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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tcctcttaatttcagcgccttaaccttaatacaagtaccagtttgagtttgtttgttcccaagttggatccggccctgggtaatttctttcttgctgaagGTGGAGAGACTGAGCTGAGCTATGGACAACTTGTGGCATCTCGGGGATGAGTTCCGTGGGCAGTCGAAGGTAGTGGAGGACCGTCAGTGGTCTCTCATGA

Basic information

species Oryza sativa
transcript LOC_Os05g41930.2
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os05g41930.2 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G033117_T01 (Zea mays), 3'ss of exon 1
tcctcttaatttcagcgc---cttaaccttaatacaagtaccagtttgagtttgtttgttcccaagt-tggatccggccctgggtaatttctttcttgctgaagGTGGAGAGACTGAGCTGAGCTATGGACAACTTGTGGCATCTCGGGGATGAGTTCCGTGGGCAGTCGAAGGTAGTGGAGGACCGTCAGTGGTCTCTCATGA
  | | |  || | || |   |  |      ||       | || | ||  |  |  ||  ||  || | ||||  | |        | | | ||||||   |||||       |   | |||||||||||| | |||||||||| ||||| ||| |||| |||||| | ||||| ||||||||||| ||||||||||||||||
cacccctgcttccggcacggacggacgggcgatctgttctctagatagacctcatgcgtgtccgtgtgttgatcttgac----actttctttctcttgcaacagGTGTGCCAGGTTGACCGAGCTATGGACAGCCTGTGGCATCTTGGGGACGAGCTCCGCGGGCAGCCCAAGGTGGTGGAGGACCGCCAGTGGTCTCTCATGA

upper sequence: LOC_Os05g41930.2 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G011923_T01 (Zea mays), 3'ss of exon 1
tcctcttaatttcagcgccttaaccttaatacaagtaccagtttga-gtttgtttgtt--cccaagttggatccggccctgggtaatttctttcttgctgaagGTGGAGAGACTGAGCTGAGCTATGGACAACTTGTGGCATCTCGGGGATGAGTTCCGTGGGCAGTCGAAGGTAGTGGAGGACCGTCAGTGGTCTCTCATGA---------
           |    |  | | |||  |||  | ||  |  |||   | | ||   |  ||  ||  |  |    | | |     | | | ||||||    ||     |||  || | |||||||||||  | |||||||||| ||||| ||| |||| |||||| | ||||| ||||||||||| |||||||| |||||||         
---------ccttgtagtataagcct--ataggaataggatcttgtcatctcttcactgacctcaggcgtgttaatctcggttctttctttctcttgcgacggggtaccagATCGA-CCGAGCTATGGACGGCCTGTGGCATCTGGGGGACGAGCTCCGCGGGCAGCCCAAGGTGGTGGAGGACCGCCAGTGGTCGCTCATGACATCCAAGC
















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|29669162|gb|CB665437.1|CB665437
EST:     CGGCGATCTCCATCTGGCGACTCGCGAGCAGAGCAGGGGAGGGGATCCTG                         GTGGAGAGACTGAGCTGAGCTATGGACAACTTGTGGCATCTCGGGGATGAG
genomic: CGGCGATCTCCATCTGGCGACTCGCGAGCAGAGCAGGGGAGGGGATCCTGgtgagcatct ... cttgctgaagGTGGAGAGACTGAGCTGAGCTATGGACAACTTGTGGCATCTCGGGGATGAG
EST: gi|33655765|gb|CF278379.1|CF278379
EST:     GGCGATCTCCATCTGGCGACTCGCGAGCAGAGCAGGGGAGGGGATCCTAC                         TTGGAGAGACTGAGCTGAGCTATGGACAACTTGTGGCATCTCGGGGATGA
genomic: GGCGATCTCCATCTGGCGACTCGCGAGCAGAGCAGGGGAGGGGATCCT-Ggtgagcatct ... cttgctgaagGTGGAGAGACTGAGCTGAGCTATGGACAACTTGTGGCATCTCGGGGATGA
EST: gi|88826009|gb|CI776574.1|CI776574
EST:     CGGCGATCTCCATCTGGCGACTCGCGAGCAGAGCAGGGGAGGGGATCCTG                         GTGGAGAGACTGAGCTGAGCTATGGACAACTTGTGGCATCTCGGGGATGAG
genomic: CGGCGATCTCCATCTGGCGACTCGCGAGCAGAGCAGGGGAGGGGATCCTGgtgagcatct ... cttgctgaagGTGGAGAGACTGAGCTGAGCTATGGACAACTTGTGGCATCTCGGGGATGAG
EST: gi|29646527|gb|CB651534.1|CB651534
EST:     CGGCGATCTCCATCTGGCGACTCGCGAGCAGAGCAGGGGAGGGGATCCTG                         GTGGAGAGACTGAGCTGAGCTATGGACAACTTGTGGCATCTCGGGGATGAG
genomic: CGGCGATCTCCATCTGGCGACTCGCGAGCAGAGCAGGGGAGGGGATCCTGgtgagcatct ... cttgctgaagGTGGAGAGACTGAGCTGAGCTATGGACAACTTGTGGCATCTCGGGGATGAG
EST: gi|88762146|gb|CI771702.1|CI771702
EST:     CGGCGATCTCCATCTGGCGACTCGCGAGCAGAGCAGGGGAGGGGATCCTG                         GTGGAGAGACTGAGCTGAGCTATGGACAACTTGTGGCATCTCGGGGATGAG
genomic: CGGCGATCTCCATCTGGCGACTCGCGAGCAGAGCAGGGGAGGGGATCCTGgtgagcatct ... cttgctgaagGTGGAGAGACTGAGCTGAGCTATGGACAACTTGTGGCATCTCGGGGATGAG
EST: gi|88299599|gb|CI574712.1|CI574712
EST:     CGGCGATCTCCATCTGGCGACTCGCGAGCAGAGCAGGGGAGGGGATCCTG                         GTGGAGAGACTGAGCTGAGCTATGGACAACTTGTGGCATCTCGGGGATGAG
genomic: CGGCGATCTCCATCTGGCGACTCGCGAGCAGAGCAGGGGAGGGGATCCTGgtgagcatct ... cttgctgaagGTGGAGAGACTGAGCTGAGCTATGGACAACTTGTGGCATCTCGGGGATGAG
EST: gi|88738100|gb|CI761608.1|CI761608
EST:     CGGCGATCTCCATCTGGCGACTCGCGAGCAGAGCAGGGGAGGGGATCCTG                         GTGGAGAGACTGAGCTGAGCTATGGACAACTTGTGGCATCTCGGGGATGAG
genomic: CGGCGATCTCCATCTGGCGACTCGCGAGCAGAGCAGGGGAGGGGATCCTGgtgagcatct ... cttgctgaagGTGGAGAGACTGAGCTGAGCTATGGACAACTTGTGGCATCTCGGGGATGAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agtttgtttgttcccaagttggatccggccctgggtaatttctttcttgctgaagGTGGAGAGACTGAGCTGAGCTATGGACAACTTGTGGCATCTCGGGGATGAGTTCCGTGGGCAGTCGAAGGTAGTGGAGGACCGTCAGTGGTCTCTCATGA
                                      tttctttcttgct  CT-rich tract
                                   taatttcttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tcctcttaatttcagcgccttaaccttaatacaagtaccagtttgagtttgtttgttcccaagttggatccggccctgggtaatttctttcttgctgaagGTGGAGAGACTGAGCTGAGCTATGGACAACTTGTGGCATCTCGGGGATGAGTTCCGTGGGCAGTCGAAGGTAGTGGAGGACCGTCAGTGGTCTCTCATGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA
- - - - - - - - - - - - - -aatacaag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tggatcc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ggccctg