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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CTAATCTATCACAATTTACCGAAAGATATTGCAAACAGGCATGTGCTGTTGTTGGATCCCATACTGGGAACAGgtatgttgatgattctcacatatccttcctgttgttacatgaattttgttcttgtgctcactggagcacttctgcctccacctatctcatgtaaaagaga...

Basic information

species Oryza sativa
transcript LOC_Os02g17320.2
intron # 13
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g17320.1 (Oryza sativa), 5'ss of exon 13
lower sequence: GRMZM2G034143_T02 (Zea mays), 5'ss of exon 14
CTAATCTATCACAATTTACCGAAAGATATTGCAAACAGGCATGTGCTGTTGTTGGATCCCATACTGGGAACAGgtatgttgatgattc----tcac------atatccttcctgttgttacatgaattttgt---------------tcttgtgctcactggagcacttctgcctccacctatctcatgtaaaagaga----------------------------------------------------------------------
|| |||||||| |||||||| |||||||||||||| |||||||| ||  ||||||| |||||| |||||||||||   ||  | ||||    ||||        | |     |  ||| |  | ||| || |               ||||     |||  ||| ||   |   |     ||  | | | |||| ||                                                                       
CTCATCTATCAAAATTTACCAAAAGATATTGCAAATAGGCATGTTCTTCTGTTGGACCCCATATTGGGAACAGgttcattttttattcctgttcactggacggcaccacctttcatgtcaattaaatcttataaaattttcaatctctcttccatgcacatgagtaccattttgtttgattacatta-gcaaaacagcactgcactagaagttacatttttttaatatttcttgttatctcattcagtctccattttatcctgatcag

upper sequence: LOC_Os02g17320.1 (Oryza sativa), 5'ss of exon 13
lower sequence: GRMZM2G169462_T01 (Zea mays), 5'ss of exon 12
CTAATCTATCACAATTTACCGAAAGATATTGCAAACAGGCATGTGCTGTTGTTGGATCCCATACTGGGAACAGgtatgttgatgattctcacatatccttcctgttgttacatgaattttgttcttgtgctcactggagcacttctgcctccacctatctcatgtaaaagaga------
|| |||||||| |||||||| |||||||||||||| |||||||| ||| ||||||| |||||| |||||||||||| |||     || | |    |  |  |||      ||  | ||||  | |       | |  |  |   || |      || |  || | | | |||       
CTCATCTATCAAAATTTACCAAAAGATATTGCAAATAGGCATGTTCTGCTGTTGGACCCCATATTGGGAACAGgtacgtt-----tttttattcctgttctctgg-acggcaccacttttcatgtcaattaaattttataaaaacttcaaatcactcttccacgcacatgagtaccatc

upper sequence: LOC_Os02g17320.1 (Oryza sativa), 5'ss of exon 13
lower sequence: GRMZM2G034143_T03 (Zea mays), 5'ss of exon 14
CTAATCTATCACAATTTACCGAAAGATATTGCAAACAGGCATGTGCTGTTGTTGGATCCCATACTGGGAACAGgtatgttgatgattctcacatatccttcctgtt-gttacatgaattttgttcttgtgctcactggagcacttctgcctccacctatctcatgtaaaagaga
|| |||||||| |||||||| |||||||||||||| |||||||| ||  ||||||| |||||| |||||||||||             |||  | |  ||||||||   |  | |        | |  ||   | |  | |   |     |                       
CTCATCTATCAAAATTTACCAAAAGATATTGCAAATAGgcatgttcttctgttggaccccatattgggaacaggt-------------tcattttttattcctgttcactggacggcaccacctttcatgtcaattaaatcttataaaatt-----------------------

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|29633369|gb|CB638378.1|CB638378
EST:     AGATATTGCAAACAGGCATGTGCTGTTGTTGGATCCCATACTGGGAACAG                         GAAATTCAGCTGTTCAAGCTATATCTCTACTCTTGAAAAAGGGTGTACAGG
genomic: AGATATTGCAAACAGGCATGTGCTGTTGTTGGATCCCATACTGGGAACAGgtatgttgat ... atcataccagGAAATTCAGCTGTTCAAGCTATATCTCTACTCTTGAAAAAGGGTGTACAGG
EST: gi|87037876|gb|CI192498.1|CI192498
EST:     AGATATTGCAAACAGGCATGTGCTGTTGTTGGATCCCATACTGGGAACAG                         GAAATTCAGCTGTTCAAGCTATATCTCTACTCTTGAAAAAGGGTGTACAGG
genomic: AGATATTGCAAACAGGCATGTGCTGTTGTTGGATCCCATACTGGGAACAGgtatgttgat ... atcataccagGAAATTCAGCTGTTCAAGCTATATCTCTACTCTTGAAAAAGGGTGTACAGG
EST: gi|3760815|gb|C98069.1|C98069
EST:     AGATATTGCAAACAGGCATGTGCTGTTGTTGGATCCCATACTGGGAACAG                         GAAATTCAGCTGTTCAAGCTATATCTCTACTCTTGAAAAAGGGTGTACAGG
genomic: AGATATTGCAAACAGGCATGTGCTGTTGTTGGATCCCATACTGGGAACAGgtatgttgat ... atcataccagGAAATTCAGCTGTTCAAGCTATATCTCTACTCTTGAAAAAGGGTGTACAGG
EST: gi|87029276|gb|CI276544.1|CI276544
EST:     AGATATTGCAAACAGGCATGTGCTGTTGTTGGATCCCATACTGGGAACAG                         GAAATTCAGCTGTTCAAGCTATATCTCTACTCTTGAAAAAGGGTGTACAGG
genomic: AGATATTGCAAACAGGCATGTGCTGTTGTTGGATCCCATACTGGGAACAGgtatgttgat ... atcataccagGAAATTCAGCTGTTCAAGCTATATCTCTACTCTTGAAAAAGGGTGTACAGG
EST: gi|88233330|gb|CI233179.1|CI233179
EST:     AGATATTGCAAACAGGCATGTGCTGTCGTTGGATCCCATACTGGGAACAG                         GAAATTCAGCTGTTCAAGCTATATCTCTACTCTTGAAAAAGGGTGTACAGG
genomic: AGATATTGCAAACAGGCATGTGCTGTTGTTGGATCCCATACTGGGAACAGgtatgttgat ... atcataccagGAAATTCAGCTGTTCAAGCTATATCTCTACTCTTGAAAAAGGGTGTACAGG
EST: gi|86498530|gb|CI141163.1|CI141163
EST:     AGATATTGCAAACAGGCATGTGCTGTTGTTGGATCCCATACTGGGAACAG                         GAAATTCAGCTGTTCAAGCTATATCTCTACTCTTGAAAAAGGGTGTACAGG
genomic: AGATATTGCAAACAGGCATGTGCTGTTGTTGGATCCCATACTGGGAACAGgtatgttgat ... atcataccagGAAATTCAGCTGTTCAAGCTATATCTCTACTCTTGAAAAAGGGTGTACAGG
EST: gi|29675373|gb|CB671648.1|CB671648
EST:     AGATATTGCAAACAGGCATGTGCTGTTGTTGGATCCCATACTGGGAACAG                         GAAATTCAGCTGTTCAAGCTATATCTCTACTCTTGAAAAAGGGTGTACAGG
genomic: AGATATTGCAAACAGGCATGTGCTGTTGTTGGATCCCATACTGGGAACAGgtatgttgat ... atcataccagGAAATTCAGCTGTTCAAGCTATATCTCTACTCTTGAAAAAGGGTGTACAGG
EST: gi|29627016|gb|CB632027.1|CB632027
EST:     AGATATTGCAAACAGGCATGTGCTGTTGTTGGATCCCATACTGGGAACAG                         GAAATTCAGCTGTTCAAGCTATATCTCTACTCTTGAAAAAGGGTGTACAGG
genomic: AGATATTGCAAACAGGCATGTGCTGTTGTTGGATCCCATACTGGGAACAGgtatgttgat ... atcataccagGAAATTCAGCTGTTCAAGCTATATCTCTACTCTTGAAAAAGGGTGTACAGG
EST: gi|86537180|gb|CI177386.1|CI177386
EST:     AGATATTGCAAACAGGCATGTGCTGTTGTTGGATCCCATACTGGGAACAG                         GAAATTCAGCTGTTCAAGCTATATCTCTACTCTTGAAAAAGGGTGTACAGG
genomic: AGATATTGCAAACAGGCATGTGCTGTTGTTGGATCCCATACTGGGAACAGgtatgttgat ... atcataccagGAAATTCAGCTGTTCAAGCTATATCTCTACTCTTGAAAAAGGGTGTACAGG
EST: gi|29669519|gb|CB665794.1|CB665794
EST:     AGGCATGTGCTGTTGTTGGATCCCATACTGGGAACAG                         GAAATTCAGCTGTTCAAGCTATATCTCTACTCTTGAAAAAGGGTGTACAGG
genomic: AGGCATGTGCTGTTGTTGGATCCCATACTGGGAACAGgtatgttgat ... atcataccagGAAATTCAGCTGTTCAAGCTATATCTCTACTCTTGAAAAAGGGTGTACAGG
EST: gi|29643326|gb|CB648333.1|CB648333
EST:     AGATATTGCAAACAGGCATGTGCTGTTGTTGGATCCCATACTGGGAACAG                         GAAATTCAGCTGTTCAAGCTATATCTCTACTCTTGAAAAAGGGTGTACAGG
genomic: AGATATTGCAAACAGGCATGTGCTGTTGTTGGATCCCATACTGGGAACAGgtatgttgat ... atcataccagGAAATTCAGCTGTTCAAGCTATATCTCTACTCTTGAAAAAGGGTGTACAGG
EST: gi|86536638|gb|CI176844.1|CI176844
EST:     AGATATTGCAAACAGGCATGTGCTGTTGTTGGATCCCATACTGGGAACAG                         GAAATTCAGCTGTTCAAGCTATATCTCTACTCTTGAAAAAGGGTGTACAGG
genomic: AGATATTGCAAACAGGCATGTGCTGTTGTTGGATCCCATACTGGGAACAGgtatgttgat ... atcataccagGAAATTCAGCTGTTCAAGCTATATCTCTACTCTTGAAAAAGGGTGTACAGG
EST: gi|86486730|gb|CI129363.1|CI129363
EST:     GTTGGATCCCATACTGGGAACAG                         GAAATTCAGCTGTTCAAGCTATATCTCTACTCTTGAAAAAGGGTGTACAGG
genomic: GTTGGATCCCATACTGGGAACAGgtatgttgat ... atcataccagGAAATTCAGCTGTTCAAGCTATATCTCTACTCTTGAAAAAGGGTGTACAGG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CTAATCTATCACAATTTACCGAAAGATATTGCAAACAGGCATGTGCTGTTGTTGGATCCCATACTGGGAACAGgtatgttgatgattctcacatatccttcctgttgttacatgaattttgttcttgtgctcactggagcacttctgcctccacctatctcatgtaaaagaga

- - - - - - - - - - - - - - - - - - - - - - GCTGTT