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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgtagggtcaagcttatagctagcttatttttttgttcttaaaccagtttttttattctaattattgaactgaatttattcttttcttttctccttgcagTGCTAACTGAACATGAGTAAGGACCAAGGATGCTGTGCCGTTTTGCATTGGTGATGCTGTGCCGTTTGAGCTTTGATCTTATCATATCCTTCAACTGAAC

Basic information

species Oryza sativa
transcript LOC_Os06g05180.4
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os06g05180.1 (Oryza sativa), 3'ss of exon 24
lower sequence: GRMZM2G095348_T02 (Zea mays), 3'ss of exon 23
-tgtagggtcaagcttatagc--tagcttatttttttgttcttaaaccagttttt-ttattctaattattgaactgaatttattcttttcttttctccttgcagTGCTAACTGAACATGAGTAAGGACCAAGGATGCTGTGCCGTTTTGCATTGGTGATGCTGTGCCGTTTGAGCTTTGATCTTATCATATCCTTCAACTGAAC---
 ||    || |   | | |    ||| |   || |        ||  |||||||   ||   |  |||||  | | |  ||| |  ||  ||| |||||||||||||||||||||||||| || || || |||         ||  |||   ||   ||| | |    |        | |    |   |  ||  ||  |  ||   
ttgcttagtaaccttgaaaatattagatgtcttctgaaaatacaatgcagttttagctaccttctttatt--attaa--ttactacttgttttgctccttgcagTGCTAACTGAACATGAATAGGGGCCGAGGGAAGCACAACGCATTG-GCTGCAAATGTTATTTTTTCCCGAGGGTAACA--AATGTGGCCCCCAGTTTTACCCT
















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|86481810|gb|CI124443.1|CI124443
EST:     AGTGGGGTACGAACAATGAAGGAACTTCGTCAGCCTAAAAGAATTGTTTG                         TGCTAACTGAACATGAGTAAGGACCAAGGATGCTGTGCCGTTTTGCATTGG
genomic: AGTGGGGTACGAACAATGAAGGAACTTCGTCAGCCTAAAAGAATTGTTTGgcaagtgtaa ... ctccttgcagTGCTAACTGAACATGAGTAAGGACCAAGGATGCTGTGCCGTTTTGCATTGG
EST: gi|86838811|gb|CI330259.1|CI330259
EST:     CCTAAAAGAATTGTTTG                         TGCTAACTGAACATGAGTAAGGACCAAGGATGCTGTGCCGTTTTGCATTGG
genomic: CCTAAAAGAATTGTTTGgcaagtgtaa ... ctccttgcagTGCTAACTGAACATGAGTAAGGACCAAGGATGCTGTGCCGTTTTGCATTGG
EST: gi|11370679|gb|AU164984.1|AU164984
EST:     AGTGGGGTACGAACAATGAAGGAA-TTCGTCAGCCTAAAAGAATTGTTTG                         TGCTAACTGAACATGAGTAAGGACCAAGGATGCTGTGCCGTTTTGCATTGG
genomic: AGTGGGGTACGAACAATGAAGGAACTTCGTCAGCCTAAAAGAATTGTTTGgcaagtgtaa ... ctccttgcagTGCTAACTGAACATGAGTAAGGACCAAGGATGCTGTGCCGTTTTGCATTGG
EST: gi|319908442|gb|HS977570.1|HS977570
EST:     GGTACCAACAATGAAGGAACTTCGTCAGCCTAAAAGAATTGTTTG                         TGCTAACTGAACATGAGTAAGGACCAAGGATGCCGTGCCGTTTTGCATTGG
genomic: GGTACGAACAATGAAGGAACTTCGTCAGCCTAAAAGAATTGTTTGgcaagtgtaa ... ctccttgcagTGCTAACTGAACATGAGTAAGGACCAAGGATGCTGTGCCGTTTTGCATTGG
EST: gi|25803773|gb|CA759734.1|CA759734
EST:     AGTGGGGTACGAACAATGAAGGAACTTTGTCAGCCTAAAAGAATTGTTTG                         TGCTAACTGAACATGAGTAAGGACCAAGGATGCTGTGCCGTTTTGCATTGG
genomic: AGTGGGGTACGAACAATGAAGGAACTTCGTCAGCCTAAAAGAATTGTTTGgcaagtgtaa ... ctccttgcagTGCTAACTGAACATGAGTAAGGACCAAGGATGCTGTGCCGTTTTGCATTGG
EST: gi|319908460|gb|HS977588.1|HS977588
EST:     GGTACNAACAATGAAGGAACTTCGTCAGCCTAAAAGAATTGTTTG                         TGCTAACTGAACATGAGTAAGGACCAAGGATGCCGTGCCGTTTTGCATTGG
genomic: GGTACGAACAATGAAGGAACTTCGTCAGCCTAAAAGAATTGTTTGgcaagtgtaa ... ctccttgcagTGCTAACTGAACATGAGTAAGGACCAAGGATGCTGTGCCGTTTTGCATTGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agtttttttattctaattattgaactgaatttattcttttcttttctccttgcagTGCTAACTGAACATGAGTAAGGACCAAGGATGCTGTGCCGTTTTGCATTGGTGATGCTGTGCCGTTTGAGCTTTGATCTTATCATATCCTTCAACTGAAC
          ttctaat  putative branch site (score: 2)
                        ctgaatttattctttt  putative PPT
     ttttattctaattatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgtagggtcaagcttatagctagcttatttttttgttcttaaaccagtttttttattctaattattgaactgaatttattcttttcttttctccttgcagTGCTAACTGAACATGAGTAAGGACCAAGGATGCTGTGCCGTTTTGCATTGGTGATGCTGTGCCGTTTGAGCTTTGATCTTATCATATCCTTCAACTGAAC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGCTT
- - - - - - - - - - - - - - - - ttgttct
- - - - - - - - - - - - - - - - - - - - aaaccag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgaactg