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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacgtgcatatggtcttctaacttacctgttctatactgtttggcaagcttttattcattcccaatatttcatctttggtactgagtctgtgcatccttgtctgtttgcagGAGATTATTACAGGAGCTGGCCATACAAGCGCTGTTGATTGGTGGGCTCTAG

Basic information

species Oryza sativa
transcript LOC_Os12g01140.5
intron # 15
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os11g01140.1 (Oryza sativa), 3'ss of exon 19
lower sequence: GRMZM2G001457_T02 (Zea mays), 3'ss of exon 18
--------gtacgtgcatatggtcttctaactt-acctgttctatactgtttggc---aagcttttattcattcccaatattt--catctttggtactga--gtctgtgc-----atccttgt-ctgtttgca-------gGAGATTATTACAGGAGCTGGCCATACAAGCGCTGTTGATTGGTGGGCTCTAG
         ||  |   ||   | || |  ||  || |  |||||    |||  |   |   ||| |||  ||  |  |||||  ||| | || || | |   |||||       ||||||||  ||| ||||       |||||||||||| |||||||||||||| || ||||| ||||||||||| ||||
gtatttatatatatatgtaatatgttgttgctccactttatctatgtgattttccctaacattttcatttcttgtctctatttgacatgtgtgatagtcatcatctgttttatcaatccttgtattgtatgcatgctgtagGAGATTATTACCGGAGCTGGCCATACGAGTGCTGTAGATTGGTGGGCGCTAG
















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|29670089|gb|CB666364.1|CB666364
EST:     CTATGCGAGCATCCAATTCATTTGTTGGCACGGAGGAGTACATTGCGCCT                         GAGATTATTACAGGAGCTGGCCATACAAGCGCTGTTGATTGGTGGGCTCTA
genomic: CTATGCGAGCATCCAATTCATTTGTTGGCACGGAGGAGTACATTGCGCCTgtacgtgcat ... ctgtttgcagGAGATTATTACAGGAGCTGGCCATACAAGCGCTGTTGATTGGTGGGCTCTA
EST: gi|29622723|gb|CB627734.1|CB627734
EST:     CTATGCGAGCATCCAATTCATTTGTTGGCACGGAGGAGTACATTGCGCCT                         GAGATTATTACAGGAGCTGGCCATAC
genomic: CTATGCGAGCATCCAATTCATTTGTTGGCACGGAGGAGTACATTGCGCCTgtacgtgcat ... ctgtttgcagGAGATTATTACAGGAGCTGGCCATAC
EST: gi|33680724|gb|CF308963.1|CF308963
EST:     CTATGCGAGCATCCAATTCATTTGTTGGCACGGAGGAGTACATTGCGCCT                         GAGATTATTACAGGAGCTGGCCATACAAGCGCTGTTGATTGGTGGGCTCTA
genomic: CTATGCGAGCATCCAATTCATTTGTTGGCACGGAGGAGTACATTGCGCCTgtacgtgcat ... ctgtttgcagGAGATTATTACAGGAGCTGGCCATACAAGCGCTGTTGATTGGTGGGCTCTA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cattcccaatatttcatctttggtactgagtctgtgcatccttgtctgtttgcagGAGATTATTACAGGAGCTGGCCATACAAGCGCTGTTGATTGGTGGGCTCTAG
                                      tccttgtct  CT-rich tract
       aatatttcatcttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtacgtgcatatggtcttctaacttacctgttctatactgtttggcaagcttttattcattcccaatatttcatctttggtactgagtctgtgcatccttgtctgtttgcagGAGATTATTACAGGAGCTGGCCATACAAGCGCTGTTGATTGGTGGGCTCTAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGTGG