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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgaagcagtgtgtttgtagaatttatgtcctatttcacgctatatttgtcttttaacttccaccttctaactgttttagGGGCATGTCCACTGTCCATGCAATGTTTATCACATTAATGTCAGTTTACCTAGTATTCTTCTCCAACCTATTCTCTGATGAGCTGGATGGCCCAGTAACA

Basic information

species Oryza sativa
transcript LOC_Os01g56230.3
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g56230.2 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM5G825226_T03 (Zea mays), 3'ss of exon 3
gtgaagcagtgtgtttgtagaatttatgtcctatttcacgctatatttgtct---------tttaacttccaccttctaactgttttagGGGCATGTCCACTGTCCATGCAATGTTTATCACATTAATGTCAGTTTACCTAGTATTCTTCTCCAACCTATTCTCTGATGAGCTGGATGGCCCAGTAACA
|| || |||| |  ||| | ||| |||| |  |||||||| ||  | | ||          || ||| |||||  | ||  ||||  ||||||||||||||| ||||||| || || |||||| |  ||||||| ||||| || ||||||||||||||||||||||||||||||||||| | |||||| 
gtcaaacagtctagttgcataatatatgcctaatttcacgttacttgtatcagcatttatgttcaacgtccactgtttacttgttc-agGGGCATGTCCACTATCCATGCGATATTCATCACAGTGGTGTCAGTGTACCTGGTTTTCTTCTCCAACCTATTCTCTGATGAGCTGGATGGACTAGTAACT
















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|29660431|gb|CB656706.1|CB656706
EST:     AAGGGTTATGGTTCTCTTACGAAAATCCAAAAGCTTGAGTGGAACAACAG                         GGGCATGTCCACTGTCCATGCAATGTTTATCACATTAATGTCAGTTTACCT
genomic: AAGGGTTATGGTTCTCTTACGAAAATCCAAAAGCTTGAGTGGAACAACAGgtgaagcagt ... actgttttagGGGCATGTCCACTGTCCATGCAATGTTTATCACATTAATGTCAGTTTACCT
EST: gi|88314263|gb|CI602595.1|CI602595
EST:     AAGGGTTATGGTTCTCTTACGAAAATCCAAAAGCTTGAGTGGAACAACAG                         GGGCATGTCCACTGTCCATGCAATGTTTATCACATTAATGTCAGTT
genomic: AAGGGTTATGGTTCTCTTACGAAAATCCAAAAGCTTGAGTGGAACAACAGgtgaagcagt ... actgttttagGGGCATGTCCACTGTCCATGCAATGTTTATCACATTAATGTCAGTT
EST: gi|300215972|gb|HO088598.1|HO088598
EST:     AAGGGTTATGGTTCTCTTACGAAAATCCAAAAGCTTGAGTGGAACAACAG                         GGGCATGTCCACTGTCCATGCAATGTTTATCACATTAATGTCAGTTTACCT
genomic: AAGGGTTATGGTTCTCTTACGAAAATCCAAAAGCTTGAGTGGAACAACAGgtgaagcagt ... actgttttagGGGCATGTCCACTGTCCATGCAATGTTTATCACATTAATGTCAGTTTACCT
EST: gi|88337687|gb|CI632189.1|CI632189
EST:     AAGGGTTATGGTTCTCTTACGAAAATCCAAAAGCTTGAGTGGAACAACAG                         GGGCATGTCCACTGTCC
genomic: AAGGGTTATGGTTCTCTTACGAAAATCCAAAAGCTTGAGTGGAACAACAGgtgaagcagt ... actgttttagGGGCATGTCCACTGTCC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atgtcctatttcacgctatatttgtcttttaacttccaccttctaactgttttagGGGCATGTCCACTGTCCATGCAATGTTTATCACATTAATGTCAGTTTACCTAGTATTCTTCTCCAACCTATTCTCTGATGAGCTGGATGGCCCAGTAACA
                                        ttctaac  putative branch site (score: 1)
                                              ctgtttt  CT-rich tract
                tatatttgtcttttaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgaagcagtgtgtttgtagaatttatgtcctatttcacgctatatttgtcttttaacttccaccttctaactgttttagGGGCATGTCCACTGTCCATGCAATGTTTATCACATTAATGTCAGTTTACCTAGTATTCTTCTCCAACCTATTCTCTGATGAGCTGGATGGCCCAGTAACA

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