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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgcgttactacaccttcacccctatcttgattttgcttttcttggcttggggtggatttggtgtgtgagattgattatttattttgttggtgatttggtgacgagcagTCTGAGAAGATCGCCACCCTGGTGAAGGCGGCCAACATCAAGGTCGAGGCCTACTGGCCCGGTCTCTTCGCCAAGCTCCTCGAGCACCGCAGCGTCGATG

Basic information

species Oryza sativa
transcript LOC_Os08g02340.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os08g02340.2 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G032315_T01 (Zea mays), 3'ss of exon 2
gtgcgttactacaccttcacccctatcttgattttgcttttcttggcttggggtggatttggtgtgtgagattgattatttattttgttggtgatttggtgacgagcagTCTGAGAAGATCGCCACCCTGGTGAAGGCGGCCAACATCAAGGTCGAGGCCTACTGGCCCGGTCTCTTCGCCAAGCTCCTCGAGCACCGCAGCGTCGATG
||||||  || | || || || |   ||   ||||   | ||   ||||       |||   | || | |  |||  |  |   |  ||| |  | |  |     |||| | ||||||||||||||  | ||||||||||||||||||||||||||| |||||||||| |  ||||||||||||||||| ||| | |||| |||||| |
gtgcgtc-cttctccctcgccgccggctc--ttttaaatctccccgctt-------attctttttgagcgggtgaggagatgcgtgattgttcctcttctt---ggcagGCCGAGAAGATCGCCACGATCGTGAAGGCGGCCAACATCAAGGTCGAGTCCTACTGGCCGGCCCTCTTCGCCAAGCTCCTGGAGAAGCGCAACGTCGAGG

upper sequence: LOC_Os08g02340.2 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G157443_T02 (Zea mays), 3'ss of exon 2
gtgcgttactacaccttcacccctatcttgattttgcttttcttggcttggggtggatttggtgtgtgagattgattatttattttgttggtgatttggtgacgagcagTCTGAGAAGATCGCCACCCTGGTGAAGGCGGCCAACATCAAGGTCGAGGCCTACTGGCCCGGTCTCTTCGCCAAGCTCCTCGAGCACCGCAGCGTCGATG
             | ||| | |         | ||  |||  |      | | |   |||  | || | | | |  |  |||| | |  |||| ||   |     |||| | ||||||||||||||| | ||||||||||||||||||||||||||| |||||||||| |  |||||||| |||||||| ||| | |||||||| || |
----------gtgcgttctctcacgctgcagtgttcttttaatc--tcagagttttcttttttttgagcggtcgcgtggttatgtggggggtgtttc--ttgtttgcagGCCGAGAAGATCGCCACCATCGTGAAGGCGGCCAACATCAAGGTCGAGTCCTACTGGCCGGCGCTCTTCGCTAAGCTCCTGGAGAAGCGCAGCGTTGAGG
















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|33674593|gb|CF302832.1|CF302832
EST:     CCTGCACGCTCGCCGCCCTCATCCTCCACGACGATGGCATCCCCATCACC                         TCTGAGAAGATCGCCACCCTGGTGAAGGCGGCCAACATCAAGGTCGAGGCC
genomic: CCTGCACGCTCGCCGCCCTCATCCTCCACGACGATGGCATCCCCATCACCgtgcgttact ... tgacgagcagTCTGAGAAGATCGCCACCCTGGTGAAGGCGGCCAACATCAAGGTCGAGGCC
EST: gi|55433761|gb|CV729994.1|CV729994
EST:     CTGCACGCTCGCCGCCCTCATCCTCCACGACGATGGC-TNCCCCATCACC                         TCTGAGAAGATCACCACCCTGGTGAAGGCGGCCAACATCAAGGTCGAGGCC
genomic: CTGCACGCTCGCCGCCCTCATCCTCCACGACGATGGCAT-CCCCATCACCgtgcgttact ... tgacgagcagTCTGAGAAGATCGCCACCCTGGTGAAGGCGGCCAACATCAAGGTCGAGGCC
EST: gi|86891478|gb|CI308094.1|CI308094
EST:     CCTGCACGCTCGCCGCCCTCATCCTCCACGACGATGGCATCCCCATCACC                         TCTGAGAAGATCGCCACCCTGGTGAAGGCGGCCAACATCAAGGTCGAGGCC
genomic: CCTGCACGCTCGCCGCCCTCATCCTCCACGACGATGGCATCCCCATCACCgtgcgttact ... tgacgagcagTCTGAGAAGATCGCCACCCTGGTGAAGGCGGCCAACATCAAGGTCGAGGCC
EST: gi|55411397|gb|CV723773.1|CV723773
EST:     CGCCCTCATCCTCCACGACGATGGCATCCCCATCACC                         TCTGAGAAGATCGCCACCCTGGTGAAGGCGGCCAACATCAAGGTCGAGGCC
genomic: CGCCCTCATCCTCCACGACGATGGCATCCCCATCACCgtgcgttact ... tgacgagcagTCTGAGAAGATCGCCACCCTGGTGAAGGCGGCCAACATCAAGGTCGAGGCC
EST: gi|427778|gb|D23916.1|D23916
EST:     CCTGCACGCTCGCCGNCCTCATCCTCCACGACGATGGCATCCCCATCACC                         TCTGAGAAGATCGCCACCCTGGTGAAGGCGGCCAACATCAAGGTCGAGGCC
genomic: CCTGCACGCTCGCCGCCCTCATCCTCCACGACGATGGCATCCCCATCACCgtgcgttact ... tgacgagcagTCTGAGAAGATCGCCACCCTGGTGAAGGCGGCCAACATCAAGGTCGAGGCC
EST: gi|87004734|gb|CI306818.1|CI306818
EST:     CCTGCACGCTCGCCGCCCTCATCCTCCACGACGATGGCATCCCCATCACC                         TCTGAGAAGATCGCCACCCTGGTGAAGGCGGCCAACATCAAGGTCGAGGCC
genomic: CCTGCACGCTCGCCGCCCTCATCCTCCACGACGATGGCATCCCCATCACCgtgcgttact ... tgacgagcagTCTGAGAAGATCGCCACCCTGGTGAAGGCGGCCAACATCAAGGTCGAGGCC
EST: gi|86901148|gb|CI306337.1|CI306337
EST:     CCTGCACGCTCGCCGCCCTCATCCTCCACGACGATCGCATCCCCATCACC                         TCTGAGAAGATCGCCACCCTGGTGAAGGCGGCCAACATCAAGGTCGAGGCC
genomic: CCTGCACGCTCGCCGCCCTCATCCTCCACGACGATGGCATCCCCATCACCgtgcgttact ... tgacgagcagTCTGAGAAGATCGCCACCCTGGTGAAGGCGGCCAACATCAAGGTCGAGGCC
EST: gi|55433803|gb|CV730015.1|CV730015
EST:     CCTGCACGCTCGCCGCCCTCATCCTCCACGACGATGGCATCCCCATCACC                         TCTGAGAAGATCGCCACCCTGGTGAAGGCGGCCAACATCAAGGTCGAGGCC
genomic: CCTGCACGCTCGCCGCCCTCATCCTCCACGACGATGGCATCCCCATCACCgtgcgttact ... tgacgagcagTCTGAGAAGATCGCCACCCTGGTGAAGGCGGCCAACATCAAGGTCGAGGCC
EST: gi|38471074|gb|CF955205.1|CF955205
EST:     CCTGCACGCTCGCCGCCCTCATCCTCCACGACGATTGCATCCCCATCACC                         TCTGAGAAGATCGCCACCCTGGTGAAGGCGGCCAACATCAAGGTCGAGGCC
genomic: CCTGCACGCTCGCCGCCCTCATCCTCCACGACGATGGCATCCCCATCACCgtgcgttact ... tgacgagcagTCTGAGAAGATCGCCACCCTGGTGAAGGCGGCCAACATCAAGGTCGAGGCC
EST: gi|87012559|gb|CI307307.1|CI307307
EST:     CCTGCACGCTCGCCGCCCTCATCCTCCACGACGATGGCATCCCCATCACC                         TCTGAGAAGATCGCCACCCTGGTGAAGGCGGCCAACATCAAGGTCGAGGCC
genomic: CCTGCACGCTCGCCGCCCTCATCCTCCACGACGATGGCATCCCCATCACCgtgcgttact ... tgacgagcagTCTGAGAAGATCGCCACCCTGGTGAAGGCGGCCAACATCAAGGTCGAGGCC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ggatttggtgtgtgagattgattatttattttgttggtgatttggtgacgagcagTCTGAGAAGATCGCCACCCTGGTGAAGGCGGCCAACATCAAGGTCGAGGCCTACTGGCCCGGTCTCTTCGCCAAGCTCCTCGAGCACCGCAGCGTCGATG
               gattgat  putative branch site (score: 4)
              agattgattatttatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgcgttactacaccttcacccctatcttgattttgcttttcttggcttggggtggatttggtgtgtgagattgattatttattttgttggtgatttggtgacgagcagTCTGAGAAGATCGCCACCCTGGTGAAGGCGGCCAACATCAAGGTCGAGGCCTACTGGCCCGGTCTCTTCGCCAAGCTCCTCGAGCACCGCAGCGTCGATG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTCCTC