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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CCTTGCCGAAAAAGGTGGCATTCCTATTGGTATTGGGAAAAATTCATGCATCAGGAGAGCAATCATTGACAAGAATGCTCGAATTGGAGACAATGTTAAGgtattccaaactgatgttccaacggtcaagaatattaatttagatttttccttaggatattacataatacttgatatgccattttgtcctcttattttta...

Basic information

species Zea mays
transcript GRMZM2G068506_T02
intron # 8
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G068506_T02 (Zea mays), 5'ss of exon 8
lower sequence: LOC_Os08g25734.1 (Oryza sativa), 5'ss of exon 8
CCTTGCCGAAAAAGGTGGCATTCCTATTGGTATTGGGAAAAATTCATGCATCAGGAGAGCAATCATTGACAAGAATGCTCGAATTGGAGACAATGTTAAGgtattccaaactgatgttccaacggtcaagaatatta-atttagatttttccttaggatattacataatacttgatatgccattttgtcctcttattttta
|||||  ||||||||||||||||| |||||||||||||| ||||    ||| || || |||||||| |||||||||||||| |||||||| ||||| ||||||||||||| |||| |||  |  || ||| || | | || |  || | | ||||   | ||  || |   ||  ||| |  | ||   |   | || |  
CCTTGGTGAAAAAGGTGGCATTCCCATTGGTATTGGGAAGAATTGCCACATTAGAAGGGCAATCATCGACAAGAATGCTCGTATTGGAGATAATGTGAAGgtattccaaattgattttcttatcgttaagcatttaatatgtttatatgttcttactttttttaatgaattttactattcggtctttctcatctcttctc-

upper sequence: GRMZM2G068506_T02 (Zea mays), 5'ss of exon 8
lower sequence: GLYMA14G01290.1 (Glycine max), 5'ss of exon 8
CCTTGCCGAAAAAGGTGGCATTCCTATTGGTATTGGGAAAAATTCATGCATCAGGAGAGCAATCATTGACAAGAATGCTCGAATTGGAGACAATGTTAAGgtattccaaactgatgttcca-acggtcaagaatattaatttagatttttccttaggatattacataatacttgatatgccattttgtcctcttattttta
 || || |  |||||  |  |||| |||||||| || |  || ||    ||||  || ||||| ||||||||||||||||||||||| || ||||| |||||  |   | ||  | ||  | ||  |   |    ||  |||| ||| |     |   | |  ||  | |   | |  | |||  |  | | |   |  | 
TCTGGCTGCCAAAGGCAGTGTTCCAATTGGTATAGGCAGGAACTCTCATATCAAAAGGGCAATTATTGACAAGAATGCTCGAATTGGGGAAAATGTCAAGgttatagcatcttctattatatacaattttgttcgttgttttacattctaagccattttttcccaagacaacaggtgaggcatagtagcttttaggtgat-

upper sequence: GRMZM2G068506_T02 (Zea mays), 5'ss of exon 8
lower sequence: PP1S2_392V6.1 (Physcomitrella patens), 5'ss of exon 8
CCTTGCCGAAAA-AGGTGGCATTCCTATTGGTATTGGGAAAAATTCATGCATCAGGAGAGCAATCATTGACAAGAATGCTCGAATTGGAGACAATGTTAAGgtattccaaactgatgttcc----aacggtcaagaatattaatttagattt------ttccttaggatattacataatacttgatatgccattttgtcctcttattttta-------------------------------
  ||||       ||||||||| || || || ||||| | ||| ||     | |  ||||||||||||||||| ||||| ||||||||||| ||||||||||||| |     |     |      | | |  |  | |||| || |  |  |      || | || | | ||  ||||||| |     |   | ||  | | ||   | |                                
-GTTGCTAGCCTCAGGTGGCATACCCATGGGCATTGGAAGAAACTCTGTAGTGAAAAGAGCAATCATTGACAAAAATGCACGAATTGGAGAGAATGTTAAGgtatgctttgttctcactttggtaagctgcaagtagtattcatatgcacataatgagtttcataag-tcttgtataatacatacatggaagtattaccattttgaatatggattaatggtcggacgttatcctttgtgtag

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|32941027|gb|CF045846.1|CF045846
EST:     TCAGGAGAGCAATCATTGACAAGAATGCTCGAATTGGAGACAATGTTAAG                         ATACTCAATGCTGACAATGTTCAAGAAGCTGCAAGGGAGACAGACGGGT
genomic: TCAGGAGAGCAATCATTGACAAGAATGCTCGAATTGGAGACAATGTTAAGgtattccaaa ... gatcttgtagATACTCAATGCTGACAATGTTCAAGAAGCTGCAATGGAGACAGACGGGT
EST: gi|32838360|gb|CD978038.1|CD978038
EST:     TCAGGAGAACAATCATTGACAAGAATGCTCGAATTGGAGACAATGTTAAG                         ATACTCAATGCTGACAATGTTCAAGAAGCTGCAAGGGAGACAGACGGGT
genomic: TCAGGAGAGCAATCATTGACAAGAATGCTCGAATTGGAGACAATGTTAAGgtattccaaa ... gatcttgtagATACTCAATGCTGACAATGTTCAAGAAGCTGCAATGGAGACAGACGGGT
EST: gi|32836730|gb|CD976408.1|CD976408
EST:     TCAGGAGAGCAATCATTGACAAGAATGCTCGAATTGGAGACAATGTTAAG                         ATACTCAATGCTGACAATGTTCAAGAAGCTGCAAGGGAGACAGACGGGTAC
genomic: TCAGGAGAGCAATCATTGACAAGAATGCTCGAATTGGAGACAATGTTAAGgtattccaaa ... gatcttgtagATACTCAATGCTGACAATGTTCAAGAAGCTGCAATGGAGACAGACGGGTAC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CCTTGCCGAAAAAGGTGGCATTCCTATTGGTATTGGGAAAAATTCATGCATCAGGAGAGCAATCATTGACAAGAATGCTCGAATTGGAGACAATGTTAAGgtattccaaactgatgttccaacggtcaagaatattaatttagatttttccttaggatattacataatacttgatatgccattttgtcctcttattttta

- - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA