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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttcacactatagtgattgtttcgaatacttataaattttttaggagatgcattttaagtcatgggcctgaaaatacttttttcttggttacagacagCAGCAGTCCTGACAACGAGACAACTCAAACTGCTCTTGAAGATGAGGAAAAAAG

Basic information

species Oryza sativa
transcript LOC_Os12g04700.1
intron # 6
splice site 3'
intron type U2

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|86827351|gb|CI270987.1|CI270987
EST:     ACCGATGCAAAGACAG                         CAGCAGTCCTGACAACGAGACTACTCAAACTGCTCTTGAAGATGAGGAAAA
genomic: ACCGATGCAAAGATATgttcacacta ... ttacagacagCAGCAGTCCTGACAACGAGACAACTCAAACTGCTCTTGAAGATGAGGAAAA
EST: gi|86498254|gb|CI140887.1|CI140887
EST:     ACTTCAAAGACCGATGCAAAGACAG                         CAGCAGTCCTGACAACGAGACAACTCAAACTGCTCTTGAAGATGAGGAAAA
genomic: ACTTCAAAGACCGATGCAAAGATATgttcacacta ... ttacagacagCAGCAGTCCTGACAACGAGACAACTCAAACTGCTCTTGAAGATGAGGAAAA
EST: gi|87016238|gb|CI271649.1|CI271649
EST:     GCGTTCACTTCAAAGACCGATGCAAAGACAG                         CAGCAGTCCTGACAACGAGACAACTCAAACTGCTCTTGAAGATGAGGAAAA
genomic: GCGTTCACTTCAAAGACCGATGCAAAGATATgttcacacta ... ttacagacagCAGCAGTCCTGACAACGAGACAACTCAAACTGCTCTTGAAGATGAGGAAAA
EST: gi|86437460|gb|CI119182.1|CI119182
EST:     CTGGTTGGCGTTCACTTCAAAGACCGATGCAAAGACAG                         CAGCAGTCCTGACAACGAGACAACTCAAACTGCTCTTGAAGATGAGGAAAA
genomic: CTGGTTGGCGTTCACTTCAAAGACCGATGCAAAGATATgttcacacta ... ttacagacagCAGCAGTCCTGACAACGAGACAACTCAAACTGCTCTTGAAGATGAGGAAAA

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 1 RNA-Seqlibrary.


Block sizes: 73 (upstream exon), 70 (downstream exon)
Score: 8

GCAAGTGGACAAAGATTGTGAGTTTCTGGAGCAAGAGAGAATTATGGATTACAGTCTTCTGGTTGGCGTTCACTTCAAAGACCGATGCAAAGATATgttcacacta ... ttacagacagCAGCAGTCCTGACAACGAGACAACTCAAACTGCTCTTGAAGATGAGGAAAAAAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ggagatgcattttaagtcatgggcctgaaaatacttttttcttggttacagacagCAGCAGTCCTGACAACGAGACAACTCAAACTGCTCTTGAAGATGAGGAAAAAAG
                                 cttttttcttggtt  CT-rich tract
                           aaaatacttttttctt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttcacactatagtgattgtttcgaatacttataaattttttaggagatgcattttaagtcatgggcctgaaaatacttttttcttggttacagacagCAGCAGTCCTGACAACGAGACAACTCAAACTGCTCTTGAAGATGAGGAAAAAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG