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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgcagtagcttccattttttgtcatataaggatcatctttcaggcatgctatctgaaaaaaaggaactgctggattgttttcatgatatagtttgttcagACAGGTTGGAGAACATACCGTAGGCCAGACGACAAGTCCGGTGGACATGGAGTTGGATGGAGCCCAATCATTCCCTACAGCTTCAAAGTTCGTGATGGCT

Basic information

species Oryza sativa
transcript LOC_Os12g08830.2
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os12g08830.2 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G087590_T01 (Zea mays), 3'ss of exon 1
tgcagtagcttccattttttgtcatataaggatcatctttcaggcatgctatctgaaaaaaaggaactgctggattgttttcatgatatagtttg-----ttcagACAGGTTGGAGAACATACCGTAGGCCAGACGACAAGTCCGGTGGACATGGAGTTGGATGGAGCCCAATCATTCCCTACAGCTTCAAAGTTCGTGATGGCT----
                    || |  |     || |||||      |  | |||| |   ||  | ||| || ||||||||||||||   | | |     ||||||||||||||||||| ||||| ||||||||||||||||||||||| || |||||||| |||||||| ||||| || ||||||||||||||||  || ||||    
--------------------gtgagctcttcttcttctttttcttct-ttctctgcagtgaaata-ctgttgaattgttttcatgatgctgatcgaatcgttcagacagGTTGGAGAACGTACCGCAGGCCAGACGACAAGTCCGGTGGCCACGGAGTTGGCTGGAGCCCCATCATCCCGTACAGCTTCAAAGTTCCAGACGGCTGGGA

upper sequence: LOC_Os12g08830.2 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G425136_T01 (Zea mays), 3'ss of exon 1
tgcagtagcttccattttttgtcatataaggatcatctttcaggcatgctatctgaaaaaaaggaactgctggattgttttcatgatatagtttg-----ttcagACAGGTTGGAGAACATACCGTAGGCCAGACGACAAGTCCGGTGGACATGGAGTTGGATGGAGCCCAATCATTCCCTACAGCTTCAAAGTTCGTGATGGCT-----
                                | | || |    | |  |     | |   |   | || || ||||||||||||||   | | |     || |||||||||||||||| ||| | ||||||||||||||||||||||| || |||||||| |||||||| |||||   ||   |||     | | ||| |||       
-------------------------------gtgagctcttcttcttctttctctacagtgaaatattgttgaattgttttcatgatgctgatcgaatcgtttagacagGTTGGAGAACGTACTGCAGGCCAGACGACAAGTCCGGTGGCCACGGAGTTGGCTGGAGCCCCATCATGTGCTGTGGCTGTGCGGCT-GTGCTGGTGGGGAG

upper sequence: LOC_Os12g08830.2 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G087590_T05 (Zea mays), 3'ss of exon 1
tgcagtagcttccattttttgtcatataaggatcatctttcaggcatgctatctgaaaaaaaggaactgctggattgttttcatgatatagtttg-----ttcagACAGGTTGGAGAACATACCGTAGGCCAGACGACAAGTCCGGTGGACATGGAGTTGGATGGAGCCCAATCATTCCCTACAGCTTCAAAGTTCGTGATGGCT
                    || |  |     || |||||      |  | |||| |   ||  | ||| || ||||||||||||||   | | |     ||||||||||||||||||| ||||| ||||||||||||||||||||||| || |||||||| |||||||| ||||| || ||||||||||||||||  || ||||
--------------------gtgagctcttcttcttctttttcttct-ttctctgcagtgaaata-ctgttgaattgttttcatgatgctgatcgaatcgttcagACAGGTTGGAGAACGTACCGCAGGCCAGACGACAAGTCCGGTGGCCACGGAGTTGGCTGGAGCCCCATCATCCCGTACAGCTTCAAAGTTCCAGACGGCT

upper sequence: LOC_Os12g08830.2 (Oryza sativa), 3'ss of exon 1
lower sequence: GLYMA04G42010.1 (Glycine max), 3'ss of exon 1
tgcagtagcttccattttttgtcatataaggatcatctttcaggcatgctatctgaaaaaaaggaactgctggattgttttcatgatatagtttgttcagACAGGTTGGAGAACATACCGTAGGCCAGACGACAAGTCCGGTGGACATGGAGTTGGATGGAGCCCAATCATTCCCTACAGCTTCAAAGTTCGTGATGGCT----
|  |  |   |   ||| |||   | | ||  |  |   |   |      |        || | || ||    | |||   ||    |   |||| ||||||||||||||| || || || ||||| || || ||||| || |||||||| ||||||||||| || || ||||| |||||||||| ||| | ||| |  |    
tcgacaaatgttagtttgttggagtgtcagttttgttaatagagaggatcaagatctttaatgaaagtgacataatgtaggca----agtatttgatcagacagGTTGGAGGACCTATCGCAGGCCGGATGAGAAGTCAGGAGGACATGGTGTTGGATGGAGTCCTATTATTCCATACAGCTTCAGAGTGCCTGAAGAATGGGA

upper sequence: LOC_Os12g08830.2 (Oryza sativa), 3'ss of exon 1
lower sequence: GLYMA06G12760.1 (Glycine max), 3'ss of exon 1
tgcagtagcttccattttttgtcatataaggatcatctttcaggcatgctatctgaaaaaaaggaactgctggattgttttcatgatata-gtttgttcagACAGGTTGGAGAACATACCGTAGGCCAGACGACAAGTCCGGTGGACATGGAGTTGGATGGAGCCCAATCATTCCCTACAGCTTCAAAGTTCGTGATGGCT----
     |||       ||  | |  || || | |||| ||    | |    |  | || |     ||     |     |  |   |  |    |||| ||||||||||||||| || || || ||||| || || ||||| || |||||||| ||||||||||| || || ||||| |||||||||| ||| |   | |  |    
-----taggcaaatgttagtttggtagaatgttcattttgttagtagagaagatcaagattttaaatgaaagtgacataatgtaggcaagcatttgatcagacagGTTGGAGGACGTATCGCAGGCCGGATGAGAAGTCTGGAGGACATGGTGTTGGATGGAGTCCTATTATTCCATACAGCTTCAGAGTGCCCAAAGAATGGGA

upper sequence: LOC_Os12g08830.2 (Oryza sativa), 3'ss of exon 1
lower sequence: AT1G77090.1 (Arabidopsis thaliana), 3'ss of exon 1
tgcagtagcttccattttttgtcatataaggatcatctttcaggcatgctatctgaaaaaa-aggaactgctggattgttttcatgatatagtt----tgttcagACAGGTTGGAGAACATACCGTAGGCCAGACGACAAGTCCGGTGGACATGGAGTTGGATGGAGCCCAATCATTCCCTACAGCTTCAAAGTTCGTGATGGCT----
        | |  || ||| | | | |    ||    | |  |   ||   | ||| |  | || |  ||     |||||    | || || ||    || ||||||||||||||||||||||||||| |||||||| ||||| || || ||||| ||||| ||||| || || || || |||  |||    |||| | | |  |    
--------cataaatctttaggctt-tggacattgattcttggagttgtattatgacagtatagtagttgggaatttgttggtgtaatgtaattgtaatgctcagacagGTTGGAGAACATACCGTAGACCAGACGAGAAGTCAGGAGGGCATGGTGTTGGTTGGAGTCCTATTATCCCTTACGCCTTTTCGGTTCCTCAAGATTGGAA

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|88351000|gb|CI620660.1|CI620660
EST:     GGGCCTTCTGGCTGGGCGGATCCCTGGGCTCTCTGACCCTGATGAAAAAG                         ---G-TTGGAGAACATACCGTAGGCC
genomic: GGGCCTTCTGGCTGGGCGGATCCCTGGGCTCTCTGACCCTGATGAAAAAGgttggttctt ... gtttgttcagACAGGTTGGAGAACATACCGTAGGCC
EST: gi|88432895|gb|CI690751.1|CI690751
EST:     GGGCCTTCTGGCTGGGCGGATCCCTGGGCTCTCTGACCCTGATGAAAAAG                         ---G-TTGGAGAACATACCGTAGG
genomic: GGGCCTTCTGGCTGGGCGGATCCCTGGGCTCTCTGACCCTGATGAAAAAGgttggttctt ... gtttgttcagACAGGTTGGAGAACATACCGTAGG
EST: gi|33801711|gb|CF326727.1|CF326727
EST:     GGGCCTTCTGGCTGGGCGGATCCCTGGGCTCTCTGACCCTGATGAAAAAG                         ---G-TTGGAGAACATACCGTAGGCCAGACGACAAGTCCGGTGGACATGGA
genomic: GGGCCTTCTGGCTGGGCGGATCCCTGGGCTCTCTGACCCTGATGAAAAAGgttggttctt ... gtttgttcagACAGGTTGGAGAACATACCGTAGGCCAGACGACAAGTCCGGTGGACATGGA
EST: gi|88429169|gb|CI690057.1|CI690057
EST:     GGGCCTTCTGGCTGGGCGGATCCCTGGGCTCTCTGACCCTGATGAAAAAG                         ---G-TTGGAGAACATACCGTAGGCCAGACGA
genomic: GGGCCTTCTGGCTGGGCGGATCCCTGGGCTCTCTGACCCTGATGAAAAAGgttggttctt ... gtttgttcagACAGGTTGGAGAACATACCGTAGGCCAGACGA
EST: gi|88579972|gb|CI691969.1|CI691969
EST:     GGGCCTTCTGGCTGGGCGGATCCCTGGGCTCTCTGACCCTGATGAAAAAG                         ---G-TTGGAGAACATACCGTAGGCCAGACGACAAGTCCG
genomic: GGGCCTTCTGGCTGGGCGGATCCCTGGGCTCTCTGACCCTGATGAAAAAGgttggttctt ... gtttgttcagACAGGTTGGAGAACATACCGTAGGCCAGACGACAAGTCCG
EST: gi|33664741|gb|CF295708.1|CF295708
EST:     GGGCCTTCTGGCTGGGCGGATCCCTGGGCTCTCTGACCCTGATGAAAAAG                         ---G-TTGGAGAACATACCGTAGGCCAGACGACAAGTCCGGTGGACATGGA
genomic: GGGCCTTCTGGCTGGGCGGATCCCTGGGCTCTCTGACCCTGATGAAAAAGgttggttctt ... gtttgttcagACAGGTTGGAGAACATACCGTAGGCCAGACGACAAGTCCGGTGGACATGGA
EST: gi|66928198|gb|CX115046.1|CX115046
EST:     GGGCCTTCTGGCTGGGAGGATCCCTGGGCTCTCTGACCCTGATGAAAAAG                         ---G-TTGGAGAACATACCGTAGGCCAGACGACAAGTCCGGTGGACATGGA
genomic: GGGCCTTCTGGCTGGGCGGATCCCTGGGCTCTCTGACCCTGATGAAAAAGgttggttctt ... gtttgttcagACAGGTTGGAGAACATACCGTAGGCCAGACGACAAGTCCGGTGGACATGGA
EST: gi|58607456|gb|CK035489.1|CK035489
EST:     GGGCCTTCTGGCTGGGAGGATCCCTGGGCTCTCTGACCCTGATGAAAAAG                         ACAGGTTGGAGAACATACCGTAGGCCAGACGACAAGTCCGGTGGACATGGA
genomic: GGGCCTTCTGGCTGGGCGGATCCCTGGGCTCTCTGACCCTGATGAAAAAGgttggttctt ... gtttgttcagACAGGTTGGAGAACATACCGTAGGCCAGACGACAAGTCCGGTGGACATGGA
EST: gi|14571429|gb|BI118797.1|BI118797
EST:     GGGCCTTCTGGCTGGGAGGATCCCTGGGCTCTCTGACCCTGATG--AAA-                         A-AGGTTGGAGAACATACCGTAGGCCAGACGACAAGTCCGGTGGACATGGA
genomic: GGGCCTTCTGGCTGGGCGGATCCCTGGGCTCTCTGACCCTGATGAAAAAGgttggttctt ... gtttgttcagACAGGTTGGAGAACATACCGTAGGCCAGACGACAAGTCCGGTGGACATGGA
EST: gi|88433746|gb|CI582068.1|CI582068
EST:     GGGCCTTCTGGCTGGGCGGATCCCTGGGCTCTCTGACCCTGATGAAAAAG                         ---G-TTGGAGAACATACCGTAGGCCAGACGACAAGTCCGGTGGACATGGA
genomic: GGGCCTTCTGGCTGGGCGGATCCCTGGGCTCTCTGACCCTGATGAAAAAGgttggttctt ... gtttgttcagACAGGTTGGAGAACATACCGTAGGCCAGACGACAAGTCCGGTGGACATGGA
EST: gi|88381593|gb|CI682257.1|CI682257
EST:     GGGCCTTCTGGCTGGGCGGATCCCTGGGCTCTCTGACCCTGATGAAAAAG                         ---G-TTGGAGAACATACCGTAGGCCAGACGACAAGTCCGGTGGACATGGA
genomic: GGGCCTTCTGGCTGGGCGGATCCCTGGGCTCTCTGACCCTGATGAAAAAGgttggttctt ... gtttgttcagACAGGTTGGAGAACATACCGTAGGCCAGACGACAAGTCCGGTGGACATGGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atgctatctgaaaaaaaggaactgctggattgttttcatgatatagtttgttcagACAGGTTGGAGAACATACCGTAGGCCAGACGACAAGTCCGGTGGACATGGAGTTGGATGGAGCCCAATCATTCCCTACAGCTTCAAAGTTCGTGATGGCT
                                              tttgttc  CT-rich tract
        tgaaaaaaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgcagtagcttccattttttgtcatataaggatcatctttcaggcatgctatctgaaaaaaaggaactgctggattgttttcatgatatagtttgttcagACAGGTTGGAGAACATACCGTAGGCCAGACGACAAGTCCGGTGGACATGGAGTTGGATGGAGCCCAATCATTCCCTACAGCTTCAAAGTTCGTGATGGCT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GATGGA
tgcagta
- - - -gcttcca
- - - - - - - - - - - - - - - - - - - - - ggcatgc
- - - - - - - - - - - - - - - - - - - - - - - - - - - -aaaaaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -actgctg