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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtaccctctcaacgatatctattaaaaaggcaccgataatctgtcaaccccattattgtttattcatactgttcttaaatgtagGTTGCAACTGATCGCTGCATCATGGCCTTGCTTTTTCTCATTGTTGCTGGAGTCATAGCAATAATAGTCGTTAAG

Basic information

species Oryza sativa
transcript LOC_Os06g50120.1
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os06g50120.1 (Oryza sativa), 3'ss of exon 8
lower sequence: GRMZM2G065105_T02 (Zea mays), 3'ss of exon 8
gtaagtaccctctcaacgatatctattaaaaaggcaccgataatctgtcaaccccattattgtttattcatactgttcttaaatgtagGTTGCAACTGATCGCTGCATCATGGCCTTGCTTTTTCTCATTGTTGCTGGAGTCATAGCAATAATAGTCGTTAAG
|||| |   |    ||   | ||| |         ||   | ||  | ||||    || || | ||||   | | || ||||||  |||||||||||||||| |||||||||||| ||||||||||||||||||||||||||||||| |||||| | ||||||
gtaaat--tcatctaatagtttcttt---------act--tcattagccaactatgttcttatctattatcaatttttttaaat--agGTTGCAACTGATCGATGCATCATGGCCATGCTTTTTCTCATTGTTGCTGGAGTCATAGCTATAATAATTGTTAAG
















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|88964764|gb|CI084762.1|CI084762
EST:     ATTTCTCCATTAAAAAGGCATCACAAATGGTGAAAGAAATTGGTAGGCAG                         GTTGCAACTGATCGCTGCATCATGGCCTTGCTTTTTCTCATTGTTGCTGGA
genomic: ATTTCTCCATTAAAAAGGCATCACAAATGGTGAAAGAAATTGGTAGGCAGgtaagtaccc ... ttaaatgtagGTTGCAACTGATCGCTGCATCATGGCCTTGCTTTTTCTCATTGTTGCTGGA
EST: gi|88964517|gb|CI055213.1|CI055213
EST:     ATTTCTCCATTAAAAAGGCATCACAAATGGTGAAAGAAATTGGTAGGCAG                         GTTGCAACTGATCGCTGCATCATGGCCTTGCTTTTTCTCATTGTTGCTGGA
genomic: ATTTCTCCATTAAAAAGGCATCACAAATGGTGAAAGAAATTGGTAGGCAGgtaagtaccc ... ttaaatgtagGTTGCAACTGATCGCTGCATCATGGCCTTGCTTTTTCTCATTGTTGCTGGA
EST: gi|88260688|gb|CI362981.1|CI362981
EST:     GAAAGAAATTGGTAGGCAG                         GTTGCAACTGATCGCTGCATCATTCCCTTGCTTTTTCTCATTGTTGCTGGA
genomic: GAAAGAAATTGGTAGGCAGgtaagtaccc ... ttaaatgtagGTTGCAACTGATCGCTGCATCATGGCCTTGCTTTTTCTCATTGTTGCTGGA
EST: gi|86603159|gb|CI357523.1|CI357523
EST:     ATTGGTAGGGCAG                         GTTGCAACTGATCGCTGCATCATGGCCTTGCTTTTTCTCATTGTTGCTGG
genomic: ATTGGTA-GGCAGgtaagtaccc ... ttaaatgtagGTTGCAACTGATCGCTGCATCATGGCCTTGCTTTTTCTCATTGTTGCTGG
EST: gi|55413904|gb|CV726280.1|CV726280
EST:     ATTTCTCCATTAAAAAGGCATCACAAATGGTGAAAGAAATTGGTAGGCAG                         GTTGCAACTGATCGCTGCATCATGGCCTTGCTTTTTCTCATTGTTGCTGGA
genomic: ATTTCTCCATTAAAAAGGCATCACAAATGGTGAAAGAAATTGGTAGGCAGgtaagtaccc ... ttaaatgtagGTTGCAACTGATCGCTGCATCATGGCCTTGCTTTTTCTCATTGTTGCTGGA
EST: gi|86497255|gb|CI139888.1|CI139888
EST:     ATTTCTCCATTAAAAAGGCATCACAAATGGTGAAAGAAATTGGTAGGCAG                         GTTGCAACTGATCGCTGCATCATGGCCTTGCTTTTTCTCATTGTTGCTGGA
genomic: ATTTCTCCATTAAAAAGGCATCACAAATGGTGAAAGAAATTGGTAGGCAGgtaagtaccc ... ttaaatgtagGTTGCAACTGATCGCTGCATCATGGCCTTGCTTTTTCTCATTGTTGCTGGA
EST: gi|58675298|gb|CK063985.1|CK063985
EST:     ATTTCTCCATTAAAAAGGCATCACAAATGGTGAAAGAAATTGGTAGGCAG                         GTTGCAACTGATCGCTGCATCATGGCCTTGCTTTTTCTCATTGTTGCTGGA
genomic: ATTTCTCCATTAAAAAGGCATCACAAATGGTGAAAGAAATTGGTAGGCAGgtaagtaccc ... ttaaatgtagGTTGCAACTGATCGCTGCATCATGGCCTTGCTTTTTCTCATTGTTGCTGGA
EST: gi|86251814|gb|CI019006.1|CI019006
EST:     ATTTCTCCATTAAAAAGGCATCACAAATGGTGAAAGAAATTGGTAGGCAG                         GTTGCAACTGATCGCTGCATCATGGCCTTGCTTTTTCTCATTGTTGCTGGA
genomic: ATTTCTCCATTAAAAAGGCATCACAAATGGTGAAAGAAATTGGTAGGCAGgtaagtaccc ... ttaaatgtagGTTGCAACTGATCGCTGCATCATGGCCTTGCTTTTTCTCATTGTTGCTGGA
EST: gi|86427669|gb|CI072766.1|CI072766
EST:     ATTTCTCCATTAAAAAGGCATCACAAATGGTGAAAGAAATTGGTAGGCAG                         GTTGCAACTGATCGCTGCATCATGGCCTTGCTTTTTCTCACTGTTGCTGGA
genomic: ATTTCTCCATTAAAAAGGCATCACAAATGGTGAAAGAAATTGGTAGGCAGgtaagtaccc ... ttaaatgtagGTTGCAACTGATCGCTGCATCATGGCCTTGCTTTTTCTCATTGTTGCTGGA
EST: gi|89185473|gb|CI051801.1|CI051801
EST:     TTTCTCCATTTAAAAAGGCATCACAAATGGTGAAAGAAATTGGTAGGCAG                         GTTTGCAACTGATCGCTGCATCATGGCCTTGCTTTTTCTCATTGTTGCTGG
genomic: TTTCTCCA-TTAAAAAGGCATCACAAATGGTGAAAGAAATTGGTAGGCAGgtaagtaccc ... ttaaatgtagG-TTGCAACTGATCGCTGCATCATGGCCTTGCTTTTTCTCATTGTTGCTGG
EST: gi|3107012|gb|D42744.1|D42744
EST:     TAAAAAGCCATCACAAATGGTGAAAGAAA-TGGTAGNCCG                         GTTGCAACTGAACGC-GCCATCATGGCCTTGCTTTTTCTCATTGTTGCTGG
genomic: TAAAAAGGCATCACAAATGGTGAAAGAAATTGGTAGGCAGgtaagtaccc ... ttaaatgtagGTTGCAACTGATCGCTG-CATCATGGCCTTGCTTTTTCTCATTGTTGCTGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gcaccgataatctgtcaaccccattattgtttattcatactgttcttaaatgtagGTTGCAACTGATCGCTGCATCATGGCCTTGCTTTTTCTCATTGTTGCTGGAGTCATAGCAATAATAGTCGTTAAG
                                       ctgttctt  CT-rich tract
                      attattgtttattcat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagtaccctctcaacgatatctattaaaaaggcaccgataatctgtcaaccccattattgtttattcatactgttcttaaatgtagGTTGCAACTGATCGCTGCATCATGGCCTTGCTTTTTCTCATTGTTGCTGGAGTCATAGCAATAATAGTCGTTAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGGA