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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tctgttgcattagattaatttatccagtttaaattgcacatgtttttttttgggggaaaaggacttattaccattgaatgtttttgtcctatttgtgcagAATATATGACATCTGCATGTCTGCAAATGCCCAGCTTTTTACAGGCATTGAACAATTGCCACAATTTTCACATCTACAAGAACTACTCGGTCTAACAGCT

Basic information

species Oryza sativa
transcript LOC_Os02g28040.1
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g28040.1 (Oryza sativa), 3'ss of exon 9
lower sequence: GRMZM2G148913_T01 (Zea mays), 3'ss of exon 9
-------tctgttgcattagattaatttat--ccagtttaaattgcacatgtttttttttgggggaaaaggacttattaccattgaatgtttttgtcctatttgtgcagAATATATGACATCTGCATGTCTGCAAATGCCCAGCTTTTTACAGGCATTGAACAATTGCCACAATTTTCACATCTACAAGAACTACTCGGTCTAACAGCT
        || |||||||  |  | ||| |       ||| || |  ||     | |  |     ||| ||||    ||| | | |||||| ||    | ||| ||||||||||||||    ||||||| ||||||||| |   ||||||| |||||||| |||||||||||||||||||||||||||||| || | ||||||||||||
gtggttgacttttgcatttaagcattttttaattgtgttatatcgttcagtcagtctcattaaataaatggac----tacaact-aatgttgtt----tctttttgcagAATATATGATTCATGCATGTGTGCAAATGCTCCCATTTTTACTGGCATTGAGCAATTGCCACAATTTTCACATCTACAAGAATTAATTGGTCTAACAGCT
















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|2427685|gb|C72148.1|C72148
EST:     GAGCGTTTGCAATCACACTCAATGAAATCTTATAGGGCTCGCTTCCAGAA                         AATATATGACATCTGCATGTCTGCAAATGCCCAGCTTTTTACAGGCATTGA
genomic: GAGCGTTTGCAATCACACTCAATGAAATCTTATAGGGCTCGCTTCCAGAAgtaagatcaa ... atttgtgcagAATATATGACATCTGCATGTCTGCAAATGCCCAGCTTTTTACAGGCATTGA
EST: gi|58592932|gb|CF991240.1|CF991240
EST:     GAGCGTTTGCAATCACACTCAATGAAATCTTATAGGGCTCGCTTCCAGAA                         AATATATGACATCTGCA
genomic: GAGCGTTTGCAATCACACTCAATGAAATCTTATAGGGCTCGCTTCCAGAAgtaagatcaa ... atttgtgcagAATATATGACATCTGCA
EST: gi|88411251|gb|CI564372.1|CI564372
EST:     GCGTTTGCAATCACACTCAATGAAATCTTATAGGGCTCGCTTCCAGAA                         AATATATGACATCTGCATGTCTGCAAATGCCCAGCTTTTTACAGGCATTGA
genomic: GCGTTTGCAATCACACTCAATGAAATCTTATAGGGCTCGCTTCCAGAAgtaagatcaa ... atttgtgcagAATATATGACATCTGCATGTCTGCAAATGCCCAGCTTTTTACAGGCATTGA
EST: gi|58655978|gb|CK044658.1|CK044658
EST:     AGCGTTTG-AATCACACTCAAGTGAAATCTTATAGGGCTCGCTTCCAGAA                         AATATATGACATCTGCATGTCTGCAAATGCCCAGCTTTTTACAGGCATTGA
genomic: AGCGTTTGCAATCACACTCAA-TGAAATCTTATAGGGCTCGCTTCCAGAAgtaagatcaa ... atttgtgcagAATATATGACATCTGCATGTCTGCAAATGCCCAGCTTTTTACAGGCATTGA
EST: gi|29674807|gb|CB671082.1|CB671082
EST:     GAGCGTTTGCAATCACACTCAATGAAATCTTATAGGGCTCGCTTCCAGAA                         AATATATGACATCTGCATGTCTGCAAATGCCCAGCTTTTTACAGGCATTGA
genomic: GAGCGTTTGCAATCACACTCAATGAAATCTTATAGGGCTCGCTTCCAGAAgtaagatcaa ... atttgtgcagAATATATGACATCTGCATGTCTGCAAATGCCCAGCTTTTTACAGGCATTGA
EST: gi|29678752|gb|CB675027.1|CB675027
EST:     GAGCGTTTGCAATCACACTCAATGAAATCCTATAAGGCTCGCTTCCAGAA                         A-TATATGACATCTGCATGTCTG
genomic: GAGCGTTTGCAATCACACTCAATGAAATCTTATAGGGCTCGCTTCCAGAAgtaagatcaa ... atttgtgcagAATATATGACATCTGCATGTCTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttttttgggggaaaaggacttattaccattgaatgtttttgtcctatttgtgcagAATATATGACATCTGCATGTCTGCAAATGCCCAGCTTTTTACAGGCATTGAACAATTGCCACAATTTTCACATCTACAAGAACTACTCGGTCTAACAGCT
                                   tttttgtcctattt  CT-rich tract
                               aatgttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tctgttgcattagattaatttatccagtttaaattgcacatgtttttttttgggggaaaaggacttattaccattgaatgtttttgtcctatttgtgcagAATATATGACATCTGCATGTCTGCAAATGCCCAGCTTTTTACAGGCATTGAACAATTGCCACAATTTTCACATCTACAAGAACTACTCGGTCTAACAGCT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAC
-ctgttgc
- - - - - - - - - - - - - - - -aattgca
- - - - - - - - - - - - - - - - - - - - - - - - - - - -gaaaagga
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ttgaatg