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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtccatctctctctctctctctcgctctccctctccctcgctctctgtgacaagttgttctcatatgtactgtatcttctttgcagCATGTCTGTTGTAGAGGACAGCTTTGAATATCTTGATGCGCCAGTTGAGAGGATTGCTGGAGCTGATGTGCCCATGCCCTACGCTGCCAACCTTGAGAGG

Basic information

species Oryza sativa
transcript LOC_Os08g42410.1
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os08g42410.2 (Oryza sativa), 3'ss of exon 10
lower sequence: GRMZM2G043198_T02 (Zea mays), 3'ss of exon 11
gtccatctctctctctctctctcgctctccctctccctcgctctctgtgacaagttgttctcata-tgtactgtatctt--ctttgcagCATGTCTGTTGTAGAGGACAGCTTTGAATATCTTGATGCGCCAGTTGAGAGGATTGCTGGAGCTGATGTGCCCATGCCCTACGCTGCCAACCTTGAGAGG
|||   | ||||| ||| ||| | |  ||||  |   |     | | |     |    |||| || ||   || |   |  ||||||||||||||||||||||||||||||||||| ||||||||||| ||||| |||||||||||||||||||||||||||||||| |||||||||||||||||||||
gtcggccactctccctccctccctccttcccaatgtataa---tgtatagtctgcgtctctcgtaatgggttgaaatgtgcctttgcagCATGTCTGTTGTAGAGGACAGCTTTGAGTATCTTGATGCACCAGTCGAGAGGATTGCTGGAGCTGATGTGCCCATGCCGTACGCTGCCAACCTTGAGAGG

upper sequence: LOC_Os08g42410.2 (Oryza sativa), 3'ss of exon 10
lower sequence: GLYMA02G46380.1 (Glycine max), 3'ss of exon 12
gtccatctctctctctctctctcgctctccctctccctcgctctctg--tgacaagttgttctcatatgtac-tgtatcttctttgcagCATGTCTGTTGTAGAGGACAGCTTTGAATATCTTGATGCGCCAGTTGAGAGGATTGCTGGAGCTGATGTGCCCATGCCCTACGCTGCCAACCTTGAGAGG
||  |||||| |   |   | |   | |   |     |  ||  |||  | ||   | |   ||||  ||   |   |||  |   |||||  |||||  | ||||| || ||||  ||||||||||| || |||||||| ||||| || |||||||| |||||||| || || || || || || || 
gtttatctctttacattgatttgtttttgtatgaatgtatcttactggttaactcttggcaatcatgagtgtgtacttctcttgcacagCACATCTGTCATTGAGGAGAGTTTTGGTTATCTTGATGCACCGGTTGAGAGAATTGCCGGGGCTGATGTTCCCATGCCATATGCAGCAAATCTGGAAAGA

upper sequence: LOC_Os08g42410.2 (Oryza sativa), 3'ss of exon 10
lower sequence: GLYMA14G36540.3 (Glycine max), 3'ss of exon 12
gtccatctctctctctctctctcgctctccctctccctcgctctctg--tgacaagttgttctcatatgtac-tgtatcttctttgca--gCATGTCTGTTGTAGAGGACAGCTTTGAATATCTTGATGCGCCAGTTGAGAGGATTGCTGGAGCTGATGTGCCCATGCCCTACGCTGCCAACCTTGAGAGG
||  |||||| |   |   | |   | ||  |   | |  ||  |||  | ||   | |   |||||||    ||||  |   |||||  |||  |||||  | || || || ||||  ||||||||||| || |||||||| |||||||| |||||||| |||||||| || || || || || || || 
gtttatctctttacattgatttgtttttctatgaacgtatcttactggttaactcttggcaatcatatgagtgtgtacttctcttgcacagCACATCTGTCATTGAAGAAAGTTTTGGTTATCTTGATGCACCCGTTGAGAGAATTGCTGGGGCTGATGTTCCCATGCCTTATGCAGCAAATCTGGAAAGA

upper sequence: LOC_Os08g42410.2 (Oryza sativa), 3'ss of exon 10
lower sequence: Vv01s0146g00310.t01 (Vitis vinifera), 3'ss of exon 13
gtccatctctctctctctctctcgctctccctctccctcgctctctgtgacaagttgtt-------ctcatatgtactgtatcttctttgcagCATGTCTGTTGTAGAGGACAGCTTTGAATATCTTGATGCGCCAGTTGAGAGGATTGCTGGAGCTGATGTGCCCATGCCCTACGCTGCCAACCTTGAGAGG
       |   ||||||||    | | | | | |    |    | | ||| |||   ||       || | |    |||  |||| |   ||||||| ||||||| ||||| |||||||  ||||||||||| ||||| || |||||||| || |||||||| |||||||| || ||||| || || ||||| 
-----gtttattctctctccactgatgttcgtttgatgcaggttgtttgataaggcattatatgtacttacactatctgcttcttttaaacagCATGGCTGTTGTTGAGGAGAGCTTTGGTTATCTTGATGCACCAGTGGAAAGGATTGCCGGGGCTGATGTTCCCATGCCTTATGCTGCTAATCTCGAGAGA

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|27921334|gb|CB097142.1|CB097142
EST:     GTTGGCGCTGAAATATG                         CATGTCTGTTGTAGAGGACAGCTTTGAATATCTTGATGCGCCAGTTGAGAG
genomic: GTTGGCGCTGAAATATGgtccatctct ... ttctttgcagCATGTCTGTTGTAGAGGACAGCTTTGAATATCTTGATGCGCCAGTTGAGAG
EST: gi|86540582|gb|CI180788.1|CI180788
EST:     GTAACCCTTGAAGAAGGATTTCCACAACATGGGGTTGGCGCTGAAATATG                         CATGTCTGTTGTAGAGGACAGCTTTGAATATCTTGATGCGCCAGTTGAGAG
genomic: GTAACCCTTGAAGAAGGATTTCCACAACATGGGGTTGGCGCTGAAATATGgtccatctct ... ttctttgcagCATGTCTGTTGTAGAGGACAGCTTTGAATATCTTGATGCGCCAGTTGAGAG
EST: gi|88961781|gb|CI096947.1|CI096947
EST:     CGCTGAAATATG                         CATGTCTGTTGTAGAGGACAGCTTTGAATATCTTGATGCGCCAGTTGAGAG
genomic: CGCTGAAATATGgtccatctct ... ttctttgcagCATGTCTGTTGTAGAGGACAGCTTTGAATATCTTGATGCGCCAGTTGAGAG
EST: gi|89191954|gb|CI250895.1|CI250895
EST:     GTAACCCTTGAAGAAGGATTTCCACAACATGGGGTTGGCGCTGAAATATG                         CATGTCTGTTGTAGAGGACAGCTTTGAATATCTTGATGCGCCAGTTGAGAG
genomic: GTAACCCTTGAAGAAGGATTTCCACAACATGGGGTTGGCGCTGAAATATGgtccatctct ... ttctttgcagCATGTCTGTTGTAGAGGACAGCTTTGAATATCTTGATGCGCCAGTTGAGAG
EST: gi|58608415|gb|CK036448.1|CK036448
EST:     GTAACCCTTGAAGAAGGATTTCCACAACATGGGGTTGGCGCTGAAATATG                         CATGTCTGTTGTAGAGGACAGCTTTGAATATCTTGATGCGCCAGTTGAGAG
genomic: GTAACCCTTGAAGAAGGATTTCCACAACATGGGGTTGGCGCTGAAATATGgtccatctct ... ttctttgcagCATGTCTGTTGTAGAGGACAGCTTTGAATATCTTGATGCGCCAGTTGAGAG
EST: gi|218478794|gb|FG960305.1|FG960305
EST:     GTAACCCTTGAAGAAGGATTTCCACAACATGGGGTTGGCGCTGAAATATG                         CATGTCTGTTGTAGAGGACAGCTTTGAATATCTTGATGCGCCAGTTGAGAG
genomic: GTAACCCTTGAAGAAGGATTTCCACAACATGGGGTTGGCGCTGAAATATGgtccatctct ... ttctttgcagCATGTCTGTTGTAGAGGACAGCTTTGAATATCTTGATGCGCCAGTTGAGAG
EST: gi|87020958|gb|CI269675.1|CI269675
EST:     GTAACCCTTGAAGAAGGATTTCCACAACATGGGGTTGGCGCTGAAATATG                         CATGTCTGTTGTAGAGGACAGCTTTGAATATCTTGATGCGCCAGTTGAGAG
genomic: GTAACCCTTGAAGAAGGATTTCCACAACATGGGGTTGGCGCTGAAATATGgtccatctct ... ttctttgcagCATGTCTGTTGTAGAGGACAGCTTTGAATATCTTGATGCGCCAGTTGAGAG
EST: gi|88251000|gb|CI349230.1|CI349230
EST:     GCTGAAATATG                         CATGTCTGTTGTAGAGGACAGCTTTGAATATCTTGATGCGCCAGTTGAGAG
genomic: GCTGAAATATGgtccatctct ... ttctttgcagCATGTCTGTTGTAGAGGACAGCTTTGAATATCTTGATGCGCCAGTTGAGAG
EST: gi|88837903|gb|CI371481.1|CI371481
EST:     ATTTCCACAACATGGGG-TGGCGCTGAAATATG                         CATGTCTGTTGTAGAGGACAGCTTTGAATATCTTGATGCGCCAGTTGAGAG
genomic: ATTTCCACAACATGGGGTTGGCGCTGAAATATGgtccatctct ... ttctttgcagCATGTCTGTTGTAGAGGACAGCTTTGAATATCTTGATGCGCCAGTTGAGAG
EST: gi|38472326|gb|CF956457.1|CF956457
EST:     GTAACCCTTGAAGAAGGATTTCCACAACATGGGGTTGGCGCTGAAATATG                         CATGTCTGTTGTAGAGGACAGCTTTGA
genomic: GTAACCCTTGAAGAAGGATTTCCACAACATGGGGTTGGCGCTGAAATATGgtccatctct ... ttctttgcagCATGTCTGTTGTAGAGGACAGCTTTGA
EST: gi|89168103|gb|CI109307.1|CI109307
EST:     TTGGCGCTGAAATATG                         CATGTCTGTTGTAGAGGACAGCTTTGAATATCTTGATGCGCCAGTTGAGAG
genomic: TTGGCGCTGAAATATGgtccatctct ... ttctttgcagCATGTCTGTTGTAGAGGACAGCTTTGAATATCTTGATGCGCCAGTTGAGAG
EST: gi|33824376|gb|CF338005.1|CF338005
EST:     TANACCCTTGAAGAAGGATTTCCACAACATGGGGTTGGCGCTGAAATATG                         CATGTCTGTTGTAGAGGACAGCTTTGAATATCTTGATGCGCCAGTTGAGAG
genomic: TA-ACCCTTGAAGAAGGATTTCCACAACATGGGGTTGGCGCTGAAATATGgtccatctct ... ttctttgcagCATGTCTGTTGTAGAGGACAGCTTTGAATATCTTGATGCGCCAGTTGAGAG
EST: gi|29614435|gb|CB619448.1|CB619448
EST:     GTAACCCTTGAAGAAGGATTTCCACAACATGGGGTTGGCGCTGAAATATG                         CATGTCTGTTGTAGAGGACAGCTTTGAATATCTTGATGCGCCAGTTGAGAG
genomic: GTAACCCTTGAAGAAGGATTTCCACAACATGGGGTTGGCGCTGAAATATGgtccatctct ... ttctttgcagCATGTCTGTTGTAGAGGACAGCTTTGAATATCTTGATGCGCCAGTTGAGAG
EST: gi|88844973|gb|CI022327.1|CI022327
EST:     GTAACCCTTGAAGAAGGATTTCCACAACATGGGGTTGGCGCTGAAATATG                         CATGTCTGTTGTAGAGGACAGCTTTGAATATCTTGATGCGCCAGTTGAGAG
genomic: GTAACCCTTGAAGAAGGATTTCCACAACATGGGGTTGGCGCTGAAATATGgtccatctct ... ttctttgcagCATGTCTGTTGTAGAGGACAGCTTTGAATATCTTGATGCGCCAGTTGAGAG
EST: gi|89192853|gb|CI050151.1|CI050151
EST:     GTAACCCTTGAAGAAGGATTTCCACAACATGGGGTTGGCGCTGAAATATG                         CATGTCTGTTGTAGAGGACAGCTTTGAATATCTTGATGCGCCAGTTGAGAG
genomic: GTAACCCTTGAAGAAGGATTTCCACAACATGGGGTTGGCGCTGAAATATGgtccatctct ... ttctttgcagCATGTCTGTTGTAGAGGACAGCTTTGAATATCTTGATGCGCCAGTTGAGAG
EST: gi|86538636|gb|CI178842.1|CI178842
EST:     GGGTTGGCGCTGAAATATG                         CATGTCTGTTGTAGAGGACAGCTTTGAATATCTTGATGCGCCAGTTGAGAG
genomic: GGGTTGGCGCTGAAATATGgtccatctct ... ttctttgcagCATGTCTGTTGTAGAGGACAGCTTTGAATATCTTGATGCGCCAGTTGAGAG
EST: gi|88991256|gb|CI108643.1|CI108643
EST:     TTGGCTCTGAAATATG                         CATGTCTGTTGTAGAGGACAGCTTTGAATATCTTGATGCGCCAGTTGAGAG
genomic: TTGGCGCTGAAATATGgtccatctct ... ttctttgcagCATGTCTGTTGTAGAGGACAGCTTTGAATATCTTGATGCGCCAGTTGAGAG
EST: gi|42591826|gb|CK738312.1|CK738312
EST:     GTAACCCTTGAAGAAGGATTTCCACAACATGGGGTTGGCGCTGAAATATG                         CATGTCTGTTGTAGAGGACAGCTTTGAATATCTTGATGCGCCAGTTGAGAG
genomic: GTAACCCTTGAAGAAGGATTTCCACAACATGGGGTTGGCGCTGAAATATGgtccatctct ... ttctttgcagCATGTCTGTTGTAGAGGACAGCTTTGAATATCTTGATGCGCCAGTTGAGAG
EST: gi|38475005|gb|CF959138.1|CF959138
EST:     GTAACCCTTGAAGAAGGATTTCCACAACATGGGGTTGGCGCTGAAATATG                         CATGTCTGTTGTAGAGGACAGCTTTGAATATCTTGATGCGCCAGTTGAGAG
genomic: GTAACCCTTGAAGAAGGATTTCCACAACATGGGGTTGGCGCTGAAATATGgtccatctct ... ttctttgcagCATGTCTGTTGTAGAGGACAGCTTTGAATATCTTGATGCGCCAGTTGAGAG
EST: gi|88960452|gb|CI006413.1|CI006413
EST:     GTAACCCTTGAAGAAGGATTTCCACAACATGGGGTTGGCGCTGAAATATG                         CATGTCTGTTGTAGAGGACAGCTTTGAATATCTTGATGCGCCAGTTGAGAG
genomic: GTAACCCTTGAAGAAGGATTTCCACAACATGGGGTTGGCGCTGAAATATGgtccatctct ... ttctttgcagCATGTCTGTTGTAGAGGACAGCTTTGAATATCTTGATGCGCCAGTTGAGAG
EST: gi|86854408|gb|CI256530.1|CI256530
EST:     GTAACCCTTGAAGAAGGATTTCCACAACATGGGGTTGGCGCTGAAATATG                         CATGTCTGTTGTAGAGGACAGCTTTGAATATCTTGATGCGCCAGTTGAGAG
genomic: GTAACCCTTGAAGAAGGATTTCCACAACATGGGGTTGGCGCTGAAATATGgtccatctct ... ttctttgcagCATGTCTGTTGTAGAGGACAGCTTTGAATATCTTGATGCGCCAGTTGAGAG
EST: gi|86427084|gb|CI072181.1|CI072181
EST:     GCTGAAATATG                         CATGTCTGTTGTAGAGGACAGCTTTGAATATCTTGATGCGCCAGTTGAGAG
genomic: GCTGAAATATGgtccatctct ... ttctttgcagCATGTCTGTTGTAGAGGACAGCTTTGAATATCTTGATGCGCCAGTTGAGAG
EST: gi|86823435|gb|CI256396.1|CI256396
EST:     GTAACCCTTGAAGAAGGATTTCCACAACATGGGGTTGGCGCTGAAATATG                         CATGTCTGTTGTAGAGGACAGCTTTGAATATCTTGATGCGCCAGTTGAGAG
genomic: GTAACCCTTGAAGAAGGATTTCCACAACATGGGGTTGGCGCTGAAATATGgtccatctct ... ttctttgcagCATGTCTGTTGTAGAGGACAGCTTTGAATATCTTGATGCGCCAGTTGAGAG
EST: gi|88245198|gb|CI245047.1|CI245047
EST:     GTAACCCTTGAAGAAGGATTTCCACAACATGGGGTTGGCGCTGAAATATG                         CATGTCTGTTGTAGAGGACAGCTTTGAATATCTTGATGCGCCAGTTGAGAG
genomic: GTAACCCTTGAAGAAGGATTTCCACAACATGGGGTTGGCGCTGAAATATGgtccatctct ... ttctttgcagCATGTCTGTTGTAGAGGACAGCTTTGAATATCTTGATGCGCCAGTTGAGAG
EST: gi|86495018|gb|CI137651.1|CI137651
EST:     GTAACCCTTGAAGAAGGATTTCCACAACATGGGGTTGGCGCTGAAATATG                         CATGTCTGTTGTAGAGGACAGCTTTGAATATCTTGATGCGCCAGTTGAGAG
genomic: GTAACCCTTGAAGAAGGATTTCCACAACATGGGGTTGGCGCTGAAATATGgtccatctct ... ttctttgcagCATGTCTGTTGTAGAGGACAGCTTTGAATATCTTGATGCGCCAGTTGAGAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tctccctcgctctctgtgacaagttgttctcatatgtactgtatcttctttgcagCATGTCTGTTGTAGAGGACAGCTTTGAATATCTTGATGCGCCAGTTGAGAGGATTGCTGGAGCTGATGTGCCCATGCCCTACGCTGCCAACCTTGAGAGG
                                         tatcttcttt  CT-rich tract
                               atatgta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtccatctctctctctctctctcgctctccctctccctcgctctctgtgacaagttgttctcatatgtactgtatcttctttgcagCATGTCTGTTGTAGAGGACAGCTTTGAATATCTTGATGCGCCAGTTGAGAGGATTGCTGGAGCTGATGTGCCCATGCCCTACGCTGCCAACCTTGAGAGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGAGG