctcatctgcaatctggctacctccagATCCTATCCAAAGCCGCAGAGAACACGGTCATGGAGACGGTAGACCAGGACATCACCGACACGTGCAAGGACCTCGGCGAGGTCAAGAAGGTGTTCCAGC
      agctaat  putative branch site (score: 3)
                                             ctacctcc  putative PPT
         taatcaaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
agggggaaaataacgctcctgtgaatgtgtgcattaatttgtaacctgccgagctaatcaaagccgctgtcctcctcatctgcaatctggctacctccagATCCTATCCAAAGCCGCAGAGAACACGGTCATGGAGACGGTAGACCAGGACATCACCGACACGTGCAAGGACCTCGGCGAGGTCAAGAAGGTGTTCCAGC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG