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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ggccattctgttgttggctgaaatctcgtaacaagataaagttatgaaaattcttgatgcaaactagtacctttgacgtactcactgttttgttttgtagGTTGTGGCAAATTTCAGTGCTTCCTGGTGTGGACCATGTCGTGTTATTGCACCTATTTATGCTGAGATGTCAAAGACTTATCCTCAACTCATGTTCTTGA

Basic information

species Oryza sativa
transcript LOC_Os05g07690.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os05g07690.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G066612_T01 (Zea mays), 3'ss of exon 1
-ggccattctgttgttggctgaaatctcgtaacaagataaagttatgaaaattcttgatgcaaactagtacctttgacgtactcactgttttgtttt-gtagGTTGTGGCAAATTTCAGTGCTTCCTGGTGTGGACCATGTCGTGTTATTGCACCTATTTATGCTGAGATGTCAAAGACTTATCCTCAACTCATGTTCTTGA
 |  |  |   ||  | | | |   | | | |  | || ||  || || |   |    |||  |  | ||| ||||    |||||| | ||| |||| ||||||||| ||||||||||| |||||||||||||| ||||| ||||| ||||| ||| | |||||||| ||||||||||||||||||||||||||||||||||
tgaactcttaatttcttg-taaggccactttattacatgaa-ctaagagatgacgatttgctgagaattacatttgttcgactcaccggtttatttttgtagGTTGTTGCAAATTTCAGCGCTTCCTGGTGTGGGCCATGCCGTGTCATTGCTCCTGTCTATGCTGAAATGTCAAAGACTTATCCTCAACTCATGTTCTTGA
















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|38473602|gb|CF957734.1|CF957734
EST:     GGAAGATTGAAGAAGCAAACAAGGATGGGAAAATT                         GTTGTGGCAAATTTCAGTGCTTCCTGGTGTGGACCATGTCGTGTTATTGCA
genomic: GGAAGATTGAAGAAGCAAACAAGGATGGGAAAATTgtaagcaagc ... tgttttgtagGTTGTGGCAAATTTCAGTGCTTCCTGGTGTGGACCATGTCGTGTTATTGCA
EST: gi|58596706|gb|CK007234.1|CK007234
EST:     AAGAGGACTGGGATAGGAAGATTGAAGAAGCAAACAAGGATGGGAAAATT                         GTTGTGGCAAATTTCAGTGCTTCCTGGTGTGGACCATGTCGTGTTATTGCA
genomic: AAGAGGACTGGGATAGGAAGATTGAAGAAGCAAACAAGGATGGGAAAATTgtaagcaagc ... tgttttgtagGTTGTGGCAAATTTCAGTGCTTCCTGGTGTGGACCATGTCGTGTTATTGCA
EST: gi|218480992|gb|FG958013.1|FG958013
EST:     AAGAGGACTGGGATAGGAAGATTGAAGAAGCAAACAAGGATGGGAAAATT                         GTTGTGGCAAATTTCAGTGCTTCCTGGTGTGGACCATGTCGTGTTATTGCA
genomic: AAGAGGACTGGGATAGGAAGATTGAAGAAGCAAACAAGGATGGGAAAATTgtaagcaagc ... tgttttgtagGTTGTGGCAAATTTCAGTGCTTCCTGGTGTGGACCATGTCGTGTTATTGCA
EST: gi|88957526|gb|CI011455.1|CI011455
EST:     ATGGGAAAATT                         GTTGTGGCAAATTTCAGTGCTTCCTGGTGTGGACCATGTCGTGTTATTGCA
genomic: ATGGGAAAATTgtaagcaagc ... tgttttgtagGTTGTGGCAAATTTCAGTGCTTCCTGGTGTGGACCATGTCGTGTTATTGCA
EST: gi|88847816|gb|CI006002.1|CI006002
EST:     GGAAGATTGAAGAAGCAAACAAGGATGGGAAAATT                         GTTGTGGCAAATTTCAGTGCTTCCTGGTGTGGACCATGTCGTGTTATTGCA
genomic: GGAAGATTGAAGAAGCAAACAAGGATGGGAAAATTgtaagcaagc ... tgttttgtagGTTGTGGCAAATTTCAGTGCTTCCTGGTGTGGACCATGTCGTGTTATTGCA
EST: gi|89199020|gb|CI253094.1|CI253094
EST:     AAGAGGACTGGGATAGGAAGATTGAAGAAGCAAACAAGGATGGGAAAATC                         GTTGTGGCAAATTTCAGTGCTTCCTGGTGTGGACCATGTCGTGTTATTGCA
genomic: AAGAGGACTGGGATAGGAAGATTGAAGAAGCAAACAAGGATGGGAAAATTgtaagcaagc ... tgttttgtagGTTGTGGCAAATTTCAGTGCTTCCTGGTGTGGACCATGTCGTGTTATTGCA
EST: gi|58683882|gb|CK072569.1|CK072569
EST:     AAGAGGACTGGGATAGGAAGATTGAAGAAGCAAACAAGGATGGGAAAATT                         GTTGTGGCAAATTTCAGTGCTTCCTGGTGTGGACCATGTCGTGTTATTGCA
genomic: AAGAGGACTGGGATAGGAAGATTGAAGAAGCAAACAAGGATGGGAAAATTgtaagcaagc ... tgttttgtagGTTGTGGCAAATTTCAGTGCTTCCTGGTGTGGACCATGTCGTGTTATTGCA
EST: gi|33661687|gb|CF292654.1|CF292654
EST:     GATAGGAAGATTGAAGAAGCAAACAAGGATGGGAAAATT                         GTTGTGGCAAATTTCAGTGCTTCCTGGTGTGGACCATGTCGTGTTATTGCA
genomic: GATAGGAAGATTGAAGAAGCAAACAAGGATGGGAAAATTgtaagcaagc ... tgttttgtagGTTGTGGCAAATTTCAGTGCTTCCTGGTGTGGACCATGTCGTGTTATTGCA
EST: gi|33821282|gb|CF336453.1|CF336453
EST:     AAGAGGACTGGGATAGGAAGATTGAAGAAGCAAACAAGGATGGGAAAATT                         GTTGTGGCAAATTTCAGTGCTTCCTGGTGTGGACCATGTCGTGTTATTGCA
genomic: AAGAGGACTGGGATAGGAAGATTGAAGAAGCAAACAAGGATGGGAAAATTgtaagcaagc ... tgttttgtagGTTGTGGCAAATTTCAGTGCTTCCTGGTGTGGACCATGTCGTGTTATTGCA
EST: gi|86596652|gb|CI286565.1|CI286565
EST:     AAGAGGACTGGGATAGGAAGATTGAAGAAGCAAACAAGGATGGGAAAATT                         GTTGTGGCAAATTCCAGTGCTTCCTGGTGTGGACCATGTCGTGTTATTGCA
genomic: AAGAGGACTGGGATAGGAAGATTGAAGAAGCAAACAAGGATGGGAAAATTgtaagcaagc ... tgttttgtagGTTGTGGCAAATTTCAGTGCTTCCTGGTGTGGACCATGTCGTGTTATTGCA
EST: gi|88321921|gb|CI673069.1|CI673069
EST:     AAGAGGACTGGGATAGGAAGATTGAAGAAGCAAACAAGGATGGGAAAATT                         GTTGTGGCAAATTTCAGTGCTTCCTGGTGTGGACCATGTCGTGTTATTGCA
genomic: AAGAGGACTGGGATAGGAAGATTGAAGAAGCAAACAAGGATGGGAAAATTgtaagcaagc ... tgttttgtagGTTGTGGCAAATTTCAGTGCTTCCTGGTGTGGACCATGTCGTGTTATTGCA
EST: gi|38480845|gb|CF964934.1|CF964934
EST:     AAGAGGACTGGGATAGGAAGATTGAAGAAGCAAACAAGGATGGGAAAATT                         GTTGTGGCAAATTTCAGTGCTTCCTGGTGTGGACCATGTCGTGTTATTGCA
genomic: AAGAGGACTGGGATAGGAAGATTGAAGAAGCAAACAAGGATGGGAAAATTgtaagcaagc ... tgttttgtagGTTGTGGCAAATTTCAGTGCTTCCTGGTGTGGACCATGTCGTGTTATTGCA
EST: gi|86593727|gb|CI266407.1|CI266407
EST:     GGAAGATTGAAGAAGCAAACAAGGATGGGAAAATT                         GTTGTGGCAAATTTCAGTGCTTCCTGGTGTGGACCATGTCGTGTTATTGCA
genomic: GGAAGATTGAAGAAGCAAACAAGGATGGGAAAATTgtaagcaagc ... tgttttgtagGTTGTGGCAAATTTCAGTGCTTCCTGGTGTGGACCATGTCGTGTTATTGCA
EST: gi|33814147|gb|CF332955.1|CF332955
EST:     AAGAGGACTGGGATAGGAAGATTGAAGAAGCAAACAAGGATGGGAAAATT                         GTTGTGGCAAATTTCAGTGCTTCCTGGTGTGGACCATGTCGTGTTATTGCA
genomic: AAGAGGACTGGGATAGGAAGATTGAAGAAGCAAACAAGGATGGGAAAATTgtaagcaagc ... tgttttgtagGTTGTGGCAAATTTCAGTGCTTCCTGGTGTGGACCATGTCGTGTTATTGCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gaaaattcttgatgcaaactagtacctttgacgtactcactgttttgttttgtagGTTGTGGCAAATTTCAGTGCTTCCTGGTGTGGACCATGTCGTGTTATTGCACCTATTTATGCTGAGATGTCAAAGACTTATCCTCAACTCATGTTCTTGA
                                 tactcac  putative branch site (score: 1)
                                          ttttgtttt  putative PPT
                                          ttttgtttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ggccattctgttgttggctgaaatctcgtaacaagataaagttatgaaaattcttgatgcaaactagtacctttgacgtactcactgttttgttttgtagGTTGTGGCAAATTTCAGTGCTTCCTGGTGTGGACCATGTCGTGTTATTGCACCTATTTATGCTGAGATGTCAAAGACTTATCCTCAACTCATGTTCTTGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGATG