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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...acttagaaatgatgatatcatgtcttagactattgtcttctgaagttttttcgtgaagcatgtaaagctgacaacctccccattcttttttttattagagCCCATGCTAACCGTGGGGAGCGTAAATCCAGTTATATGGTCCGATGACTGGACAGCGGTGACTGAAGACGGCAGCTTGTCAGCACAGTTTGAGCACACAA

Basic information

species Oryza sativa
transcript LOC_Os02g52420.3
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g52420.3 (Oryza sativa), 3'ss of exon 9
lower sequence: GRMZM2G101438_T03 (Zea mays), 3'ss of exon 8
acttagaaatgatgatatcatgtcttagactattgtcttctgaagttttttcgtgaagcatgtaaagctgaca-acctccccattctttttt-----------ttattagagCCCATGCTAACCGTGGGGAGCGTAAATCCAGTTATATGGTCCGATGACTGGACAGCGGTGACTGAAGACGGCAGCTTGTCAGCACAGTTTGAGCACACAA
       | |||||  ||    | ||     |||| ||  | ||        || |||||| | |||||  |  || ||  ||  ||||| |           | || |||||||||||||||| | |||||| | || || || || ||||||||||||||||| || ||||| |||||||||||||||||||||||||||||||||||  
------cactgatgccatgcgatgttttttcattggctagtaaa----caaggtaaagcatatgaagctatctcacttcatcacccttttctatcattccatgtcatcagAGCCCATGCTAACCATAGGGAGCATCAACCCTGTCATGTGGTCCGATGACTGGACCGCAGTGACAGAAGACGGCAGCTTGTCAGCACAGTTTGAGCACAC--
















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|86492814|gb|CI135447.1|CI135447
EST:     GAAACAATGAATGGGGCCGTATGACATTGAACCCAACATTTACTATAG                         A
genomic: GAAACAATGAATGGGGCCGTATGACATTGAACCAAACATTTACTATAGgtacatgttt ... tttattagag-
EST: gi|86492814|gb|CI135447.1|CI135447
EST:     GAAACAATGAATGGGGCCGTATGACATTGAACCCAACATTTACTATAG                         A
genomic: GAAACAATGAATGGGGCCGTATGACATTGAACCAAACATTTACTATAGgtacatgttt ... tttattagag-
EST: gi|86492814|gb|CI135447.1|CI135447
EST:     GAAACAATGAATGGGGCCGTATGACATTGAACCCAACATTTACTATAG                         A
genomic: GAAACAATGAATGGGGCCGTATGACATTGAACCAAACATTTACTATAGgtacatgttt ... tttattagag-
EST: gi|38482500|gb|CF966534.1|CF966534
EST:     GAAACAATGAATGGGGCCGTATGACATTGAACCAAACATTTACTATAG                         A
genomic: GAAACAATGAATGGGGCCGTATGACATTGAACCAAACATTTACTATAGgtacatgttt ... tttattagag-
EST: gi|38482500|gb|CF966534.1|CF966534
EST:     GAAACAATGAATGGGGCCGTATGACATTGAACCAAACATTTACTATAG                         A
genomic: GAAACAATGAATGGGGCCGTATGACATTGAACCAAACATTTACTATAGgtacatgttt ... tttattagag-
EST: gi|38482500|gb|CF966534.1|CF966534
EST:     GAAACAATGAATGGGGCCGTATGACATTGAACCAAACATTTACTATAG                         A
genomic: GAAACAATGAATGGGGCCGTATGACATTGAACCAAACATTTACTATAGgtacatgttt ... tttattagag-
EST: gi|86494445|gb|CI137078.1|CI137078
EST:     GAAACAATGAATGGGGCCGTATGACATTGAACCAAACATTTACTATAG                         CCCATGCTAACCGTGGGGAGCGTAAATCCAGTTATATGGTCCGATGACTGG
genomic: GAAACAATGAATGGGGCCGTATGACATTGAACCAAACATTTACTATAGgtacatgttt ... tttattagagCCCATGCTAACCGTGGGGAGCGTAAATCCAGTTATATGGTCCGATGACTGG
EST: gi|29657570|gb|CB653845.1|CB653845
EST:     GAAACAATGAATGGGGCCGTATGACATTGAACCAAACATTTACTATAG                         A
genomic: GAAACAATGAATGGGGCCGTATGACATTGAACCAAACATTTACTATAGgtacatgttt ... tttattagag-
EST: gi|29657570|gb|CB653845.1|CB653845
EST:     GAAACAATGAATGGGGCCGTATGACATTGAACCAAACATTTACTATAG                         A
genomic: GAAACAATGAATGGGGCCGTATGACATTGAACCAAACATTTACTATAGgtacatgttt ... tttattagag-
EST: gi|29657570|gb|CB653845.1|CB653845
EST:     GAAACAATGAATGGGGCCGTATGACATTGAACCAAACATTTACTATAG                         A
genomic: GAAACAATGAATGGGGCCGTATGACATTGAACCAAACATTTACTATAGgtacatgttt ... tttattagag-


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttttttcgtgaagcatgtaaagctgacaacctccccattcttttttttattagagCCCATGCTAACCGTGGGGAGCGTAAATCCAGTTATATGGTCCGATGACTGGACAGCGGTGACTGAAGACGGCAGCTTGTCAGCACAGTTTGAGCACACAA
                    agctgac  putative branch site (score: 3)
                             cctccccattcttttt  putative PPT
                                    attcttttttttatta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
acttagaaatgatgatatcatgtcttagactattgtcttctgaagttttttcgtgaagcatgtaaagctgacaacctccccattcttttttttattagagCCCATGCTAACCGTGGGGAGCGTAAATCCAGTTATATGGTCCGATGACTGGACAGCGGTGACTGAAGACGGCAGCTTGTCAGCACAGTTTGAGCACACAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGCT
- - - - atgatga
- - - - - - - - atcatgt
- - - - - - - - - - - - - - - - - - cttctga
- - - - - - - - - - - - - - - - - - - - - - - - - - - - -gcatgta
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gctgaca