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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtagtattatgaaatcctaattttctgatggtttctgggcaactaattcaagatcgaattcatcgttttgtaccacattgtctctcattcagaacatgcagaaattcttgttctaaatttcaccatatcttcgctgtgtgcagAAAGCGCAAACCTCGGTGATCAAAGCCAACCTGAACCCTGTCTGGAACGAAGAACTCAAGCTCTCTGTTCCTCAGCAATACGGCCCTCTCAAACTG

Basic information

species Oryza sativa
transcript LOC_Os02g10480.3
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g10480.1 (Oryza sativa), 3'ss of exon 7
lower sequence: GRMZM2G138349_T04 (Zea mays), 3'ss of exon 3
gtagtattatgaaatcctaattttctgatggtttctgggcaactaattcaagatcgaattcatcgttttgtaccacattgtctctcattcagaacatgcagaaattcttgttctaaatttcaccatatcttcgctgtgtgcagAAAGCGCAAACCTCGGTGATCAAAGCCAACCTGAACCCTGTCTGGAACGAAGAACTCAAGCTCTCTGTTCCTCAGCAATACGGCCCTCTCAAACTG
                                                     |    ||  |||||||||      | |  || ||  || || |  || | | | |  |   ||||| || |      | | ||  |||||||||| ||||| || || ||||| | ||||||||| ||||||||||| |||||||| |||||||||||||| |||||||| || ||||| || |||
----------------------------------------------------gtaattttggtcgttttgt------tagaatcacaa-caaaataaacatatactttgttatcaaattacagcgccctcttgttgattgcagAAAGCACAAACTTCAGTAATCAATGGCAACCTGAATCCTGTCTGGAATGAAGAACTGAAGCTCTCTGTTCCCCAGCAATATGGACCTCTGAAGCTG

upper sequence: LOC_Os02g10480.1 (Oryza sativa), 3'ss of exon 7
lower sequence: GRMZM2G138349_T02 (Zea mays), 3'ss of exon 6
gtagtattatgaaatcctaattttctgatggtttctgggcaactaattcaagatcgaattcatcgttttgtaccacattgtctctcattcagaacatgcagaaattcttgttctaaatttcaccatatcttcgctgtgtgcagAAAGCGCAAACCTCGGTGATCAAAGCCAACCTGAACCCTGTCTGGAACGAAGAACTCAAGCTCTCTGTTCCTCAGCAATACGGCCCTCTCAAACTG----
                                                     |    ||  |||||||||      | |  || ||  || || |  || | | | |  |   ||||| || |      | | ||  |||||||||| ||||| || || ||||| | ||||||||| ||||||||||| |||||||| |||||||||||||| |||||||| || ||||| || |||    
----------------------------------------------------gtaattttggtcgttttgt------tagaatcacaa-caaaataaacatatactttgttatcaaattacagcgccctcttgttgattgcagAAAGCACAAACTTCAGTAATCAATGGCAACCTGAATCCTGTCTGGAATGAAGAACTGAAGCTCTCTGTTCCCCAGCAATATGGACCTCTGAAGCTGGTAA

upper sequence: LOC_Os02g10480.1 (Oryza sativa), 3'ss of exon 7
lower sequence: AT4G21160.4 (Arabidopsis thaliana), 3'ss of exon 6
gtagtattatgaaatcctaattttc-tgatggtttctgggcaactaattcaagatcgaattcatcgttttgtaccacattgtctctcattcagaacatgcagaaattcttgttctaaatttcaccatatcttcgctgtgtgcagAAAGCGCAAACCTCGGTGATCAAAGCCAACCTGAACCCTGTCTGGAACGAAGAACTCAAGCTCTCTGTTCCTCAGCAATACGGCCCTCTCAAACTG
                 ||||| |  |||    || ||   | ||         |    || ||   ||  |||||     | | | | | |  |        |  |||| |||| |   | | |||   ||  |      ||||| || ||| |  | ||  | ||   |||| | |||||||||||||| || ||||||| |||||||||||||||  | || ||| |  | ||| ||
----------------gtaattatagtgaatacttttgaa-atcttgaaaggttttctctttatatgttcttaccat----tgtttaagtgatcattattgtcatctctttttctgatcgttatcatcgttttac------cagAAGGCTCAATCTACTGTAGTGAAGAGCAACTTAAACCCTGTCTGGAATGAGGAACTCATGCTCTCTGTTCCTCATAACTATGGCTCAGTGAAATTG

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|87005483|gb|CI285705.1|CI285705
EST:     GAGACATGTCAAGCAGTGATCCTTATGTAGTCCTGACCCTTGGGCAACAG                         AAAGCGCAAACCTCGGTG
genomic: GAGACATGTCAAGCAGTGATCCTTATGTAGTCCTGACCCTTGGGCAACAGgtagtattat ... ctgtgtgcagAAAGCGCAAACCTCGGTG
EST: gi|29645547|gb|CB650554.1|CB650554
EST:     GAGACATGTCAAGCAGTGATCCTTATGTAGTCCTGACCCTTGGGCAACAG                         AAAGCGCAAACCTCGGTGATCAAAGCCAACCTGAACCCTGTCTGGAACGAA
genomic: GAGACATGTCAAGCAGTGATCCTTATGTAGTCCTGACCCTTGGGCAACAGgtagtattat ... ctgtgtgcagAAAGCGCAAACCTCGGTGATCAAAGCCAACCTGAACCCTGTCTGGAACGAA
EST: gi|9866250|gb|AU102000.1|AU102000
EST:     GAGACATGTCAAGCAGTGATCCTTATGTAGTCCTGACCCTTGGGCAACAG                         AAAGCGCAAACCTCGGTGATCAAAGCCAACCTGAACCCTGTCTGGAACGAA
genomic: GAGACATGTCAAGCAGTGATCCTTATGTAGTCCTGACCCTTGGGCAACAGgtagtattat ... ctgtgtgcagAAAGCGCAAACCTCGGTGATCAAAGCCAACCTGAACCCTGTCTGGAACGAA
EST: gi|13806102|gb|AU181353.1|AU181353
EST:     TCCTGACCCTTGGGCAACAAG                         AAAGCGCAAACCTCGGTGATCAAAGCCAACCTGAACCCTGTCTGGAACGA
genomic: TCCTGACCCTTGGGCAAC-AGgtagtattat ... ctgtgtgcagAAAGCGCAAACCTCGGTGATCAAAGCCAACCTGAACCCTGTCTGGAACGA
EST: gi|29657516|gb|CB653791.1|CB653791
EST:     GAGACATGTCAAGCAGTGATCCTTATGTAGTCCTGACCCTTGGGCAACAG                         AAAGCGCAAACCTCGGTGATCAAAGCCAACCTGAACCCTGTCTGGAACGAA
genomic: GAGACATGTCAAGCAGTGATCCTTATGTAGTCCTGACCCTTGGGCAACAGgtagtattat ... ctgtgtgcagAAAGCGCAAACCTCGGTGATCAAAGCCAACCTGAACCCTGTCTGGAACGAA
EST: gi|86507268|gb|CI149901.1|CI149901
EST:     GAGACATGTCAAGCAGTGATCCTTATGTAGTCCTGACCCTTGGGCAACAG                         AAAGCGCAAACCTCGGTGATCAAAGCCAACCTGAACCCTGTCTGGAACGAA
genomic: GAGACATGTCAAGCAGTGATCCTTATGTAGTCCTGACCCTTGGGCAACAGgtagtattat ... ctgtgtgcagAAAGCGCAAACCTCGGTGATCAAAGCCAACCTGAACCCTGTCTGGAACGAA
EST: gi|86502666|gb|CI145299.1|CI145299
EST:     CAGTGATCCTTATGTAGTCCTGACCCTTGGGCAACAG                         TAAGCGCAAACCTCGGTGATCAAAGCCAACCTGAACCCTGTCTGGAACGAA
genomic: CAGTGATCCTTATGTAGTCCTGACCCTTGGGCAACAGgtagtattat ... ctgtgtgcagAAAGCGCAAACCTCGGTGATCAAAGCCAACCTGAACCCTGTCTGGAACGAA
EST: gi|29645546|gb|CB650553.1|CB650553
EST:     GAGACATGTCAAGCAGTGATCCTTATGTAGTCCTGACCCTTGGGCAACAG                         AAAGCGCAAACCTCGGTGATCAAAGCCA-CCTGAAACCTGTCTGGAACG
genomic: GAGACATGTCAAGCAGTGATCCTTATGTAGTCCTGACCCTTGGGCAACAGgtagtattat ... ctgtgtgcagAAAGCGCAAACCTCGGTGATCAAAGCCAACCTGAACCCTGTCTGGAACG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcagaacatgcagaaattcttgttctaaatttcaccatatcttcgctgtgtgcagAAAGCGCAAACCTCGGTGATCAAAGCCAACCTGAACCCTGTCTGGAACGAAGAACTCAAGCTCTCTGTTCCTCAGCAATACGGCCCTCTCAAACTG
                      ttctaaa  putative branch site (score: 2)
                                       tcttcgct  putative PPT
                      ttctaaattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtagtattatgaaatcctaattttctgatggtttctgggcaactaattcaagatcgaattcatcgttttgtaccacattgtctctcattcagaacatgcagaaattcttgttctaaatttcaccatatcttcgctgtgtgcagAAAGCGCAAACCTCGGTGATCAAAGCCAACCTGAACCCTGTCTGGAACGAAGAACTCAAGCTCTCTGTTCCTCAGCAATACGGCCCTCTCAAACTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAAGCT