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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagctttttgctactattacctctcctgcttttaggacccgagtacagtatgttagtgattactttatccacatctctctaatatggtcaatgtcgcccaattatttcagATGAAGTGAAGGTTGGTGCTACTGCAGGCAAAACTGACCTACCTGCTGCACAAAAGAAAATTCAAACAAATATGAGGACCCTTAGAGGACATACAGGTGC

Basic information

species Oryza sativa
transcript LOC_Os01g39380.2
intron # 22
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g39380.2 (Oryza sativa), 3'ss of exon 22
lower sequence: GRMZM2G074466_T01 (Zea mays), 3'ss of exon 3
gtaagctttttgctactattacctctcctgcttttaggacccgagtacagtatgttagtgattactttatccacatctctctaatatggtcaatgtcgcccaattatttcagATGAAGTGAAGGTTGGTGCTACTGCAGGCAAAACTGACCTACCTGCTGCACAAAAGAAAATTCAAACAAATATGAGGACCCTTAGAGGACATACAGGTGC
  ||  |      || ||  |     | |  | ||||     | ||||| ||   |   || || | |||   ||  | |||||||| | || ||| |    || || |||| ||| |  || | || |||| |  | |||||||| ||  |  | |||||||||||||||| |||||| || ||||||||||||||||| |||||||||||
-caaattggaccttaatacaataaagctta-tattag----tgggtacattac--tgcagacta-tatatttccacatttctaatatagccattgttgt---atcatgtcagGTGATGGAAATGCTGTTGCTGCCACGGGCAAAACCGAAATCTCAGCTGCACAAAAGAAAACTCAAACTAACATGAGGACCCTTAGAGGGCATACAGGTGC
















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|29641894|gb|CB646901.1|CB646901
EST:     CATGTTTAGTAGGGACAGAAGCTTAAGGGCTAGCTCTTTCAACCGAACTA                         ATGAAGTGAAGGTTGGTGCTACTGCAGGCAAAACTGACCTACCTGCTGCAC
genomic: CATGTTTAGTAGGGACAGAAGCTTAAGGGCTAGCTCTTTCAACCGAACTAgtaagctttt ... attatttcagATGAAGTGAAGGTTGGTGCTACTGCAGGCAAAACTGACCTACCTGCTGCAC
EST: gi|33690825|gb|CF319064.1|CF319064
EST:     AAGCTTAAGGGCTAGCTCTTTCAACCGAACTA                         ATGAAGTGAAGGTTGGTGCTACTGCAGGCAAAACTGACCTACCTGCTGCAC
genomic: AAGCTTAAGGGCTAGCTCTTTCAACCGAACTAgtaagctttt ... attatttcagATGAAGTGAAGGTTGGTGCTACTGCAGGCAAAACTGACCTACCTGCTGCAC
EST: gi|87023608|gb|CI286359.1|CI286359
EST:     CATGTTTAGTAGGGACAGAAGCTTAAGGGCTAGCTCTTTCAACCGAACTA                         ATGAAGTGAAGGTTGGTGCTACTGCAGGCAAAACTGACCTACCTGCTGCAC
genomic: CATGTTTAGTAGGGACAGAAGCTTAAGGGCTAGCTCTTTCAACCGAACTAgtaagctttt ... attatttcagATGAAGTGAAGGTTGGTGCTACTGCAGGCAAAACTGACCTACCTGCTGCAC
EST: gi|3763545|gb|AU030297.1|AU030297
EST:     CATGTTTAGTAGGGACAGAAGCTTAAGGGCTAGCTCTTTCAACCGAACTA                         ATGAAGTGAAGGTTGGTGCTACTGCAGGCAAAACTGACCTACCTGCTGCAC
genomic: CATGTTTAGTAGGGACAGAAGCTTAAGGGCTAGCTCTTTCAACCGAACTAgtaagctttt ... attatttcagATGAAGTGAAGGTTGGTGCTACTGCAGGCAAAACTGACCTACCTGCTGCAC
EST: gi|58694147|gb|CK082834.1|CK082834
EST:     CATGTTTAGTAGGGACAGAAGCTTAAGGGCTAGCTCTTTCAACCGAACTA                         ATGAAGTGAAGGTTGGTGCTACTGCAGGCAAAACTGACCTACCTGCTGCAC
genomic: CATGTTTAGTAGGGACAGAAGCTTAAGGGCTAGCTCTTTCAACCGAACTAgtaagctttt ... attatttcagATGAAGTGAAGGTTGGTGCTACTGCAGGCAAAACTGACCTACCTGCTGCAC
EST: gi|163918523|gb|EG713217.1|EG713217
EST:     CATGTTTAGTAGGGACAGAAGCTTAAGGGCTAGCTCTTTCAACCGAACTA                         ATGAAGTGAAGGTTGGTGCTACTGCAGGCAAAACTGACCTACCTGCTGCAC
genomic: CATGTTTAGTAGGGACAGAAGCTTAAGGGCTAGCTCTTTCAACCGAACTAgtaagctttt ... attatttcagATGAAGTGAAGGTTGGTGCTACTGCAGGCAAAACTGACCTACCTGCTGCAC
EST: gi|163926766|gb|EG715054.1|EG715054
EST:     CATGTTTAGTAGGGACAGAAGCTTAAGGGCTAGCTCTTTCAACCGAACTA                         ATGAAGTGAAGGTTGGTGCTACTGCAGGCAAAACTGACCTACCTGCTGCAC
genomic: CATGTTTAGTAGGGACAGAAGCTTAAGGGCTAGCTCTTTCAACCGAACTAgtaagctttt ... attatttcagATGAAGTGAAGGTTGGTGCTACTGCAGGCAAAACTGACCTACCTGCTGCAC

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: 63 (upstream exon), 69 (downstream exon)
Score: 19

AGCCAACAACCTGCCGAGGCATCTGGATTGGGTCGAAATTGGGTGCAAAGCATGTTTAGTAGGGACAGAAGCTTAAGGGCTAGCTCTTTCAACCGAACTAgtaagctttt ... attatttcagATGAAGTGAAGGTTGGTGCTACTGCAGGCAAAACTGACCTACCTGCTGCACAAAAGAAAATTCAAACAAATATGAGGACCCTTAGAGGACATACAGGTGC




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtgattactttatccacatctctctaatatggtcaatgtcgcccaattatttcagATGAAGTGAAGGTTGGTGCTACTGCAGGCAAAACTGACCTACCTGCTGCACAAAAGAAAATTCAAACAAATATGAGGACCCTTAGAGGACATACAGGTGC
                     ctctaat  putative branch site (score: 19)
                                              ttatttc  putative PPT
                                            aattatttca  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagctttttgctactattacctctcctgcttttaggacccgagtacagtatgttagtgattactttatccacatctctctaatatggtcaatgtcgcccaattatttcagATGAAGTGAAGGTTGGTGCTACTGCAGGCAAAACTGACCTACCTGCTGCACAAAAGAAAATTCAAACAAATATGAGGACCCTTAGAGGACATACAGGTGC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGGA