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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgtatatatcccaaaaatattcggcatgctgggtcaccagtactcggtatttgccaaaatttaataattgctatgagaacacctagaaatggaacccacaaacaacattctactgataagcttgtattcattaaacagGTAGCATGAGACCTGGAACTGCGCAGGCGACAGGAGGATCCTTAGCCAAGCCTTCCAAAAGACGGTAGAAATAGAATCTGACGAAGCATCCATGCAAGTT

Basic information

species Oryza sativa
transcript LOC_Os01g54080.1
intron # 21
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|86844514|gb|CI338561.1|CI338561
EST:     GCCATCAACTTCTAGACCAAAACCAAGGGAGGTTGTTCCGAAAACTCAAG                         GTAGCATGAGACCTGGAACTGCGCAGGCGACAGGAGGATCCTTAGCCAAGC
genomic: GCCATCAACTTCTAGACCAAAACCAAGGGAGGTTGTTCCGAAAACTCAAGgtatgtatat ... cattaaacagGTAGCATGAGACCTGGAACTGCGCAGGCGACAGGAGGATCCTTAGCCAAGC
EST: gi|86839103|gb|CI331414.1|CI331414
EST:     CCCATCAACTTCTAGACCAAAACCAAGGGAGGTTTTTCCGAAAACTCAAG                         GTAGCATGAGACCTGGAACTGCCCAGGCGACAGGAGGATCCTTAGCCAAGC
genomic: GCCATCAACTTCTAGACCAAAACCAAGGGAGGTTGTTCCGAAAACTCAAGgtatgtatat ... cattaaacagGTAGCATGAGACCTGGAACTGCGCAGGCGACAGGAGGATCCTTAGCCAAGC
EST: gi|88458511|gb|CI550051.1|CI550051
EST:     GCCATCAACTTCTAGACCAAAACCAAGGGAGGTTGTTCCGAAAACTCAAG                         GTAGCATGAGACCTGGAACTGCGCAGGCGACAGGAGGATCCTTAGCCAAGC
genomic: GCCATCAACTTCTAGACCAAAACCAAGGGAGGTTGTTCCGAAAACTCAAGgtatgtatat ... cattaaacagGTAGCATGAGACCTGGAACTGCGCAGGCGACAGGAGGATCCTTAGCCAAGC
EST: gi|88375958|gb|CI528262.1|CI528262
EST:     GCCATCAACTTTTAGACCAAAACCAAGGGAGGTTGTTCCGGAAACTCAAG                         GTAGCATGAGACCTGGAACTGCGCAGGCGACAGGAGGATCCTTANCCAAGC
genomic: GCCATCAACTTCTAGACCAAAACCAAGGGAGGTTGTTCCGAAAACTCAAGgtatgtatat ... cattaaacagGTAGCATGAGACCTGGAACTGCGCAGGCGACAGGAGGATCCTTAGCCAAGC
EST: gi|88457088|gb|CI531687.1|CI531687
EST:     GCCATCAACTTCTAGACCAAAACCAAGGGAGGTTGTTCCGAAAACTCAAG                         GTAGCATGAGACCTGGAACTGCGCAGGCGACAGGAGGATCCTTAGCCAAGC
genomic: GCCATCAACTTCTAGACCAAAACCAAGGGAGGTTGTTCCGAAAACTCAAGgtatgtatat ... cattaaacagGTAGCATGAGACCTGGAACTGCGCAGGCGACAGGAGGATCCTTAGCCAAGC
EST: gi|88261478|gb|CI365054.1|CI365054
EST:     GCCATCAACTTCTAGACCAAAACCAAGGGAGGTTGTTCCGAAAACTCAAG                         GTAGCATGAGACCTGGAACTGCGCAGGCGACAGGAGGATCCTTAGCCAACC
genomic: GCCATCAACTTCTAGACCAAAACCAAGGGAGGTTGTTCCGAAAACTCAAGgtatgtatat ... cattaaacagGTAGCATGAGACCTGGAACTGCGCAGGCGACAGGAGGATCCTTAGCCAAGC
EST: gi|88456863|gb|CI529064.1|CI529064
EST:     GCCATCAACTTTTAGACCAAAACCAAGGGAGGTTGTTCCGAAAACTCAAG                         GTAGCATGAGACCTGGAACTGCGCAGGCGACAGGAGGATCCTTAGCCAAGC
genomic: GCCATCAACTTCTAGACCAAAACCAAGGGAGGTTGTTCCGAAAACTCAAGgtatgtatat ... cattaaacagGTAGCATGAGACCTGGAACTGCGCAGGCGACAGGAGGATCCTTAGCCAAGC
EST: gi|88977806|gb|CI384288.1|CI384288
EST:     GCCATCAACTTCTAGACCAAAACCAAGGGAGGTTGTTCCGAAAACTCAAG                         GTAGCATGAGACCTGGAAGCTGCGCAGGCGACAGGAGGATCCTTAGCCAAG
genomic: GCCATCAACTTCTAGACCAAAACCAAGGGAGGTTGTTCCGAAAACTCAAGgtatgtatat ... cattaaacagGTAGCATGAGACCTGGAA-CTGCGCAGGCGACAGGAGGATCCTTAGCCAAG
EST: gi|88323110|gb|CI550789.1|CI550789
EST:     GCCATCAACTTCTAGACCAAAACCAAGGGAGGTTGTTCCGAAAACTCAAG                         GTAGCATGAGACCTGGAACTGCGCAGGCGACAGGAGGATCCTTAGCCAAGC
genomic: GCCATCAACTTCTAGACCAAAACCAAGGGAGGTTGTTCCGAAAACTCAAGgtatgtatat ... cattaaacagGTAGCATGAGACCTGGAACTGCGCAGGCGACAGGAGGATCCTTAGCCAAGC
EST: gi|88321372|gb|CI535324.1|CI535324
EST:     GCCATCAACTTCTAGACCAAAACCAAGGGAGGTTGTTCCGAAAACTCAAG                         GTAGCATGAGACCTGGAACTGCGCAGGCGACAGGAGGATCCTTAGCCAAGC
genomic: GCCATCAACTTCTAGACCAAAACCAAGGGAGGTTGTTCCGAAAACTCAAGgtatgtatat ... cattaaacagGTAGCATGAGACCTGGAACTGCGCAGGCGACAGGAGGATCCTTAGCCAAGC
EST: gi|88274815|gb|CI388273.1|CI388273
EST:     GCCATCAACTTCTAGACCAAAACCAAGGGAGGTTGTTCCGAAAACTCAAG                         GTAGCATGAGACCTGGAACTGCGCAGGCGACAGGAGGATCCTTAGCCAAGC
genomic: GCCATCAACTTCTAGACCAAAACCAAGGGAGGTTGTTCCGAAAACTCAAGgtatgtatat ... cattaaacagGTAGCATGAGACCTGGAACTGCGCAGGCGACAGGAGGATCCTTAGCCAAGC
EST: gi|88834219|gb|CI000583.1|CI000583
EST:     GCCATCAACTTGTAGACCAAAACCAAGGGAGGTTGTTCCGAAAACTCAAG                         GTGGCATGAGACCTGGAACTGCGCAGGCGACAGGAGGATCCTTAGCCAAGC
genomic: GCCATCAACTTCTAGACCAAAACCAAGGGAGGTTGTTCCGAAAACTCAAGgtatgtatat ... cattaaacagGTAGCATGAGACCTGGAACTGCGCAGGCGACAGGAGGATCCTTAGCCAAGC
EST: gi|88457718|gb|CI539514.1|CI539514
EST:     GCCATCAACTTTTAGACCAAAACCAAGGGAGGTTGTTCCGAAAACTCAAG                         GTAGCATGAGACCTGGAACTGCGCAGGCGACAGGAGGATCCTTAGCCAAGC
genomic: GCCATCAACTTCTAGACCAAAACCAAGGGAGGTTGTTCCGAAAACTCAAGgtatgtatat ... cattaaacagGTAGCATGAGACCTGGAACTGCGCAGGCGACAGGAGGATCCTTAGCCAAGC
EST: gi|88455616|gb|CI521836.1|CI521836
EST:     GCCATCAACTTTTAGACCAAAACCAAGGGAGGTTGTTCCGAAAACTCAAG                         GTAGCATGAGACCTGGAACTGCCCAGGCGACAGGAGGATCCTTAGCCAAGC
genomic: GCCATCAACTTCTAGACCAAAACCAAGGGAGGTTGTTCCGAAAACTCAAGgtatgtatat ... cattaaacagGTAGCATGAGACCTGGAACTGCGCAGGCGACAGGAGGATCCTTAGCCAAGC
EST: gi|88902249|gb|CI374857.1|CI374857
EST:     GCCATCAACTTTTAGACCAAAACCAAGGGAGGTTGTTCCGAAAACTCAAG                         GTAGCATGAGACCTGGAACTGCGCAGGCGACAGGAGGATCCTTAGCCAAGC
genomic: GCCATCAACTTCTAGACCAAAACCAAGGGAGGTTGTTCCGAAAACTCAAGgtatgtatat ... cattaaacagGTAGCATGAGACCTGGAACTGCGCAGGCGACAGGAGGATCCTTAGCCAAGC
EST: gi|88383175|gb|CI538203.1|CI538203
EST:     GCCATCAACTTCTAGACCAAAACCAAGGGAGGTTGTTCCGAAAACTCAAG                         GTAGCATGAGACCTGGAACTGCGCAGGCGACAGGAGGATCCTTAGCCAAGC
genomic: GCCATCAACTTCTAGACCAAAACCAAGGGAGGTTGTTCCGAAAACTCAAGgtatgtatat ... cattaaacagGTAGCATGAGACCTGGAACTGCGCAGGCGACAGGAGGATCCTTAGCCAAGC
EST: gi|88366735|gb|CI558909.1|CI558909
EST:     GCCATCAACTTTTAGACCAAAACCAAGGGAGGTTGTTCCGAAAACTCAAG                         GTAGCATGAGACCTGGAACTGCGCAGGCGACAGGAGGATCCTTAGCCAAGC
genomic: GCCATCAACTTCTAGACCAAAACCAAGGGAGGTTGTTCCGAAAACTCAAGgtatgtatat ... cattaaacagGTAGCATGAGACCTGGAACTGCGCAGGCGACAGGAGGATCCTTAGCCAAGC
EST: gi|88971914|gb|CI390497.1|CI390497
EST:     GCCATCAACTTCTAGACCAAAACCAAGGGAGGTTGTTCCGAAAACTCAAG                         GTAGCATGAGACCTGGAACTGCGCAGGCGACAGGAGGATCCGTAGCCAAGC
genomic: GCCATCAACTTCTAGACCAAAACCAAGGGAGGTTGTTCCGAAAACTCAAGgtatgtatat ... cattaaacagGTAGCATGAGACCTGGAACTGCGCAGGCGACAGGAGGATCCTTAGCCAAGC
EST: gi|157650722|gb|EX450356.1|EX450356
EST:     GCCATCAACTTCTAGACCAAAACCAAGGGAGGTTGTTCCGAAAACTCAAG                         GTAGCATGAGACCTGGAACTGCGCAGGCGACAGGAGGATCCTTAGCCAAGC
genomic: GCCATCAACTTCTAGACCAAAACCAAGGGAGGTTGTTCCGAAAACTCAAGgtatgtatat ... cattaaacagGTAGCATGAGACCTGGAACTGCGCAGGCGACAGGAGGATCCTTAGCCAAGC

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: 71 (upstream exon), 71 (downstream exon)
Score: 22

CATAAAGCGCCATCAAGAATAACCAGATTCTTTCTCACGAAGAACGGGCAGCCATCAACTTCTAGACCAAAACCAAGGGAGGTTGTTCCGAAAACTCAAGgtatgtatat ... cattaaacagGTAGCATGAGACCTGGAACTGCGCAGGCGACAGGAGGATCCTTAGCCAAGCCTTCCAAAAGACGGTAGAAATAGAATCTGACGAAGCATCCATGCAAGTT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tagaaatggaacccacaaacaacattctactgataagcttgtattcattaaacagGTAGCATGAGACCTGGAACTGCGCAGGCGACAGGAGGATCCTTAGCCAAGCCTTCCAAAAGACGGTAGAAATAGAATCTGACGAAGCATCCATGCAAGTT
                           tactgat  putative branch site (score: 22)
                                      ttgtattcattaaa  TA-rich tract