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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttgtgttcagtgattatatagtttttttttaatgcagaatggacaagtggtatttataacctgctatttaagatgtttttaactggatctttaattttagGTCTTCTCAATCAGAGATGCTGCTGCAAACAACTTGAAGCGCCTAGCTGAGGAGTTTGGTCCAGAATGGGCGATGCAGCATATAATCCCTCAG

Basic information

species Oryza sativa
transcript LOC_Os09g07510.1
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os09g07510.1 (Oryza sativa), 3'ss of exon 9
lower sequence: GLYMA20G24790.1 (Glycine max), 3'ss of exon 9
ttgtgttcagtgattatatagtttttttttaatgcagaatggacaagtggtatttataacctgctatttaagatgttt-ttaactggatctttaattttagGTCTTCTCAATCAGAGATGCTGCTGCAAACAACTTGAAGCGCCTAGCTGAGGAGTTTGGTCCAGAATGGGCGATGCAGCATATAATCCCTCAG
    |||  ||| |  |  | ||  ||  || ||  |  || |    ||| |  |  |   |||   | |   | ||| |||||    |   | ||| |||||    |||||  | || || ||||| ||||||||||| ||||| ||||| || ||||| || || ||||| |||||||| ||||| ||||||
----gttt-gtgctc-tccacttccttgctagtgt-gggtgcattt-tgggaactgcatattgcacatgactgtttttgttaacaaccttagttattgtagGTTCATTCAATTCGCGAAGCAGCTGCTAACAACTTGAAACGCCTTGCTGAAGAATTTGGACCTGAGTGGGCTATGCAGCACATAATTCCTCAG

upper sequence: LOC_Os09g07510.1 (Oryza sativa), 3'ss of exon 9
lower sequence: GLYMA02G10790.1 (Glycine max), 3'ss of exon 9
ttgtgttcagtgattatatagtttttttttaatgcagaatggacaagtggtatttataacctgctatttaagatgtttttaactggatctttaattttagGTCTTCTCAATCAGAGATGCTGCTGCAAACAACTTGAAGCGCCTAGCTGAGGAGTTTGGTCCAGAATGGGCGATGCAGCATATAATCCCTCAG
    |||    || | || |   |  ||| |    |   | |  ||      ||| ||     |||||      ||  |||||   ||  ||  || |||||    || ||| | || || ||||| ||||| ||||||||||||||||| || |||||||| || ||||| ||||| || ||||| || |||
----gtttgtggactctacatgctagtttgagcatattttaggaaaccaccttttctacatgactatt------gtcgttaacctcattgtttgttgtagGTTCATTCGATCCGTGAGGCAGCTGCTAACAATTTGAAGCGCCTAGCTGAAGAATTTGGTCCTGAGTGGGCTATGCAACACATAATTCCACAG

upper sequence: LOC_Os09g07510.1 (Oryza sativa), 3'ss of exon 9
lower sequence: GLYMA10G42250.1 (Glycine max), 3'ss of exon 9
ttgtgttcagtgattatatagtttttttttaatgcagaatggacaagtggtatttataacctgctatttaagatgttt-ttaactggatctttaattttagGTCTTCTCAATCAGAGATGCTGCTGCAAACAACTTGAAGCGCCTAGCTGAGGAGTTTGGTCCAGAATGGGCGATGCAGCATATAATCCCTCAG
    |||  ||| |  || | ||  ||  || ||  |  || |    ||| |  |  |   |||   | | | | ||| |||||    |   | ||| |||||    |||||  | || || ||||| ||||||||||| ||||| ||||| || |||||||| || ||||| |||||||| ||||| ||||||
----gttt-gtgctc-tacacttccttgctagtgt-gggtgcattt-tgggaactgcatattgcacatgacggtttttgttaaccaccttagttattgtagGTTCATTCAATTCGTGAAGCAGCTGCTAACAACTTGAAACGCCTTGCTGAAGAATTTGGTCCTGAGTGGGCTATGCAGCACATAATTCCTCAG

upper sequence: LOC_Os09g07510.1 (Oryza sativa), 3'ss of exon 9
lower sequence: AT1G13320.2 (Arabidopsis thaliana), 3'ss of exon 9
ttgtgttcagtgattatatagtttttttttaatgcagaatggacaagtggtatttataacctgctatttaagatgtttttaactggatctttaattttagGTCTTCTCAATCAGAGATGCTGCTGCAAACAACTTGAAGCGCCTAGCTGAGGAGTTTGGTCCAGAATGGGCGATGCAGCATATAATCCCTCAG
      ||  | ||| | ||  ||  ||  |          || || |   |||| |   ||    |    ||  |||| || |   | |  | | | ||||   ||||||| | || ||||||||||||||  ||||||| || ||||| ||||||||||| |||||||| |||||||||||| | ||||||
-----gtccctcattctctaccttcattgaatcatc---cagataaataa-atttgtcgtctctactgcttgaaattttgaaataattataaattgtcagGTTCACTCAATCCGTGAAGCTGCTGCAAACAATCTGAAGCGTCTTGCTGAAGAGTTTGGTCCTGAATGGGCAATGCAGCATATAGTTCCTCAG

upper sequence: LOC_Os09g07510.1 (Oryza sativa), 3'ss of exon 9
lower sequence: AT3G25800.1 (Arabidopsis thaliana), 3'ss of exon 8
--------------------------ttgtgttcagt--gattatatagtttttttttaatgcagaatggacaagtggtatttataacctgctatttaagatgtttttaactggatctttaattttagGTCTTCTCAATCAGAGATGCTGCTGCAAACAACTTGAAGCGCCTAGCTGAGGAGTTTGGTCCAGAATGGGCGATGCAGCATATAATCCCTCAG
                           || |     |  |||||||  | || || || ||  | | ||      |  | ||| |    |  | |||      |||||  | |   || | |||  ||||   ||||||| | ||||||||||| |||||  | ||||| || |||||||| |||||||| |||||||| ||||| |||||| | ||||||
gtatttctttctctctcttacttttactgggaatgatcagattataccgcttcttatttatagaaattgattttttttttttttttttttttttttt------ttttttgcggatgctctcatt--agGTTCACTCAATCCGCGATGCTGCTGCTAACAATCTCAAGCGGCTTGCTGAGGAATTTGGTCCTGAATGGGCAATGCAACATATAGTTCCTCAG

upper sequence: LOC_Os09g07510.1 (Oryza sativa), 3'ss of exon 9
lower sequence: AT1G25490.1 (Arabidopsis thaliana), 3'ss of exon 9
ttgtgttcagtgattatatagtttttttttaatgcagaatggacaagtggtatttataacctgctatttaagatgtttttaactggatctttaattttagGTCTTCTCAATCAGAGATGCTGCTGCAAACAACTTGAAGCGCCTAGCTGAGGAGTTTGGTCCAGAATGGGCGATGCAGCATATAATCCCTCAG
              | ||   |   | ||| |||     || | || |  | |   | || || ||||  |||| ||   |    | |||     || |||||| ||| ||| | || ||||| ||||||||| | |||||||| || |||||||||||||| |||||||| ||||||||  || | || |||
-------------gtttaccttgaatctttgatgtt---tgcataaatt-tctcattcacttgttattgtagatattgaca--ctgttctcctccttcagGTCTACTCTATCCGCGAAGCTGCAGCAAACAACCTAAAGCGCCTCGCAGAGGAGTTTGGTCCTGAATGGGCAATGCAGCACTTAGTTCCCCAG

upper sequence: LOC_Os09g07510.1 (Oryza sativa), 3'ss of exon 9
lower sequence: Vv01s0011g03280.t01 (Vitis vinifera), 3'ss of exon 8
ttgtgttcagtgattatatagtttttttttaat-gcagaatggacaagtggtatttataacctgctatttaagatgtttttaactggatctttaattttagGTCTTCTCAATCAGAGATGCTGCTGCAAACAACTTGAAGCGCCTAGCTGAGGAGTTTGGTCCAGAATGGGCGATGCAGCATATAATCCCTCAG
 | | || || |    |  |   | ||| | || |     |      ||  | | | ||      || || | | |     ||    ||| |    |  |||| | ||| ||  | ||||||||||| |||||||| |||||||| || || || |||||||| || ||||| ||||||||  |||| || |||
-tattttaagagggctttcatcatctttgtcatcgttttctttgtctgtcatctatgtatttatgtagttcaaaagggacaaatattatcatgttgtgcagGTTTACTCCATTCGTGATGCTGCTGCTAACAACTTAAAGCGCCTTGCAGAAGAATTTGGTCCTGACTGGGCAATGCAGCACTTAATTCCACAG

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|29658916|gb|CB655191.1|CB655191
EST:     TTTTCGATGACAAGCTGGGGGCACTTTGCATGCAATGGTTGGAAGATAAG                         GTCTTCTCAATCAGAGATGCTGCTGCAAACAACTTGAAGCGCCTAGCTGAG
genomic: TTTTCGATGACAAGCTGGGGGCACTTTGCATGCAATGGTTGGAAGATAAGgtatttacca ... ttaattttagGTCTTCTCAATCAGAGATGCTGCTGCAAACAACTTGAAGCGCCTAGCTGAG
EST: gi|58683974|gb|CK072661.1|CK072661
EST:     TTTTCGATGACAAGCTGGGGGCACTTTGCATGCAATGGTTGGAAGATAAG                         GTCTTCTCAATCAGAGATGCTGCTGCAAACAACTTGAAGCGCCTAGCTGAG
genomic: TTTTCGATGACAAGCTGGGGGCACTTTGCATGCAATGGTTGGAAGATAAGgtatttacca ... ttaattttagGTCTTCTCAATCAGAGATGCTGCTGCAAACAACTTGAAGCGCCTAGCTGAG
EST: gi|29641703|gb|CB646710.1|CB646710
EST:     TTTTCGATGACAAGCTGGGGGCACTTTGCATGCAATGGTTGGAAGATAAG                         GTCTTCTCAATCAGAGATGCTGCTGCAAACAACTTGAAGCGCCTAGCTGAG
genomic: TTTTCGATGACAAGCTGGGGGCACTTTGCATGCAATGGTTGGAAGATAAGgtatttacca ... ttaattttagGTCTTCTCAATCAGAGATGCTGCTGCAAACAACTTGAAGCGCCTAGCTGAG
EST: gi|38476835|gb|CF960968.1|CF960968
EST:     CGATGACAAGCTGGGGGCACTTTGCATGCAATGGTTGGAAGATAAG                         GTCTTCTCAGTCGAGAGATGCTGCTGCAAACAACTTGAAGCGCCTAGCTGA
genomic: CGATGACAAGCTGGGGGCACTTTGCATGCAATGGTTGGAAGATAAGgtatttacca ... ttaattttagGTCTTCTCAATC-AGAGATGCTGCTGCAAACAACTTGAAGCGCCTAGCTGA
EST: gi|87017349|gb|CI301385.1|CI301385
EST:     TTTTCGATGACAAGCTGGGGGCACTTTGCATGCAATGGTTGGAAGATAAG                         GTCTTCTCAATCAGAGATGCTGCTGCAAACAACTTGAAGCGCCTAGCTGAG
genomic: TTTTCGATGACAAGCTGGGGGCACTTTGCATGCAATGGTTGGAAGATAAGgtatttacca ... ttaattttagGTCTTCTCAATCAGAGATGCTGCTGCAAACAACTTGAAGCGCCTAGCTGAG
EST: gi|29642127|gb|CB647134.1|CB647134
EST:     GCTGGGGGCACTTTGCATGCAATGGTTGGAAGATAAG                         GTCTTCTCAATCAGAGATGCTGCTGCAAACAACTTGAAGCGCCTAGCTGAG
genomic: GCTGGGGGCACTTTGCATGCAATGGTTGGAAGATAAGgtatttacca ... ttaattttagGTCTTCTCAATCAGAGATGCTGCTGCAAACAACTTGAAGCGCCTAGCTGAG
EST: gi|87038212|gb|CI192834.1|CI192834
EST:     ATGCAATGGTTGGAAGATAAG                         GTCTTCTCAATCAGAGATGCTGCTGCAAACAACTTGAAGCGCCTAGCTGAG
genomic: ATGCAATGGTTGGAAGATAAGgtatttacca ... ttaattttagGTCTTCTCAATCAGAGATGCTGCTGCAAACAACTTGAAGCGCCTAGCTGAG
EST: gi|87036423|gb|CI191045.1|CI191045
EST:     TTTTCGATGACAAGCTGGGGGCACTTTGCATGCAATGGTTGGAAGATAAG                         GTCTTCTCAATCAGAGATGCTGCTGCAAACAACTTGAAGCGCCTAGCTGAG
genomic: TTTTCGATGACAAGCTGGGGGCACTTTGCATGCAATGGTTGGAAGATAAGgtatttacca ... ttaattttagGTCTTCTCAATCAGAGATGCTGCTGCAAACAACTTGAAGCGCCTAGCTGAG
EST: gi|29667131|gb|CB663406.1|CB663406
EST:     TTTTCGATGACAAGCTGGGGGCACTTTGCATGCAATGGTTGGAAGATAAG                         GTCTTCTCAATCAGAGATGCTGCTGCAAACAACTTGAAGCGCCTAGCTGAG
genomic: TTTTCGATGACAAGCTGGGGGCACTTTGCATGCAATGGTTGGAAGATAAGgtatttacca ... ttaattttagGTCTTCTCAATCAGAGATGCTGCTGCAAACAACTTGAAGCGCCTAGCTGAG
EST: gi|58685311|gb|CK073998.1|CK073998
EST:     TGGAAGATAAG                         TTCTTCTCAATCAGAGATGCTGCTGCAAACAACTTGAAGCGCCTAGCTGAG
genomic: TGGAAGATAAGgtatttacca ... ttaattttagGTCTTCTCAATCAGAGATGCTGCTGCAAACAACTTGAAGCGCCTAGCTGAG
EST: gi|218487576|gb|FG960599.1|FG960599
EST:     TTATCGATGACAAGCTGGGGGCACTTTGCATGCAATGGTTGGACGATAAG                         GTCTTCTCAATCAGAGATGCTGCTGCAAACAACTTG
genomic: TTTTCGATGACAAGCTGGGGGCACTTTGCATGCAATGGTTGGAAGATAAGgtatttacca ... ttaattttagGTCTTCTCAATCAGAGATGCTGCTGCAAACAACTTG
EST: gi|86899096|gb|CI296244.1|CI296244
EST:     TTTTCGATGACAAGCTGGGGGCACTTTGCATGCAATGGTTGGAAGATAAG                         GTCTTCTCAATCAGAGATGCTGCTGCAAACAACTTGAAGCGCCTAGCTGAG
genomic: TTTTCGATGACAAGCTGGGGGCACTTTGCATGCAATGGTTGGAAGATAAGgtatttacca ... ttaattttagGTCTTCTCAATCAGAGATGCTGCTGCAAACAACTTGAAGCGCCTAGCTGAG
EST: gi|33656227|gb|CF278841.1|CF278841
EST:     TTTTCGATGACAAGCTGGGGGCACTTTGCATGCAATGGTTGGAAGATAAG                         GTCTTCTCAATCAGAGATGCTGCTGCAAACAACTTGAAGCGCCTAGCTGAG
genomic: TTTTCGATGACAAGCTGGGGGCACTTTGCATGCAATGGTTGGAAGATAAGgtatttacca ... ttaattttagGTCTTCTCAATCAGAGATGCTGCTGCAAACAACTTGAAGCGCCTAGCTGAG
EST: gi|29621782|gb|CB626793.1|CB626793
EST:     TGGTTGGAAGATAAG                         GTCTTCTCAATCAGAGATGCTGCTGCAAACAACTTGAAGCGCCTAGCTGAG
genomic: TGGTTGGAAGATAAGgtatttacca ... ttaattttagGTCTTCTCAATCAGAGATGCTGCTGCAAACAACTTGAAGCGCCTAGCTGAG
EST: gi|58678838|gb|CK067525.1|CK067525
EST:     TTTTCGATGACAAGCTGGGGGCACTTTGCATGCAATGGTTGGAAGATAAG                         GTCTTCTCAATCAGAGATGCTGCTGCAAACAACTTGAAGCGCCTAGCTGAG
genomic: TTTTCGATGACAAGCTGGGGGCACTTTGCATGCAATGGTTGGAAGATAAGgtatttacca ... ttaattttagGTCTTCTCAATCAGAGATGCTGCTGCAAACAACTTGAAGCGCCTAGCTGAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agtggtatttataacctgctatttaagatgtttttaactggatctttaattttagGTCTTCTCAATCAGAGATGCTGCTGCAAACAACTTGAAGCGCCTAGCTGAGGAGTTTGGTCCAGAATGGGCGATGCAGCATATAATCCCTCAG
                                          tcttt  CT-rich tract
                   tatttaagatgttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttgtgttcagtgattatatagtttttttttaatgcagaatggacaagtggtatttataacctgctatttaagatgtttttaactggatctttaattttagGTCTTCTCAATCAGAGATGCTGCTGCAAACAACTTGAAGCGCCTAGCTGAGGAGTTTGGTCCAGAATGGGCGATGCAGCATATAATCCCTCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG
ttgtgtt
- - - - - - - - - - - - - - -taatgca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -cctgcta
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ctggatc