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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TCGCTGCTGCTCTTGCATATCGTAATCCATTTGTGCTCCCAATAGATAGGAAAGAAGAAGCTGATGCTGTCAAAAGATCATTTGCTGGTGACTCCTGCAGgtaattaatataatcttttctctgttccgtattgattccttttgtcttacctgtactaaaatatctttgtcaccatataatgcaaagaatgtgagtgtta...

Basic information

species Oryza sativa
transcript LOC_Os10g33275.1
intron # 14
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os10g33275.1 (Oryza sativa), 5'ss of exon 14
lower sequence: GRMZM2G399212_T01 (Zea mays), 5'ss of exon 15
TCGCTGCTGCTCTTGCATATCGTAATCCATTTGTGCTCCCAATAGATAGGAAAGAAGAAGCTGATGCTGTCAAAAGATCATTTGCTGGTGACTCCTGCAGgtaattaatataatcttttctctgttccgtattgattccttttgtcttacctgtacta-aaatatctttgtcaccatataatgcaaagaatgtgagtgtta
| ||||||||||| |||||||| |||||||||||||||||||||||||| |||||||||||||||||||||||||||||||||||||||||||| |||||||||||| ||||    ||   |   | ||     | ||||   | || |      ||| ||  ||  || |  | |   |    |     ||  | |  | 
TTGCTGCTGCTCTCGCATATCGAAATCCATTTGTGCTCCCAATAGATAGAAAAGAAGAAGCTGATGCTGTCAAAAGATCATTTGCTGGTGACTCGTGCAGgtaattattatagcaattctgccacttcgataaaaatcctaaggactgagggaacctataaggattcttttttcgaggcacctgattagttgatatttct-

upper sequence: LOC_Os10g33275.1 (Oryza sativa), 5'ss of exon 14
lower sequence: AT2G35920.1 (Arabidopsis thaliana), 5'ss of exon 13
TCGCTGCTGCTCTTGCATATCGTAATCCATTTGTGCTCCCAATAGATAGGAAAGAAGAAGCTGATGCTGTCAAAAGATCATTTGCTGGTGACTCCTGCAGgtaattaatataatcttttctctgttccgtattgattccttttgtcttacctgt-actaaaatatctttgtcaccatataatgcaaagaatgtgagtgtta-----
||||||||||||| || |||||||  ||||||||  | ||| || |||||||||| ||||||||||  | |||| |||  ||||||||||| |||||||||||    || ||        |    |   | || |  || |  |||   |  || |||    | | ||| | ||   | ||      | || |  |||||      
TCGCTGCTGCTCTGGCGTATCGTAGCCCATTTGTCTTACCATTAAATAGGAAAGAGGAAGCTGATGAAGCCAAACGATATTTTGCTGGTGATTCCTGCAGgtatgacatctataggcaaattacgtttat-ttcacaccgtcagtcaaccaggtcactgtgttctgtttcttacgg-aaaagatttggcatatatgtgttgtgcag

upper sequence: LOC_Os10g33275.1 (Oryza sativa), 5'ss of exon 14
lower sequence: Vv08s0032g01230.t01 (Vitis vinifera), 5'ss of exon 13
TCGCTGCTGCTCTTGCATATCGTAATCCATTTGTGCTCCCAATAGATAGGAAAGAAGAAGCTGATGCTGTCAAAAGATCATTTGCTGGTGACTCCTGCAGgt------aattaatataatctt----ttctctgttccgt-attgattccttttgtcttacctgtactaaaatatctttgtcaccatataatg--caaagaatgtgagtgtta
| || |||||||||||| ||||| | |||||||| || |||||| ||||||||||||||||| ||||||  |||||||| |||||||| || || |||||||      | |||| | | || |    ||||||| |  |  | |  |    | | |   |  | |||    || |  |||  |   |  |||   | |    | | | ||   
TTGCAGCTGCTCTTGCACATCGTGACCCATTTGTCCTTCCAATAAATAGGAAAGAAGAAGCTAATGCTGCAAAAAGATCCTTTGCTGGCGATTCTTGCAGgttcagttatttaacaaagtcatgctgttctctgctttgagaattgtagaatcttttcaaaatttacattgattttgttgataaggtgaaattttccacaccttttaatgcag

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|58611624|gb|CK039336.1|CK039336
EST:     GCTGATGCTGTCAAAAGATCATTTGCTGGTGACTCCTGCAG                         TGATCACATTGCTCTTGGGTAAGGCGTTCGAAGCATGGAAGGAAGCAAGAC
genomic: GCTGATGCTGTCAAAAGATCATTTGCTGGTGACTCCTGCAGgtaattaata ... atttttccagTGATCACATTGCTCTT-GTTAAGGCGTTCGAAGCATGGAAGGAAGCAAGAC
EST: gi|33381742|gb|CF197085.1|CF197085
EST:     AAAGAAGAAGCTGATGCTGTCAAAAGATCATTTGCTGGTGACTCCTGCAG                         TGATCACATTGCTCTTGTTAAGGCGTTCGANGCATG
genomic: AAAGAAGAAGCTGATGCTGTCAAAAGATCATTTGCTGGTGACTCCTGCAGgtaattaata ... atttttccagTGATCACATTGCTCTTGTTAAGGCGTTCGAAGCATG
EST: gi|29681906|gb|CB678181.1|CB678181
EST:     AAAGAAGAAGCTGATGCTGTCAAAAGATCATTTGCTGGTGACTCCTGCAG                         TGATCACATTGCTCTTGTTAAGGCGTTCGAAGCATGGAAGGAAGCAAGACG
genomic: AAAGAAGAAGCTGATGCTGTCAAAAGATCATTTGCTGGTGACTCCTGCAGgtaattaata ... atttttccagTGATCACATTGCTCTTGTTAAGGCGTTCGAAGCATGGAAGGAAGCAAGACG
EST: gi|58600773|gb|CK011301.1|CK011301
EST:     AAAGAAGAAGCTGATGCTGTCAAAAGATCATTTGCTGGTGACTCCTGCAG                         TGATCACATTGCTCTTGTTAAGGCGTTCGA
genomic: AAAGAAGAAGCTGATGCTGTCAAAAGATCATTTGCTGGTGACTCCTGCAGgtaattaata ... atttttccagTGATCACATTGCTCTTGTTAAGGCGTTCGA
EST: gi|218492590|gb|FG952568.1|FG952568
EST:     AAAGAAGAAGCTGATGCTGTCACAAGATCATTTGCTGGTGACTCCTGCAG                         TGATCACATTGCTCTTGTTAAGGCGTTCGAAGCATGGAAGGAAGCAAGACG
genomic: AAAGAAGAAGCTGATGCTGTCAAAAGATCATTTGCTGGTGACTCCTGCAGgtaattaata ... atttttccagTGATCACATTGCTCTTGTTAAGGCGTTCGAAGCATGGAAGGAAGCAAGACG
EST: gi|29675438|gb|CB671713.1|CB671713
EST:     AAAGAAGAAGCTGATGCTGTCAAAAGATCATTTGCTGGTGACTCCTGCAG                         TGATCACATTGCTCTTGTTAAGGCGTTCGAAGCATGGAAGGAAGCAAGACG
genomic: AAAGAAGAAGCTGATGCTGTCAAAAGATCATTTGCTGGTGACTCCTGCAGgtaattaata ... atttttccagTGATCACATTGCTCTTGTTAAGGCGTTCGAAGCATGGAAGGAAGCAAGACG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TCGCTGCTGCTCTTGCATATCGTAATCCATTTGTGCTCCCAATAGATAGGAAAGAAGAAGCTGATGCTGTCAAAAGATCATTTGCTGGTGACTCCTGCAGgtaattaatataatcttttctctgttccgtattgattccttttgtcttacctgtactaaaatatctttgtcaccatataatgcaaagaatgtgagtgtta

- - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGATCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG