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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagatagtggatggtaccaatctacctactatgatagcgattcccgcagcgcattttacgcaatacaagttacttaatccacaacctctttttcactgcagGAGGAATACAAGCATGAGGACACACTTGGGAGGCTGAAATGCGGCCACGGGTTTCACTGCAATTGCATCAAGAAGTGGCTGCAGGTGAAGAACACCTGCC

Basic information

species Oryza sativa
transcript LOC_Os05g07070.1
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os05g07070.8 (Oryza sativa), 3'ss of exon 7
lower sequence: GRMZM2G118344_T05 (Zea mays), 3'ss of exon 8
----------------------------------------------gtaagatagtggatggtaccaatctacctactatgatagcgattcccgcagcgcattttacgcaatacaagttact--taatccacaacctctttttcactgcagGAGGAATACAAGCATGAGGACACACTTGGGAGGCTGAAATGCGGCCACGGGTTTCACTGCAATTGCATCAAGAAGTGGCTGCAGGTGAAGAACACCTGCC
                                              ||    ||||  |  ||   | | |    | |   |||   |     | ||    | |||   | | ||||| | |  | ||| |  ||   |   |  ||||||||||| |||||    |||||| |  | |||| ||| ||||||   |||  || ||||    | ||||||||||| |||||||||||||||||| | ||||
gtaagaagatgacacccttgtacaacagccggtttttttatttgacgttttttagtataaagttgtactgttgagagtcaaataaaaagaaatggaggtagtattatttatttcaagtcaatgcttatcaaacactggtggctggctgcagGAGGATTACAAATTCGAGGACTCTGTCGGGAAGCTAAAATGCAATCACAAGTATCACGCAGACTGCATCAAGAAATGGCTGCAGGTGAAGAACGCTTGCC
















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|88849533|gb|CI089441.1|CI089441
EST:     GTAGTCATTTGCAGGATGATCAGGACAATGAAAGATGTGTAATCTGCCTG                         GAGGAATACAAGCATGAGGACACACTTGGGAGGCTGAAATGCGGCCACGGG
genomic: GTAGTCATTTGCAGGATGATCAGGACAATGAAAGATGTGTAATCTGCCTGgtaagatagt ... ttcactgcagGAGGAATACAAGCATGAGGACACACTTGGGAGGCTGAAATGCGGCCACGGG
EST: gi|88991207|gb|CI108594.1|CI108594
EST:     TGCAGGATGATCAGGACAATGAAAGATGTGTAATCTGCCTG                         GAGGAATACAAGCATGAGGACACACTTGGGAGGCTGAAATGCGGCCACGGG
genomic: TGCAGGATGATCAGGACAATGAAAGATGTGTAATCTGCCTGgtaagatagt ... ttcactgcagGAGGAATACAAGCATGAGGACACACTTGGGAGGCTGAAATGCGGCCACGGG
EST: gi|88967083|gb|CI392045.1|CI392045
EST:     GTAGTCATTTGCAGGATGATCAGGACAATGAAAGATGTGTAATCTGCCTG                         GAGGAATACAAGCATGAGGACACACTTGGGAGGCTGAAATGCGGCCACGGG
genomic: GTAGTCATTTGCAGGATGATCAGGACAATGAAAGATGTGTAATCTGCCTGgtaagatagt ... ttcactgcagGAGGAATACAAGCATGAGGACACACTTGGGAGGCTGAAATGCGGCCACGGG
EST: gi|109712957|gb|CI105565.1|CI105565
EST:     GTAGTCATTTGCAGGATGATCAGGACAATGAAAGATGTGTAATCTGCCTG                         GAGGAATACAAGCATGAGGACACACTTGGGAGGCTGAAATGCGGCCACGGG
genomic: GTAGTCATTTGCAGGATGATCAGGACAATGAAAGATGTGTAATCTGCCTGgtaagatagt ... ttcactgcagGAGGAATACAAGCATGAGGACACACTTGGGAGGCTGAAATGCGGCCACGGG
EST: gi|88243449|gb|CI244571.1|CI244571
EST:     GTAGTCATTTGCAGGATGATCAGGACCATGAAAGATGTGTAATCTGCCTG                         GAGGAATACAAGCATGAGGACACACTTGGGAGTCTGAAATGCGGCCACGGG
genomic: GTAGTCATTTGCAGGATGATCAGGACAATGAAAGATGTGTAATCTGCCTGgtaagatagt ... ttcactgcagGAGGAATACAAGCATGAGGACACACTTGGGAGGCTGAAATGCGGCCACGGG
EST: gi|86890276|gb|CI321453.1|CI321453
EST:     GTAGTCATTTGCAGGATGATCAGGACAATGAAAGATGTGTAATCTGCCTG                         GAGGAATACAAGCATGAGGACACACTTGGGAGGGCTGAAATGCGGCCACGG
genomic: GTAGTCATTTGCAGGATGATCAGGACAATGAAAGATGTGTAATCTGCCTGgtaagatagt ... ttcactgcagGAGGAATACAAGCATGAGGACACACTTGGGA-GGCTGAAATGCGGCCACGG
EST: gi|88982886|gb|CI250490.1|CI250490
EST:     GTAGTCATTTGCAGGATGATCAGGACAATGAAAGATGTGTAATCTGCCTG                         GAGGAATACAAGCATGAGGACACACTTGGGAGGCTGAAATGCGGCCACGGG
genomic: GTAGTCATTTGCAGGATGATCAGGACAATGAAAGATGTGTAATCTGCCTGgtaagatagt ... ttcactgcagGAGGAATACAAGCATGAGGACACACTTGGGAGGCTGAAATGCGGCCACGGG
EST: gi|88842597|gb|CI081853.1|CI081853
EST:     GTAGTCATTTGCAGGATGATCAGGACAATGAAAGATGTGTAATCTGCCTG                         GAGGAATACAAGCATGAGGACACACTTGGGAGGCTGAAATGCGGCCACGGG
genomic: GTAGTCATTTGCAGGATGATCAGGACAATGAAAGATGTGTAATCTGCCTGgtaagatagt ... ttcactgcagGAGGAATACAAGCATGAGGACACACTTGGGAGGCTGAAATGCGGCCACGGG
EST: gi|88420557|gb|CI562191.1|CI562191
EST:     GGATGATCAGGACAATGAAAGATGTGTAATCTGCCTG                         GAGGAATACAAGCATGAGGACACACTTGGGAGGCTGAAATGCGGCCACGGG
genomic: GGATGATCAGGACAATGAAAGATGTGTAATCTGCCTGgtaagatagt ... ttcactgcagGAGGAATACAAGCATGAGGACACACTTGGGAGGCTGAAATGCGGCCACGGG
EST: gi|29615678|gb|CB620690.1|CB620690
EST:     GTAGTCATTTGCAGGATGATCAGGACAATGAAAGATGTGTAATCTGCCTG                         GAGGAATACAAGCATGAGGACACACTTGGGAGGCTGAAATGCGGCCACGGG
genomic: GTAGTCATTTGCAGGATGATCAGGACAATGAAAGATGTGTAATCTGCCTGgtaagatagt ... ttcactgcagGAGGAATACAAGCATGAGGACACACTTGGGAGGCTGAAATGCGGCCACGGG
EST: gi|88275524|gb|CI396128.1|CI396128
EST:     GTAGTCATTTGCAGGATGATCAGGACAATGAAAGATGTGTAATCTGCCTG                         GAGGAATACAAGCATGAGGACACACTTGGGAGGCTGAAATGCGGCCACGGG
genomic: GTAGTCATTTGCAGGATGATCAGGACAATGAAAGATGTGTAATCTGCCTGgtaagatagt ... ttcactgcagGAGGAATACAAGCATGAGGACACACTTGGGAGGCTGAAATGCGGCCACGGG
EST: gi|88438699|gb|CI546181.1|CI546181
EST:     CAGGACAATGAAAGATGTGTAATCTGCCTG                         GAGGAATACAAGCATGAGGACACACTTGGGAGGCTGAAATGCGGCCACGGG
genomic: CAGGACAATGAAAGATGTGTAATCTGCCTGgtaagatagt ... ttcactgcagGAGGAATACAAGCATGAGGACACACTTGGGAGGCTGAAATGCGGCCACGGG
EST: gi|88460450|gb|CI531923.1|CI531923
EST:     AAAGATGTGTAATCTGCCTG                         GAGGAATACAAGCATGAGGACACACTTGGGAGGCTGAAATGCGGCCACGGG
genomic: AAAGATGTGTAATCTGCCTGgtaagatagt ... ttcactgcagGAGGAATACAAGCATGAGGACACACTTGGGAGGCTGAAATGCGGCCACGGG
EST: gi|88549938|gb|CI479874.1|CI479874
EST:     GATGTNTAATCTGCCTG                         GAGGAATACAAGCATGAGGACACACTTGGGAGGCTGAAATGCGGCCACGGG
genomic: GATGTGTAATCTGCCTGgtaagatagt ... ttcactgcagGAGGAATACAAGCATGAGGACACACTTGGGAGGCTGAAATGCGGCCACGGG
EST: gi|88259241|gb|CI363534.1|CI363534
EST:     GTAGTCATTTGCAGGATGATCAGGACAATGAAAGATGTGTAATCTGCCTG                         GAGGAATACAAGCATGAGGACACACTTGGGAGGCTGAAATCCGGCCACGGG
genomic: GTAGTCATTTGCAGGATGATCAGGACAATGAAAGATGTGTAATCTGCCTGgtaagatagt ... ttcactgcagGAGGAATACAAGCATGAGGACACACTTGGGAGGCTGAAATGCGGCCACGGG
EST: gi|44665886|gb|CR279320.1|CR279320
EST:     GTAGTCATTTGCAGGATGATCAGGACAATGAAAGATGTGTAATCTGCCTG                         GAGGAATACAAGCATGAGGACACACTTGGGAGGCTGAAATGCGGCCACGGG
genomic: GTAGTCATTTGCAGGATGATCAGGACAATGAAAGATGTGTAATCTGCCTGgtaagatagt ... ttcactgcagGAGGAATACAAGCATGAGGACACACTTGGGAGGCTGAAATGCGGCCACGGG
EST: gi|86487200|gb|CI129833.1|CI129833
EST:     GTAGTCATTTGCAGGATGATCAGGACAATGAAAGATGTGTAATCTGCCTG                         GAGGAATACAAGCATGAGGACACACTTGGGAGGCTGAAATGCGGCCACGGG
genomic: GTAGTCATTTGCAGGATGATCAGGACAATGAAAGATGTGTAATCTGCCTGgtaagatagt ... ttcactgcagGAGGAATACAAGCATGAGGACACACTTGGGAGGCTGAAATGCGGCCACGGG
EST: gi|88967187|gb|CI392143.1|CI392143
EST:     GTAGTCATTTGCAGGATGATCAGGACAATGAAATATGTGTAATCTGCCTG                         GAGGAATACAAGCATGAGGACACACTTGGGAGGCTG-AATGCGGCCACGGG
genomic: GTAGTCATTTGCAGGATGATCAGGACAATGAAAGATGTGTAATCTGCCTGgtaagatagt ... ttcactgcagGAGGAATACAAGCATGAGGACACACTTGGGAGGCTGAAATGCGGCCACGGG
EST: gi|88274547|gb|CI394953.1|CI394953
EST:     GTAGTCATTTGCAGGATGATCAGGACAATGAAAGATGTGTAATCTGCCTG                         GAGGAATACAAGCATGAGGACACACTTGGGAGGCTGAAATGCGGCCACGGG
genomic: GTAGTCATTTGCAGGATGATCAGGACAATGAAAGATGTGTAATCTGCCTGgtaagatagt ... ttcactgcagGAGGAATACAAGCATGAGGACACACTTGGGAGGCTGAAATGCGGCCACGGG
EST: gi|88304748|gb|CI520603.1|CI520603
EST:     AAGATGTGTAATCTGCCTG                         GAGGAATACAAGCATGAGGACACACTTGGGAGGCTGAAATGCGGCCACGGG
genomic: AAGATGTGTAATCTGCCTGgtaagatagt ... ttcactgcagGAGGAATACAAGCATGAGGACACACTTGGGAGGCTGAAATGCGGCCACGGG
EST: gi|89174305|gb|CI110503.1|CI110503
EST:     GTAGTCATTTGCAGGATGATCAGGACAATGAAAGATGTGTAATCTGCCTG                         GAGGAATACAAGCATGAGGACACACTTGGGAGGCTGAAATGCGGCCACGGG
genomic: GTAGTCATTTGCAGGATGATCAGGACAATGAAAGATGTGTAATCTGCCTGgtaagatagt ... ttcactgcagGAGGAATACAAGCATGAGGACACACTTGGGAGGCTGAAATGCGGCCACGGG
EST: gi|88842610|gb|CI081866.1|CI081866
EST:     GTAGTCATTTGCAGGATGATCAGGACAATGAAAGATGTGTAATCTGCCTG                         GAGGAATACAAGCATGAGGACACACTTGGGAGGCTGAAATGCGGCCACGGG
genomic: GTAGTCATTTGCAGGATGATCAGGACAATGAAAGATGTGTAATCTGCCTGgtaagatagt ... ttcactgcagGAGGAATACAAGCATGAGGACACACTTGGGAGGCTGAAATGCGGCCACGGG
EST: gi|86490334|gb|CI132967.1|CI132967
EST:     GTAGTCATTTGCAGGATGATCAGGACAATGAAAGATGTGTAATCTGCCTG                         GAGGAATACAAGCATGAGGACACACTTGGGAGGCTGAAATGCGGCCACGGG
genomic: GTAGTCATTTGCAGGATGATCAGGACAATGAAAGATGTGTAATCTGCCTGgtaagatagt ... ttcactgcagGAGGAATACAAGCATGAGGACACACTTGGGAGGCTGAAATGCGGCCACGGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cagcgcattttacgcaatacaagttacttaatccacaacctctttttcactgcagGAGGAATACAAGCATGAGGACACACTTGGGAGGCTGAAATGCGGCCACGGGTTTCACTGCAATTGCATCAAGAAGTGGCTGCAGGTGAAGAACACCTGCC
                         acttaat  putative branch site (score: 4)
                                      cctctttttcactgc  putative PPT
                       ttacttaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagatagtggatggtaccaatctacctactatgatagcgattcccgcagcgcattttacgcaatacaagttacttaatccacaacctctttttcactgcagGAGGAATACAAGCATGAGGACACACTTGGGAGGCTGAAATGCGGCCACGGGTTTCACTGCAATTGCATCAAGAAGTGGCTGCAGGTGAAGAACACCTGCC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC