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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CCAGATAAACTCAGGCGCAGAAAATGCTTATAATTCTTCACAGTGTGATTCTTTGCTGATTGGGGATAACGCTGCTGCCAACACCTATCCGACTATTCAGgtaactgctctgctgttcttgatttgcctggcatgaagggccaattgcatttttataatgcaaactattaagagtaggttgttaatcctttgttctgtat...

Basic information

species Oryza sativa
transcript LOC_Os01g61400.1
intron # 1
splice site 5'
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|88218125|gb|CI217974.1|CI217974
EST:     TGGGGATAACGCTGCTGCCAACACCTATCCGACTATTCAG                         GTGGGTTGCATTTCTAGTCGTGTTGAGCATGAGGCAAGCACTTCAAAAATA
genomic: TGGGGATAACGCTGCTGCCAACACCTATCCGACTATTCAGgtaactgctc ... gtgataacagGTGGGTTGCATTTCTAGTCGTGTTGAGCATGAGGCAAGCACTTCAAAAATA
EST: gi|86497502|gb|CI140135.1|CI140135
EST:     CTTTGCTGATTGGGGATAACGCTGCTGCCAACACCTATCCGACTATTCAG                         GTGGGTTGCATTTCTAGTCGTGTTGAGCATGAGGCAAGCACTTCAAAAATA
genomic: CTTTGCTGATTGGGGATAACGCTGCTGCCAACACCTATCCGACTATTCAGgtaactgctc ... gtgataacagGTGGGTTGCATTTCTAGTCGTGTTGAGCATGAGGCAAGCACTTCAAAAATA
EST: gi|113930856|gb|DQ883962.1|DQ883962
EST:     CTNTGCTNATTGGGGATAACGCTGCTGCCAACACCTATCCGACTATTCAG                         GTGGGTTGCATTTCTAGTCGTGTTGAGCATGAGGCAAGCACTTCAAAAATA
genomic: CTTTGCTGATTGGGGATAACGCTGCTGCCAACACCTATCCGACTATTCAGgtaactgctc ... gtgataacagGTGGGTTGCATTTCTAGTCGTGTTGAGCATGAGGCAAGCACTTCAAAAATA
EST: gi|38470819|gb|CF954950.1|CF954950
EST:     CTTTGCTGATTGGGGATAACGCTGCTGCCAACACCTATCCGACTATTCAG                         GTGGGTTGCATTTCTAGTCGTGTTGAGCATGAGGCAAGCACTTCAAAAATA
genomic: CTTTGCTGATTGGGGATAACGCTGCTGCCAACACCTATCCGACTATTCAGgtaactgctc ... gtgataacagGTGGGTTGCATTTCTAGTCGTGTTGAGCATGAGGCAAGCACTTCAAAAATA
EST: gi|22307487|gb|BQ908709.1|BQ908709
EST:     ATAACGCTGCTGCCAACACCTATCCGACTATTCAG                         GTGGGTTGCATTTCTAGTCGTGTTGAGCATGAGGCAAGCACTTCAAAAATA
genomic: ATAACGCTGCTGCCAACACCTATCCGACTATTCAGgtaactgctc ... gtgataacagGTGGGTTGCATTTCTAGTCGTGTTGAGCATGAGGCAAGCACTTCAAAAATA
EST: gi|218482075|gb|FG958767.1|FG958767
EST:     CTTTGCTGATTGGGGATAACGCTGCTGCCAACACCTATCCGACTATTCAG                         GTGGGTTGCATTTCTAGTCGTGTTGAGCATGAGGCAAGCACTTCAAAAATA
genomic: CTTTGCTGATTGGGGATAACGCTGCTGCCAACACCTATCCGACTATTCAGgtaactgctc ... gtgataacagGTGGGTTGCATTTCTAGTCGTGTTGAGCATGAGGCAAGCACTTCAAAAATA
EST: gi|113931024|gb|DQ884118.1|DQ884118
EST:     CTTTGCTGATTGGGGATAACGCTGCTGCCAACACCTATCCGACTATTCAG                         GTGGGTTGCATTTCTAGTCGTGTTGAGCATGAGGCAAGCACTTCAAAAATA
genomic: CTTTGCTGATTGGGGATAACGCTGCTGCCAACACCTATCCGACTATTCAGgtaactgctc ... gtgataacagGTGGGTTGCATTTCTAGTCGTGTTGAGCATGAGGCAAGCACTTCAAAAATA
EST: gi|89192609|gb|CI049907.1|CI049907
EST:     ATCCGACTATTCAG                         GTGGNTTGCATTTCTAGTCGTGTTGAGCATGAGGCAAGCACTTCAAAAATA
genomic: ATCCGACTATTCAGgtaactgctc ... gtgataacagGTGGGTTGCATTTCTAGTCGTGTTGAGCATGAGGCAAGCACTTCAAAAATA
EST: gi|88993604|gb|CI110425.1|CI110425
EST:     CTTTGCTGATTGGGGATAACGCTGCTGCCAACACCTATCCGACTAGTCAG                         GTGGGTTGCATTTCTAGTCGTGTTGAGCATGAGGCAAGCACTTCAAAAATA
genomic: CTTTGCTGATTGGGGATAACGCTGCTGCCAACACCTATCCGACTATTCAGgtaactgctc ... gtgataacagGTGGGTTGCATTTCTAGTCGTGTTGAGCATGAGGCAAGCACTTCAAAAATA
EST: gi|22304774|gb|BQ905996.1|BQ905996
EST:     CTTTGCTGATTGGGGATAACGCTGCTGCCAACACCTATCCGACTATTCAG                         GTGGGTTGCATTTCTAGTCGTGTTGAGCATGAGGCAAGCACTTCAAAAATA
genomic: CTTTGCTGATTGGGGATAACGCTGCTGCCAACACCTATCCGACTATTCAGgtaactgctc ... gtgataacagGTGGGTTGCATTTCTAGTCGTGTTGAGCATGAGGCAAGCACTTCAAAAATA
EST: gi|88226852|gb|CI224837.1|CI224837
EST:     TTTGCTGATTGGGGATAACGCTGCTGCCAACACCTATCCGACTATTCAG                         GTGGGTTGCATTTCTAGTCGTGTTGAGCATGAGGCAAGCACTTCAAAAATA
genomic: TTTGCTGATTGGGGATAACGCTGCTGCCAACACCTATCCGACTATTCAGgtaactgctc ... gtgataacagGTGGGTTGCATTTCTAGTCGTGTTGAGCATGAGGCAAGCACTTCAAAAATA
EST: gi|88245735|gb|CI245584.1|CI245584
EST:     GATTGGGGATAACGCTGCTGCCAACACCTATCCGACTATTCAG                         GTGGGTTGCATTTCTAGTCGTGTTGAGCATGAGGCAAGCACTTCAAAAATA
genomic: GATTGGGGATAACGCTGCTGCCAACACCTATCCGACTATTCAGgtaactgctc ... gtgataacagGTGGGTTGCATTTCTAGTCGTGTTGAGCATGAGGCAAGCACTTCAAAAATA
EST: gi|86426259|gb|CI071356.1|CI071356
EST:     ATTGGGGATAACGCTGCTGCCAACACCTATCCGACTATTCAG                         GT-GGCTGCATTTCTAGTCGTGTTGAGCATGAGGCAAGCACTTCAAAAATA
genomic: ATTGGGGATAACGCTGCTGCCAACACCTATCCGACTATTCAGgtaactgctc ... gtgataacagGTGGGTTGCATTTCTAGTCGTGTTGAGCATGAGGCAAGCACTTCAAAAATA
EST: gi|113930857|gb|DQ883963.1|DQ883963
EST:     TTGCTGATTGGGGATAACCGCCTGCTGCCAACACCTATCCGACTATTCAG                         GTGGGTTGCATTTCTAGTCGTGTTGAGCATGAGGCAAGCACTTTCAAAAAT
genomic: TTGCTGATTGGGGATAA-CG-CTGCTGCCAACACCTATCCGACTATTCAGgtaactgctc ... gtgataacagGTGGGTTGCATTTCTAGTCGTGTTGAGCATGAGGCAAGCAC-TTCAAAAAT
EST: gi|86426173|gb|CI071270.1|CI071270
EST:     CTTTGCTGATTGGGGATAACGCTGCTGCCAACACCTATCCGACTATTCAG                         GTGGGTTGCATTTCTAGTCGTGTTGAGCATGAGGCAAGCACTTCAAAAATA
genomic: CTTTGCTGATTGGGGATAACGCTGCTGCCAACACCTATCCGACTATTCAGgtaactgctc ... gtgataacagGTGGGTTGCATTTCTAGTCGTGTTGAGCATGAGGCAAGCACTTCAAAAATA
EST: gi|87024301|gb|CI257042.1|CI257042
EST:     CTTTGCTGATTGGGGATAACGCTGCTGCCAACACCTATCCGACTATTCAG                         GTGGGTTGCATTTCTAGTCGTGTTGAGCATGAGGCAAGCACTTCAAAAATA
genomic: CTTTGCTGATTGGGGATAACGCTGCTGCCAACACCTATCCGACTATTCAGgtaactgctc ... gtgataacagGTGGGTTGCATTTCTAGTCGTGTTGAGCATGAGGCAAGCACTTCAAAAATA

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: 42

CCAGATAAACTCAGGCGCAGAAAATGCTTATAATTCTTCACAGTGTGATTCTTTGCTGATTGGGGATAACGCTGCTGCCAACACCTATCCGACTATTCAGgtaactgctc ... gtgataacagGTGGGTTGCATTTCTAGTCGTGTTGAGCATGAGGCAAGCACTTCAAAAATAGGGGAGGACCAGCTATTTTATTTCCAACAAAGGGGGATAGACCATGAAA




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CCAGATAAACTCAGGCGCAGAAAATGCTTATAATTCTTCACAGTGTGATTCTTTGCTGATTGGGGATAACGCTGCTGCCAACACCTATCCGACTATTCAGgtaactgctctgctgttcttgatttgcctggcatgaagggccaattgcatttttataatgcaaactattaagagtaggttgttaatcctttgttctgtat

- - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC