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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tcaatcaacccaacaccacgcccctgtcacaaaatttaccactctgagttttcttgtctacattaaaatgtctgccaattaatcatttacctctgtgcagTGATATCCGTATACAGAGTAATATATCTTGTCCCGTATCTCCATGTGGAAGTCCTCTTCTAAGATCAAGATCTCCACAACATCAAAATGGTAGAATGTCG

Basic information

species Zea mays
transcript GRMZM2G093316_T01
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G093316_T02 (Zea mays), 3'ss of exon 11
lower sequence: LOC_Os02g44642.1 (Oryza sativa), 3'ss of exon 11
--tcaatcaacccaacaccacgcccctgtcacaaaatttaccactctgagttttcttgtctacattaaaatgtctgccaattaatcatttacctctgtgcagTGATATCCGTATACAGAGTAATATATCTTGTCCCGTATCTCCATGTGGAAGTCCTCTTCTAAGATCAAGATCTCCACAACATCAAAATGGTAGAATGTCG
    ||  ||  ||   || ||    | | | ||||   ||   || | |  |   | ||| |||  |||||| ||     |||||||       ||  ||||||||| | | |||  ||  |||||||||| || || ||||||||||| || |||| ||| || |||||||||||||||||||||||||||| |||||| 
ctataagaaatacagttcctcgttttttttaaaaaaaaaacagttcagtgaatgtatatctgcatggaaatgtatgtactctaatcatcggtgcttg--cagTGATATTCATGTACGAAGCTATATATCTTGCCCTGTTTCTCCATGTGGGAGCCCTCATCTGAGGTCAAGATCTCCACAACATCAAAATGGTATAATGTCA
















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|211167296|gb|FL126871.1|FL126871
EST:     TACCAATCAATTTTGCAGAGAAGAGCTGCCAAATTTTCTTTGCCAAATAG                         TGATATCCGTATACAGAGTAATATATCTTGTCCTGTATCTCCATGTGGAAG
genomic: TACCAATCAATTTTGCAGAGAAGAGCTGCCAAATTTTCTTTGCCAAATAGgtaacaattc ... ctctgtgcagTGATATCCGTATACAGAGTAATATATCTTGTCCCGTATCTCCATGTGGAAG
EST: gi|78116720|gb|DV535107.1|DV535107
EST:     TACCAATCAATTTTGCAGAGAAGAGCTGCCAAATTTTCTTTGCCAAATAG                         TGATATCCGTATACAGAGTAATATATCTTGTCCCGTATCTCCATGTGGAAG
genomic: TACCAATCAATTTTGCAGAGAAGAGCTGCCAAATTTTCTTTGCCAAATAGgtaacaattc ... ctctgtgcagTGATATCCGTATACAGAGTAATATATCTTGTCCCGTATCTCCATGTGGAAG
EST: gi|211167295|gb|FL126870.1|FL126870
EST:     TACCAATCAATTTTGCAGAGAAGAGCTGCCAAATTTTCTTTGCCAAATAG                         TGATATCCGTATACAGAGTAATATATCTTGTCCTGTATCTCCATGTGGAAG
genomic: TACCAATCAATTTTGCAGAGAAGAGCTGCCAAATTTTCTTTGCCAAATAGgtaacaattc ... ctctgtgcagTGATATCCGTATACAGAGTAATATATCTTGTCCCGTATCTCCATGTGGAAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gagttttcttgtctacattaaaatgtctgccaattaatcatttacctctgtgcagTGATATCCGTATACAGAGTAATATATCTTGTCCCGTATCTCCATGTGGAAGTCCTCTTCTAAGATCAAGATCTCCACAACATCAAAATGGTAGAATGTCG
                               aattaat  putative branch site (score: 3)
                                        tttacctct  putative PPT
                               aattaatcattta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tcaatcaacccaacaccacgcccctgtcacaaaatttaccactctgagttttcttgtctacattaaaatgtctgccaattaatcatttacctctgtgcagTGATATCCGTATACAGAGTAATATATCTTGTCCCGTATCTCCATGTGGAAGTCCTCTTCTAAGATCAAGATCTCCACAACATCAAAATGGTAGAATGTCG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGATCA