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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgggccaacgcttaaccaaatattattaactggttttctgctgctgtttattcccagcaaactaacttgccaactgcatctgcagGAATTGTCATCAGATTCATCTCAGCATGTTCGTTCAGCTTTGGCTTCAGTTATTATGGGAATGGCCCCGGTCTTGGGAAAG

Basic information

species Oryza sativa
transcript LOC_Os09g07510.1
intron # 6
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 6
lower sequence: GRMZM2G102858_T01 (Zea mays), 3'ss of exon 6
gtgggccaacgcttaac-caaatattattaactggttttctgctgctgtttattcccagcaaactaacttgccaactgcatctgcagGAATTGTCATCAGATTCATCTCAGCATGTTCGTTCAGCTTTGGCTTCAGTTATTATGGGAATGGCCCCGGTCTTGGGAAAG
||| |   | || |  | |||| | |||| |   | | |   |   | || | |    |  ||||    ||||   || |     ||||||| |||||||||||||||||||||||||||||||||||||| || ||||||||||||||||| || || |||||||||
gtgtgtttaagcattgcacaaacactattga---gctctgcaccaatattcagt---ggttaact--tgtgccttttgtactcatagGAATTATCATCAGATTCATCTCAGCATGTTCGTTCAGCTTTGGCATCGGTTATTATGGGAATGGCTCCTGTATTGGGAAAG

upper sequence: LOC_Os09g07510.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GLYMA02G10790.2 (Glycine max), 3'ss of exon 6
gtgggccaacgcttaaccaaatattattaactggttttctgctgctgtttattcccagcaaactaacttgccaactgcatctgcagGAATTGTCATCAGATTCATCTCAGCATGTTCGTTCAGCTTTGGCTTCAGTTATTATGGGAATGGCCCCGGTCTTGGGAAAG
|||   |   | ||       | ||   |    || |||||    | | | | |     ||| ||  |||| |  |   | |||||||||||||| | ||||| |  ||||||||||| || ||||||||||| || || ||||||||||| || || || ||||||
gtgtctctttggtt---ttggtcttgaaattcagtattctga-attatatttacaggctaaaatactttgcaagatc--tttgcagGAATTGTCAACGGATTCTTTGCAGCATGTTCGCTCTGCTTTGGCTTCCGTGATAATGGGAATGGCTCCAGTGTTAGGAAAG

upper sequence: LOC_Os09g07510.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GLYMA07G10000.1 (Glycine max), 3'ss of exon 5
--gtgggccaacgcttaaccaaatattatta--actggtt-----ttctgctgct-gtttattcccagcaaactaa-cttgccaactgcatctgcagGAATTGTCATCAGATTCATCTCAGCATGTTCGTTCAGCTTTGGCTTCAGTTATTATGGGAATGGCCCCGGTCTTGGGAAAG
   ||     ||  | ||  || |   |||   || ||||     || || | || ||||  |  || |  |  ||  ||||| |||        |||| || ||| ||||||||||||| |||||||| || ||  ||||||| ||||| ||||| ||||| ||||| || || |||
gtatgtagtcacagtaaaaaaattgggattgttacaggttaacatttatgatactagtttgattacaactgatcaagtttgcctacta------tagGAGTTATCAACAGATTCATCTCAACATGTTCGCTCTGCACTGGCTTCTGTTATAATGGGTATGGCACCGGTGTTAGGGAAG

upper sequence: LOC_Os09g07510.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GLYMA20G24790.1 (Glycine max), 3'ss of exon 6
-----------------------------------------------gtgggccaacgcttaaccaaatatta-ttaactggttttctgctgctg-tttattcccagcaaactaacttgcc---aactgcatctgcagGAATTGTCATCAGATTCATCTCAGCATGTTCGTTCAGCTTTGGCTTCAGTTATTATGGGAATGGCCCCGGTCTTGGGAAAG
                                                |   |  | ||||  |    | ||  ||      ||   |        |||||    |      ||| ||      |||  | | |||||||||||||||||||||| || |||||||| || || |||||||||||||| || ||||||||||| || || |||||||||
gtatacatctttggaaaagaaattataacacattaatattactgattatatacagaggctttccttggttttggtttgtcaattcagtaggataaatttatatttacaggtttaagttctttgaaacaacttttgcagGAATTGTCATCAGATTCTTCACAGCATGTCCGGTCTGCTTTGGCTTCAGTAATAATGGGAATGGCTCCAGTGTTGGGAAAG

upper sequence: LOC_Os09g07510.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GLYMA10G42250.1 (Glycine max), 3'ss of exon 6
-----------------------------------------------gtgggccaacgcttaaccaaatattattaactggttttctgctgctg--tttattcccagcaaactaacttgcc---aactgcatctgcagGAATTGTCATCAGATTCATCTCAGCATGTTCGTTCAGCTTTGGCTTCAGTTATTATGGGAATGGCCCCGGTCTTGGGAAAG
                                                |   |  | ||||  |    | ||  |   |   ||     ||||   |||||    |      ||| ||      |||  | | |||||||||||||||||||||| ||||||||||| || || |||||||||||||| || ||||||||||| || || |||||||||
gtatacatctttggaaaagaaattataacacattagtattactgattatatacagaggcttttcttggttttggttggtcaattcagtatgctaaatttatatttacaggtttaagttctttgaaacaacttttgcagGAATTGTCATCAGATTCTTCTCAGCATGTCCGGTCTGCTTTGGCTTCAGTAATAATGGGAATGGCTCCAGTGTTGGGAAAG

upper sequence: LOC_Os09g07510.1 (Oryza sativa), 3'ss of exon 6
lower sequence: AT1G13320.2 (Arabidopsis thaliana), 3'ss of exon 6
---------gtgggccaacgc-ttaaccaaatattattaactggttttctgctgctgtttattcccagcaaactaacttgccaactgcatctgcagGAATTGTCATCAGATTCATCTCAGCATGTTCGTTCAGCTTTGGCTTCAGTTATTATGGGAATGGCCCCGGTCTTGGGAAAG
            |   |  |  || |    |||||||  |  ||        | ||||   |       || || || |   || |  |   | ||||||| |||||||| || |||||||| ||  | || || ||||| |||||||| ||||||||||| || |||||||| |||
gtacacacttaagaagagtgtgttgatttcatattatgcaaaggaccaaaa-tactgtcggtgtttgctaagcttacctat-aaatctacacgtagGAATTATCATCAGACTCTTCTCAGCACGTCAGATCTGCATTGGCATCAGTTATAATGGGAATGGCTCCAGTCTTGGGTAAG

upper sequence: LOC_Os09g07510.1 (Oryza sativa), 3'ss of exon 6
lower sequence: AT3G25800.2 (Arabidopsis thaliana), 3'ss of exon 5
-------------gtgggccaacgcttaaccaaatattatt-----aactggttttctgctgctgtttattcccagcaaactaacttgccaactgcatctgcagGAATTGTCATCAGATTCATCTCAGCATGTTCGTTCAGCTTTGGCTTCAGTTATTATGGGAATGGCCCCGGTCTTGGGAAAG
                   |||   ||  |||| |    |      ||      |   | || ||  |||| |     |     | |   ||    | ||| ||||  | |||||||| || |||||||||||  | || || ||||| |||||||| ||||||||||| || |||||||| |||
gtacatgcttaagagaattcaattgttttccaagttccttacagaaaatcaacgtatagttgttgcatattactgatgatt---cctcttaatgctacctgtagGAGCTATCATCAGACTCTTCTCAGCATGTCAGATCTGCATTGGCCTCAGTTATAATGGGAATGGCTCCAGTCTTGGGTAAG

upper sequence: LOC_Os09g07510.1 (Oryza sativa), 3'ss of exon 6
lower sequence: Vv17s0000g03870.t01 (Vitis vinifera), 3'ss of exon 7
--------------------------------------------------gtgggccaacgcttaaccaaatattattaactggttttctgctgctgtttattcccagca----aactaacttgccaactg--catctgcagGAATTGTCATCAGATTCATCTCAGCATGTTCGTTCAGCTTTGGCTTCAGTTATTATGGGAATGGCCCCGGTCTTGGGAAAG
                                                   |||||  ||   |       |  |||| ||   |  |   |||   | | |    |        ||||  ||   || ||  | |||||||||||| ||||||||||| || |||||||||||||| ||||||||||||||||||||||||||||| || || || ||||||
gtatacatgcttgcaaaagttttaagtttcattatgctatgaagtttcttatgggcttaca--tggtggggttctatttaccactgcttatctgtcatctgtcttaaaatttgtgactagattagaaaatgtccttctgcagGAATTATCATCAGATTCTTCCCAGCATGTTCGTTCTGCTTTGGCTTCAGTTATTATGGGAATGGCACCTGTTTTAGGAAAG

upper sequence: LOC_Os09g07510.1 (Oryza sativa), 3'ss of exon 6
lower sequence: Vv01s0011g03280.t01 (Vitis vinifera), 3'ss of exon 5
-------------------------------------------gtgggccaacgcttaaccaaatattattaa-ctggttttctgctgctgtttattcccagcaaactaacttgccaactgcatct-gcagGAATTGTCATCAGATTCATCTCAGCATGTTCGTTCAGCTTTGGCTTCAGTTATTATGGGAATGGCCCCGGTCTTGGGAAAG
                                           ||   |    | | |   |  || |||| | ||  | | |  ||| ||    ||| ||  |       |||   |   ||| | | |||||||||||| |||||| || |||||||| || || || |||||||||||| | ||||||||||| || ||||| ||||||
gtgctcacgtttattaaaagagtgtttctctgtattatataatgtctccttttgttcacgaacttactattgagctaatgtgcacctgttgagctttctcaata------tttggtgatgtcattttgtagGAATTGTCATTAGATTCGTCCCAGCATGTCCGCTCTGCCTTGGCTTCAGTTTTAATGGGAATGGCTCCCGTCTTAGGAAAG

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|58683974|gb|CK072661.1|CK072661
EST:     GGATGTTAAGTCCTCAGCTTGCAATTCAGCATATTCTTCCTTGTGTCAAG                         GAATTGTCATCAGATTCATCTCAGCATGTTCGTTCAGCTTTGGCTTCAGTT
genomic: GGATTTTAAGTCCTCAGCTTGCAATTCAGCATATTCTTCCTTGTGTCAAGgtgggccaac ... gcatctgcagGAATTGTCATCAGATTCATCTCAGCATGTTCGTTCAGCTTTGGCTTCAGTT
EST: gi|30226842|gb|CB964734.1|CB964734
EST:     GGATTTTAAGTCCTCAGCTGGCAATTCAGCATATTCTTCCTTGTGTCAAG                         GAATTGTCATCAGATTCATCTCAGCATGTTCGTTCAGCTTTGGCTTCAGTT
genomic: GGATTTTAAGTCCTCAGCTTGCAATTCAGCATATTCTTCCTTGTGTCAAGgtgggccaac ... gcatctgcagGAATTGTCATCAGATTCATCTCAGCATGTTCGTTCAGCTTTGGCTTCAGTT
EST: gi|300215963|gb|HO088589.1|HO088589
EST:     GGATTTTAAGTCCTCAGCTTGCAATTCAGCATATTCTTCCTTGTGTCAAG                         GAATTGTCATCAGATTCATCTCAGCATGTTCGTTCAGCTTTGGCTTCAGTT
genomic: GGATTTTAAGTCCTCAGCTTGCAATTCAGCATATTCTTCCTTGTGTCAAGgtgggccaac ... gcatctgcagGAATTGTCATCAGATTCATCTCAGCATGTTCGTTCAGCTTTGGCTTCAGTT
EST: gi|58654414|gb|CK043094.1|CK043094
EST:     GGATTTTAAGTCCTCAGCTTGCAATTCAGCATATTCTTCCTTGTGTCAAG                         GAATTGTCATCAGATTCATCTCAGCATGTTCGTTCAGCTTTGGCTTCAGTT
genomic: GGATTTTAAGTCCTCAGCTTGCAATTCAGCATATTCTTCCTTGTGTCAAGgtgggccaac ... gcatctgcagGAATTGTCATCAGATTCATCTCAGCATGTTCGTTCAGCTTTGGCTTCAGTT
EST: gi|86904336|gb|CI306754.1|CI306754
EST:     GGATTTTAAGTCCTCAGCTTGCAATTCAGCATATTCTTCCTTGTGTCAAG                         GAATTGTCATCAGATTCATCTCAGCATGTTCGTTCAGCTTTGGCTTCAGTT
genomic: GGATTTTAAGTCCTCAGCTTGCAATTCAGCATATTCTTCCTTGTGTCAAGgtgggccaac ... gcatctgcagGAATTGTCATCAGATTCATCTCAGCATGTTCGTTCAGCTTTGGCTTCAGTT
EST: gi|58652709|gb|CK041389.1|CK041389
EST:     GGATTTTAAGTCCTCAGCTTGCAATTCAGCATATTCTTCCTTGTGTCAAG                         GAATTGTCATCAGATTCATCTCAGCATGTTCGTTCAGCTTTGGCTTCAGTT
genomic: GGATTTTAAGTCCTCAGCTTGCAATTCAGCATATTCTTCCTTGTGTCAAGgtgggccaac ... gcatctgcagGAATTGTCATCAGATTCATCTCAGCATGTTCGTTCAGCTTTGGCTTCAGTT
EST: gi|38474762|gb|CF958895.1|CF958895
EST:     GGATTTTAAGTCCTCAGCTTGCAATTCAGCATATTCTTCCTTGTGTCAAG                         GAATTGTCATCAGATTCATCTCAGCATGTTCGTTCAGCTTTGGCTTCAGTT
genomic: GGATTTTAAGTCCTCAGCTTGCAATTCAGCATATTCTTCCTTGTGTCAAGgtgggccaac ... gcatctgcagGAATTGTCATCAGATTCATCTCAGCATGTTCGTTCAGCTTTGGCTTCAGTT
EST: gi|33654809|gb|CF277423.1|CF277423
EST:     GGATTTTAAGTCCTCAGCTTGCAATTCAGCATATTCTTCCTTGTGTCAAG                         GAATTGTCATCAGATTCATCTCAGCATGGTTCGTTCAGCTTTGGCTTCAGT
genomic: GGATTTTAAGTCCTCAGCTTGCAATTCAGCATATTCTTCCTTGTGTCAAGgtgggccaac ... gcatctgcagGAATTGTCATCAGATTCATCTCAGCATG-TTCGTTCAGCTTTGGCTTCAGT
EST: gi|58593044|gb|CF991352.1|CF991352
EST:     GGATTTTAAGTCCTCAGCTTGCAATTCAGCATATTCTTCCTTGTGTCAAG                         GAATTGTCATCAGATTCATCTCAGCATGTTCGTTCAGCTTTGGCTTCAGTT
genomic: GGATTTTAAGTCCTCAGCTTGCAATTCAGCATATTCTTCCTTGTGTCAAGgtgggccaac ... gcatctgcagGAATTGTCATCAGATTCATCTCAGCATGTTCGTTCAGCTTTGGCTTCAGTT
EST: gi|33796143|gb|CF323937.1|CF323937
EST:     GGATTTTAAGTCCTCAGCTTGCAATTCAGCATATTCTTCCTTGTGTCAAG                         GAATTGTCATCAGATTCATCTCAGCATGTTCGTTCAGCTTTGGCTTCAGTT
genomic: GGATTTTAAGTCCTCAGCTTGCAATTCAGCATATTCTTCCTTGTGTCAAGgtgggccaac ... gcatctgcagGAATTGTCATCAGATTCATCTCAGCATGTTCGTTCAGCTTTGGCTTCAGTT
EST: gi|29635602|gb|CB640611.1|CB640611
EST:     GGATTTTAAGTCCTCAGCTTGCAATTCAGCATATTCTTCCTTGTGTCAAG                         GAATTGTCATCAGATTCATCTCATCATGTTCGTTCAGCTTTGGCTTCAGTT
genomic: GGATTTTAAGTCCTCAGCTTGCAATTCAGCATATTCTTCCTTGTGTCAAGgtgggccaac ... gcatctgcagGAATTGTCATCAGATTCATCTCAGCATGTTCGTTCAGCTTTGGCTTCAGTT
EST: gi|58598714|gb|CK009242.1|CK009242
EST:     GGATTTTAAGTCCTCAGCTTGCAATTCAGCATATTCTTCCTTGTGTCAAG                         GAATTGTCATCAGATTCATCTCAGCATGTTCGTTCAGCTTTGGCTTCAGTT
genomic: GGATTTTAAGTCCTCAGCTTGCAATTCAGCATATTCTTCCTTGTGTCAAGgtgggccaac ... gcatctgcagGAATTGTCATCAGATTCATCTCAGCATGTTCGTTCAGCTTTGGCTTCAGTT
EST: gi|218487576|gb|FG960599.1|FG960599
EST:     GATTTTAAGCTCCTCAGCTTGCAATTCAGCATATTCTTCCTTTTGTCAAG                         GAATTGTCATCAGATTCATCTCAGCATGTGCGTTCAGCTTTGGCTTCAGTT
genomic: GATTTTAAG-TCCTCAGCTTGCAATTCAGCATATTCTTCCTTGTGTCAAGgtgggccaac ... gcatctgcagGAATTGTCATCAGATTCATCTCAGCATGTTCGTTCAGCTTTGGCTTCAGTT
EST: gi|300215769|gb|HO088395.1|HO088395
EST:     GGATTTTAAGTCCTCAGCTTGCAATTCAGCATATTCTTCCTTGTGTCAAG                         GAATTGTCATCAGATTCATCTCAGCATGTTCGTTCAGCTTTGGCTTC
genomic: GGATTTTAAGTCCTCAGCTTGCAATTCAGCATATTCTTCCTTGTGTCAAGgtgggccaac ... gcatctgcagGAATTGTCATCAGATTCATCTCAGCATGTTCGTTCAGCTTTGGCTTC
EST: gi|3768380|gb|AU032407.1|AU032407
EST:     GGATTTTAAGTCCTCAGCTTGCAATTCAGCATATTCTTCCTTGTGTCAAG                         GAATTGTCATCAGATTCATCTCAGCATGTTCGTTCAGCTTTGGCTTCAGTT
genomic: GGATTTTAAGTCCTCAGCTTGCAATTCAGCATATTCTTCCTTGTGTCAAGgtgggccaac ... gcatctgcagGAATTGTCATCAGATTCATCTCAGCATGTTCGTTCAGCTTTGGCTTCAGTT
EST: gi|58655438|gb|CK044118.1|CK044118
EST:     GGATTTTAAGTCCTCAGCTTGCAATTCAGCATATTCTTCCTTGTGTCAAG                         GAATTGTCATCAGATTCATCTCAGCATGTTCGTTCAGCTTTGGCTTCAGTT
genomic: GGATTTTAAGTCCTCAGCTTGCAATTCAGCATATTCTTCCTTGTGTCAAGgtgggccaac ... gcatctgcagGAATTGTCATCAGATTCATCTCAGCATGTTCGTTCAGCTTTGGCTTCAGTT
EST: gi|55409620|gb|CV721996.1|CV721996
EST:     GGATTTTAAGTCCTCAGCTTGCAATTCAGCATATTCTTCCTTGTGTCAAG                         GAATTGTCATTAGATTCATCTCAGCATGTTCGTTCAGCTTTGGCTTCAGTT
genomic: GGATTTTAAGTCCTCAGCTTGCAATTCAGCATATTCTTCCTTGTGTCAAGgtgggccaac ... gcatctgcagGAATTGTCATCAGATTCATCTCAGCATGTTCGTTCAGCTTTGGCTTCAGTT
EST: gi|33676187|gb|CF304426.1|CF304426
EST:     GGATTTTAAGTCCTCAGCTTGCAATTCAGCATATTCTTCCTTGTGTCAAG                         GAATTGTCATCAGATTCATCTCAGCATGTTCGTTCAGCTTTGGCTTCAGTT
genomic: GGATTTTAAGTCCTCAGCTTGCAATTCAGCATATTCTTCCTTGTGTCAAGgtgggccaac ... gcatctgcagGAATTGTCATCAGATTCATCTCAGCATGTTCGTTCAGCTTTGGCTTCAGTT
EST: gi|33656227|gb|CF278841.1|CF278841
EST:     GGATTTTAAGTCCTCAGCTTGCAATTCAGCATATTCTTCCTTGTGTCAAG                         GAATTGTCATCAGATTCATCTCAGCATGTTCGTTCAGCTTTGGCTTCAGTT
genomic: GGATTTTAAGTCCTCAGCTTGCAATTCAGCATATTCTTCCTTGTGTCAAGgtgggccaac ... gcatctgcagGAATTGTCATCAGATTCATCTCAGCATGTTCGTTCAGCTTTGGCTTCAGTT
EST: gi|58678838|gb|CK067525.1|CK067525
EST:     GGATTTTAAGTCCTCAGCTTGCAATTCAGCATATTCTTCCTTGTGTCAAG                         GAATTGTCATCAGATTCATCTCAGCATGTTCGTTCAGCTTTGGCTTCAGTT
genomic: GGATTTTAAGTCCTCAGCTTGCAATTCAGCATATTCTTCCTTGTGTCAAGgtgggccaac ... gcatctgcagGAATTGTCATCAGATTCATCTCAGCATGTTCGTTCAGCTTTGGCTTCAGTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tggttttctgctgctgtttattcccagcaaactaacttgccaactgcatctgcagGAATTGTCATCAGATTCATCTCAGCATGTTCGTTCAGCTTTGGCTTCAGTTATTATGGGAATGGCCCCGGTCTTGGGAAAG
                             aactaac  putative branch site (score: 1)
              tgtttatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgggccaacgcttaaccaaatattattaactggttttctgctgctgtttattcccagcaaactaacttgccaactgcatctgcagGAATTGTCATCAGATTCATCTCAGCATGTTCGTTCAGCTTTGGCTTCAGTTATTATGGGAATGGCCCCGGTCTTGGGAAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TCAGCT