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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgtcaaatgctaatatcgtgtctatttgaaacacaaatggattggttctataactaatccatcaacttctccatttctgcgttacagTCTATGAAGTTGCTTTCTACAATGGCTGCAATTCGATTGGATGAGGATGGTGACAACATTGAGAACACCCTGTCCCTTGCTCTAGTTGACACAGCAAGGC

Basic information

species Oryza sativa
transcript LOC_Os01g39310.1
intron # 18
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g39310.1 (Oryza sativa), 3'ss of exon 18
lower sequence: AC196426.3_FGT007 (Zea mays), 3'ss of exon 17
------------------------------------------------------gta-tgtcaaatgctaatatcg-----tgtctatttgaaacacaaatggattggttctataactaatccatcaac-ttctccatttctgcgttacagTCTATGAAGTTGCTTTCTACAATGGCTGCAATTCGATTGGATGAGGATGGTGACAACATTGAGAACACCCTGTCCCTTGCTCTAGTTGACACAGCAAGGC
                                                      ||| ||||||||||||||||       | | ||| |||||||  || | ||||  |    |||| |  |||   | ||||||  || |||  |||||||| ||||||||||||||||||||||||||||||| ||||| ||||||||||| |||||||||||||| || ||||||||||| ||||||||  |||| |
gtgtggacaggaaaggaggacataaaagctataactaaaaccgctcgctcagctgtactgtcaaatgctaatatttaatattatatatgtgaaacagtaaggaattgtcttaggaactgaagcatattcattctcccattttgc--tacagTCTGTGAAGTTGCTTTCTACAATGGCTGCAATTCGGTTGGAGGAGGATGGTGATAACATTGAGAACACTCTTTCCCTTGCTCTTGTTGACACTTCAAGAC
















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|29641074|gb|CB646081.1|CB646081
EST:     GGACCGGAAAGGAGGACATAAAGGCCATTACTAAAACTGCTCGTTCAGCT                         TCTATGAAGTTGCTTTCTACAATGGCTGCAATTCGATTGGATGAGGATGGT
genomic: GGACCGGAAAGGAGGACATAAAGGCCATTACTAAAACTGCTCGTTCAGCTgtatgtcaaa ... tgcgttacagTCTATGAAGTTGCTTTCTACAATGGCTGCAATTCGATTGGATGAGGATGGT
EST: gi|157650537|gb|EX450171.1|EX450171
EST:     GGACCGGAAAGGAGGACATAAAGGCCATTACTAAAACTGCTCGTTCAGCT                         TCTATGAAGTTGCTTTCTACAATGGCTGCAATTCGATTGGATGAGGATGGT
genomic: GGACCGGAAAGGAGGACATAAAGGCCATTACTAAAACTGCTCGTTCAGCTgtatgtcaaa ... tgcgttacagTCTATGAAGTTGCTTTCTACAATGGCTGCAATTCGATTGGATGAGGATGGT
EST: gi|38474188|gb|CF958320.1|CF958320
EST:     GGACCGGAAAGGAGGACATAAAGGCCATTACTAAAACTGCTCGTTCAGCT                         TCTATGAAGTTGCTTTCTACAATGGCTGCAATTCGATTGGATGAGGATGGT
genomic: GGACCGGAAAGGAGGACATAAAGGCCATTACTAAAACTGCTCGTTCAGCTgtatgtcaaa ... tgcgttacagTCTATGAAGTTGCTTTCTACAATGGCTGCAATTCGATTGGATGAGGATGGT
EST: gi|88584803|gb|CI702382.1|CI702382
EST:     GGACCGGAAAGGAGGACATAAAGGCCATTACTAAAACTGCTCATTCAGCT                         TCTATGAAGTTGCTTTCTACA
genomic: GGACCGGAAAGGAGGACATAAAGGCCATTACTAAAACTGCTCGTTCAGCTgtatgtcaaa ... tgcgttacagTCTATGAAGTTGCTTTCTACA
EST: gi|66924925|gb|CX111773.1|CX111773
EST:     GGACCGGAAAGGAGGACATAAAGGCCATTACTAAAACTGCTCGTTCAGCT                         TCTATGAAGTTGCTTTCTACAATGGCTGCAATTCGATTGGAT
genomic: GGACCGGAAAGGAGGACATAAAGGCCATTACTAAAACTGCTCGTTCAGCTgtatgtcaaa ... tgcgttacagTCTATGAAGTTGCTTTCTACAATGGCTGCAATTCGATTGGAT
EST: gi|58661468|gb|CK050148.1|CK050148
EST:     GGAGGACATAAAGGCCATTACTAAAACTGCTCGTTCAGCT                         TCTATGAAGTTGCTTTCTACAATGGCTGCAATTCGATTGGATGAGGATGGT
genomic: GGAGGACATAAAGGCCATTACTAAAACTGCTCGTTCAGCTgtatgtcaaa ... tgcgttacagTCTATGAAGTTGCTTTCTACAATGGCTGCAATTCGATTGGATGAGGATGGT
EST: gi|95100913|gb|CI692635.1|CI692635
EST:     GGACCGGAAAGGAGGACATAAAGGCCATTACTAAAACTGCTCATTCAGCT                         TCTATGAAGTTGCTTTCTACAAT
genomic: GGACCGGAAAGGAGGACATAAAGGCCATTACTAAAACTGCTCGTTCAGCTgtatgtcaaa ... tgcgttacagTCTATGAAGTTGCTTTCTACAAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

acaaatggattggttctataactaatccatcaacttctccatttctgcgttacagTCTATGAAGTTGCTTTCTACAATGGCTGCAATTCGATTGGATGAGGATGGTGACAACATTGAGAACACCCTGTCCCTTGCTCTAGTTGACACAGCAAGGC
                   aactaat  putative branch site (score: 2)
                                 cttctccatttctgc  putative PPT
                tataactaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgtcaaatgctaatatcgtgtctatttgaaacacaaatggattggttctataactaatccatcaacttctccatttctgcgttacagTCTATGAAGTTGCTTTCTACAATGGCTGCAATTCGATTGGATGAGGATGGTGACAACATTGAGAACACCCTGTCCCTTGCTCTAGTTGACACAGCAAGGC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG