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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttgtgctttcttaaaactgaaatctctaccacaacatgatatttagtcctttcggttgtaacaaataactgagaaactccaatggaactctttgatctttggtacagAGGCCCTAGAGGAACAACGAATTATTCTAGCTGCTGCTGCAGCAGCAGCTAATTCAACTGCTGGGGAATCGTCACCTGTTGCTGGTCCTCAAGAAAATGA

Basic information

species Oryza sativa
transcript LOC_Os08g31470.1
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os08g31470.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G150212_T03 (Zea mays), 3'ss of exon 7
gtttgtgctttcttaaaactgaaatctctaccacaacatg-atatttagtcctttcggttgtaacaaataactgagaaactccaatggaactctttgatctttggtacagAG--GCCCTAGAGGAACAACGAATTATTCTAGCTGCTGCTGCAGCAGCAGC---TAATTCAACTGCTGGGGAATCGTCACCTGTTGCTGGTCCTCAAGAAAATGA
    ||  |||    |  |  || |||||  || ||     || || |||| | |  || ||| ||  |   | |    |||  ||||   |  ||| ||||| ||||| ||  ||| | || |||||| | |||| ||||||||| ||||| || |||||   ||||||||||||    |||||||||||||||||||| ||||||||  |   
----gtttttttcccagccaaaagtctctgtcaaaatgaatatgttaagtcttatttgtagtaccatct---tcatttcctctgatgg---ttattgttcttttgtacacagCTGCCTTGGAAGAACAAAGGATTACTCTAGCTGCCGCTGCGGCTGCAGCCACTAATTCAACTGCCACAGAATCGTCACCTGTTGCTGGCCCTCAAGAGGA---

upper sequence: LOC_Os08g31470.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G078541_T01 (Zea mays), 3'ss of exon 6
gtttgtgctttcttaaaactgaaatctctaccacaacatgatat--ttagtcctttcggttgtaacaaataactgagaaactccaatggaactctttgatctttggtacagAG--GCCCTAGAGGAACAACGAATTATTCTAGCTGC---TGCTGCAGCAGCAGCTAATTCAACTGCTGGGGAATCGTCACCTGTTGCTGGTCCTCAAGAAAATGA
    ||  ||||   |  |  || |||  | || |||   ||||  | |||| | |   |||||| |      |      |||  ||||   || ||| ||||  ||||| ||  ||| | || |||||| | |||| |||||| ||   |||||| || ||| |||||||||||||    |||||||||||||||||||| |||||||| ||   
----gttttttccccagccaaaagtcttgatcaaaactaaatatgttcagtcttct---ttgtaatatcatcttcgtttcctctgatgg---tcattgttcttgtgtacacagCTGCCTTGGAAGAACAAAGGATTACTCTAGCCGCCGCTGCTGCTGCGGCAACTAATTCAACTGCCACAGAATCGTCACCTGTTGCTGGCCCTCAAGAGAA---
















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|58675762|gb|CK064449.1|CK064449
EST:     TCTGGATCTATTGGAGCTTGATCTAATCACTACAAGTGAAGGACTACAAG                         AGGCCCTAGAGGAACAACGAATTATTCTAGCTGCTGCTGCAGCAGCAGCTA
genomic: TCTGGATCTATTGGAGCTTGATCTAATCACTACAAGTGAAGGACTACAAGgtttgtgctt ... tttggtacagAGGCCCTAGAGGAACAACGAATTATTCTAGCTGCTGCTGCAGCAGCAGCTA
EST: gi|86500374|gb|CI143007.1|CI143007
EST:     TGGATCTATTGGAGCTTGATCTAATCACTACCAAGTGAAGGACTACCAAG                         AGGCCCTAGAGGAACAACGAATTATTCTAGCTGCTGCTGCAGCAGCAGCT
genomic: TGGATCTATTGGAGCTTGATCTAATCACTA-CAAGTGAAGGACTA-CAAGgtttgtgctt ... tttggtacagAGGCCCTAGAGGAACAACGAATTATTCTAGCTGCTGCTGCAGCAGCAGCT
EST: gi|27576534|gb|CA999228.1|CA999228
EST:     TCTGGATCTATTGGAGCTTGATCTAATCACTACAAGTGAAGGACTACAAG                         AGGCCCTAGAGGAACAACGAATTATTCTAGCTGCTGCTGCAGCAGCAGCTA
genomic: TCTGGATCTATTGGAGCTTGATCTAATCACTACAAGTGAAGGACTACAAGgtttgtgctt ... tttggtacagAGGCCCTAGAGGAACAACGAATTATTCTAGCTGCTGCTGCAGCAGCAGCTA
EST: gi|58661547|gb|CK050227.1|CK050227
EST:     TCTGGATCTATTGGAGCTTGATCTAATCACTACAAGTGAAGGACTACAAG                         AGGCCCTAGAGGAACAACGAATTATTCTAGCTGCTGCTGCAGCAGCAGCTA
genomic: TCTGGATCTATTGGAGCTTGATCTAATCACTACAAGTGAAGGACTACAAGgtttgtgctt ... tttggtacagAGGCCCTAGAGGAACAACGAATTATTCTAGCTGCTGCTGCAGCAGCAGCTA
EST: gi|27576907|gb|CA999601.1|CA999601
EST:     TCTGGATCTATTGGAGCTTGATCTAATCACTACAAGTGAAGGACTACAAG                         AGGCCCTAGAGGAACAACGAATTATTCTAGCTGCTGCTGCAGCAGCAGCTA
genomic: TCTGGATCTATTGGAGCTTGATCTAATCACTACAAGTGAAGGACTACAAGgtttgtgctt ... tttggtacagAGGCCCTAGAGGAACAACGAATTATTCTAGCTGCTGCTGCAGCAGCAGCTA
EST: gi|29616427|gb|CB621439.1|CB621439
EST:     TCTGGATCTATTGGAGCTTGATCTAATCACTACAAGTGAAGGACTACAAG                         AGGCCCTAGAGGAACAACGAATTATTCTAGCTGCTGCTGCAGCAGCAGCTA
genomic: TCTGGATCTATTGGAGCTTGATCTAATCACTACAAGTGAAGGACTACAAGgtttgtgctt ... tttggtacagAGGCCCTAGAGGAACAACGAATTATTCTAGCTGCTGCTGCAGCAGCAGCTA
EST: gi|29616113|gb|CB621125.1|CB621125
EST:     TCTGGATCTATTGGAGCTTGATCTAATCACTACAAGTGAAGGACTACAAG                         AGGCCCTAGAGGAACAACGAATTATTCTAGCTGCTGCTGCAGCAGCAGCTA
genomic: TCTGGATCTATTGGAGCTTGATCTAATCACTACAAGTGAAGGACTACAAGgtttgtgctt ... tttggtacagAGGCCCTAGAGGAACAACGAATTATTCTAGCTGCTGCTGCAGCAGCAGCTA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cggttgtaacaaataactgagaaactccaatggaactctttgatctttggtacagAGGCCCTAGAGGAACAACGAATTATTCTAGCTGCTGCTGCAGCAGCAGCTAATTCAACTGCTGGGGAATCGTCACCTGTTGCTGGTCCTCAAGAAAATGA
                                           tcttt  CT-rich tract
      taacaaataa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtttgtgctttcttaaaactgaaatctctaccacaacatgatatttagtcctttcggttgtaacaaataactgagaaactccaatggaactctttgatctttggtacagAGGCCCTAGAGGAACAACGAATTATTCTAGCTGCTGCTGCAGCAGCAGCTAATTCAACTGCTGGGGAATCGTCACCTGTTGCTGGTCCTCAAGAAAATGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA