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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aggtaatgaagttaaattgttaatagttccgtaaacatcttttgagaatcatagactggttttcttcattgtgttaagtaatgggtggtgtaatttgcagTATGGTCTGGTGCACATTTCTGCTGGAGATTTGCTAAGGGCAGAAATTGCTGCAGGCAGTGAGAATGGGAAGCGAGCTAAGGAATTTATGGAGAAGGGTC

Basic information

species Oryza sativa
transcript LOC_Os08g01770.2
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os08g01770.2 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G178192_T03 (Zea mays), 3'ss of exon 3
aggtaatgaagttaaattgttaatagttccgtaaacatcttttgagaatcatagactggttttcttcattgt-gttaagtaatgggtggt---gtaatttgcagTATGGTCTGGTGCACATTTCTGCTGGAGATTTGCTAAGGGCAGAAATTGCTGCAGGCAGTGAGAATGGGAAGCGAGCTAAGGAATTTATGGAGAAGGGTC
  | |     || |   | | |     | | |  |   ||  |  | | ||   ||||         |  |  | | |||||| | |  |    |||||||||||||   |||| |||||| || |||||||||||| |  |||| ||||| ||||| |||  ||||||||||||||| || |||||||| ||||||||||| |
-aggagaatcgtcagtatatcatgtcctacatgcaatcctccttcgcagca---actgcagagaaaaacagcagcttagtaatcgtttttctgataatttgcagTATCAACTGGCGCACATCTCCGCTGGAGATTTGTTGCGGGCGGAAATCGCTGCTGGCTCTGAGAATGGGAAGCGGGCCAAGGAATTCATGGAGAAGGGCC

upper sequence: LOC_Os08g01770.2 (Oryza sativa), 3'ss of exon 2
lower sequence: GLYMA09G36900.4 (Glycine max), 3'ss of exon 2
aggtaatgaagttaaattgttaatagttccgtaaacatcttttgagaatcatagactggttttcttcattgtgttaagtaatgggtggtgta-atttgcagTATGGTCTGGTGCACATTTCTGCTGGAGATTTGCTAAGGGCAGAAATTGCTGCAGGCAGTGAGAATGGGAAGCGAGCTAAGGAATTTATGGAGAAGGGTC
      | |  |||  || |   |  |||| |       ||   | |   |||||   | ||  |   |  | || |  ||         |  |  ||||||| ||| |||| || ||| ||||||||||||| || ||||||||||||||  | || ||||| ||||| |||||||| ||  | | |||||||||||| |
-----gttagcttaccttctc--tttttccttccttcaattactaaatagatagataagcttcttagttcttatttatgaacaaacacaattcaaatgcagTACGGTTTGGTTCATATTGCTGCTGGAGATTTACTTAGGGCAGAAATTGCCACTGGAAGTGATAATGGAAAGCGAGCCAAACAGTATATGGAGAAGGGAC

upper sequence: LOC_Os08g01770.2 (Oryza sativa), 3'ss of exon 2
lower sequence: AT5G47840.1 (Arabidopsis thaliana), 3'ss of exon 2
----------aggtaatgaagttaaattgttaatagttccgtaaacatcttttgagaatcatagactggttttcttcattgtgttaagtaatgggtggtgtaatttgcagTATGGTCTGGTGCACATTTCTGCTGGAGATTTGCTAAGGGCAGAAATTGCTGCAGGCAGTGAGAATGGGAAGCGAGCTAAGGAATTTATGGAGAAGGGTC
          |  | ||    || || |  |  | | | | | |   | | |   ||| || |  | | ||      |   | ||      | | |||| |     |||||||||| ||||||| || ||||||||||||||||| ||||| ||||| ||| | || ||||| ||||| |  || ||||| |||  ||||||||| || |
tccatggaagacttcatactttttaagttctctttgctgcatgagattttctcatgaaacagaagcagattg-----aaaattttcctcttttgttggtat-----gcagTATGGTTTGGTGCATATCTCTGCTGGAGATTTGCTGAGGGCTGAAATCGCTTCTGGAAGTGAAAATGGAAGACGTGCTAAAGAACATATGGAGAAAGGAC

upper sequence: LOC_Os08g01770.2 (Oryza sativa), 3'ss of exon 2
lower sequence: Vv18s0041g01280.t01 (Vitis vinifera), 3'ss of exon 3
aggtaatgaagttaaattgttaatagttccgtaaacatcttttgagaatcatagactggttttcttcattgtgttaagtaatgg-gtggtgtaatttgcagTATGGTCTGGTGCACATTTCTGCTGGAGATTTGCTAAGGGCAGAAATTGCTGCAGGCAGTGAGAATGGGAAGCGAGCTAAGGAATTTATGGAGAAGGGTC
   | |      ||| ||  |   | | | | | | || | |        || | || ||       |     || | | | |   |  |   || ||||| ||| | ||||||| ||| |||||||||||||  | ||||||||| |||| || || ||||| ||||||| |||||| ||||| || ||||| || ||  
-tattacttgcataagttactggcattactgcataaatttctcatttggaattgcctcgtgaagaaaaacagattgaatcaagtcatcctcgtatatgcagCATGATTTGGTGCATATTGCTGCTGGAGATTTATTGAGGGCAGAAGTTGCAGCTGGTAGTGAAAATGGGAGGCGAGCGAAGGAGTTCATGGAAAAAGGGA

upper sequence: LOC_Os08g01770.2 (Oryza sativa), 3'ss of exon 2
lower sequence: EFJ34288 (Selaginella moellendorffii), 3'ss of exon 2
aggtaatgaagttaaattgttaatagttccgtaaacatcttttgagaatcatagactggttttcttcattgtgttaagtaatgggtggtgtaatttgcagTATGGTCTGGTGCACATTTCTGCTGGAGATTTGCTAAGGGCAGAAATTGCTGCAGGCAGTGAGAATGGGAAGCGAGCTAAGGAATTTATGGAGAAGGGTC
                                          |  ||  |||  ||||    |  |  |          | || |||    ||||   ||||   |||||| || ||||| ||||||||||||||| | || ||| |||| ||||||| |||  |||||||| | || ||||| ||||||||  | ||  
-----------------------------------------gtatgatccatccactgaaagttgtgttgcaagcttacattgtgtgtgacaattc-tagTACAATCTGGTCCATATTTCCGCTGGAGATTTGCTACGAGCGGAAGTTGCCGCAGGCACTGATTATGGGAAGAGGGCCAAGGAGTTTATGGATCAAGGCA

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|58691964|gb|CK080651.1|CK080651
EST:     GGGCTCCAGCATCTGGAAAGGGAACGCAGTGTGAGCTCATCAAGAGCAAA                         TATGGTCTGGTGCACATTTCTGCTGGAGATTTGCTAAGGGCAGAAATTGCT
genomic: GGGCTCCAGCATCTGGAAAGGGAACGCAGTGTGAGCTCATCAAGAGCAAAgtaagtgagt ... taatttgcagTATGGTCTGGTGCACATTTCTGCTGGAGATTTGCTAAGGGCAGAAATTGCT
EST: gi|58608711|gb|CK036744.1|CK036744
EST:     GGGCTCCAGCATCTGGAAAGGGAACGCAGTGTGAGCTCATCAAGAGCAAA                         TAATGGTCTGGTGCACATTTCTGCTGGAGATTTGCTAAGGGCAGAAATTGC
genomic: GGGCTCCAGCATCTGGAAAGGGAACGCAGTGTGAGCTCATCAAGAGCAAAgtaagtgagt ... taatttgcagT-ATGGTCTGGTGCACATTTCTGCTGGAGATTTGCTAAGGGCAGAAATTGC
EST: gi|88351694|gb|CI617419.1|CI617419
EST:     GGGCTCCAGCATCTGGAAAGGGAACGCAGTGTGAGCTCATCAAGAGCAAA                         TATGGTCTGGTGCACATTTCTGCTGGAGATTTGCTAAGGGCAGAAATTGCT
genomic: GGGCTCCAGCATCTGGAAAGGGAACGCAGTGTGAGCTCATCAAGAGCAAAgtaagtgagt ... taatttgcagTATGGTCTGGTGCACATTTCTGCTGGAGATTTGCTAAGGGCAGAAATTGCT
EST: gi|88313599|gb|CI671726.1|CI671726
EST:     GGGCTCCAGCATCTGGAAAGGGAACGCAGTGTGAGCTCATCAAGAGCAAA                         TATGGTCTGGTGCACATTTCTACTGGAGATTTGCTAACGGCAGAAATTGCT
genomic: GGGCTCCAGCATCTGGAAAGGGAACGCAGTGTGAGCTCATCAAGAGCAAAgtaagtgagt ... taatttgcagTATGGTCTGGTGCACATTTCTGCTGGAGATTTGCTAAGGGCAGAAATTGCT
EST: gi|88324446|gb|CI566259.1|CI566259
EST:     GGGCTCCACCATCTGGAAAGGGAACGCAGTGTGAGCTCATCAAGAGCAAA                         TATGGTCTGGTGCACATTTCTGCTGGAGATTTGCTA-GGGCACAAATTGCT
genomic: GGGCTCCAGCATCTGGAAAGGGAACGCAGTGTGAGCTCATCAAGAGCAAAgtaagtgagt ... taatttgcagTATGGTCTGGTGCACATTTCTGCTGGAGATTTGCTAAGGGCAGAAATTGCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gaatcatagactggttttcttcattgtgttaagtaatgggtggtgtaatttgcagTATGGTCTGGTGCACATTTCTGCTGGAGATTTGCTAAGGGCAGAAATTGCTGCAGGCAGTGAGAATGGGAAGCGAGCTAAGGAATTTATGGAGAAGGGTC
                            ttaagtaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aggtaatgaagttaaattgttaatagttccgtaaacatcttttgagaatcatagactggttttcttcattgtgttaagtaatgggtggtgtaatttgcagTATGGTCTGGTGCACATTTCTGCTGGAGATTTGCTAAGGGCAGAAATTGCTGCAGGCAGTGAGAATGGGAAGCGAGCTAAGGAATTTATGGAGAAGGGTC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAA
- - - - - - - - - - - - - - - - - - -tcttttg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ggtggtg