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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgggtacaatatccttttcgccaacaccttctgtttaatgcattcactttattgagctatgaagtctagtttatggctgtcaagatcagtagcaatcgacccatctgagttgcatcgtggctattgatttgcaacttatatatgttaaatctttgcagGTTCTTATTGATTTTGGGCTGAGTTTCACTTCGACAATTCCCGAGGACAAAGCGGTGGACCTATATGTGCTAGAGAGAGCTTTGATTTCCATGCATTCGT

Basic information

species Zea mays
transcript GRMZM2G313649_T06
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G313649_T05 (Zea mays), 3'ss of exon 6
lower sequence: LOC_Os10g28640.1 (Oryza sativa), 3'ss of exon 4
gtgggtacaatatccttttcgccaacaccttctgtttaatgcattcactttattgagctatgaagtctagtttatggctgtcaa--gatcagtagcaatcgacccatctgag--ttgcatcgtggctattgatttgcaacttatatatgttaaatctttgcagGTTCTTATTGATTTTGGGCTGAGTTTCACTTCGACAATTCCCGAGGACAAAGCGGTGGACCTATATGTGCTAGAGAGAGCTTTGATTTCCATGCATTCGT
                                                          | |  |   |  ||| || | ||  |   ||       | ||     ||   ||  || ||||   |||||| || ||| ||| | || |||| |    || |||||||||||||||||||| ||||||||||  || || ||||| ||||||||||| |||||| |||||||||| |||||||| |||||||| |||||||| |
-------------------------------------------------------gtgtgtagaacttcctttctgtcagttcatgcattttcttgagtcatttaattcaagacttacatccgagctattaatgtgccactca-atgtgttca--tattccagGTTCTTATTGATTTTGGTCTGAGTTTCATATCAACTATTCCTGAGGACAAAGCAGTGGACTTATATGTGCTTGAGAGAGCATTGATTTCTATGCATTCAT
















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|76294398|gb|DV033966.1|DV033966
EST:     TTGACCACGTCAAACATGATAATTAAGAACAGTAACAATCAATTG        
genomic: ATAATTAAGAACAGTAACAATCAATTGgtgggtacaa ... atctttgcagG
EST: gi|71427980|gb|DR809030.1|DR809030
EST:     TTGACCACGTCAAACATGATAATTAAGAACAGTAACAATCAATTG        
genomic: ATAATTAAGAACAGTAACAATCAATTGgtgggtacaa ... atctttgcagG
EST: gi|32942234|gb|CF047053.1|CF047053
EST:     TTGACCACGTCAAACATGATAATTAAGAACAGTAACAATCAATTG        
genomic: ATAATTAAGAACAGTAACAATCAATTGgtgggtacaa ... atctttgcagG
EST: gi|88748493|gb|DY532634.1|DY532634
EST:     TTGACCACGTCAAACATGATAATTAAGAACAGTAACAATCAATTG        
genomic: ATAATTAAGAACAGTAACAATCAATTGgtgggtacaa ... atctttgcagG
EST: gi|71442372|gb|DR823422.1|DR823422
EST:     TTGACCACGTCAAACATGATAATTAAGAACAGTAACAATCAATTG        
genomic: ATAATTAAGAACAGTAACAATCAATTGgtgggtacaa ... atctttgcagG
EST: gi|149084732|gb|EE174225.2|EE174225
EST:     TTGACCACGTCAAACATGATAATTAAGAACAGTAACAATCAATTG        
genomic: ATAATTAAGAACAGTAACAATCAATTGgtgggtacaa ... atctttgcagG
EST: gi|71762245|gb|DR960182.1|DR960182
EST:     TTGACCACGTCAAACATGATAATTAAGAACAGTAACAATCAATTG        
genomic: ATAATTAAGAACAGTAACAATCAATTGgtgggtacaa ... atctttgcagG
EST: gi|88748628|gb|DY532769.1|DY532769
EST:     TTGACCACGTCAAACATGATAATTAAGAACAGTAACAATCAATTG        
genomic: ATAATTAAGAACAGTAACAATCAATTGgtgggtacaa ... atctttgcagG
EST: gi|60343573|gb|DN210546.1|DN210546
EST:     TTGACCACGTCAAACATGATAATTAAGAACAGTAACAATCAATTG        
genomic: ATAATTAAGAACAGTAACAATCAATTGgtgggtacaa ... atctttgcagG
EST: gi|32836689|gb|CD976367.1|CD976367
EST:     TTGACCACGTCAAACATGATAATTAAGAACAGTAACAATCAATTG        
genomic: ATAATTAAGAACAGTAACAATCAATTGgtgggtacaa ... atctttgcagG
EST: gi|213182702|gb|FM195363.1|FM195363
EST:     TTGACCACGTCAAACATGATAATTAAGAACAGTAACAATCAATTG        
genomic: ATAATTAAGAACAGTAACAATCAATTGgtgggtacaa ... atctttgcagG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tctgagttgcatcgtggctattgatttgcaacttatatatgttaaatctttgcagGTTCTTATTGATTTTGGGCTGAGTTTCACTTCGACAATTCCCGAGGACAAAGCGGTGGACCTATATGTGCTAGAGAGAGCTTTGATTTCCATGCATTCGT
                  tattgat  putative branch site (score: 3)
                                              tctttgc  putative PPT
                             aacttatatatgttaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgggtacaatatccttttcgccaacaccttctgtttaatgcattcactttattgagctatgaagtctagtttatggctgtcaagatcagtagcaatcgacccatctgagttgcatcgtggctattgatttgcaacttatatatgttaaatctttgcagGTTCTTATTGATTTTGGGCTGAGTTTCACTTCGACAATTCCCGAGGACAAAGCGGTGGACCTATATGTGCTAGAGAGAGCTTTGATTTCCATGCATTCGT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGCTT