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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tatctgcagaaagtcagcagtagaatattgtcttctctaattaaggtgttgtcagtactcaataatgcttcaagaaaatgatgtggttgtgaccgtgcagGTAATTGGATTGCATGGTGGTGCTTTGCTTGGTGTCACATACCGTACATCTCGTAGAATCAGTCCTGTGACAGCAACAGCTATATCAACTGTTCAATCTA

Basic information

species Oryza sativa
transcript LOC_Os01g46510.2
intron # 12
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g46510.2 (Oryza sativa), 3'ss of exon 12
lower sequence: GRMZM5G824843_T02 (Zea mays), 3'ss of exon 1
-----tatctgcagaaagtcagcagtagaatattgtcttctctaattaaggtgttgtcagtactcaataatgcttcaagaaaatgatgtggttgtgaccgtgcagGTAATTGGATTGCATGGTGGTGCTTTGCTTGGTGTCACATACCGTACATCTCGTAGAATCAGTCCTGTGACAGCAACAGCTATATCAACTGTTCAATCTA
     |  |   |||||   |      |||  || | | |  || |  | || | | |||    ||  ||  ||||     | ||   ||| | |||   | ||||| ||||||||||||||||||||||| ||||||||||||||||||||||||||||||||||||||| ||||||||||||||||||||||||||||||| |
ttgtttgaccatagaaataaaaacactgaactttctgtccattagtataagt-tcggcag----cagaaagtcttctgtctagtgtaatggctatgatatttcagGTTATTGGATTGCATGGTGGTGCTTTACTTGGTGTCACATACCGTACATCTCGTAGAATCAGTCCTTTGACAGCAACAGCTATATCAACTGTTCAATCGA
















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|58664662|gb|CK053348.1|CK053348
EST:     AGCACATGTTTTGCAGCGATCCATTGATGGCCGCAGTGAACCG                         GTAATTGGATTGCATGGTGGTGCTTTGCTTGGTGTCACATACCGTACATCT
genomic: AGCACATGTTTTGCAGCGATCCATTGATGGCCGCAGTGAACCGgttggcaatc ... gaccgtgcagGTAATTGGATTGCATGGTGGTGCTTTGCTTGGTGTCACATACCGTACATCT
EST: gi|29626669|gb|CB631680.1|CB631680
EST:     ATGGAACAGCACATGTTTTGCAGCGATCCATTGATGGCCGCAGTGAACCG                         GTAATTGGATTGCAT
genomic: ATGGAACAGCACATGTTTTGCAGCGATCCATTGATGGCCGCAGTGAACCGgttggcaatc ... gaccgtgcagGTAATTGGATTGCAT
EST: gi|58658218|gb|CK046898.1|CK046898
EST:     ATGGAACAGCACATGTTTTGCAGCGATCCATTGATGGCCGCAGTGAACCG                         GTAATTGGATTGCATGGTGGTGCTTTGCTTGGTGTCACATACCGTACATCT
genomic: ATGGAACAGCACATGTTTTGCAGCGATCCATTGATGGCCGCAGTGAACCGgttggcaatc ... gaccgtgcagGTAATTGGATTGCATGGTGGTGCTTTGCTTGGTGTCACATACCGTACATCT
EST: gi|86889062|gb|CI314678.1|CI314678
EST:     GCAGCGATCCATTGATGGCCGCAGTGAACCG                         GTAATTGGATTGCATGGTGGTGCTTTGCTTGGTGTCACATACCGTACATCT
genomic: GCAGCGATCCATTGATGGCCGCAGTGAACCGgttggcaatc ... gaccgtgcagGTAATTGGATTGCATGGTGGTGCTTTGCTTGGTGTCACATACCGTACATCT
EST: gi|25804329|gb|CA760290.1|CA760290
EST:     ATGGAACAGCACATGTTNTGCAGCGATCCATTGATGGCCGCAGTGAACCG                         GTAATTGGATTGCATGGTGGTGCTNTGCTTGGTGTCACATACCGTACATCT
genomic: ATGGAACAGCACATGTTTTGCAGCGATCCATTGATGGCCGCAGTGAACCGgttggcaatc ... gaccgtgcagGTAATTGGATTGCATGGTGGTGCTTTGCTTGGTGTCACATACCGTACATCT
EST: gi|58656516|gb|CK045196.1|CK045196
EST:     AACAGCACATGTTTTGCAGCGATCCATTGATGGCCGCAGTGAACCG                         GTAATTGGATTGCATGGTGGTGCTTTGCTTGGTGTCACATACCGTACATCT
genomic: AACAGCACATGTTTTGCAGCGATCCATTGATGGCCGCAGTGAACCGgttggcaatc ... gaccgtgcagGTAATTGGATTGCATGGTGGTGCTTTGCTTGGTGTCACATACCGTACATCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtgttgtcagtactcaataatgcttcaagaaaatgatgtggttgtgaccgtgcagGTAATTGGATTGCATGGTGGTGCTTTGCTTGGTGTCACATACCGTACATCTCGTAGAATCAGTCCTGTGACAGCAACAGCTATATCAACTGTTCAATCTA
             tcaataat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tatctgcagaaagtcagcagtagaatattgtcttctctaattaaggtgttgtcagtactcaataatgcttcaagaaaatgatgtggttgtgaccgtgcagGTAATTGGATTGCATGGTGGTGCTTTGCTTGGTGTCACATACCGTACATCTCGTAGAATCAGTCCTGTGACAGCAACAGCTATATCAACTGTTCAATCTA

-atctgca
- - - - - - - cagcagt
- - - - - - - - - - - - - - - - - - - - - - ggtgttg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgcttca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -atgatgt