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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgattaaatgtattttgtgtcactcacattttctgtatcaacttgtgccttcatttgaaattgatgttttctgctatttgctactctttgaagGTGGATTGGATTGGCCAGAGGAATCAAATAGATGCTG

Basic information

species Oryza sativa
transcript LOC_Os05g01970.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os05g01970.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G047219_T03 (Zea mays), 3'ss of exon 2
-----------------------------------gtgattaaatgtattttgtgtcactcacat------tttctgtatcaacttgtgccttcatttgaaattgatgttttctgctatttgctactctttgaagGTGGATTGGATTGGCCAGAGGAATCAAATAGATGCTG
                                   ||  |||  |  | |  |||   |||  |       | | ||| |||| |      ||  |||| |||||||||| | || | ||||   || ||| |||||||||||||||||||| | ||||||||| |||||||
gtgcctgaaattattcgatatacagtgctcttacagtatttatctaaaatacgtggtgctcttacggtagctgtatgtgtcaattcccaaatttgtttggaattgatgttctatgttgtttgtctctgtttcaagGTGGATTGGATTGGCCAAAAGAATCAAATTGATGCTG

upper sequence: LOC_Os05g01970.1 (Oryza sativa), 3'ss of exon 2
lower sequence: EFJ06085 (Selaginella moellendorffii), 3'ss of exon 1
gtgattaaatgtattttgtgtcactcacattttctgtatcaacttgtgccttcatttgaaattgatgttttctgctatttgctactctttgaagGTGGATTGGATTGGCCAGAGGAATCAAATAGATGCTG
                 || | ||   |||| ||  | |    |||||||      ||  ||   |  | |||  | ||  | | | | |  |||||||||||||||||||||  |||||||| |||||||
-----------------gtatgacgatcattctcctttt----ttgtgcc------tgtgatctctcatctct-tttttctccattgtctccagGTGGATTGGATTGGCCAGAAAAATCAAATTGATGCTG

upper sequence: LOC_Os05g01970.1 (Oryza sativa), 3'ss of exon 2
lower sequence: EFJ29885 (Selaginella moellendorffii), 3'ss of exon 1
gtgattaaatgtattttgtgtcactcacattttctgtatcaacttgtgccttcatttgaaattgatgttttctgctatttgctactctttgaagGTGGATTGGATTGGCCAGAGGAATCAAATAGATGCTG
                | || |  |||   |   | | ||  | ||||   ||         | || | || |    ||  | | | | |  ||||||||||||||||||||| ||||||||| |||||||
---------------gtatgacggtcattctccttttctctgcctgtgatctc---------tcatctctttt----ttctccattgtctccagGTGGATTGGATTGGCCAGAAGAATCAAATTGATGCTG

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|29637321|gb|CB642330.1|CB642330
EST:     AGGGGGGACGCCCAGAGTTCTACTTTGAGGATGGCTCTTATCCTGAGCAG                         GTGGATTGGATTGGCCAGAGGAATCAAATAGATGCTG
genomic: AGGGGGGACGCCCAGAGTTCTACTTTGAGGATGGCTCTTATCCTGAGCAGgtgattaaat ... ctctttgaagGTGGATTGGATTGGCCAGAGGAATCAAATAGATGCTG
EST: gi|29637203|gb|CB642212.1|CB642212
EST:     AGGGGGGACGCCCAGAGTTCTACTTTGAGGATGGCTCTTATCCTGAGCAG                         GTGGATTGGATTGGCCAGAGGAATCAAATAGATGCTG
genomic: AGGGGGGACGCCCAGAGTTCTACTTTGAGGATGGCTCTTATCCTGAGCAGgtgattaaat ... ctctttgaagGTGGATTGGATTGGCCAGAGGAATCAAATAGATGCTG
EST: gi|88372139|gb|CI641774.1|CI641774
EST:     AGGGGGGACGCCCAGAGTTCTACTTTGAGGATGGCTCTTATCCTGAGCAG                         GTGGATTGGATTGGCCAGAGGAATCAAATAGATGCTG
genomic: AGGGGGGACGCCCAGAGTTCTACTTTGAGGATGGCTCTTATCCTGAGCAGgtgattaaat ... ctctttgaagGTGGATTGGATTGGCCAGAGGAATCAAATAGATGCTG
EST: gi|29614613|gb|CB619626.1|CB619626
EST:     AGGGGGGACGCCCAGAGTTCTACTTTGAGGATGGCTCTTATCCTGAGCAG                         GTGGATTGGATTGGCCAGAAGAATCAAATAGATGCTG
genomic: AGGGGGGACGCCCAGAGTTCTACTTTGAGGATGGCTCTTATCCTGAGCAGgtgattaaat ... ctctttgaagGTGGATTGGATTGGCCAGAGGAATCAAATAGATGCTG
EST: gi|29637365|gb|CB642374.1|CB642374
EST:     AGGGGGGACGCCCAGAGTTCTACTTTGAGGATGGCTCTTATCCTGAGCAG                         GTGGATTGGATTGGCCACAGGAATCAAATAAATGCTG
genomic: AGGGGGGACGCCCAGAGTTCTACTTTGAGGATGGCTCTTATCCTGAGCAGgtgattaaat ... ctctttgaagGTGGATTGGATTGGCCAGAGGAATCAAATAGATGCTG
EST: gi|84117300|gb|CD151067.1|CD151067
EST:     AGGGGGGACGCCCAGAGTTCTACTTTGAGGATGGCTCTTATCCTGAGCAG                         GTGGATTGGATTGGCCAGAAGAATCAAATAGATGCTG
genomic: AGGGGGGACGCCCAGAGTTCTACTTTGAGGATGGCTCTTATCCTGAGCAGgtgattaaat ... ctctttgaagGTGGATTGGATTGGCCAGAGGAATCAAATAGATGCTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

caacttgtgccttcatttgaaattgatgttttctgctatttgctactctttgaagGTGGATTGGATTGGCCAGAGGAATCAAATAGATGCTG
                    aattgat  putative branch site (score: 4)
                                          ctactcttt  putative PPT
              atttgaaatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgattaaatgtattttgtgtcactcacattttctgtatcaacttgtgccttcatttgaaattgatgttttctgctatttgctactctttgaagGTGGATTGGATTGGCCAGAGGAATCAAATAGATGCTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  ATGCTG