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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TACTTGACGCCAATCTCAATCCTAAGATCTCGGATTTCGGGCTAGCCAAACTTTATGATGACAAGATGACTCATGTTAGCACAAAAGTTGCTGGTACATTgtaagtatattccatctttgcattttttcttttaaaaaaaataactattttaatggcatgcaagaaataagaggacatcctcttaaggggcaaaaaaaag...

Basic information

species Oryza sativa
transcript LOC_Os04g52640.3
intron # 22
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os04g52640.1 (Oryza sativa), 5'ss of exon 22
lower sequence: GRMZM2G155837_T02 (Zea mays), 5'ss of exon 18
TACTTGACGCCAATCTCAATCCTAAGATCTCGGATTTCGGGCTAGCCAAACTTTATGATGACAAGATGACTCATGTTAGCACAAAAGTTGCTGGTACATTgtaagtatattccatctttgcattttttcttttaaaaaaaataactattttaatggcatgcaagaaataagaggacatcctcttaaggggcaaaaaaaag
| ||||| || |||||||| ||||||||||||||||||||||| ||||||||||| |||||||||| ||||||||| ||||| |||||||| ||||||||||||||  ||| |    ||||     | || |  |   || | | |  || ||  |   ||  |    ||      |  ||  |  |  |          
TGCTTGATGCAAATCTCAACCCTAAGATCTCGGATTTCGGGCTCGCCAAACTTTACGATGACAAGAAGACTCATGTCAGCACCAAAGTTGCGGGTACATTgtaagtgcatttccatattgc----ctcctctacacccaagttatt--ttcaaatgtgagctggtgtcaatttcttactcttctgtgaag----------

upper sequence: LOC_Os04g52640.1 (Oryza sativa), 5'ss of exon 22
lower sequence: GRMZM2G126858_T02 (Zea mays), 5'ss of exon 20
TACTTGACGCCAATCTCAATCCTAAGATCTCGGATTTCGGGCTAGCCAAACTTTATGATGACAAGATGACTCATGTTAGCACAAAAGTTGCTGGTACATTgtaagtatattccatctttgcattttttcttttaaaaaaaataactattttaatggcatgcaagaaataagaggacatcctcttaagg--ggcaaaaaaaag
||||||| |||| | | || |||||||| |||||||||||||| |||||||||||||| || || | ||| ||||||||||||||||||||||||||||||||||   || |          | |   |   ||     ||||| || |||      |||   ||  |||  | |  |||| || |    |        |||
TACTTGATGCCACTTTGAACCCTAAGATTTCGGATTTCGGGCTCGCCAAACTTTATGACGATAAAAAGACACATGTTAGCACAAAAGTTGCTGGTACATTgtaagggcatac-------atgtctccccccatatgtttaataattagtttccactaatgtctgagctaatggaagttccttttcactttgatttcttgaag

upper sequence: LOC_Os04g52640.1 (Oryza sativa), 5'ss of exon 22
lower sequence: GRMZM2G031536_T01 (Zea mays), 5'ss of exon 7
TACTTGACGCCAATCTCAATCCTAAGATCTCGGATTTCGGGCTAGCCAAACTTTATGATGACAAGATGACTCATGTTAGCACAAAAGTTGCTGGTACATTgtaagtatattccatctttgcattttttcttttaaaaaaaataactattttaatggcatgcaagaaataagaggacatcctcttaaggggcaaaaaaaag
| |||||||| ||| |||| ||||||||||| ||||| ||||| |||||||||||||| ||||||| ||||||||| |||||||||||||| ||||||||||||||| ||| |    |||     |  |||||| ||      | |||||| |     || |  ||     |   | | |||||  | |           
TGCTTGACGCAAATTTCAACCCTAAGATCTCAGATTTTGGGCTCGCCAAACTTTATGACGACAAGAAGACTCATGTCAGCACAAAAGTTGCGGGTACATTgtaagtacatttccatcttg-----tgccttttacaagtgcatattattttcaca-tgtgaactaatgccaatttcttgctcttctgtgaag--------

upper sequence: LOC_Os04g52640.1 (Oryza sativa), 5'ss of exon 22
lower sequence: GRMZM2G126858_T01 (Zea mays), 5'ss of exon 20
TACTTGACGCCAATCTCAATCCTAAGATCTCGGATTTCGGGCTAGCCAAACTTTATGATGACAAGATGACTCATGTTAGCACAAAAGTTGCTGGTACATTgtaagtatattccatctttgcattttttcttttaaaaaaaataactattttaatggcatgcaagaaataagaggacatcctcttaaggggcaaaaaaaag----------------------------------------------------------------------------------
||||||| |||| | | || |||||||| |||||||||||||| |||||||||||||| || || | ||| ||||||||||||||||||||||||||||||||||   || |     |  |    | | ||| | ||  | |  | |   ||||| |       |   |||      | | |||      |   ||   |                                                                                  
TACTTGATGCCACTTTGAACCCTAAGATTTCGGATTTCGGGCTCGCCAAACTTTATGACGATAAAAAGACACATGTTAGCACAAAAGTTGCTGGTACATTgtaagggcatacatgtctccccccatatgtttaataattagtttccac--taatgtctgagctaatggaagttccttttcactttgatttcttgaagtggctatctttcacctgagtacgccatgagaggtcacatgactgagaaagttgatatttttgcttttggtgtggtcatgttggag

upper sequence: LOC_Os04g52640.1 (Oryza sativa), 5'ss of exon 22
lower sequence: Vv12s0055g00640.t01 (Vitis vinifera), 5'ss of exon 1
TACTTGACGCCAATCTCAATCCTAAGATCTCGGATTTCGGGCTAGCCAAACTTTATGATGACAAGATGACTCATGTTAGCACAAAAGTTGCTGGTACATTgtaagtatatt-----------ccatctttgcattttttcttttaaaaaaaataactattttaatggcatgcaagaaataagaggacatcctcttaaggggcaaaaaaaag
| ||||||    |||||||||||||||| || ||||| ||  | |||||||| ||||||||||  ||||||||  | |||||    || || || ||| ||||||    |            || |   | | || ||| || |          | | |||| ||   || |   || |   |       || ||| |   |  ||  |  
TGCTTGACTATTATCTCAATCCTAAGATTTCAGATTTTGGTTTGGCCAAACTGTATGATGACACAATGACTCACATAAGCACCCGTGTGGCAGGCACAATgtaagatcctcaaaagtcaaggcccttagttccttgtttattctcttttttgggatttttttcatt-tatccccaaagtttaaaactgggcttttatgttactgaagtag-

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|29661115|gb|CB657390.1|CB657390
EST:     CTTTATGATGACAAGATGACTCATGTTAGCACAAAAGTTGCTGGTACATT                         TGGTTATCTTGCACCTGAGTACGCCATGAGAGGACATATGACTGAGAAAGT
genomic: CTTTATGATGACAAGATGACTCATGTTAGCACAAAAGTTGCTGGTACATTgtaagtatat ... ctctttccagTGGTTATCTTGCACCTGAGTACGCCATGAGAGGACATATGACTGAGAAAGT




















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TACTTGACGCCAATCTCAATCCTAAGATCTCGGATTTCGGGCTAGCCAAACTTTATGATGACAAGATGACTCATGTTAGCACAAAAGTTGCTGGTACATTgtaagtatattccatctttgcattttttcttttaaaaaaaataactattttaatggcatgcaagaaataagaggacatcctcttaaggggcaaaaaaaag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG