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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tggtgtaatgttattgactgttttagtggaagttgcaagtcggtgatgcatttgagtacttgagtcatgatggcttactgtttggcaaccattggtgcagAATACGTGAAGTGGAGTTGAAGCGCGACTACGCGTTTATT

Basic information

species Oryza sativa
transcript LOC_Os03g17710.2
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g17710.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G099317_T05 (Zea mays), 3'ss of exon 3
tggtgtaatgttattgactgttttagtggaagttgcaagtcggtgatgcatttgagtacttgagtcatgatggcttactgtttg--gcaaccattggtgcagAATACGTGAAGTGGAGTTGAAGCGCGACTACGCGTTTATT
    |||||||||||||||||||||||||||||| ||||| |||||||||||||||||||||| |||||| |||||||||||||  |||||| ||   |||||||||| ||||||||||||||||||||||| || ||||||
----gtaatgttattgactgttttagtggaagttccaagttggtgatgcatttgagtacttgactcatgaaggcttactgtttgtggcaaccctttccgcagAATACGAGAAGTGGAGTTGAAGCGCGACTATGCATTTATT

upper sequence: LOC_Os03g17710.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G099317_T02 (Zea mays), 3'ss of exon 2
tggtgtaatgttattgactgttttagtggaagttgcaagtcggtgatgcatttgagtacttgagtcatgatggcttactgtttg--gcaaccattggtgcagAATACGTGAAGTGGAGTTGAAGCGCGACTACGCGTTTATT
  |||||||||||||||||||||||||||||||| ||||| |||||||||||||||||||||| |||||| |||||||||||||  |||||| ||   |||||||||| ||||||||||||||||||||||| || ||||||
--gtgtaatgttattgactgttttagtggaagttccaagttggtgatgcatttgagtacttgactcatgaaggcttactgtttgtggcaaccctttccgcagAATACGAGAAGTGGAGTTGAAGCGCGACTATGCATTTATT
















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|33654664|gb|CF277278.1|CF277278
EST:     TCGCGCACTCGTTCTCGTGACCTAGAATATCTTTTCGGCAGATATGGAAG                         AATACGTGAAGTGGAGTTGAAGCGCGACTACGCGTTTATT
genomic: TCGCGCACTCGTTCTCGTGACCTAGAATATCTTTTCGGCAGATATGGAAGgtaagaacag ... attggtgcagAATACGTGAAGTGGAGTTGAAGCGCGACTACGCGTTTATT
EST: gi|88422877|gb|CI615177.1|CI615177
EST:     TCGCGCACTCGTTCTCGTGACCTAGAATATCTTTTCGGCAGATATGGAAG                         AATACGTGAAGTGGAGTTGAAGCGCGACTACGCGTTTATT
genomic: TCGCGCACTCGTTCTCGTGACCTAGAATATCTTTTCGGCAGATATGGAAGgtaagaacag ... attggtgcagAATACGTGAAGTGGAGTTGAAGCGCGACTACGCGTTTATT
EST: gi|58673537|gb|CK062223.1|CK062223
EST:     TCGCGCACTCGTTCTCGTGACCTAGAATATCTTTTCGGCAGATATGGAAG                         AATACGTGAAGTGGAGTTGAAGCGCGACTACGCGTTTATT
genomic: TCGCGCACTCGTTCTCGTGACCTAGAATATCTTTTCGGCAGATATGGAAGgtaagaacag ... attggtgcagAATACGTGAAGTGGAGTTGAAGCGCGACTACGCGTTTATT
EST: gi|58602955|gb|CK013483.1|CK013483
EST:     GCGCACTCGTTCTCGTGACCTAGAATATCTTTTCGGCAGATATGGAAG                         AATACGTGAAGTGGAGTTGAAGCGCGACTACGCGTTTATT
genomic: GCGCACTCGTTCTCGTGACCTAGAATATCTTTTCGGCAGATATGGAAGgtaagaacag ... attggtgcagAATACGTGAAGTGGAGTTGAAGCGCGACTACGCGTTTATT
EST: gi|58653740|gb|CK042420.1|CK042420
EST:     TCGCGCACTCGTTCTCGTGACCTAGAATATCTTTTCGGCAGATATGGAAG                         AATACGTGAAGTGGAGTTGAAGCGCGACTACGCGTTTATT
genomic: TCGCGCACTCGTTCTCGTGACCTAGAATATCTTTTCGGCAGATATGGAAGgtaagaacag ... attggtgcagAATACGTGAAGTGGAGTTGAAGCGCGACTACGCGTTTATT
EST: gi|88573286|gb|CI664857.1|CI664857
EST:     TCGCGCACTCGTTCTCGTGACCTAGAATATCTTTTCGGCAGATATGGAAG                         AATACGTGAAGTGGAGTTGAAGCGCGACTACGCGTTTATT
genomic: TCGCGCACTCGTTCTCGTGACCTAGAATATCTTTTCGGCAGATATGGAAGgtaagaacag ... attggtgcagAATACGTGAAGTGGAGTTGAAGCGCGACTACGCGTTTATT
EST: gi|33654208|gb|CF276822.1|CF276822
EST:     TCGCGCACTCGTTCTCGTGACCTAGAATATCTTTTCGGCAGATATGGAAG                         AATACGTGAAGTGGAGTTGAAGCGCGACTACGCGTTTATT
genomic: TCGCGCACTCGTTCTCGTGACCTAGAATATCTTTTCGGCAGATATGGAAGgtaagaacag ... attggtgcagAATACGTGAAGTGGAGTTGAAGCGCGACTACGCGTTTATT
EST: gi|88327495|gb|CI646681.1|CI646681
EST:     TCGCGCACTCGTTCTCGTGACCTAGAATATCTTTTCGGCAGATATGGAAG                         AATACGTGAAGTGGAGTTGAAGCGCGACTACGCGTTTATT
genomic: TCGCGCACTCGTTCTCGTGACCTAGAATATCTTTTCGGCAGATATGGAAGgtaagaacag ... attggtgcagAATACGTGAAGTGGAGTTGAAGCGCGACTACGCGTTTATT
EST: gi|88729424|gb|CI752934.1|CI752934
EST:     TCGCGCACTCGTTCTCGTGACCTACAATATCTTTTCGGCAGATATGGAAG                         AATACGTGAAGTGGAGTTGAAGCGCGACTACGCGTTTATT
genomic: TCGCGCACTCGTTCTCGTGACCTAGAATATCTTTTCGGCAGATATGGAAGgtaagaacag ... attggtgcagAATACGTGAAGTGGAGTTGAAGCGCGACTACGCGTTTATT
EST: gi|66917360|gb|CX104208.1|CX104208
EST:     TCGCGCACTCGTTCTCGTGACCTATAATATCTTTTCGGCAGATATGGAAG                         AATACGTGAAGTGGAGTTGAAGCGCCACTACGCGTCTTATT
genomic: TCGCGCACTCGTTCTCGTGACCTAGAATATCTTTTCGGCAGATATGGAAGgtaagaacag ... attggtgcagAATACGTGAAGTGGAGTTGAAGCGCGACTACGCGT-TTATT
EST: gi|218497275|gb|FG960321.1|FG960321
EST:     TCGCGCACTCGTTCTCGTGACCTAGAATATCCTTTCGGCAGATATGGAAG                         AATACGTGAAGTGGAGTTGAAGCGCGACTACGCGTTTATT
genomic: TCGCGCACTCGTTCTCGTGACCTAGAATATCTTTTCGGCAGATATGGAAGgtaagaacag ... attggtgcagAATACGTGAAGTGGAGTTGAAGCGCGACTACGCGTTTATT
EST: gi|88572064|gb|CI663635.1|CI663635
EST:     TCGCGCACTCGTTCTCGTGACCTAGAATATCTTTTCGGCAGATATGGAAG                         AATACGTGAAGTGGAGTTGAAGCGCGACTACGCGTTTATT
genomic: TCGCGCACTCGTTCTCGTGACCTAGAATATCTTTTCGGCAGATATGGAAGgtaagaacag ... attggtgcagAATACGTGAAGTGGAGTTGAAGCGCGACTACGCGTTTATT
EST: gi|109974555|gb|DT806973.1|DT806973
EST:     TCGCGCACTCGTTCTCGTGACCTAGAATATCTTTTCGGCAGATATGGAAG                         AATACGTGAAGTGGAGTTGAAGCGCGACTACGCGTTTATT
genomic: TCGCGCACTCGTTCTCGTGACCTAGAATATCTTTTCGGCAGATATGGAAGgtaagaacag ... attggtgcagAATACGTGAAGTGGAGTTGAAGCGCGACTACGCGTTTATT
EST: gi|88349704|gb|CI632839.1|CI632839
EST:     TCGCGCACTCGTTCTCGTGACCTANAATATCTTTTCGGCAGATATGGAAG                         AATACGTGAAGTGGAGTTGAAGCGCGACTACGCGTTTATT
genomic: TCGCGCACTCGTTCTCGTGACCTAGAATATCTTTTCGGCAGATATGGAAGgtaagaacag ... attggtgcagAATACGTGAAGTGGAGTTGAAGCGCGACTACGCGTTTATT
EST: gi|58674796|gb|CK063483.1|CK063483
EST:     TCGCGCACTCGTTCTCGTGACCTAGAATATCTTTTCGGCAGATATGGAAG                         AATACGTGAAGTGGAGTTGAAGCGCGACTACGCGTTTATT
genomic: TCGCGCACTCGTTCTCGTGACCTAGAATATCTTTTCGGCAGATATGGAAGgtaagaacag ... attggtgcagAATACGTGAAGTGGAGTTGAAGCGCGACTACGCGTTTATT
EST: gi|88328329|gb|CI651340.1|CI651340
EST:     TCGCGCACTCGTTCTCGTGACCTAGAATATCTTTTCGGCAGATATGGAAG                         AATACGTGAAGTGGAGTTGAAGCGCGACTACGCGTTTATT
genomic: TCGCGCACTCGTTCTCGTGACCTAGAATATCTTTTCGGCAGATATGGAAGgtaagaacag ... attggtgcagAATACGTGAAGTGGAGTTGAAGCGCGACTACGCGTTTATT
EST: gi|117220967|gb|CT861417.1|CT861417
EST:     TCGCGCACTCGTTCTCGTGACCTAGAATATCTTTTCGGCAGATATGGAAG                         AATACGTGAAGTGGAGTTGAAGCGCGACTACGCGTTTATT
genomic: TCGCGCACTCGTTCTCGTGACCTAGAATATCTTTTCGGCAGATATGGAAGgtaagaacag ... attggtgcagAATACGTGAAGTGGAGTTGAAGCGCGACTACGCGTTTATT
EST: gi|88720424|gb|CI743723.1|CI743723
EST:     TCGCGCACTCGTTCTCGTGACCTAGAATATCTTTTCGGCAGATATGGAAG                         AATACGTGAAGTGGAGTTGAAGCGCGACTACGCGTTTATT
genomic: TCGCGCACTCGTTCTCGTGACCTAGAATATCTTTTCGGCAGATATGGAAGgtaagaacag ... attggtgcagAATACGTGAAGTGGAGTTGAAGCGCGACTACGCGTTTATT
EST: gi|88761659|gb|CI771215.1|CI771215
EST:     TCGCGCACTCGTTCTCGTGACCTANAATATCTTTTCGGCAGATATGGAAG                         AATACGTGAAGTGGAGTTGAAGCGCGACTACGCGTTTATT
genomic: TCGCGCACTCGTTCTCGTGACCTAGAATATCTTTTCGGCAGATATGGAAGgtaagaacag ... attggtgcagAATACGTGAAGTGGAGTTGAAGCGCGACTACGCGTTTATT
EST: gi|88424660|gb|CI606459.1|CI606459
EST:     TCGCGCACTCGTTCTCGTGACCTAGAATATCTTTTCGGCAGATATGGAAG                         AATACGTGAAGTGGAGTTGAAGCGCGACTACGCGTTTATT
genomic: TCGCGCACTCGTTCTCGTGACCTAGAATATCTTTTCGGCAGATATGGAAGgtaagaacag ... attggtgcagAATACGTGAAGTGGAGTTGAAGCGCGACTACGCGTTTATT
EST: gi|88342002|gb|CI644339.1|CI644339
EST:     TCGCGCACTCGTTCTCGTGACCTAGAATATCTTTTCGGCAGATATGGAAG                         AATACGTGAAGTGGAGTTGAAGCGCGACTACGCGTTTATT
genomic: TCGCGCACTCGTTCTCGTGACCTAGAATATCTTTTCGGCAGATATGGAAGgtaagaacag ... attggtgcagAATACGTGAAGTGGAGTTGAAGCGCGACTACGCGTTTATT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atgcatttgagtacttgagtcatgatggcttactgtttggcaaccattggtgcagAATACGTGAAGTGGAGTTGAAGCGCGACTACGCGTTTATT
                          ggcttac  putative branch site (score: 3)
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tggtgtaatgttattgactgttttagtggaagttgcaagtcggtgatgcatttgagtacttgagtcatgatggcttactgtttggcaaccattggtgcagAATACGTGAAGTGGAGTTGAAGCGCGACTACGCGTTTATT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGC