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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaaatgctattttctttctcttttcaagctgaattctcctgggattttactattatctgactgaaccagttatttctgtccagATCTTTGTTCCTATACACAAGGAAGTGCATTGGTGTTTAGCAGTCATAAACATAAGGGACAAAAAGTTTCAATTTCTGGATTCACTTGGCAGCATGGACA

Basic information

species Oryza sativa
transcript LOC_Os01g25370.1
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g25370.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G012601_T02 (Zea mays), 3'ss of exon 5
gtaaaatgctattttctttctcttttcaagctgaattctc-ctgggattttactattatctg-actgaaccagttatttctgtccagATCTTTGTTCCTATACACAAGGAAGTGCATTGGTGTTTAGCAGTCATAAACATAAGGGACAAAAAGTTTCAATTTCTGGATTCACTTGGCAGCATGGACA
|||| |  || |||   ||||||||||| | | |   ||  || || ||| ||| |  | || | | |||| |   ||  | ||||||| |||||||| |||||||||||||| |||||||||||||||||||| ||||||||||||||||||||||| | |||||||||||||||  |||||||||
gtaacacact-tttgggttctcttttcaggtttagaccttactagggtttaact-tagtatgcatttaaccggaacttattatccagATATTTGTTCCCATACACAAGGAAGTCCATTGGTGTTTAGCAGTCATCAACATAAGGGACAAAAAGTTTCAGTATCTGGATTCACTTGGTGGCATGGACA

upper sequence: LOC_Os01g25370.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G088653_T01 (Zea mays), 3'ss of exon 5
gtaaaatgctattttctttctcttttcaagctgaattctc-ctgggattttactattatctg-actgaaccagttatttctgtccagATCTTTGTTCCTATACACAAGGAAGTGCATTGGTGTTTAGCAGTCATAAACATAAGGGACAAAAAGTTTCAATTTCTGGATTCACTTGGCAGCATGGACA
|||||   || |||   |||| ||||||   | |  |||  || || ||| ||| || | || | |  |||     ||  | ||||||| |||||||| |||||||||||||| |||||||||||||||||||| ||||| ||||||||||||||||| | ||| || ||||||||  |||||||||
gtaaagcactttttggattctgttttcagctttagatcttactagggtttaact-ttgtatgcatttgaccgaaacttattatccagATATTTGTTCCCATACACAAGGAAGTCCATTGGTGTTTAGCAGTCATCAACATCAGGGACAAAAAGTTTCAGTATCTAGACTCACTTGGTGGCATGGACA
















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|33692526|gb|CF320765.1|CF320765
EST:     GATGGACAACTAAAAGGAAGTTAGGTTACAGCCTACTTGAATGTGATAAG                         ATCTTTGTTCCTATACACAAGGAAGTGCATTGGTGTTTAGCAGTCATAAAC
genomic: GATGGACAACTAAAAGGAAGTTAGGTTACAGCCTACTTGAATGTGATAAGgtaaaatgct ... ttctgtccagATCTTTGTTCCTATACACAAGGAAGTGCATTGGTGTTTAGCAGTCATAAAC
EST: gi|218485916|gb|FG967011.1|FG967011
EST:     GATGGACAACTAAAAGGAAGTTAGGTTACAGCCTACTTGAATGTGATAAG                         ATCTTTGTTCCTATACACAAGGAAGTGCATTGGTGTTTAGCAGTCATAAAC
genomic: GATGGACAACTAAAAGGAAGTTAGGTTACAGCCTACTTGAATGTGATAAGgtaaaatgct ... ttctgtccagATCTTTGTTCCTATACACAAGGAAGTGCATTGGTGTTTAGCAGTCATAAAC
EST: gi|29662158|gb|CB658433.1|CB658433
EST:     GATGGACAACTAAAAGGAAGTTAGGTTACAGCCTACTTGAATGTGATAAG                         ATCTTTGTTCCTATACACAAGGAAGTGCATTGGTGTTTAGCAGTCATAAAC
genomic: GATGGACAACTAAAAGGAAGTTAGGTTACAGCCTACTTGAATGTGATAAGgtaaaatgct ... ttctgtccagATCTTTGTTCCTATACACAAGGAAGTGCATTGGTGTTTAGCAGTCATAAAC
EST: gi|58590052|gb|CF988360.1|CF988360
EST:     GATGGACAACTAAAAGGAAGTTAGGTTACAGCCTACTTGAATGTGATAAG                         ATCTTTGTTCCTATACACAAGGAAGTGCATTGGTGTTTAGCAGTCATAAAC
genomic: GATGGACAACTAAAAGGAAGTTAGGTTACAGCCTACTTGAATGTGATAAGgtaaaatgct ... ttctgtccagATCTTTGTTCCTATACACAAGGAAGTGCATTGGTGTTTAGCAGTCATAAAC
EST: gi|426920|gb|D22996.1|D22996
EST:     GATGGACAACTAAAAGGAAGTTAGGTTACAGCCTACTTGAATGTGATAAG                         ATCTTTGTTCCTATACACAAGGAAGTGCATTGGTGTTTAGCAGTCATAAAC
genomic: GATGGACAACTAAAAGGAAGTTAGGTTACAGCCTACTTGAATGTGATAAGgtaaaatgct ... ttctgtccagATCTTTGTTCCTATACACAAGGAAGTGCATTGGTGTTTAGCAGTCATAAAC
EST: gi|218488315|gb|FG953540.1|FG953540
EST:     GATGGACAACTAAAAGGAAGTTAGGTTACAGCCTACTTGAATGTGATAAG                         ATCTTTGTTCCTATACACAAGGAAGTGCATTGGTGTTTAGCAGTCATAAAC
genomic: GATGGACAACTAAAAGGAAGTTAGGTTACAGCCTACTTGAATGTGATAAGgtaaaatgct ... ttctgtccagATCTTTGTTCCTATACACAAGGAAGTGCATTGGTGTTTAGCAGTCATAAAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctgaattctcctgggattttactattatctgactgaaccagttatttctgtccagATCTTTGTTCCTATACACAAGGAAGTGCATTGGTGTTTAGCAGTCATAAACATAAGGGACAAAAAGTTTCAATTTCTGGATTCACTTGGCAGCATGGACA
                          atctgac  putative branch site (score: 3)
                                            tttctgtcc  putative PPT
               attttactattatct  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaaaatgctattttctttctcttttcaagctgaattctcctgggattttactattatctgactgaaccagttatttctgtccagATCTTTGTTCCTATACACAAGGAAGTGCATTGGTGTTTAGCAGTCATAAACATAAGGGACAAAAAGTTTCAATTTCTGGATTCACTTGGCAGCATGGACA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CATGGA