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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgtttacctactatgctcataaacctctgtccaaaattaatgagaaaaatccaacaaatgccattgacgaactaaatttggcagGTACAGGTGCTGTTGCTACAAATAACTGCTCTAGTAGCATAGAGAGTCCTTCTACTACTTGGCCAACTTCTGAAGCAGTTGAACAAGAAAATATGCTTCG

Basic information

species Oryza sativa
transcript LOC_Os06g45840.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os06g45840.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G057408_T01 (Zea mays), 3'ss of exon 4
gtatgtttacctactatgctcataaacctctgtccaaaattaatgagaaaaatccaacaaatgccattg--acgaactaaatttggcagGTACAGGTGCTGTTGCTACAAATAACTGCTCTAGTAGCATAGAGAGTCCTTCTACTACTTGGCCAACTTCTGAAGCAGTTGAACAAGAAAATATGCTTCG------
|| ||| ||   | || |       ||||   | |||||      | ||| | ||     |  | |||   ||     |  | | |  | | ||||||| | ||| ||||||||||| || |||||||| |||||||| |||  |||||||||||||||||||||||| || |||||||||||| |||       
gtttgtgtaatcattacg-------acctgcatacaaaa------acaaataacctgtggagccaattataacttctcacgtattggtgatgcagGTGCAGCTGCAACAAATAACTGTTCAAGTAGCATGGAGAGTCCATCTGGTACTTGGCCAACTTCTGAAGCAGTCGAGCAAGAAAATATGGTTCCACCACT

upper sequence: LOC_Os06g45840.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G170148_T01 (Zea mays), 3'ss of exon 4
gtatgtttacctactatgctcataaacctctgtccaaaattaatgagaaaaatccaacaaatgccattgacgaactaaatttggcagGTACAGGTGCTGT---TGCTACAAATAACTGCTCTAGTAGCATAGAGAGTCCTTCTACTACTTGGCCAACTTCTGAAGCAGTTGAACAAGAAAATATGCTTCG-----------
                 | |    || | ||||    |  |    | |||||   ||  | |      | | |    || ||  || |||  |||| ||    ||| ||||||||||| || ||||||||||||||||| |||  ||||||||||||||||||||||||||| ||||||| | || |||            
-----------------gtttcgtaatcactgt---gacctgcatacaaaaaataaatgacttgtggagccaattgtaacttttcatgtattggtggtgcagGTGCAACAAATAACTGTTCAAGTAGCATAGAGAGTCCATCTGGTACTTGGCCAACTTCTGAAGCAGTTGAGCAAGAAATTGTGGTTCCATCACTCCATG
















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|218481447|gb|FG951027.1|FG951027
EST:     CTCCTGGGACAATTCTATTGCTCAACCTTTAAGTGCAAGTCGCACGCAAG                         GTACAGGTGCTGTTGCTACAAATAACTGCTCTAGTAGCATAGAGAGTCCTT
genomic: CTCCTGGGACAATTCTATTGCTCAACCTTTAAGTGCAAGTCGCACGCAAGgtatgtttac ... aatttggcagGTACAGGTGCTGTTGCTACAAATAACTGCTCTAGTAGCATAGAGAGTCCTT
EST: gi|218489538|gb|FG952484.1|FG952484
EST:     CAATTCTATTGCTCAACCTTTAAGTGCAAGTCGCACGCAAG                         GTACAGGTGCTGTTGCTACAAATAACTGCTCTAGTAGCATAGAGAGTCCTT
genomic: CAATTCTATTGCTCAACCTTTAAGTGCAAGTCGCACGCAAGgtatgtttac ... aatttggcagGTACAGGTGCTGTTGCTACAAATAACTGCTCTAGTAGCATAGAGAGTCCTT
EST: gi|218494859|gb|FG953214.1|FG953214
EST:     CCTGGGACAATTCTATTGCTCAACCTTTAAGTGCAAGTCGCACGCAAG                         GTACAGGTGCTGTTGCTACAAATAACTTGCTCTAGTAGCATAGAGAGTCCT
genomic: CCTGGGACAATTCTATTGCTCAACCTTTAAGTGCAAGTCGCACGCAAGgtatgtttac ... aatttggcagGTACAGGTGCTGTTGCTACAAATAAC-TGCTCTAGTAGCATAGAGAGTCCT
EST: gi|33678202|gb|CF306441.1|CF306441
EST:     CTCCTGGGACAATTCTATTGCTCAACCTTTAAGTGCAAGTCGCACGCAAG                         G----G-TGCTGTTGCTACAAATAACTGCTCTAGTAGCATAGAGAGTCCTT
genomic: CTCCTGGGACAATTCTATTGCTCAACCTTTAAGTGCAAGTCGCACGCAAGgtatgtttac ... aatttggcagGTACAGGTGCTGTTGCTACAAATAACTGCTCTAGTAGCATAGAGAGTCCTT
EST: gi|55408531|gb|CV720907.1|CV720907
EST:     CTCCTGGGACAATTCTATTGCTCAACCTTTAAGTGCAAGTCGCACGCAAG                         GTACAGGTGCTGTTGCTACAAATAACTGCTCTAGTAGCATAGAGAGTCCTT
genomic: CTCCTGGGACAATTCTATTGCTCAACCTTTAAGTGCAAGTCGCACGCAAGgtatgtttac ... aatttggcagGTACAGGTGCTGTTGCTACAAATAACTGCTCTAGTAGCATAGAGAGTCCTT
EST: gi|27577453|gb|CB000148.1|CB000148
EST:     CAAGTCGCACGCAAG                         GTACAGGGTGCTGTTGCTACAAATAACTGGCTCTAGTAGCATAGAGAGTCC
genomic: CAAGTCGCACGCAAGgtatgtttac ... aatttggcagGTACA-GGTGCTGTTGCTACAAATAACT-GCTCTAGTAGCATAGAGAGTCC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tccaaaattaatgagaaaaatccaacaaatgccattgacgaactaaatttggcagGTACAGGTGCTGTTGCTACAAATAACTGCTCTAGTAGCATAGAGAGTCCTTCTACTACTTGGCCAACTTCTGAAGCAGTTGAACAAGAAAATATGCTTCG
                                        aactaaa  putative branch site (score: 2)
     aattaatgagaaaaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgtttacctactatgctcataaacctctgtccaaaattaatgagaaaaatccaacaaatgccattgacgaactaaatttggcagGTACAGGTGCTGTTGCTACAAATAACTGCTCTAGTAGCATAGAGAGTCCTTCTACTACTTGGCCAACTTCTGAAGCAGTTGAACAAGAAAATATGCTTCG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA