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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagcattcatatccattacattatggtttcggctgtttctaccagaaaactgtaaaaacagccaaatcatctgaatttgcaaattgcacttttactttgtagTGTTTACCTATCACGATTGATGTTGGTACAAACAATGAGCAATTGTTGAATGATGAATTCTACATTGGGCTCCGGCAAAGGCGTGCTACTGGCAAG

Basic information

species Oryza sativa
transcript LOC_Os01g09320.1
intron # 7
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|58668338|gb|CK057024.1|CK057024
EST:     TTGGTAAACTTTCTCTGTACACTGCCCTTGGAGGAGTTCGCCCGTCAGCT                         TGTTTACCTATCACGATTGATGTTGGTACAAACAATGAGCAATTGTTGAAT
genomic: TTGGTAAACTTTCTCTGTACACTGCCCTTGGAGGAGTTCGCCCGTCAGCTgtaagcattc ... tactttgtagTGTTTACCTATCACGATTGATGTTGGTACAAACAATGAGCAATTGTTGAAT
EST: gi|58612495|gb|CK040207.1|CK040207
EST:     TTGGTAAACTTTCTCTGTACACTGCCCTTGGAGGAGTTCGCCCGTCAGCT                         TGTTTACCTATCACGATTGATGTTGGTACAAACAATGAGCAATTG
genomic: TTGGTAAACTTTCTCTGTACACTGCCCTTGGAGGAGTTCGCCCGTCAGCTgtaagcattc ... tactttgtagTGTTTACCTATCACGATTGATGTTGGTACAAACAATGAGCAATTG
EST: gi|29642462|gb|CB647469.1|CB647469
EST:     TTGGTAAACTTTCTCTGTACACTGCCCTTGGAGGAGTTCGCCCGTCAGCT                         TGTTTACCTATCACGATTGATGTTGGTACAAACAATGAGCAATTGTTGAAT
genomic: TTGGTAAACTTTCTCTGTACACTGCCCTTGGAGGAGTTCGCCCGTCAGCTgtaagcattc ... tactttgtagTGTTTACCTATCACGATTGATGTTGGTACAAACAATGAGCAATTGTTGAAT
EST: gi|218495881|gb|FG947063.1|FG947063
EST:     TTGGTAAACTTTCTCTGTACACTGCCCTTGGAGGAGTTCGCCCGTCAGCT                         TGTTTACCTATCACGATTGATGTTGGTACAAACAATGAGCAATTGTTGAAT
genomic: TTGGTAAACTTTCTCTGTACACTGCCCTTGGAGGAGTTCGCCCGTCAGCTgtaagcattc ... tactttgtagTGTTTACCTATCACGATTGATGTTGGTACAAACAATGAGCAATTGTTGAAT
EST: gi|58608599|gb|CK036632.1|CK036632
EST:     TGGTAGACTTTCTCTGTACACTGCCCTTGGAGGAGTTCGCCCGCTCAGCT                         TGTTTACCTATCACGATTGATGTTGGTACAAACAATGAGCAATTGTTGAA
genomic: TGGTAAACTTTCTCTGTACACTGCCCTTGGAGGAGTTCGCCCG-TCAGCTgtaagcattc ... tactttgtagTGTTTACCTATCACGATTGATGTTGGTACAAACAATGAGCAATTGTTGAA
EST: gi|29645565|gb|CB650572.1|CB650572
EST:     TTGGTAAACTTTCTCTGTACACTGCCCTTGGAGGAGTTCGCCCGTCAGCT                         TGTTTACCTATCACGATTGATGTTGGTACAAACAATGAGCAATTGTTGAAT
genomic: TTGGTAAACTTTCTCTGTACACTGCCCTTGGAGGAGTTCGCCCGTCAGCTgtaagcattc ... tactttgtagTGTTTACCTATCACGATTGATGTTGGTACAAACAATGAGCAATTGTTGAAT
EST: gi|2309667|gb|C25822.1|C25822
EST:     TTGGTAAACTTTCTCTGTACACTGCCCTTTGAGGAGTTCGCCCGTCAGCT                         TGTTTACCTATCACG
genomic: TTGGTAAACTTTCTCTGTACACTGCCCTTGGAGGAGTTCGCCCGTCAGCTgtaagcattc ... tactttgtagTGTTTACCTATCACG
EST: gi|428653|gb|D24805.1|D24805
EST:     TTGGTAAACTTTCTCTGTACACTGCCCTTGGAGGAGTTCGCCCGTCAGCT                         TGTTTACCTATCACGNTTGATGTTGGTACAAACAATGNGCAATTGTTGAAT
genomic: TTGGTAAACTTTCTCTGTACACTGCCCTTGGAGGAGTTCGCCCGTCAGCTgtaagcattc ... tactttgtagTGTTTACCTATCACGATTGATGTTGGTACAAACAATGAGCAATTGTTGAAT
EST: gi|58595714|gb|CK006242.1|CK006242
EST:     TTGGTAAACTTTCTCTGTACACTGCCCTTGGAGGAGTTCGCCCGTCAGCT                         TGTTTACCTATCACGATTGATGTTGGTACAAACAATGAGCAATTGTTGAAT
genomic: TTGGTAAACTTTCTCTGTACACTGCCCTTGGAGGAGTTCGCCCGTCAGCTgtaagcattc ... tactttgtagTGTTTACCTATCACGATTGATGTTGGTACAAACAATGAGCAATTGTTGAAT
EST: gi|58674300|gb|CK062986.1|CK062986
EST:     TTGGTAAACTTTCTCTGTACACTGCCCTTGGAGGAGTTCGCCCGTCAGCT                         TGTTTACCTATCACGATTGATGTTGGTACAAACAATGAGCAATTGTTGAAT
genomic: TTGGTAAACTTTCTCTGTACACTGCCCTTGGAGGAGTTCGCCCGTCAGCTgtaagcattc ... tactttgtagTGTTTACCTATCACGATTGATGTTGGTACAAACAATGAGCAATTGTTGAAT
EST: gi|33793137|gb|CF322449.1|CF322449
EST:     TTGGTAAACTTTCTCTGTACACTGCCCTTGGAGGAGTTCGCCCGTCAGCT                         TGTTTACCTATCACGATTGATGTTGGTACAAACAATGAGCAATTGTTGAAT
genomic: TTGGTAAACTTTCTCTGTACACTGCCCTTGGAGGAGTTCGCCCGTCAGCTgtaagcattc ... tactttgtagTGTTTACCTATCACGATTGATGTTGGTACAAACAATGAGCAATTGTTGAAT
EST: gi|58598862|gb|CK009390.1|CK009390
EST:     TTGGTAAACTTTCTCTGTACACTGCCCTTGGAGGAGTTCG-GCGTCAGCT                         TGTTTACCTATCACGATTGATGTTGGTACAAACAATGAGCAATTGTTGAAT
genomic: TTGGTAAACTTTCTCTGTACACTGCCCTTGGAGGAGTTCGCCCGTCAGCTgtaagcattc ... tactttgtagTGTTTACCTATCACGATTGATGTTGGTACAAACAATGAGCAATTGTTGAAT
EST: gi|58670000|gb|CK058686.1|CK058686
EST:     GAGG-GTTCGCCCGTCAGCT                         TGTTTACCTATCACGATTGATGTTGGTACAAGCGATGAGCAATTGTTGAAT
genomic: GAGGAGTTCGCCCGTCAGCTgtaagcattc ... tactttgtagTGTTTACCTATCACGATTGATGTTGGTACAAACAATGAGCAATTGTTGAAT
EST: gi|29668942|gb|CB665217.1|CB665217
EST:     TTGGTAAACTTTCTCTGTACACTGCCCTTGGAGGAGTTCGCCCGTCAGCT                         TGTTTACCTATCACGATTGATGTTGGTACAAACAATGAGCAATTGTTGAAT
genomic: TTGGTAAACTTTCTCTGTACACTGCCCTTGGAGGAGTTCGCCCGTCAGCTgtaagcattc ... tactttgtagTGTTTACCTATCACGATTGATGTTGGTACAAACAATGAGCAATTGTTGAAT
EST: gi|58671508|gb|CK060194.1|CK060194
EST:     TTGGTAAACTTTCTCTGTACACTGCCCTTGGAGGAGTTCGCCCGTCAGCT                         TGTTTACCTATCACGATTGATGTTGGTACAAACAATGAGCAATTGTTGAAT
genomic: TTGGTAAACTTTCTCTGTACACTGCCCTTGGAGGAGTTCGCCCGTCAGCTgtaagcattc ... tactttgtagTGTTTACCTATCACGATTGATGTTGGTACAAACAATGAGCAATTGTTGAAT
EST: gi|58665642|gb|CK054328.1|CK054328
EST:     TTGGTAAACTTTCTCTGTACACTGCCCTTGGAGGAGTTCGCCCGTCAGCT                         TGTTTACCTATCACGATTGATGTTGGTACAAACAATGAGCAATTGTTGAAT
genomic: TTGGTAAACTTTCTCTGTACACTGCCCTTGGAGGAGTTCGCCCGTCAGCTgtaagcattc ... tactttgtagTGTTTACCTATCACGATTGATGTTGGTACAAACAATGAGCAATTGTTGAAT

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: 75 (upstream exon), 54 (downstream exon)
Score: 66

GGAATGGGTATTCCTGTTGGTAAACTTTCTCTGTACACTGCCCTTGGAGGAGTTCGCCCGTCAGCTgtaagcattc ... tactttgtagTGTTTACCTATCACGATTGATGTTGGTACAAACAATGAGCAATTGTTGAATGATGAATTCTACATTGGGCTCCGGCAAAGGCGTGCTACTGGCAAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aactgtaaaaacagccaaatcatctgaatttgcaaattgcacttttactttgtagTGTTTACCTATCACGATTGATGTTGGTACAAACAATGAGCAATTGTTGAATGATGAATTCTACATTGGGCTCCGGCAAAGGCGTGCTACTGGCAAG
                                         cttttacttt  CT-rich tract
                                          ttttacttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagcattcatatccattacattatggtttcggctgtttctaccagaaaactgtaaaaacagccaaatcatctgaatttgcaaattgcacttttactttgtagTGTTTACCTATCACGATTGATGTTGGTACAAACAATGAGCAATTGTTGAATGATGAATTCTACATTGGGCTCCGGCAAAGGCGTGCTACTGGCAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG