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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...attcttagttttctgtagtactggccatttattgttcttgactctctaatttccatggctgaatctacaatgtcctacttgactcatcccttttcatcagGTCAGGAGTCAAGGTATATCAGATGATGGATCTGTCCACGACTTCAGTAGTGGCTGCTAAGGCCTACAAGTACAGAGCAGAATCACTTGTTAAGGACTAC

Basic information

species Oryza sativa
transcript LOC_Os01g56230.2
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g56230.5 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM5G825226_T03 (Zea mays), 3'ss of exon 1
-attcttagttttc----tgtagtactggccatttattgttcttg-actctctaatttccatggctgaatctacaatgtcctacttgactcatccctt---ttcatcagGTCAG-GAGTCAAGGTATATCAGATGATGGATCTGTCCACGACTTCAGTAGTGGCTGCTAAGGCCTACAAGTACAGAGCAGAATCACTTGTTAAGGACTAC
 ||||  |||| |     ||| ||  | |||||||||||| |||  |  | |||   |  |  | ||    |    | ||  ||||| ||| | |  |   ||||  ||||    ||||| ||  ||| ||||||||||| |||||||||||||||||  |||| ||||| || ||||| |||| |||||||||||||||||        
gattcaaagttgttgatatgtggtggtagccatttattgtgcttatatgccctatggttgaatggtgtgcttcatttatctgacttgtctctttcactagGTTCAGTAGGTTGTTGAGTCTAG--ATACCAGATGATGGACCTGTCCACGACTTCAGTGCTGGCAGCTAAAGCTTACAAATACAAAGCAGAATCACTTGTTA--------

upper sequence: LOC_Os01g56230.5 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM5G825226_T04 (Zea mays), 3'ss of exon 2
attcttagttttctgtagtactggccatttattgttcttg-actctctaatttccatggctgaatctacaatgtcctacttgactcatccctt---ttcatcagGTCAG-GAGTCAAGGTATATCAGATGATGGATCTGTCCACGACTTCAGTAGTGGCTGCTAAGGCCTACAAGTACAGAGCAGAATCACTTGTTAAGGACTAC
    ||  |  | ||| ||  | |||||||||||| |||  |  | |||   |  |  | ||    |    | ||  ||||| ||| | |  |   ||||  ||||    ||||| ||  ||| ||||||||||| |||||||||||||||||  |||| ||||| || ||||| |||| ||||||||||||||||||||| |  
-aagttgttgatatgtggtggtagccatttattgtgcttatatgccctatggttgaatggtgtgcttcatttatctgacttgtctctttcactaggttcagTAGGTTGTTGAGTCTAG--ATACCAGATGATGGACCTGTCCACGACTTCAGTGCTGGCAGCTAAAGCTTACAAATACAAAGCAGAATCACTTGTTAAGGAGT--
















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|29660431|gb|CB656706.1|CB656706
EST:     GAGGCATCCTTCCACCGCCGACCTCCACCTCGGCCGGAATAGAACTGAAG                         GTCAGGAGTCAAGGTATATCAGATGATGGATCTGTCCACGACTTCAGTAGT
genomic: GAGGCATCCTTCCACCGCCGACCTCCACCTCGGCCGGAATAGAACTGAAGgtattcgttc ... ttttcatcagGTCAGGAGTCAAGGTATATCAGATGATGGATCTGTCCACGACTTCAGTAGT
EST: gi|88732948|gb|CI756125.1|CI756125
EST:     AGGCATCCTTCCACCGCCGACCTCCACCTCGGCCCGGAATAGAACTGAAG                         GTCAGGAGTCAAGGTATATCAGATGATGGATCTGTCCACGACTTCAGTACT
genomic: AGGCATCCTTCCACCGCCGACCTCCACCTCGGCC-GGAATAGAACTGAAGgtattcgttc ... ttttcatcagGTCAGGAGTCAAGGTATATCAGATGATGGATCTGTCCACGACTTCAGTAGT
EST: gi|88578737|gb|CI687685.1|CI687685
EST:     GAGGCATCCTTCCACCGCCGACCTCCACCTCGGCCGGAATAGAACTGAAG                         GTCAGGAGTCAAGGTATATCAGATGATGGATCTGTCCACGACTTCAGTAGT
genomic: GAGGCATCCTTCCACCGCCGACCTCCACCTCGGCCGGAATAGAACTGAAGgtattcgttc ... ttttcatcagGTCAGGAGTCAAGGTATATCAGATGATGGATCTGTCCACGACTTCAGTAGT
EST: gi|15008478|gb|AU222866.1|AU222866
EST:     GAGGCATCCTTCCACCGCCGACCTCCACCTCGGNCGGAATAGAACTGAAG                         GTCAGGAGTCAAGGTATATCAGATGATGGATCTGTCCACGACTTCAGTAGT
genomic: GAGGCATCCTTCCACCGCCGACCTCCACCTCGGCCGGAATAGAACTGAAGgtattcgttc ... ttttcatcagGTCAGGAGTCAAGGTATATCAGATGATGGATCTGTCCACGACTTCAGTAGT
EST: gi|300215972|gb|HO088598.1|HO088598
EST:     GAGGCATCCTTCCACCGCCGACCTCCACCTCGGCCGGAATAGAACTGAAG                         GTCAGGAGTCAAGGTATATCAGATGATGGATCTGTCCACGACTTCAGTAGT
genomic: GAGGCATCCTTCCACCGCCGACCTCCACCTCGGCCGGAATAGAACTGAAGgtattcgttc ... ttttcatcagGTCAGGAGTCAAGGTATATCAGATGATGGATCTGTCCACGACTTCAGTAGT
EST: gi|88314263|gb|CI602595.1|CI602595
EST:     GAGGCATCCTTCCACCGCCGACCTCCACCTCGGCCGGAATAGAACTG-A-                         ---AGGAGTCAAGGTATATCAGATGATGGATCTGTCCACGACTTCAGTAGT
genomic: GAGGCATCCTTCCACCGCCGACCTCCACCTCGGCCGGAATAGAACTGAAGgtattcgttc ... ttttcatcagGTCAGGAGTCAAGGTATATCAGATGATGGATCTGTCCACGACTTCAGTAGT
EST: gi|88337687|gb|CI632189.1|CI632189
EST:     GAGGCATCCTTCCACCGCCGACCTCCACCTCGGCCGGAATAGAACTGAAG                         GTCAGGAGTCAAGGTATATCAGATGATGGATCTGTCCACGACTTCAGTAGT
genomic: GAGGCATCCTTCCACCGCCGACCTCCACCTCGGCCGGAATAGAACTGAAGgtattcgttc ... ttttcatcagGTCAGGAGTCAAGGTATATCAGATGATGGATCTGTCCACGACTTCAGTAGT
EST: gi|38468775|gb|CF952906.1|CF952906
EST:     GAGGCATCCTTCCACCGCCGAACTCCACCTCGGCCGGAATAGAACTGAAG                         GTCAGGAGTCAAGGTATATCAGATGATGGATCTGTCCACGACTTCAGTAGT
genomic: GAGGCATCCTTCCACCGCCGACCTCCACCTCGGCCGGAATAGAACTGAAGgtattcgttc ... ttttcatcagGTCAGGAGTCAAGGTATATCAGATGATGGATCTGTCCACGACTTCAGTAGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctaatttccatggctgaatctacaatgtcctacttgactcatcccttttcatcagGTCAGGAGTCAAGGTATATCAGATGATGGATCTGTCCACGACTTCAGTAGTGGCTGCTAAGGCCTACAAGTACAGAGCAGAATCACTTGTTAAGGACTAC
                                     ctcatcccttttcatc  CT-rich tract
                                             ttttcat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
attcttagttttctgtagtactggccatttattgttcttgactctctaatttccatggctgaatctacaatgtcctacttgactcatcccttttcatcagGTCAGGAGTCAAGGTATATCAGATGATGGATCTGTCCACGACTTCAGTAGTGGCTGCTAAGGCCTACAAGTACAGAGCAGAATCACTTGTTAAGGACTAC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCAG