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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtctggttacaccagcaattccacctcttaatgttttgtgacacaaacagattgaatattgttcatgcattccactgaaccgtcctttttcttctcttcagAAAGCATCACGTGGCTGGTGCGAGAAGATGGTGGATCTTGCAGAAGACTCATC

Basic information

species Oryza sativa
transcript LOC_Os01g40620.1
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g40620.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G086052_T03 (Zea mays), 3'ss of exon 6
-------------gtctggttacaccagcaatt--ccacctcttaatgttttgtgacacaaacagattgaatattgttcatgcattccactgaaccgtcctttttcttctctt-cagAAAGCATCACGTGGCTGGTGCGAGAAGATGGTGGATCTTGCAGAAGACTCATC
              |   |||      |   ||  ||| | |  | ||  || |    | |    | |||||| | | | |    | | ||   ||   |  |  || |   | ||||||||||||||||| |||||||| |||||||||||| |||||||||| || | 
gtttgttcccatgattaagttcttattgtggttatccatcaccaactgagtt-tatagccattgcactgaataatctccctctccttctctctccccctccctccctccctgtacagAAAGCATCACGTGGATGGTGCGAAAAGATGGTGGATATTGCAGAAGATTCTTT

upper sequence: LOC_Os01g40620.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G086052_T02 (Zea mays), 3'ss of exon 6
-------------gtctggttacaccagcaatt--ccacctcttaatgttttgtgacacaaacagattgaatattgttcatgcattccactgaaccgtcctttttcttctctt-cagAAAGCATCACGTGGCTGGTGCGAGAAGATGGTGGATCTTGCAGAAGACTCATC-----------------------------------------------
              |   |||      |   ||  ||| | |  | ||  || |    | |    | |||||| | | | |    | | ||   ||   |  |  || |   | ||||||||||||||||| |||||||| |||||||||||| |||||||||| || |                                                
gtttgttcccatgattaagttcttattgtggttatccatcaccaactgagtt-tatagccattgcactgaataatctccctctccttctctctccccctccctccctccctgtacagAAAGCATCACGTGGATGGTGCGAAAAGATGGTGGATATTGCAGAAGATTCTTTGTAAGCTTTACAGGCTATGTTTATGTAATTGTAACCGTAAGGAAACG

upper sequence: LOC_Os01g40620.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GLYMA11G10540.1 (Glycine max), 3'ss of exon 6
gtctggttacaccagcaattccacctcttaat-gttttgtgacacaaacagattgaatattgttcatgcattccactgaaccgtcctttttcttc------tcttcagAAAGCATCACGTGGCTGGTGCGAGAAGATGGTGGATCTTGCAGAAGACTCATC
        | |   | ||||| || |||   |    |  || |      | ||||  | ||| |  | |||| |  |||| |||  ||| | |||      ||| ||||||||||| ||||||||||| ||||| ||||| ||| | |||||||| |||||
-------aaaaaatgaaattcaacttctctgtcaaatcctgccttttctatattgc-tcttggtgttacatttctgtgaagcgtgatttcttttcctgggctctgcagAAAGCATCTCGTGGCTGGTGTGAGAAAATGGTTGATGTGGCAGAAGATTCATC

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|25800535|gb|CA756496.1|CA756496
EST:     TAATTATTGCACATGAATTCTATGATGCCTTGCCAATTCATCAATTTCAG                         AAAGCATCACGTGGCTGGTGCGAGAAGATGGTGGATCTTGCAGAAGACTCA
genomic: TAATTATTGCACATGAATTCTATGATGCCTTGCCAATTCATCAATTTCAGgtctggttac ... ttctcttcagAAAGCATCACGTGGCTGGTGCGAGAAGATGGTGGATCTTGCAGAAGACTCA
EST: gi|29644655|gb|CB649662.1|CB649662
EST:     TAATTATTGCACATGAATTCTATGATGCCTTGCCAATTCATCAATTTCAG                         AAAGCATCACGTGGCTGGTGCGAGAAGATGGTGGATCTTGCAGAAGACTCA
genomic: TAATTATTGCACATGAATTCTATGATGCCTTGCCAATTCATCAATTTCAGgtctggttac ... ttctcttcagAAAGCATCACGTGGCTGGTGCGAGAAGATGGTGGATCTTGCAGAAGACTCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

acagattgaatattgttcatgcattccactgaaccgtcctttttcttctcttcagAAAGCATCACGTGGCTGGTGCGAGAAGATGGTGGATCTTGCAGAAGACTCATC
                                 ccgtcctttttcttct  CT-rich tract
     ttgaatatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtctggttacaccagcaattccacctcttaatgttttgtgacacaaacagattgaatattgttcatgcattccactgaaccgtcctttttcttctcttcagAAAGCATCACGTGGCTGGTGCGAGAAGATGGTGGATCTTGCAGAAGACTCATC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA