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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtgactggatacctgaacataatatgaacttgcgcgatatcatttccagggaaaatgttggcggcatttggtgattgaaaaaccaactgcatttaattgatctttactacattctgcagGATCCATGCTCCAGGAGAGATTGCTGGCACAAGCAGTGAGGGTCCACTTGGTCTATTGCCGCATCAGATACGAGGATCACTCTCGCAGTACAACTTACTA

Basic information

species Oryza sativa
transcript LOC_Os01g42850.1
intron # 18
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g42850.2 (Oryza sativa), 3'ss of exon 18
lower sequence: GRMZM2G005304_T01 (Zea mays), 3'ss of exon 12
gtaagtgactggatacctgaacataatatgaacttgcgcgatatcatttccagggaaaatgttggcggcatttggtgattgaaaaaccaactgcatttaat--tgatctttactacattctgcagGATCCATGCTCCAGGAGAGATTGCTGGCACAAGCAGTGAGGGTCCACTTGGTCTATTGCCGCATCAGATACGAGGATCACTCTCGCAGTACAACTTACTA
                                     |  | || |  |  | |   | || ||    ||  |  || ||   ||  | ||    |       | |   | |   | || | |||||| |  || ||||| || | |||||| |||   |  ||   || ||||||||||||||| |||||| |||||||||||||| |  |||   | ||| | 
-------------------------------------gtaagat-accttaaagattattgctgagtccaacttatgtttatgaagtccaccatgtggtgccataagtatcataccctttttcagGATACGGGCCCCAGGCGATACTGCTGGTACAGAAACAGAACATCAACTTGGTCTATTGCCACATCAGCTACGAGGATCACTCCCCAAGTGTGATTTATTT

upper sequence: LOC_Os01g42850.2 (Oryza sativa), 3'ss of exon 18
lower sequence: GRMZM2G005304_T01 (Zea mays), 3'ss of exon 18
gtaagtgactggatacctgaacataatatgaacttgcgcga--tatcatttccagggaaaatgttggcggcatttggtgattgaaaaaccaactgcatttaattgatctttactacattctgcagGATCCATGCTCCAGGAGAGATTGCTGGCACAAGCAGTGAGGGTCCACTTGGTCTATTGCCGCATCAGATACGAGGATCACTCTCGCAGTACAACTTACTA
                          |  |   ||||||||  |||||||||||  ||| ||| |  | | ||   ||||   |||||  |||    | | ||  ||  ||  ||| |  |||||||| ||||||||||||||||||||||| ||| ||||||    |   |  || || || || || ||||| || |||||||| |||||||||||| || ||
-----------------------ctctgaggctttgcgcgagctatcatttccaaagaacatgctaactgtatccagtgaacaaaaaag-aaccaagtctgataaatacttg-tacgtgttgcagGATACATGCTCCAGGAGAGATTGCTGGTACAGGCAGTGGTCATGAGCACGGCCTTTTACCTCACCAGATGCGTGGATCACTATCGCAGTACAACATATTA
















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|29677767|gb|CB674042.1|CB674042
EST:     TCTGGCTGTGCGGCAGACCTCTTCACAAGAATGTTACATCATCCAGATGG                         GATCCATGCTCCAGGAGAGATTGCTGGCACAAGCAGTGAGGGTCCACTTGG
genomic: TCTGGCTGTGCGGCAGACCTCTTCACAAGAATGTTACATCATCCAGATGGgtaagtgact ... cattctgcagGATCCATGCTCCAGGAGAGATTGCTGGCACAAGCAGTGAGGGTCCACTTGG
EST: gi|29672225|gb|CB668500.1|CB668500
EST:     TCTGGCTGTGCGGCAGACCTCTTCACAAGAATGTTACATTATGGAGATGG                         GATCCATGCTCCAGGAGAGATTGCTGGCACAAGCAGTGAGGGTCCACTTGG
genomic: TCTGGCTGTGCGGCAGACCTCTTCACAAGAATGTTACATCATCCAGATGGgtaagtgact ... cattctgcagGATCCATGCTCCAGGAGAGATTGCTGGCACAAGCAGTGAGGGTCCACTTGG
EST: gi|29667791|gb|CB664066.1|CB664066
EST:     TCTGGCTGTGCGGCAGACCTCTTCACAAGAATGTTACATCATCCAGATGG                         GATCCATGCTCCAGGAGAGATTGCTGGCACAAGCAGTGAGGGTCCACTTGG
genomic: TCTGGCTGTGCGGCAGACCTCTTCACAAGAATGTTACATCATCCAGATGGgtaagtgact ... cattctgcagGATCCATGCTCCAGGAGAGATTGCTGGCACAAGCAGTGAGGGTCCACTTGG
EST: gi|29641126|gb|CB646133.1|CB646133
EST:     TCTGGCTGTGCGGCAGACCTCTTCACAAGAATGTTACATCATCCAGATGG                         GATCCATGCTCCAGGAGAGATTGCTGGCACAAGCAGTGAGGGTCCACTTGG
genomic: TCTGGCTGTGCGGCAGACCTCTTCACAAGAATGTTACATCATCCAGATGGgtaagtgact ... cattctgcagGATCCATGCTCCAGGAGAGATTGCTGGCACAAGCAGTGAGGGTCCACTTGG
EST: gi|33682080|gb|CF310319.1|CF310319
EST:     TCTGGCTGTGCGGCAGACCTCTTCACAAGAATGTTACATCATCCAGATGG                         GATCCATGCTCCAGGAGAGATTGCTGGCACAAGCAGTGAGGGTCCACTTGG
genomic: TCTGGCTGTGCGGCAGACCTCTTCACAAGAATGTTACATCATCCAGATGGgtaagtgact ... cattctgcagGATCCATGCTCCAGGAGAGATTGCTGGCACAAGCAGTGAGGGTCCACTTGG
EST: gi|29674598|gb|CB670873.1|CB670873
EST:     TCTGGCTGTGCGGCAGACCTCTTCACAAGAATGTTACATCATCCAGATGG                         GATCCATGCTCCAGGAGAGATTGCTGGCACAAGCAGTGAGGGTCCACTTGG
genomic: TCTGGCTGTGCGGCAGACCTCTTCACAAGAATGTTACATCATCCAGATGGgtaagtgact ... cattctgcagGATCCATGCTCCAGGAGAGATTGCTGGCACAAGCAGTGAGGGTCCACTTGG
EST: gi|29640245|gb|CB645254.1|CB645254
EST:     TCTGGCTGTGCGGCAGACCTCTTCACAAGAATGTTACATCATCCAGATGG                         GATCCATGCTCCAGGAGAGATTGCTGGCACAAGCAGTGAGGGTCCACTTGG
genomic: TCTGGCTGTGCGGCAGACCTCTTCACAAGAATGTTACATCATCCAGATGGgtaagtgact ... cattctgcagGATCCATGCTCCAGGAGAGATTGCTGGCACAAGCAGTGAGGGTCCACTTGG
EST: gi|29627979|gb|CB632990.1|CB632990
EST:     TCTGGCTGTGCGGCAGACCTCTTCACAAGAATGTTACATCGTCCAGATGG                         GATCCATGCTCCAGGAGAGATTGCTGGCACAAGCAGTGAGGGTCCACTTGG
genomic: TCTGGCTGTGCGGCAGACCTCTTCACAAGAATGTTACATCATCCAGATGGgtaagtgact ... cattctgcagGATCCATGCTCCAGGAGAGATTGCTGGCACAAGCAGTGAGGGTCCACTTGG
EST: gi|29629460|gb|CB634469.1|CB634469
EST:     TCTGGCTGTGCGGCAGACCTCTTCACAAGAATGTTACATCATCCAGGTGG                         GATCCATGCTCCAGGAGAGATTGCTGGCACAAGCAGTGAGGGTCCACTTGG
genomic: TCTGGCTGTGCGGCAGACCTCTTCACAAGAATGTTACATCATCCAGATGGgtaagtgact ... cattctgcagGATCCATGCTCCAGGAGAGATTGCTGGCACAAGCAGTGAGGGTCCACTTGG
EST: gi|29674600|gb|CB670875.1|CB670875
EST:     TCTGGCTGTGCGGCAGACCTCTTCACAAGAATGTTACATCATCCAGATGG                         GATCCATGCTCCAGGAGAGATTGCTGGCACAAGCAGTGAGGGTCCACTTGG
genomic: TCTGGCTGTGCGGCAGACCTCTTCACAAGAATGTTACATCATCCAGATGGgtaagtgact ... cattctgcagGATCCATGCTCCAGGAGAGATTGCTGGCACAAGCAGTGAGGGTCCACTTGG
EST: gi|29642677|gb|CB647684.1|CB647684
EST:     TCTGGCTGTGCGGCAGACCTCTTCACAAGAATGTTACATCATCCAGATGG                         GATCCATGCTCCAGGAGAGATTGCTGGCACAAGCAGTGAGGGTCCACTTGG
genomic: TCTGGCTGTGCGGCAGACCTCTTCACAAGAATGTTACATCATCCAGATGGgtaagtgact ... cattctgcagGATCCATGCTCCAGGAGAGATTGCTGGCACAAGCAGTGAGGGTCCACTTGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

catttggtgattgaaaaaccaactgcatttaattgatctttactacattctgcagGATCCATGCTCCAGGAGAGATTGCTGGCACAAGCAGTGAGGGTCCACTTGGTCTATTGCCGCATCAGATACGAGGATCACTCTCGCAGTACAACTTACTA
                              aattgat  putative branch site (score: 4)
                          atttaattgatcttta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagtgactggatacctgaacataatatgaacttgcgcgatatcatttccagggaaaatgttggcggcatttggtgattgaaaaaccaactgcatttaattgatctttactacattctgcagGATCCATGCTCCAGGAGAGATTGCTGGCACAAGCAGTGAGGGTCCACTTGGTCTATTGCCGCATCAGATACGAGGATCACTCTCGCAGTACAACTTACTA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAT