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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGATGACTTCCGAGACAGGGACTATGATGTGGCGGCACTTGCTAATAACCTGAGCCAGGCATTCCGGTATGGAATGTACAGCAATGATGACATTGAAGAGgtgattgtctgaacttgcagcagcctgagctttggtagcatgctagaatttacatacctgaggaaatgggcactgatgtcttatgctcttattaccttcactgatatagtcctctctagcattatggaacatgttagtaatgtgtcaatgtttgcttattgcag

Basic information

species Oryza sativa
transcript LOC_Os05g51490.1
intron # 16
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os05g51490.1 (Oryza sativa), 5'ss of exon 16
lower sequence: GRMZM5G812498_T01 (Zea mays), 5'ss of exon 6
TGATGACTTCCGAGACAGGGACTATGATGTGGCGGCACTTGCTAATAACCTGAGCCAGGCATTCCGGTATGGAATGTACAGCAATGATGACATTGAAGAGgtgattgtc-tgaacttgcagcag------cctgagctttgg-tagcatgctagaatttacatacctgaggaaatgggcactgatgtcttatgctcttattaccttcactgatatagtcctctctagcattatggaacatgttagtaatgtgtcaatgtttgcttattgcag
 || |||||||||||||| ||||| |||||||| |||||  |||||||  ||||||||||||| || | ||| || ||||| |||||||||||||||||||| ||| || | |  ||    ||       | |||| ||||   | |||| |    |||   |   |      |   || | | ||   |  ||  | ||||                                                                      
CGACGACTTCCGAGACAGAGACTACGATGTGGCAGCACTCACTAATAATATGAGCCAGGCATTTCGATTTGGGATATACAGGAATGATGACATTGAAGAGgtaattttcgtcagttttttacaagattttcttgagttttgaacatcatgttcttctttgtttttttttctcga-atgcgcaggtgaactgcgca-tcatta----------------------------------------------------------------------

upper sequence: LOC_Os05g51490.1 (Oryza sativa), 5'ss of exon 16
lower sequence: AT1G30470.2 (Arabidopsis thaliana), 5'ss of exon 16
TGATGACTTCCGAGACAGGGACTATGATGTGGCGGCACTTGCTAATAACCTGAGCCAGGCATTCCGGTATGGAATGTACAGCAATGATGACATTGAAGAGgtgattgtctgaacttgcagcagcctgagctttggtagcatgctagaatttacatacctgaggaaatgggcactgatgtcttatgctcttattaccttcactgatatagtcctctctagcattatggaacatgttagtaatgtgtcaatgtttgcttattgcag
|||||| | ||  || || || ||||||||||| || || || || ||  |||||||||| || || |||||||| ||||||||||||||||| || ||||||||  |||    || |            |||  |||| |||||    | || |  ||  ||||||  | | |    ||  |   | |     | |      ||| |||  |                                                   
TGATGATTACCACGATAGAGATTATGATGTGGCAGCCCTAGCAAACAATTTGAGCCAGGCTTTTCGATATGGAATTTACAGCAATGATGACATGGATGAGgtgatgttctcgtgtttcc----------ttttcatagc-tgctacgtgtgacttttctttggaaattagtatt---atccaagattttggccgcatatttcaata-agttttgg-------------------------------------------------
















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|58612771|gb|CK040483.1|CK040483
EST:     TGAGCCAGGCATTCCGGTATGGAATGTACAGCAATGATGACATTGAAGAG                         GCACAAGTAATTGAACGAGATGATGAG
genomic: TGAGCCAGGCATTCCGGTATGGAATGTACAGCAATGATGACATTGAAGAGgtgattgtct ... cttattgcagGCACAAGTAATTGAACGAGATGATGAG
EST: gi|58608385|gb|CK036418.1|CK036418
EST:     TGAGCCAGGCATTCCGGTATGGAATGTACAGCAATGATGACATTGAGGAG                         GCACAAGTAATTGAACGAGATGATGAG
genomic: TGAGCCAGGCATTCCGGTATGGAATGTACAGCAATGATGACATTGAAGAGgtgattgtct ... cttattgcagGCACAAGTAATTGAACGAGATGATGAG
EST: gi|58653975|gb|CK042655.1|CK042655
EST:     TGAGCCAGGCATTCCGGTATGGAATGTACAGCAATGATGACATTGAAGAG                         GCACAAGTAATTGAACGAGATGATGAG
genomic: TGAGCCAGGCATTCCGGTATGGAATGTACAGCAATGATGACATTGAAGAGgtgattgtct ... cttattgcagGCACAAGTAATTGAACGAGATGATGAG
EST: gi|218484458|gb|FG943361.1|FG943361
EST:     TGAGCCAGGCATTCCGGTATGGAATGTACAGCAATGATGACATTGAAGAG                         GCACAAGTAATTGAACGAGATGATGAG
genomic: TGAGCCAGGCATTCCGGTATGGAATGTACAGCAATGATGACATTGAAGAGgtgattgtct ... cttattgcagGCACAAGTAATTGAACGAGATGATGAG
EST: gi|58660503|gb|CK049183.1|CK049183
EST:     TGAGCCAGGCATTCCGGTATGGAATGTACAGCAATGATGACATTGAAGAG                         GCACAAGTAATTGAACGAGATGATGAG
genomic: TGAGCCAGGCATTCCGGTATGGAATGTACAGCAATGATGACATTGAAGAGgtgattgtct ... cttattgcagGCACAAGTAATTGAACGAGATGATGAG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGATGACTTCCGAGACAGGGACTATGATGTGGCGGCACTTGCTAATAACCTGAGCCAGGCATTCCGGTATGGAATGTACAGCAATGATGACATTGAAGAGgtgattgtctgaacttgcagcagcctgagctttggtagcatgctagaatttacatacctgaggaaatgggcactgatgtcttatgctcttattaccttcactgatatagtcctctctagcattatggaacatgttagtaatgtgtcaatgtttgcttattgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA