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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaatgtacattaataataaacctgtcgctgctagtactgttattttgcacttcaactttgatacttttttttatagtaggaatgtagtaggtacatatttcggtgtttaggcgcccctactgttctattgtaaagtgtgtgatgccacacttgtagGAACCCTGCCCTGCTTACTGTTGGTGGCTGGTCTATTCTTCATTCCGGAATCTCCAAGATGGCTG

Basic information

species Zea mays
transcript GRMZM2G160430_T01
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G160430_T01 (Zea mays), 3'ss of exon 6
lower sequence: LOC_Os05g49260.1 (Oryza sativa), 3'ss of exon 6
----------------------gtaatgtacattaataataaacctgtcgctgctagtactgttattttgcacttcaac-tttgatacttttttttatagtaggaatgtagtaggtacatatttcggtgtttaggcgcccctactgttctattgtaaagtgtgtgatgccacacttgtagGAACCCTGCCCTGCTTACTGTTGGTGGCTGGTCTATTCTTCATTCCGGAATCTCCAAGATGGCTG
                        |||||    || | |   |  |||      || || ||   ||||    ||  |  |||| || |   ||||  | |   | || | |  |||  |   |      |  ||  || ||  | |   |||  ||  | || | |||||  |||||||||| | | || ||   | ||||  |  ||||||||||||||||||||||||| ||||||||||||
gtacaaatcaatacctgatgtctgaatgttttctatttagggatatgtaataaataataatgaatttttaacttttgatatttgctagtaccttttggactt--attgcaatttgtatgtgcgttaaatgtctggtacctctgat-tctgattcaaatatctgggttgccatgcttgtagGAAGCATCCCATGTACATTGTTAATACCTGGTCTATTCTTCATTCCGGAATCCCCAAGATGGCTG
















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|148950294|gb|EC895853.2|EC895853
EST:     TTCCTATGTGCTTGGCTTGTTTTTCCCTTGGAGGCTTCTTGCATTAATAG                         GAACCCTGCCCTGCTTACTGTTGGTGGCTGGTCTATTCTTCATTCCGGAAT
genomic: TTCCTATGTGCTTGGCTTGTTTTTCCCTTGGAGGCTTCTTGCATTAATAGgtaatgtaca ... acacttgtagGAACCCTGCCCTGCTTACTGTTGGTGGCTGGTCTATTCTTCATTCCGGAAT
EST: gi|32832539|gb|CD972217.1|CD972217
EST:     TTCCTATGTGCTTGGCTTGTTTTTCCCTTGGAGGCTTCTTGCATTAATAG                         GAACCCTGCCCTGCTTACTGTTGGTGGCTGGTCTATTCTTCGTTCCGGAAT
genomic: TTCCTATGTGCTTGGCTTGTTTTTCCCTTGGAGGCTTCTTGCATTAATAGgtaatgtaca ... acacttgtagGAACCCTGCCCTGCTTACTGTTGGTGGCTGGTCTATTCTTCATTCCGGAAT
EST: gi|32929449|gb|CF034261.1|CF034261
EST:     TTCCTATGTGCTTGGCTTGTTTTTCCCTTGGAGGCTTCTTGCATTAATAG                         GAACCCTGCCCTGCTTACTGTTGGTGGCTGGTCTATTCTTCGTTCCGGAAT
genomic: TTCCTATGTGCTTGGCTTGTTTTTCCCTTGGAGGCTTCTTGCATTAATAGgtaatgtaca ... acacttgtagGAACCCTGCCCTGCTTACTGTTGGTGGCTGGTCTATTCTTCATTCCGGAAT
EST: gi|32834892|gb|CD974570.1|CD974570
EST:     TTCCTATGTGCTTGGCTTGTTTTTCCCTTGGAGGCTTCTTGCATTAATAG                         GAACCCTGCCCTGCTTACTGTTGGTGGCTGGTCTATTCTTCGTTCCGGAAT
genomic: TTCCTATGTGCTTGGCTTGTTTTTCCCTTGGAGGCTTCTTGCATTAATAGgtaatgtaca ... acacttgtagGAACCCTGCCCTGCTTACTGTTGGTGGCTGGTCTATTCTTCATTCCGGAAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ggtgtttaggcgcccctactgttctattgtaaagtgtgtgatgccacacttgtagGAACCCTGCCCTGCTTACTGTTGGTGGCTGGTCTATTCTTCATTCCGGAATCTCCAAGATGGCTG
                        tattgtaaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaatgtacattaataataaacctgtcgctgctagtactgttattttgcacttcaactttgatacttttttttatagtaggaatgtagtaggtacatatttcggtgtttaggcgcccctactgttctattgtaaagtgtgtgatgccacacttgtagGAACCCTGCCCTGCTTACTGTTGGTGGCTGGTCTATTCTTCATTCCGGAATCTCCAAGATGGCTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG