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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCACATAATCAGCCATCTGAAGAAAGAGATGCCTGCACTGATGGGCAAGGCCAAGGCTCAGCAGAAGCTGCTCGACGGGCTGGATCAACAGTTCGCCAAGgttcactgctcatcccttgcaagttgcacactggcacctataggtgtagtgtaggtgtaggcgtgtagcccacatgcatgcaatgcacgttcgtgttcttgtctctgaatccgagctgcatgcccttgctctgtgcag

Basic information

species Zea mays
transcript GRMZM2G065012_T01
intron # 15
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G065012_T02 (Zea mays), 5'ss of exon 15
lower sequence: GLYMA09G01160.1 (Glycine max), 5'ss of exon 13
GCACATAATCAGCCATCTGAAGAAAGAGATGCCTGCACTGATGGGCAAGGCCAAGGCTCAGCAGAAGCTGCTCGACGGGCTGGATCAACAGTTCGCCAAGgttcactgctcatcccttgcaagttgcacactggcacctataggtgtagtgtaggtgtaggcgtgtagcccacatgcatgcaatgcacgttcgtgttcttgtctctgaatccgagctgcatgcccttgctctgtgcag
  | ||||| |||||||| ||||| |||||||||||  | |||||||| ||||||||||  || |  || || ||    || ||  || | || || |||||       || | || | |   ||             |    |  || | |    |||  | |      || ||   |||||  ||                                                   
ATATATAATTAGCCATCTTAAGAAGGAGATGCCTGCTATAATGGGCAAAGCCAAGGCTCGACAAAGACTTCTTGATAATCTTGAGGAAGAATTTGCAAAGgtctttctttcctacccttcctctta---------gtttgattgcttaattttcaggta--cttaccattcatatttttgcaa-acag--------------------------------------------------

upper sequence: GRMZM2G065012_T02 (Zea mays), 5'ss of exon 15
lower sequence: Vv19s0090g01130.t01 (Vitis vinifera), 5'ss of exon 15
GCACATAATCAGCCATCTGAAGAAAGAGATGCCTGCACTGATGGGCAAGGCCAAGGCTCAGCAGAAGCTGCTCGACGGGCTGGATCAACAGTTCGCCAAGgttcactgctcatcccttgcaagttgcacactggcacctataggtgtagtgtag-gtgtaggcgtgtagcccacatgcatgcaatgcacgttcgtgttcttgtctctgaatccgagctgcatgcccttgctctgtgcag
  |||| ||||||||||| ||||| ||||||||| |  |||||||||| |||||| ||||||||| |||  |||||   |||||  |  | || || |||||||        || | ||||| |  |    |   ||| | |  |  | |  |   |  |  | |  | |  ||          |  |  |   | | |                                        
CTACATCATCAGCCATCTAAAGAAGGAGATGCCTACTATGATGGGCAAAGCCAAGACTCAGCAGAGGCTTATCGACAATCTGGAAGATGAATTTGCAAAGgttccacatctctctcctgcaaataaccttgtaa-accaacacattcaattcaccattcatacattaatcgtactcattcttggttaatatatatatacag--------------------------------------
















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|26455418|gb|CA827001.1|CA827001
EST:     CCAAGGCTCAGCAGAAGCTGCTCGACGGGCTGGATCAACAGTTCGCCAAG                         GTCCAGAAGGAGCTGCACCTGCCGCCAGGGGACTTCCCGAGCGTGGAGGAG
genomic: CCAAGGCTCAGCAGAAGCTGCTCGACGGGCTGGATCAACAGTTCGCCAAGgttcactgct ... ctctgtgcagGTCCAGAAGGAGCTGCACCTGCCGCCAGGGGACTTCCCGAGCGTGGAGGAG
EST: gi|71333236|gb|DR803672.1|DR803672
EST:     CCAAGGCTCAGCAGAAGCTGCTCGACGGGCTGGATCAACAGTTCGCCAAG                         GTCCAGAAGGAGCTGCACCTGCCGCCAGGGGACTTCCCGAGCGTGGAGGAG
genomic: CCAAGGCTCAGCAGAAGCTGCTCGACGGGCTGGATCAACAGTTCGCCAAGgttcactgct ... ctctgtgcagGTCCAGAAGGAGCTGCACCTGCCGCCAGGGGACTTCCCGAGCGTGGAGGAG
EST: gi|89106667|gb|DY576884.1|DY576884
EST:     CCAAGGCTCAGCAGAAGCTGCTCGACGGGCTGGATCAACAGTTCGCCAAG                         GTCCAGAAGGAGCTGCACCTGCCGCCAGGGGACTTCCCGAGCGTGGAGGAG
genomic: CCAAGGCTCAGCAGAAGCTGCTCGACGGGCTGGATCAACAGTTCGCCAAGgttcactgct ... ctctgtgcagGTCCAGAAGGAGCTGCACCTGCCGCCAGGGGACTTCCCGAGCGTGGAGGAG
EST: gi|21390315|gb|BQ528364.1|BQ528364
EST:     CCAAGGCTCAGCAGAAGCTGCTCGACGGGCTGGATCAACAGTTCGCCAAG                         GTCCAGAAGGAGCTGCACCTGCCGCCAGGGGACTTCCCGAGCGTGGAGGAG
genomic: CCAAGGCTCAGCAGAAGCTGCTCGACGGGCTGGATCAACAGTTCGCCAAGgttcactgct ... ctctgtgcagGTCCAGAAGGAGCTGCACCTGCCGCCAGGGGACTTCCCGAGCGTGGAGGAG
EST: gi|76283613|gb|DV023181.1|DV023181
EST:     GATCAACAGTTCGCCAAG                         GTCCAGAAGGAGCTGCACCTGCCGCCAGGGGACTTCCCGAGCGTGGAGGAG
genomic: GATCAACAGTTCGCCAAGgttcactgct ... ctctgtgcagGTCCAGAAGGAGCTGCACCTGCCGCCAGGGGACTTCCCGAGCGTGGAGGAG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GCACATAATCAGCCATCTGAAGAAAGAGATGCCTGCACTGATGGGCAAGGCCAAGGCTCAGCAGAAGCTGCTCGACGGGCTGGATCAACAGTTCGCCAAGgttcactgctcatcccttgcaagttgcacactggcacctataggtgtagtgtaggtgtaggcgtgtagcccacatgcatgcaatgcacgttcgtgttcttgtctctgaatccgagctgcatgcccttgctctgtgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA