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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgtgtattcataaccaaatgtttctcttaacactgagcacatagttatgactctgtgattgacttgtattatatgaatatcaagGGTTTAAAGAACTTCTCAAAAGCTGCAAGGGATCTAATCACACGACTGCAGAAGATCGACAATGACAACTACCCAGAG

Basic information

species Oryza sativa
transcript LOC_Os05g46720.2
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os05g46720.2 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G174990_T02 (Zea mays), 3'ss of exon 5
gtatg-tgtatt----cataaccaaatgtttctcttaacactgag---cacatagttatgactctgtgattgact-tgtattatatga-atatcaagGGTTTAAAGAACTTCTCAAAAGCTGCAAGGGATCTAATCACACGACTGCAGAAGATCGACAATGACAACTACCCAGAG
||||| || | |     ||| | || | ||  |||| |||   |    ||||| | || || |   |  ||   | | || |   ||  | ||||||||||| ||||||||||| ||| |||| || ||  ||||||||||| | ||||||||||||| ||| ||||||||||||
gtatgctgcactatattatagctaagtattgttctttacatataaagccacattgctaagagttaatactttgttctttacttcttggtaaatcaagGGTTTCAAGAACTTCTCGAAATCTGCCAGAGAATTAATCACACGATTACAGAAGATCGACAGTGATAACTACCCAGAG

upper sequence: LOC_Os05g46720.2 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G355610_T01 (Zea mays), 3'ss of exon 5
gtatg-tgtattc----ataaccaaatgtttctcttaacactgag---cacatagttatgactctgtgattgacttgta--ttatatgaatatcaagGGTTTAAAGAACTTCTCAAAAGCTGCAAGGGATCTAATCACACGACTGCAGAAGATCGACAATGACAACTACCCAGAG
||||| || |||     ||| | |||| ||  | || |||   |    |||||   || || |   || ||   |  |   || | || | || |||||||| ||||||||||||||| |||| |||||  ||||||||||| | |||||||||||||| || ||||||||||||
gtatgctgcattatatgatagctaaatattgttgtttacatataaatccacattactaagaattaatgctttgttctttatttctttgtaaattaagGGTTTCAAGAACTTCTCAAAATCTGCCAGGGAATTAATCACACGATTACAGAAGATCGACAACGATAACTACCCAGAG
















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|29628429|gb|CB633440.1|CB633440
EST:     CAAAAAGGCCCATAGATTCATCTACTACTATTCTGGACGTGCAAGGCGTG                         GGTTTAAAGAACTTCTCAAAAGCTGCAAGGGATCTAATCACACGACTGCAG
genomic: CAAAAAGGCCCATAGATTCATCTACTACTATTCTGGACGTGCAAGGCGTGgtatgtgtat ... gaatatcaagGGTTTAAAGAACTTCTCAAAAGCTGCAAGGGATCTAATCACACGACTGCAG
EST: gi|29636608|gb|CB641617.1|CB641617
EST:     CAAAAAGGCCCATAGATTCATCTACTACTATTCTGGACGTGCAAGGCGTG                         GGTTTAAAGAACTTTCTCAAA-GCTGCAAGGGATCTAATCACACGACTGCA
genomic: CAAAAAGGCCCATAGATTCATCTACTACTATTCTGGACGTGCAAGGCGTGgtatgtgtat ... gaatatcaagGGTTTAAAGAACTT-CTCAAAAGCTGCAAGGGATCTAATCACACGACTGCA
EST: gi|29623352|gb|CB628363.1|CB628363
EST:     CAAAAAGGCCCATAGATTCATCTACTACTATTCTGGACGTGCAAGGCGTG                         NGTTTAAAGAACT
genomic: CAAAAAGGCCCATAGATTCATCTACTACTATTCTGGACGTGCAAGGCGTGgtatgtgtat ... gaatatcaagGGTTTAAAGAACT
EST: gi|29624625|gb|CB629636.1|CB629636
EST:     CAAAAAGGCCCATAGATTCATCTACTACTATTCTGGACGTGCAAGGCGTG                         GGTTTAAAGAACTTCTCAAAAGCTGCAAGGGGATCTAATCACACGACTGCA
genomic: CAAAAAGGCCCATAGATTCATCTACTACTATTCTGGACGTGCAAGGCGTGgtatgtgtat ... gaatatcaagGGTTTAAAGAACTTCTCAAAAGCTGCAAGGG-ATCTAATCACACGACTGCA
EST: gi|29630847|gb|CB635856.1|CB635856
EST:     CAAAAAGGCCCATAGATTCATCTACTACTATTCTGGACGTGCAAGGCGTG                         GGTTTAAAGAACTTCTCAAAAGCTGCAAGGGATCTAATCACACGACTGCAG
genomic: CAAAAAGGCCCATAGATTCATCTACTACTATTCTGGACGTGCAAGGCGTGgtatgtgtat ... gaatatcaagGGTTTAAAGAACTTCTCAAAAGCTGCAAGGGATCTAATCACACGACTGCAG
EST: gi|29628211|gb|CB633222.1|CB633222
EST:     CAAAAAGGCCCATAGATTCATCTACTACTATTCTGGACGTGCAAGGCGTG                         GGTTTAAAGAACTTCTCAAAAGCTGCAAGGGATCTAATCACACGACTGCAG
genomic: CAAAAAGGCCCATAGATTCATCTACTACTATTCTGGACGTGCAAGGCGTGgtatgtgtat ... gaatatcaagGGTTTAAAGAACTTCTCAAAAGCTGCAAGGGATCTAATCACACGACTGCAG
EST: gi|33676922|gb|CF305161.1|CF305161
EST:     CAAAAAGGCCCATAGATTCATCTACTACTATTCTGGACGTGCAAGGCGTG                         GGTTTAAAGAACTTCTCAAAAGCTGCAAGGGATCTAATCACACGACTGCAG
genomic: CAAAAAGGCCCATAGATTCATCTACTACTATTCTGGACGTGCAAGGCGTGgtatgtgtat ... gaatatcaagGGTTTAAAGAACTTCTCAAAAGCTGCAAGGGATCTAATCACACGACTGCAG
EST: gi|29628534|gb|CB633545.1|CB633545
EST:     CAAAAAGGCCCATAGATTCATCTACTACTATTCTGGACGTGCAAGGCGTG                         GGTTTAAAGAACTTCTCAAAAGCTGCAAGGGATCTAATCACACGACTG
genomic: CAAAAAGGCCCATAGATTCATCTACTACTATTCTGGACGTGCAAGGCGTGgtatgtgtat ... gaatatcaagGGTTTAAAGAACTTCTCAAAAGCTGCAAGGGATCTAATCACACGACTG
EST: gi|29669409|gb|CB665684.1|CB665684
EST:     CAAAAAGGCCCATAGATTCATCTACTACTATTCTGGACGTGCAAGGCGTG                         GGTTTAAAGAACTTCTCAAAAGCTGCAAGGGATCTAATCACACGACTGCAG
genomic: CAAAAAGGCCCATAGATTCATCTACTACTATTCTGGACGTGCAAGGCGTGgtatgtgtat ... gaatatcaagGGTTTAAAGAACTTCTCAAAAGCTGCAAGGGATCTAATCACACGACTGCAG
EST: gi|29665229|gb|CB661504.1|CB661504
EST:     CAAAAAGGCCCATAGATTCATCTACTACTATTCTGGACGTGCAAGGCGTG                         GGTTTAAAGAACTTCTCAAAAGCTGCAAGGGATCTAATCACACGACTGCAG
genomic: CAAAAAGGCCCATAGATTCATCTACTACTATTCTGGACGTGCAAGGCGTGgtatgtgtat ... gaatatcaagGGTTTAAAGAACTTCTCAAAAGCTGCAAGGGATCTAATCACACGACTGCAG
EST: gi|29628535|gb|CB633546.1|CB633546
EST:     CAAAAAGGCCCATAGATTCATCTACTACTATTCTGGACGTGCAAGGCGTG                         GGTTTAAAGAACTTCTCAAAAGCTGCAAGGGATCTAATCACACGACTGCAG
genomic: CAAAAAGGCCCATAGATTCATCTACTACTATTCTGGACGTGCAAGGCGTGgtatgtgtat ... gaatatcaagGGTTTAAAGAACTTCTCAAAAGCTGCAAGGGATCTAATCACACGACTGCAG
EST: gi|29640888|gb|CB645895.1|CB645895
EST:     CAAAAAGGCCCATAGATTCATCTACTACTATTCTGGACGTGCAAGGCGTG                         GGTTTAAAGAACTTCTCAAAAGCTGCAAGGGATCTAATCACACGACTGCAG
genomic: CAAAAAGGCCCATAGATTCATCTACTACTATTCTGGACGTGCAAGGCGTGgtatgtgtat ... gaatatcaagGGTTTAAAGAACTTCTCAAAAGCTGCAAGGGATCTAATCACACGACTGCAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

acactgagcacatagttatgactctgtgattgacttgtattatatgaatatcaagGGTTTAAAGAACTTCTCAAAAGCTGCAAGGGATCTAATCACACGACTGCAGAAGATCGACAATGACAACTACCCAGAG
                                  ttgtattatatgaata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgtgtattcataaccaaatgtttctcttaacactgagcacatagttatgactctgtgattgacttgtattatatgaatatcaagGGTTTAAAGAACTTCTCAAAAGCTGCAAGGGATCTAATCACACGACTGCAGAAGATCGACAATGACAACTACCCAGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG