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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGTACCTGTCACTGTCAGTGCTCCTACCCCAACTGCCACAGCTTCCCCAGCTCCTGCTGTTGCTGTATCgtgagttcctgatgttccatccattctataaatttgattattctcatgtgaatgtagtttctgcttgaggatgtgctgtaatttactgaacccattttgacttgatcttttcttcttgccatttgagcag

Basic information

species Oryza sativa
transcript LOC_Os09g24200.1
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os09g24200.1 (Oryza sativa), 5'ss of exon 5
lower sequence: GRMZM2G105772_T01 (Zea mays), 5'ss of exon 5
TGTACCTGTCACTGTCAGTGCTCCTACCCCAACTGCCACAGCTTCCCCAGCTCCTGCTGTTGCTGTATCgtgagttcctgatgttccatccattctata-aatttgattattctcatg-tgaatgtagtttctgcttgaggatgtgctg-taatttactgaacccattttgacttgatcttttcttcttgccatttgagcag
      |||  |||||||||| |   |  ||||||| ||||| ||  |||||||||||||||||||||||| ||||||||||  ||| |||||  || |  |||| | || |||  |  | |   || ||| || |||| ||||   || || ||     ||     |                                  
------TGTACCTGTCAGTGCACTGGCTGCAACTGCTACAGCCTCAGCAGCTCCTGCTGTTGCTGTATCgtaagttcctgattctccttccatcttagatgatttaactaatcttgtaataagcataatttttgtttgatgatgcattggtatttcgtaaaatttgctacag------------------------------

upper sequence: LOC_Os09g24200.1 (Oryza sativa), 5'ss of exon 5
lower sequence: GRMZM2G061620_T05 (Zea mays), 5'ss of exon 5
TGTACCTGTCACTGTCAGTGCTCCTACCCCAACTGCCACAGCTTCCCCAGCTCCTGCTGTTGCTGTATCgtgagttcctgatgttccatccattctataaatttgattattctcatg-tgaatgtagtttctgcttgaggatgtgctgtaatttactga-------acccattttgacttg------------------atcttttcttct-tgc-catttgagcag
      |||  |||||||||| ||  |  ||||||| ||||| ||  ||||||||||||||||||| |||| |||| ||||| |||| || ||  || | |||| | || |||  |  | ||  || ||  ||||||| |||||  ||  |||| ||         | |  ||   | |||                  |||||||||| | ||  || |||| |||
------TGTACCTGTCAGTGCACCGGCTGCAACTGCTACAGCCTCAGCAGCTCCTGCTGTTGCTGTCTCgtaagtttctgattttccttctatcttagatatttaactaatcttgtaataaacataattgttgcttgatgatgtattgatatttcctattaaaaatagctgttgaaagttgctaatcacattcacgtatatcttttcttttatgttcacttgaacag

upper sequence: LOC_Os09g24200.1 (Oryza sativa), 5'ss of exon 5
lower sequence: GRMZM2G061620_T04 (Zea mays), 5'ss of exon 5
TGTACCTGTCACTGTCAGTGCTCCTACCCCAACTGCCACAGCTTCCCCAGCTCCTGCTGTTGCTGTATCgtgagttcctgatgttccatccattctataaatttgattattctcatg-tgaatgtagtttctgcttgaggatgtgctgtaatttactga-------acccattttgacttg------------------atcttttcttct-tgc-catttgagcag
                  ||| ||  |  ||||||| ||||| ||  ||||||||||||||||||| |||| |||| ||||| |||| || ||  || | |||| | || |||  |  | ||  || ||  ||||||| |||||  ||  |||| ||         | |  ||   | |||                  |||||||||| | ||  || |||| |||
------------------TGCACCGGCTGCAACTGCTACAGCCTCAGCAGCTCCTGCTGTTGCTGTCTCgtaagtttctgattttccttctatcttagatatttaactaatcttgtaataaacataattgttgcttgatgatgtattgatatttcctattaaaaatagctgttgaaagttgctaatcacattcacgtatatcttttcttttatgttcacttgaacag

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|58672603|gb|CK061289.1|CK061289
EST:     GCTCCTACCCCAACTGCCACAGCTTCCCCAGCTCCTGCTGTTGCTGTATC                         CTCTGAAGCTGATAACTACGGTCAGGCCACCTCAAACCTTGTTGCTGGCAG
genomic: GCTCCTACCCCAACTGCCACAGCTTCCCCAGCTCCTGCTGTTGCTGTATCgtgagttcct ... atttgagcagCTCTGAAGCTGATAACTACGGTCAGGCCACCTCAAACCTTGTTGCTGGCAG
EST: gi|33691318|gb|CF319557.1|CF319557
EST:     GCTCCTACCCCAACTGCCACAGCTTCCCCAGCTCCTGCTGTTGCTGTATC                         CTCTGAAGCTGATAACTACGGTCAGGCCACCTCAAACCTTGTTGCTGGCAG
genomic: GCTCCTACCCCAACTGCCACAGCTTCCCCAGCTCCTGCTGTTGCTGTATCgtgagttcct ... atttgagcagCTCTGAAGCTGATAACTACGGTCAGGCCACCTCAAACCTTGTTGCTGGCAG
EST: gi|56157493|gb|D24336.3|D24336
EST:     CTCCTACCCCAACTGGCCACAGCTTCCCCAGCTCCTGCTGTTGCTGTATC                         CTCTGAAGCTGGATAACTACGGTCAGGCCANCTCAAACCTTGTTGCTGGCA
genomic: CTCCTACCCCAACTG-CCACAGCTTCCCCAGCTCCTGCTGTTGCTGTATCgtgagttcct ... atttgagcagCTCTGAAGCTG-ATAACTACGGTCAGGCCACCTCAAACCTTGTTGCTGGCA
EST: gi|58686007|gb|CK074694.1|CK074694
EST:     GCTCCTACCCCAACTGCCACAGCTTCCCCAGCTCCTGCTGTTGCTGTATC                         CTCTGAAGCTGATAACTACGGTCAGGCCACCTCAAACCTTGTTGCTGGCAG
genomic: GCTCCTACCCCAACTGCCACAGCTTCCCCAGCTCCTGCTGTTGCTGTATCgtgagttcct ... atttgagcagCTCTGAAGCTGATAACTACGGTCAGGCCACCTCAAACCTTGTTGCTGGCAG
EST: gi|88377574|gb|CI605409.1|CI605409
EST:     GCTCCTACCCCAACTGCCACAGCTTCCCCAGCTCCTGCTGTTGCTGTATC                         CTCTGAAGCTGATAACTACGGTCAGGCCACCTCAAACCTTGTTGCTGGCAG
genomic: GCTCCTACCCCAACTGCCACAGCTTCCCCAGCTCCTGCTGTTGCTGTATCgtgagttcct ... atttgagcagCTCTGAAGCTGATAACTACGGTCAGGCCACCTCAAACCTTGTTGCTGGCAG
EST: gi|58665783|gb|CK054469.1|CK054469
EST:     GCTCCTACCCCAACTGCCACAGCTTCCCCAGCTCCTGCTGTTGCTGTATC                         CTCTGAAGCTGATAACTACGGTCAGGCCACCTCAAACCTTGTTGCTGGCAG
genomic: GCTCCTACCCCAACTGCCACAGCTTCCCCAGCTCCTGCTGTTGCTGTATCgtgagttcct ... atttgagcagCTCTGAAGCTGATAACTACGGTCAGGCCACCTCAAACCTTGTTGCTGGCAG
EST: gi|29678389|gb|CB674664.1|CB674664
EST:     GCTCCTACCCCAACTGCCACAGCTTCCCCAGCTCCTGCTGTTGCTGTATC                         CTCTGAAGCTGATAACTACGGTCAGGCCACCTCAAACCTTGTTGCTGGCAG
genomic: GCTCCTACCCCAACTGCCACAGCTTCCCCAGCTCCTGCTGTTGCTGTATCgtgagttcct ... atttgagcagCTCTGAAGCTGATAACTACGGTCAGGCCACCTCAAACCTTGTTGCTGGCAG
EST: gi|58609238|gb|CK037271.1|CK037271
EST:     GCTCCTACCCCAACTGCCACAGATTCCCCAGCTCCTGCTGTAGCTGTATC                         CTCTGAAGCTGATAACTACGGTCAGGC
genomic: GCTCCTACCCCAACTGCCACAGCTTCCCCAGCTCCTGCTGTTGCTGTATCgtgagttcct ... atttgagcagCTCTGAAGCTGATAACTACGGTCAGGC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGTACCTGTCACTGTCAGTGCTCCTACCCCAACTGCCACAGCTTCCCCAGCTCCTGCTGTTGCTGTATCgtgagttcctgatgttccatccattctataaatttgattattctcatgtgaatgtagtttctgcttgaggatgtgctgtaatttactgaacccattttgacttgatcttttcttcttgccatttgagcag

- - - - - - - - - - - - - - - - - - - - - - -  CAGCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGTT