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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttttctcttcttgctggtctgtacattttttaagcatatctgcgtgcattcctaattaattgtgattgtagtatatctgatgaattaccatattattcagAATGAAATGAATGAACGAGAGCTGTCTGCCTTGAAAGCTGCTATTAAGTGTATCGAGGAGCACAAACTTGATGAGAAATATCCGATTGACCTGCTTCAGA

Basic information

species Oryza sativa
transcript LOC_Os09g07360.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os09g07360.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G160316_T02 (Zea mays), 3'ss of exon 3
ttttctcttcttgctggtctgtacattttttaagcatatctgcgtgcat-tcctaattaattgtgattgtagtatatctgatgaa--ttaccatattattcagAATGAAATGAATGAACGAGAGCTGTCTGCCTTGAAAGCTGCTATTAAGTGTATCGAGGAGCACAAACTTGATGAGAAATATCCGATTGACCTGCTTCAGA
  ||   |      ||  ||   |       ||  ||    |  || |  |  ||||  || ||  ||   ||  | ||| |||   | ||  |  | |||||||||| ||||||||||| ||| | |||||  ||||| |||  |||||||| || || ||||||||||||||  || | || ||  | || |  |||||||
--ttagttcaaaaatgaacta-gcgagcgacaaatattcaagaatggaggtagtaatacatagtatttactgttaaactgttgatgctcacttttgttttcagAATGAGATGAATGAACGTGAGTTATCTGCGCTGAAATCTGTCATTAAGTGCATTGAAGAGCACAAACTTGAGCAGCAGTACCCTGTGGATCCACTTCAGA
















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|58674976|gb|CK063663.1|CK063663
EST:     AAGACTGGAAAGATATCTCTGCAAGTACAG                         AATGAAATGAATGAACGAGAGCTGTCTGCCTTGAAAGCTGCTATTAAGTGT
genomic: AAGACTGGAAAGATATCTCTGCAAGTACAGgtgcactttt ... tattattcagAATGAAATGAATGAACGAGAGCTGTCTGCCTTGAAAGCTGCTATTAAGTGT
EST: gi|33804268|gb|CF328008.1|CF328008
EST:     TCAAGAGTGTGCCACATTTCAAGACTGGAAAGATATCTCTGCAAGTACAG                         AATGAAATGAATG
genomic: TCAAGAGTGTGCCACATTTCAAGACTGGAAAGATATCTCTGCAAGTACAGgtgcactttt ... tattattcagAATGAAATGAATG
EST: gi|29615074|gb|CB620087.1|CB620087
EST:     TCAAGAGTGTGCCACATTTCAAGACTGGAAAGATATCTCTGCAAGTACAG                         AATGAAATGAATGAACGAGAGCTGTCTGCCTTGAAAGCTGCTATTAAGTGT
genomic: TCAAGAGTGTGCCACATTTCAAGACTGGAAAGATATCTCTGCAAGTACAGgtgcactttt ... tattattcagAATGAAATGAATGAACGAGAGCTGTCTGCCTTGAAAGCTGCTATTAAGTGT
EST: gi|66923856|gb|CX110704.1|CX110704
EST:     TCAAGAGTGTGCCACATTTCAAGACTGGAAAGATATCTCTGCAAGTACAG                         AATGAAATGAATGAACGAGAGCTGTCTGCCTTGAAAGCTGCTATTAAGTGT
genomic: TCAAGAGTGTGCCACATTTCAAGACTGGAAAGATATCTCTGCAAGTACAGgtgcactttt ... tattattcagAATGAAATGAATGAACGAGAGCTGTCTGCCTTGAAAGCTGCTATTAAGTGT
EST: gi|29684197|gb|CB680472.1|CB680472
EST:     TCAAGAGTGTGCCACATTTCAAGACTGGAAAGATATCTCTGCAAGTACAG                         AATGAAATGAATGAACGAGAGCTGTCTGCCTTGAAAGCTGTTATTAAGTGT
genomic: TCAAGAGTGTGCCACATTTCAAGACTGGAAAGATATCTCTGCAAGTACAGgtgcactttt ... tattattcagAATGAAATGAATGAACGAGAGCTGTCTGCCTTGAAAGCTGCTATTAAGTGT
EST: gi|58683783|gb|CK072470.1|CK072470
EST:     TCAAGAGTGTGCCACATTTCAAGACTGGAAAGATATCTCTGCAAGTACAG                         AATGAAATGAATGAACGAGAGCTGTCTGCCTTGAAAGCTGCTATTAAGTGT
genomic: TCAAGAGTGTGCCACATTTCAAGACTGGAAAGATATCTCTGCAAGTACAGgtgcactttt ... tattattcagAATGAAATGAATGAACGAGAGCTGTCTGCCTTGAAAGCTGCTATTAAGTGT
EST: gi|15072272|gb|D15310.2|D15310
EST:     TCAAGAGTGTGCCACATTTCAAGACTGGAAAGATATCTCTGCAAGTNCAG                         AATGAAATGNATGAACGAGAGCTGTCTGCCTTGAAAGCTGCTATTAAGTGT
genomic: TCAAGAGTGTGCCACATTTCAAGACTGGAAAGATATCTCTGCAAGTACAGgtgcactttt ... tattattcagAATGAAATGAATGAACGAGAGCTGTCTGCCTTGAAAGCTGCTATTAAGTGT
EST: gi|33793495|gb|CF322631.1|CF322631
EST:     TCAAGAGTGTGCCACATTTCAAGACTGGAAAGATATCTCTGCAAGTACAG                         AATGAAATGAATGAACGAGAGCTGTCTGCCTTGAAAGCTGCTATTAAGTGT
genomic: TCAAGAGTGTGCCACATTTCAAGACTGGAAAGATATCTCTGCAAGTACAGgtgcactttt ... tattattcagAATGAAATGAATGAACGAGAGCTGTCTGCCTTGAAAGCTGCTATTAAGTGT
EST: gi|163926844|gb|EG710188.1|EG710188
EST:     TCAAGAGTGTGCCACATTTCAAGACTGGAAAGATATCTCTGCAAGTACAG                         AATGAAATGAATGAACGAGAGCTGTCTGCCTTGAAAGCTGCTATTAAGTGT
genomic: TCAAGAGTGTGCCACATTTCAAGACTGGAAAGATATCTCTGCAAGTACAGgtgcactttt ... tattattcagAATGAAATGAATGAACGAGAGCTGTCTGCCTTGAAAGCTGCTATTAAGTGT
EST: gi|163928758|gb|EG709711.1|EG709711
EST:     TCAAGAGTGTGCCACATTTCAAGACTGGAAAGATATCTCTGCAAGTACAG                         AATGAAATGAATGAACGAGAGCTGTCTGCCTTGAAAGCTGCTATTAAGTGT
genomic: TCAAGAGTGTGCCACATTTCAAGACTGGAAAGATATCTCTGCAAGTACAGgtgcactttt ... tattattcagAATGAAATGAATGAACGAGAGCTGTCTGCCTTGAAAGCTGCTATTAAGTGT
EST: gi|29616279|gb|CB621291.1|CB621291
EST:     TCAAGAGTGTGCCACATTTCAAGACTGGAAAGATATCTCTGCAAGTACAG                         AATGAAATGAATGAACGAGAGCTGTCTGCCTTGAAAGCTGCTATTAAGTGT
genomic: TCAAGAGTGTGCCACATTTCAAGACTGGAAAGATATCTCTGCAAGTACAGgtgcactttt ... tattattcagAATGAAATGAATGAACGAGAGCTGTCTGCCTTGAAAGCTGCTATTAAGTGT
EST: gi|29626988|gb|CB631999.1|CB631999
EST:     TCAAGAGTGTGCCACATTTCAAGACTGGAAAGATATCTCTGCAAGTACAG                         AATGAAATGAATGAACGAGAGCTGTCTGCCTTGAAAGCTGCTATTAAGTGT
genomic: TCAAGAGTGTGCCACATTTCAAGACTGGAAAGATATCTCTGCAAGTACAGgtgcactttt ... tattattcagAATGAAATGAATGAACGAGAGCTGTCTGCCTTGAAAGCTGCTATTAAGTGT
EST: gi|29621932|gb|CB626943.1|CB626943
EST:     TCAAGAGTGTGCCACATTTCAAGACTGGAAAGATATCTCTGCAAGTACAG                         AATGAAATGAATGAACGAGAGCTGTCTGCCTTGAAAGCTGCTATTAAGTGT
genomic: TCAAGAGTGTGCCACATTTCAAGACTGGAAAGATATCTCTGCAAGTACAGgtgcactttt ... tattattcagAATGAAATGAATGAACGAGAGCTGTCTGCCTTGAAAGCTGCTATTAAGTGT
EST: gi|29636947|gb|CB641956.1|CB641956
EST:     TCAAGAGTGTGCCACATTTCAAGACTGGAAAGATATCTCTGCAAGTACAG                         AATGAAATGAATGAACGAGAGCTGTCTGCCTTGAAAGCTGCTATTAAGTGT
genomic: TCAAGAGTGTGCCACATTTCAAGACTGGAAAGATATCTCTGCAAGTACAGgtgcactttt ... tattattcagAATGAAATGAATGAACGAGAGCTGTCTGCCTTGAAAGCTGCTATTAAGTGT
EST: gi|33795483|gb|CF323611.1|CF323611
EST:     CACATTTCAAGACTGGAAAGATATCTCTGCAAGTACAG                         AATGAAATGAATGAACGAGAGCTGTCTGCCTTGAAAGCTGCTATTAAGTGT
genomic: CACATTTCAAGACTGGAAAGATATCTCTGCAAGTACAGgtgcactttt ... tattattcagAATGAAATGAATGAACGAGAGCTGTCTGCCTTGAAAGCTGCTATTAAGTGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gcattcctaattaattgtgattgtagtatatctgatgaattaccatattattcagAATGAAATGAATGAACGAGAGCTGTCTGCCTTGAAAGCTGCTATTAAGTGTATCGAGGAGCACAAACTTGATGAGAAATATCCGATTGACCTGCTTCAGA
       taattaattgtgatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttttctcttcttgctggtctgtacattttttaagcatatctgcgtgcattcctaattaattgtgattgtagtatatctgatgaattaccatattattcagAATGAAATGAATGAACGAGAGCTGTCTGCCTTGAAAGCTGCTATTAAGTGTATCGAGGAGCACAAACTTGATGAGAAATATCCGATTGACCTGCTTCAGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCA