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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...atgtgctggttacatcactgattttcttttccctttagtttttttttaaatgtcctttggtgtattattttggctgacactgataagaacccgcttgcagGAGTTAGCTATTACTTCAGATGAGGCCTTAAGTTTGGAGGAGCTACCAAAACGTGCTGTAATCCTTGGTGGCGG

Basic information

species Oryza sativa
transcript LOC_Os02g56850.3
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g56850.4 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM5G806449_T01 (Zea mays), 3'ss of exon 5
atgtgctggttacatcactgattttcttttccctttagtttttttttaaatgtcctttggtgtattattttggctgac-actgataagaacccgc----ttgcagGAGTTAGCTATTACTTCAGATGAGGCCTTAAGTTTGGAGGAGCTACCAAAACGTGCTGTAATCCTTGGTGGCGG
   |  | ||||  |   ||   ||  ||    || | ||| |  || | |  | | ||||| |||||| |     || | ||| || || | |     || |||||  | ||||||||||| ||||||||||| || ||||||||||| ||||| || ||||||||||| ||||||||
--atatttgttatgtt-ttggcctttgttcgttttcattttgtccttcatt--catctggtgaattattgttaaaaactagtgaaaacaatctgtcttttttcagGATCTGGCTATTACTTCTGATGAGGCCTTGAGCTTGGAGGAGCTTCCAAAGCGCGCTGTAATCCTGGGTGGCGG
















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|88433133|gb|CI569802.1|CI569802
EST:     TATTGATAGCAACTGGTAGCCGAGCTCAACGTGTCAACATTCCTGGGAAG                         GAGTTAGCTATTACTTCAGATGAGGC-TTAAGTTTGGAGGAGCTACCAAAA
genomic: TATTGATAGCAACTGGTAGCCGAGCTCAACGTGTCAACATTCCTGGGAAGgtaacaaaat ... ccgcttgcagGAGTTAGCTATTACTTCAGATGAGGCCTTAAGTTTGGAGGAGCTACCAAAA
EST: gi|58586132|gb|CF984440.1|CF984440
EST:     TATTGATAGCAACTGGTAGCCGAGCTCAACGTGTCAACATTCCTGGGAAG                         GAGTTAGCTATTACTTCAGATGAGGCCTTAAGTTTGGAGGAGCTACCAAAA
genomic: TATTGATAGCAACTGGTAGCCGAGCTCAACGTGTCAACATTCCTGGGAAGgtaacaaaat ... ccgcttgcagGAGTTAGCTATTACTTCAGATGAGGCCTTAAGTTTGGAGGAGCTACCAAAA
EST: gi|58601900|gb|CK012428.1|CK012428
EST:     TATTGATAGCAACTGGTAGCCGAGCTCAACGTGTCAACATTCCTGGGAAG                         GAGTTAGCTATTACTTCAGATGAGGCCTTAAGTTTGGAGGAGCTACCAAAA
genomic: TATTGATAGCAACTGGTAGCCGAGCTCAACGTGTCAACATTCCTGGGAAGgtaacaaaat ... ccgcttgcagGAGTTAGCTATTACTTCAGATGAGGCCTTAAGTTTGGAGGAGCTACCAAAA
EST: gi|29675048|gb|CB671323.1|CB671323
EST:     TATTGATAGCAACTGGTAGCCGAGCTCAACGTGTCAACATTCCTGGGAAG                         GAGTTAGCTATTACTTCAGATGAGGCCTTAAGTTTGGAGGAGCTACCAAAA
genomic: TATTGATAGCAACTGGTAGCCGAGCTCAACGTGTCAACATTCCTGGGAAGgtaacaaaat ... ccgcttgcagGAGTTAGCTATTACTTCAGATGAGGCCTTAAGTTTGGAGGAGCTACCAAAA
EST: gi|319908658|gb|HS977786.1|HS977786
EST:     TATTGATAGCAACTGGTAGCCGAGCTCAACGTGTCAACATTCCTGGGAAG                         GAGTTAGCTATTACTTCAGATGAGGCCTTAAGTTTGGAGGAGCTACCAAAA
genomic: TATTGATAGCAACTGGTAGCCGAGCTCAACGTGTCAACATTCCTGGGAAGgtaacaaaat ... ccgcttgcagGAGTTAGCTATTACTTCAGATGAGGCCTTAAGTTTGGAGGAGCTACCAAAA
EST: gi|4714976|gb|AU056093.1|AU056093
EST:     TATTGATAGCAACTGGTAGCCGAGCTCAACGTGTCAACATTCCTGGGAAG                         GAGTTAGCTATTACTTCAGATGAGGCCTTAAGTTTGGAGGAGCTACCAAAA
genomic: TATTGATAGCAACTGGTAGCCGAGCTCAACGTGTCAACATTCCTGGGAAGgtaacaaaat ... ccgcttgcagGAGTTAGCTATTACTTCAGATGAGGCCTTAAGTTTGGAGGAGCTACCAAAA
EST: gi|88407233|gb|CI583691.1|CI583691
EST:     ATTGATAGCAACTGGTAGCCCGAGCTCAACGTGTCAACATTCCTGGGAAG                         GAGTTAGCTATTACTTCAGATGAGGCCTTAAGTTTGGAGGAGCTACCAAAA
genomic: ATTGATAGCAACTGGTAGCC-GAGCTCAACGTGTCAACATTCCTGGGAAGgtaacaaaat ... ccgcttgcagGAGTTAGCTATTACTTCAGATGAGGCCTTAAGTTTGGAGGAGCTACCAAAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttaaatgtcctttggtgtattattttggctgacactgataagaacccgcttgcagGAGTTAGCTATTACTTCAGATGAGGCCTTAAGTTTGGAGGAGCTACCAAAACGTGCTGTAATCCTTGGTGGCGG
                                cactgat  putative branch site (score: 3)
                                            cccgctt  putative PPT
               tgtattatttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
atgtgctggttacatcactgattttcttttccctttagtttttttttaaatgtcctttggtgtattattttggctgacactgataagaacccgcttgcagGAGTTAGCTATTACTTCAGATGAGGCCTTAAGTTTGGAGGAGCTACCAAAACGTGCTGTAATCCTTGGTGGCGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGTGG