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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tctacccaatatgctatctttcttataccttaagagcatatatgctggactgttgttttcttcaaaatttatatatgctccatatttgtttatgctgtagGTTTTCTTAACAAAACATTACAGGAATAGGCGGTGTAACGACCCAGATTTTTTCCTTGATTTTGAAGAGATATATGTTATTGACTCGAAAGCAAGGTCAA

Basic information

species Oryza sativa
transcript LOC_Os11g01890.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os11g01890.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM5G829928_T02 (Zea mays), 3'ss of exon 3
tctacccaatatgctatctttcttatacct--taagagcatatatgctggactgt---tgttttcttcaaaattta---tatatgctccatatttgtttatgctgtagGTTTTCTTAACAAAACATTACAGGAATAGGCGGTGTAACGACCCAGATTTTTTCCTTGATTTTGAAGAGATATATGTTATTGACTCGAAAGCAAGGTCAA
        || |||  |  |  ||    ||  ||||||      ||  |   |||   |||||| ||  | ||| |    |||||||  || ||  ||    | | |||||||||| || || || ||||| || |||||   | | |||||||||||||| ||||||||||| ||||| |||||||||||||||| | |||||||||
--------atgtgcattaatgtttgacactggtaagaggccccttgtggccttgtgagtgtttttttttatattcagaacatatgctgtattttgtttcgcaccgcagGTTTTCTTGACCAAGCACTACAGAAACAGGCGCGCTGATGACCCAGATTTTTTTCTTGATTTTGAGGAGATCTATGTTATTGACTCGAGAACAAGGTCAA

upper sequence: LOC_Os11g01890.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GLYMA06G12370.1 (Glycine max), 3'ss of exon 3
---tctacccaatatgctatctttcttataccttaagagcatatatgctggactgttgttttcttcaaaatttatatatgctccatatttgtttatgctgtagGTTTTCTTAACAAAACATTACAGGAATAGGCGGTGTAACGACCCAGATTTTTTCCTTGATTTTGAAGAGATATATGTTATTGACTCGAAAGCAAGGTCAA
   || |  || | |   |      |||   | ||    |  | ||| ||  || | || ||    | ||| | |   |  |     ||  ||  || |  |||| | ||| |||||||| ||||  ||| |  ||      ||  | || ||| | ||||||||||||||||| ||||||||||| || ||| | | |||||
aagtccaatcattgtaaaaaagaaattaa--catagttactgaaatgatgctct-tggtctttgctagaatgtctccctcataggacttctttcctgttacagGTGTACTTGACAAAACACTACAAAAATCGAAGGAAGGGTGATTCTGAGTTTGTGCTTGATTTTGAAGAGATTTATGTTATTGATTCCAAATCCAAGTCAA

upper sequence: LOC_Os11g01890.1 (Oryza sativa), 3'ss of exon 3
lower sequence: AT1G21600.2 (Arabidopsis thaliana), 3'ss of exon 3
tctacccaatatgctatctttcttat-accttaagagcatatatgctggactgttgttttcttcaaaatttat-atatgctccatatttgtttatgctgtagGTTTTCTTAACAAAACATTACAGGAATAGGCGGTGTAACGACCCAGATTTTTTCCTTGATTTTGAAGAGATATATGTTATTGACTCGAAAGCAAGGTCAA
  |     |     ||    |   || | |   | |  |  || | |     |||    | |   | |   ||  | | |  | | ||| ||| |  || |||||||||| |||||||||||| |||| ||  ||   ||||| ||||| ||| | || ||| |||||||||||||||||||||| || ||  ||| |||||
-gttttttaagcattaaggatgagatcaacacgaaactactta-gtttagtagttacagtttctgatacaaattgtcttcatcgtgtttattttttatgcagGTTTTCTTGACAAAACATTACCGGAACAGAAGGACAAACGATCCAGAATTTGTGCTAGATCTTGAAGAGATATATGTTATTGATTCCAAGACAAAGTCAA

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|29662883|gb|CB659158.1|CB659158
EST:     TTGAGCATTTGCGTGATCCCCTATACAAGACAGAAAGGGAGATCATGAAG                         GTTTTCTTAACAAAACATTACAGGAATAGGCGGTGTAACGACCCAGATTTT
genomic: TTGAGCATTTGCGTGATCCCCTATACAAGACAGAAAGGGAGATCATGAAGgtatgtgtga ... tatgctgtagGTTTTCTTAACAAAACATTACAGGAATAGGCGGTGTAACGACCCAGATTTT
EST: gi|87025956|gb|CI257114.1|CI257114
EST:     GATCCCCTATACAAGACAGAAAGGGAGATCATGAAG                         GTTTTCTTAACAAAACATTACAGGAATAGGCGGTGTAACGACCCAGATTTT
genomic: GATCCCCTATACAAGACAGAAAGGGAGATCATGAAGgtatgtgtga ... tatgctgtagGTTTTCTTAACAAAACATTACAGGAATAGGCGGTGTAACGACCCAGATTTT
EST: gi|29662875|gb|CB659150.1|CB659150
EST:     TTGAGCATTTGCGTGATCCCCTATACAAGACAGAAAGGGAGATCATGAAG                         GTTTTCTTAACAAAACATTACAGGAATAGGCGGTGTAACGACCCAGATTTT
genomic: TTGAGCATTTGCGTGATCCCCTATACAAGACAGAAAGGGAGATCATGAAGgtatgtgtga ... tatgctgtagGTTTTCTTAACAAAACATTACAGGAATAGGCGGTGTAACGACCCAGATTTT
EST: gi|58603685|gb|CK014213.1|CK014213
EST:     TTGAGCATTTGCGTGATCCCCTATACAAGACAGAAAGGGAGATCATGAAG                         GTTTTCTTAACGAAACATTACAGGAATAGGCGGTGTAACGACCCAGATTTT
genomic: TTGAGCATTTGCGTGATCCCCTATACAAGACAGAAAGGGAGATCATGAAGgtatgtgtga ... tatgctgtagGTTTTCTTAACAAAACATTACAGGAATAGGCGGTGTAACGACCCAGATTTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tggactgttgttttcttcaaaatttatatatgctccatatttgtttatgctgtagGTTTTCTTAACAAAACATTACAGGAATAGGCGGTGTAACGACCCAGATTTTTTCCTTGATTTTGAAGAGATATATGTTATTGACTCGAAAGCAAGGTCAA
                                       tttgttt  CT-rich tract
       ttgttttcttcaaaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tctacccaatatgctatctttcttataccttaagagcatatatgctggactgttgttttcttcaaaatttatatatgctccatatttgtttatgctgtagGTTTTCTTAACAAAACATTACAGGAATAGGCGGTGTAACGACCCAGATTTTTTCCTTGATTTTGAAGAGATATATGTTATTGACTCGAAAGCAAGGTCAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCAAG
- - - - -tatgcta
- - - - - - - - - - - - - - - - - - - - tatgctg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgctcca