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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATTGGAGGTTACTCTGGAAGCAATCTGCAGTTTCCTTGATGCACGCACTACTGAGCTTGAGACCGATGCTTACCCAGCTTTGGATGAGTTGACATCCAAGgtgagtggatgtgcttgtatactgtgtttcattagtatgcatttgatttgaacatcctagtgtgttttaataaagcaaaaatataggggtaaggcttgcc...

Basic information

species Zea mays
transcript GRMZM2G159295_T02
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G159295_T01 (Zea mays), 5'ss of exon 4
lower sequence: LOC_Os03g53110.1 (Oryza sativa), 5'ss of exon 4
ATTGGAGGTTACTCTGGAAGCAATCTGCAGTTTCCTTGATGCACGCACTACTGAGCTTGAGACCGATGCTTACCCAGCTTTGGATGAGTTGACATCCAAGgtgagtggatgt--gcttgt-atactgtgtttcattagtatgcatttgatt----tgaacatcctagtgtgttttaataaagcaaaaata-taggggtaaggcttgcc
| ||||||||||| ||||||| || |||||||| |||| |||||||||||||||| | ||||  | |||||||||||||||||||||  ||||||||||||||| || || |  ||||   ||||||| || | ||  |||| | ||||||      |  | | |  | ||| | | |  |    ||  |  | |  |||        
ACTGGAGGTTACTTTGGAAGCCATTTGCAGTTTTCTTGGTGCACGCACTACTGAGTTGGAGAGTGCTGCTTACCCAGCTTTGGATGAACTGACATCCAAGgtgactgaatatatgcttaccatactgtattcccttgttatgaacttgattactcctagaaacatgatatgtgtgattttatttgaagcaacaagcataa--------
















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|32843052|gb|CD982733.1|CD982733
EST:     CTGAGCTTGAGACCGATGCTTACCCAGCTTTGGATGAGTTGACATCCAAG                         ATCAGCAGCCGCAACTTGGATAGGGTAC
genomic: CTGAGCTTGAGACCGATGCTTACCCAGCTTTGGATGAGTTGACATCCAAGgtgagtggat ... gacatcgcagATCAGCAGCCGCAACTTGGATAGGGTAC
EST: gi|149107575|gb|EE189457.2|EE189457
EST:     CTGAGCTTGAGACCGATGCTTACCCAGCTTTGGATGAGTTGACATCCAAG                         ATCAGCAGCCGCAACTTGGATAGGGTACGTAAGTTAAAAAGCGGGATGACA
genomic: CTGAGCTTGAGACCGATGCTTACCCAGCTTTGGATGAGTTGACATCCAAGgtgagtggat ... gacatcgcagATCAGCAGCCGCAACTTGGATAGGGTACGTAAGTTAAAAAGCGGGATGACA
EST: gi|26557372|gb|CA829607.1|CA829607
EST:     CTGAGCTTGAGACCGATGCTTACCCAGCTTTGGATGAGTTGACATCCAAG                         ATCAGCAGCCGCAACTTGGATAGGGTACGTAAGTTAAAAAGCGGGATGACA
genomic: CTGAGCTTGAGACCGATGCTTACCCAGCTTTGGATGAGTTGACATCCAAGgtgagtggat ... gacatcgcagATCAGCAGCCGCAACTTGGATAGGGTACGTAAGTTAAAAAGCGGGATGACA
EST: gi|32843159|gb|CD982840.1|CD982840
EST:     CTGAGCTTGAGACCGATGCTTACCCAGCTTTGGATGAGTTGACATCCAAG                         ATCAGCAGCCGCAACTTGGATAGGGTAC
genomic: CTGAGCTTGAGACCGATGCTTACCCAGCTTTGGATGAGTTGACATCCAAGgtgagtggat ... gacatcgcagATCAGCAGCCGCAACTTGGATAGGGTAC
EST: gi|29544404|gb|CB604784.1|CB604784
EST:     CTGAGCTTGAGACCGATGCTTACCCAGCTTTGGATGAGTTGACATCCAAG                         ATCAGCAGCCGCAACTTGGATAGGGTACGTAAGTTAAAAAGCGGGATGACA
genomic: CTGAGCTTGAGACCGATGCTTACCCAGCTTTGGATGAGTTGACATCCAAGgtgagtggat ... gacatcgcagATCAGCAGCCGCAACTTGGATAGGGTACGTAAGTTAAAAAGCGGGATGACA
EST: gi|32836386|gb|CD976064.1|CD976064
EST:     CTGAGCTTGAGACCGATGCTTACCCAGCTTTGGATGAGTTGACATCCAAG                         ATCAGCAGCCGCAACTTGGATAGGGT
genomic: CTGAGCTTGAGACCGATGCTTACCCAGCTTTGGATGAGTTGACATCCAAGgtgagtggat ... gacatcgcagATCAGCAGCCGCAACTTGGATAGGGT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ATTGGAGGTTACTCTGGAAGCAATCTGCAGTTTCCTTGATGCACGCACTACTGAGCTTGAGACCGATGCTTACCCAGCTTTGGATGAGTTGACATCCAAGgtgagtggatgtgcttgtatactgtgtttcattagtatgcatttgatttgaacatcctagtgtgttttaataaagcaaaaatataggggtaaggcttgcc

- - - - - - - - - - - - - - - - - - - - - - - - - - GAGCTT