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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...caacaagctcaaacatttttttttcaaattcaaaatatatctcattcttgctagggggcttatagaagtttttttttttttttactttttgttccttcagGTTGTCGTTAACAGTGAAATGATCGAGTACTATGACATATCCGGTTGTTATATCTTGAGGCCATGGGCGATGGAGATCTGGGAATTGCTTAAA

Basic information

species Oryza sativa
transcript LOC_Os12g25710.4
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os12g25710.3 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G094123_T01 (Zea mays), 3'ss of exon 2
-caacaagctcaaacatttttttttcaaattcaaaatatatctcattcttgctagggggcttatagaagtttttttttttttttactttttgttccttcagGTTGTCGTTAACAGTGAAATGATCGAGTACTATGACATATCCGGTTGTTATATCTTGAGGCCATGGGCGATGGAGATCTGGGAATTGCTTAAA
   ||| |   ||| || |||  |  |||||      ||  ||  || |  ||       ||   |    | |||  |    || || ||||||||| |||||||| ||||||||||||||||| |||||||||||||| || ||||||||||| |||||||||||||||||||| ||||||||  | || |||
gacacatgacaaaatatctttcctcgaaatttggt-catcgctttttgtacctctttcttttcatgtgactatttcataacattgctatttgttcctacagGTTGTTGTTAACAGTGAAATGATTGAGTACTATGACATTTCTGGTTGTTATATATTGAGGCCATGGGCGATGGAAATCTGGGAGCTACTGAAA

upper sequence: LOC_Os12g25710.3 (Oryza sativa), 3'ss of exon 2
lower sequence: Vv07s0005g02620.t01 (Vitis vinifera), 3'ss of exon 3
-caacaagctcaaacatttttttttcaaattcaaaat-atatctcattcttgctagggggcttatagaagtttttttttttttttactttttgttccttcagGTTGTCGTTAACAGTGAAATGATCGAGTACTATGACATATCCGGTTGTTATATCTTGAGGCCATGGGCGATGGAGATCTGGGAATTGCTTAAA
  |   |  |   | ||  |  || |    |    || |||| | |   |   ||   |  || | |   ||     | |    |   ||| |||  || |||||  ||| ||  |||||||||| ||||||||||| ||||| || ||||| ||  ||||||||||| | ||||   |||||||   | |  ||
tgattcatgttcgatataatgcttccttgctagctatcatattttagaatg--tacaagtattgttgcccttgaccatctaagctttctttggtttgtttagGTTTGCGTCAATGGTGAAATGATTGAGTACTATGATATATCAGGCTGTTACATTCTGAGGCCATGGACTATGGCAGTCTGGGAGACGATGCAA
















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|58690340|gb|CK079027.1|CK079027
EST:     TCGGGATGGCGTACAAGAAGGATGACAACTTCGGGGAGTGGTACTCCGAG                         GTTGTCGTTAACAGTGAAATGATCGAGTACTATGACATATCCGGTTGTTAT
genomic: TCGGGATGGCGTACAAGAAGGATGACAACTTCGGGGAGTGGTACTCCGAGgttggttttt ... gttccttcagGTTGTCGTTAACAGTGAAATGATCGAGTACTATGACATATCCGGTTGTTAT
EST: gi|58674015|gb|CK062701.1|CK062701
EST:     TCGGGATGGCGTACAAGAAGGATGACAACTTCGGGGAGTGGTACTCCGAG                         GTTGTCGTTAACAGTGAAATGATCGAGTACTATGACATATCCGGTTGTTAT
genomic: TCGGGATGGCGTACAAGAAGGATGACAACTTCGGGGAGTGGTACTCCGAGgttggttttt ... gttccttcagGTTGTCGTTAACAGTGAAATGATCGAGTACTATGACATATCCGGTTGTTAT
EST: gi|29635079|gb|CB640088.1|CB640088
EST:     TCGGGATGGCGTACAAGAAGGATGACAACTTCGGGGAGTGGTACTCCGAG                         GTTGTCGTTAACAGTGAAATGATCGAGTACTATGACATATCCGGTTGTTAT
genomic: TCGGGATGGCGTACAAGAAGGATGACAACTTCGGGGAGTGGTACTCCGAGgttggttttt ... gttccttcagGTTGTCGTTAACAGTGAAATGATCGAGTACTATGACATATCCGGTTGTTAT
EST: gi|58652586|gb|CK041266.1|CK041266
EST:     CGGGAATGGCGTACAAGAAGGATGACAACTTCGGGGAGTGGTACTCCGAG                         GTTGTCGTTAACAGTGAAATGATCGAGTACTATGACATATCCGGTTGGGAT
genomic: CGGG-ATGGCGTACAAGAAGGATGACAACTTCGGGGAGTGGTACTCCGAGgttggttttt ... gttccttcagGTTGTCGTTAACAGTGAAATGATCGAGTACTATGACATATCCGGTTGTTAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcttgctagggggcttatagaagtttttttttttttttactttttgttccttcagGTTGTCGTTAACAGTGAAATGATCGAGTACTATGACATATCCGGTTGTTATATCTTGAGGCCATGGGCGATGGAGATCTGGGAATTGCTTAAA
                       ttttttttttttttta  CT-rich tract
              ttatagaagttttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
caacaagctcaaacatttttttttcaaattcaaaatatatctcattcttgctagggggcttatagaagtttttttttttttttactttttgttccttcagGTTGTCGTTAACAGTGAAATGATCGAGTACTATGACATATCCGGTTGTTATATCTTGAGGCCATGGGCGATGGAGATCTGGGAATTGCTTAAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATC