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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaatccaaattaatcttttttacctgatgacttcttgaatgatttacaatttaacaaaaatgactgggcattgggcaatgtggaggaacagcatgttgaagatatgataataatacctttgtgtttatcagGAGAGGAACGAGAGGCTCTTCTACAAGCTTTTGATTGATAATGTGGAGGAGCTTCTCCCTGTGGTGTATACACCAACAGTAGGTGAGGCCTGCCAGAAGT

Basic information

species Oryza sativa
transcript LOC_Os01g09320.1
intron # 4
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|58673289|gb|CK061975.1|CK061975
EST:     GCCAGTACAGTGTACCTTTGCAGCGTTACATGGCCATGATGGATCTCCAG                         GAGAGGAACGAGAGGCTCTTCTACAAGCTTTTGATTGATAATGTGGAGGAG
genomic: GCCAGTACAGTGTACCTTTGCAGCGTTACATGGCCATGATGGATCTCCAGgtaatccaaa ... tgtttatcagGAGAGGAACGAGAGGCTCTTCTACAAGCTTTTGATTGATAATGTGGAGGAG
EST: gi|58612495|gb|CK040207.1|CK040207
EST:     GCCAGTACAGTGTACCTTTGCAGCGTTACATGGCCATGAGGGATCTCCAG                         GAGAGGAACGAGAGGCTCTTCTACAAGCTTTTGATTGATAATGTGGAGGAG
genomic: GCCAGTACAGTGTACCTTTGCAGCGTTACATGGCCATGATGGATCTCCAGgtaatccaaa ... tgtttatcagGAGAGGAACGAGAGGCTCTTCTACAAGCTTTTGATTGATAATGTGGAGGAG
EST: gi|58600382|gb|CK010910.1|CK010910
EST:     GCCAGTACAGTGTACCTTTGCAGCGTTACATGGCCATGATGGATCTCCAG                         GAGAGGAACGAGAGGCTCTTCTACAAGCTTTTGATTGATAATGTGGAGGAG
genomic: GCCAGTACAGTGTACCTTTGCAGCGTTACATGGCCATGATGGATCTCCAGgtaatccaaa ... tgtttatcagGAGAGGAACGAGAGGCTCTTCTACAAGCTTTTGATTGATAATGTGGAGGAG
EST: gi|29645565|gb|CB650572.1|CB650572
EST:     GCCAGTACAGTGTACCTTTGCAGCGTTACATGGCCATGATGGATCTCCAG                         GAGAGGAACGAGAGGCTCTTCTACAAGCTTTTGATTGATAATGTGGAGGAG
genomic: GCCAGTACAGTGTACCTTTGCAGCGTTACATGGCCATGATGGATCTCCAGgtaatccaaa ... tgtttatcagGAGAGGAACGAGAGGCTCTTCTACAAGCTTTTGATTGATAATGTGGAGGAG
EST: gi|2309667|gb|C25822.1|C25822
EST:     GCCAGTACAGTGTACCTTTNCAGCGTTACATGGCCATGATGGATCTCCAG                         GAGAGGAACGAGAGGCTCTTCTACAAGCTTTTNATTGATAATGTGGAGGAG
genomic: GCCAGTACAGTGTACCTTTGCAGCGTTACATGGCCATGATGGATCTCCAGgtaatccaaa ... tgtttatcagGAGAGGAACGAGAGGCTCTTCTACAAGCTTTTGATTGATAATGTGGAGGAG
EST: gi|58667623|gb|CK056309.1|CK056309
EST:     GCCAGTACAGTGTACCTTTGCAGCGTTACATGGCCATGATGGATCTCCAG                         GAGAGGAACGAGAGGCTCTTCTACAAGCTTTTGATTGATAATGTGGAGGAG
genomic: GCCAGTACAGTGTACCTTTGCAGCGTTACATGGCCATGATGGATCTCCAGgtaatccaaa ... tgtttatcagGAGAGGAACGAGAGGCTCTTCTACAAGCTTTTGATTGATAATGTGGAGGAG
EST: gi|58595714|gb|CK006242.1|CK006242
EST:     GCCAGTACAGTGTACCTTTGCAGCGTTACATGGCCATGATGGATCTCCAG                         GAGAGGAACGAGAGGCTCTTCTACAAGCTTTTGATTGATAATGTGGAGGAG
genomic: GCCAGTACAGTGTACCTTTGCAGCGTTACATGGCCATGATGGATCTCCAGgtaatccaaa ... tgtttatcagGAGAGGAACGAGAGGCTCTTCTACAAGCTTTTGATTGATAATGTGGAGGAG
EST: gi|33796303|gb|CF324019.1|CF324019
EST:     GCCAGTACAGTGTACCTTTGCAGCGTTACATGGCCATGATGGATCTCCAG                         GAGAGGAACGAGAGGCTCTTCTACAAGCTTTTGATTGATAATGTGGAGGAG
genomic: GCCAGTACAGTGTACCTTTGCAGCGTTACATGGCCATGATGGATCTCCAGgtaatccaaa ... tgtttatcagGAGAGGAACGAGAGGCTCTTCTACAAGCTTTTGATTGATAATGTGGAGGAG
EST: gi|58674300|gb|CK062986.1|CK062986
EST:     GCCAGTACAGTGTACCTTTGCAGCGTTACATGGCCATGATGGATCTCCAG                         GAGAGGAACGAGAGGCTCTTCTACAAGCTTTTGATTGATAATGTGGAGGAG
genomic: GCCAGTACAGTGTACCTTTGCAGCGTTACATGGCCATGATGGATCTCCAGgtaatccaaa ... tgtttatcagGAGAGGAACGAGAGGCTCTTCTACAAGCTTTTGATTGATAATGTGGAGGAG
EST: gi|33793137|gb|CF322449.1|CF322449
EST:     GCCAGTACAGTGTACCTTTGCAGCGTTACATGGCCATGATGGATCTCCAG                         GAGAGGAACGAGAGGCTCTTCTACAAGCTTTTGATTGATAATGTGGAGGAG
genomic: GCCAGTACAGTGTACCTTTGCAGCGTTACATGGCCATGATGGATCTCCAGgtaatccaaa ... tgtttatcagGAGAGGAACGAGAGGCTCTTCTACAAGCTTTTGATTGATAATGTGGAGGAG
EST: gi|29668942|gb|CB665217.1|CB665217
EST:     GCCAGTACAGTGTACCTTTGCAGCGTTACATGGCCATGATGGATCTCCAG                         GAGAGGAACGAGAGGCTCTTCTACAAGCTTTTGATTGATAATGTGGAGGAG
genomic: GCCAGTACAGTGTACCTTTGCAGCGTTACATGGCCATGATGGATCTCCAGgtaatccaaa ... tgtttatcagGAGAGGAACGAGAGGCTCTTCTACAAGCTTTTGATTGATAATGTGGAGGAG
EST: gi|157651462|gb|EX451096.1|EX451096
EST:     GTACCTTTGCAGCGTTACATGGCCATGATGGATCTCCAG                         GAGAGGAACGAGAGGCTCTTCTACAAACTTTTGATTGATAATGTGGAGGAG
genomic: GTACCTTTGCAGCGTTACATGGCCATGATGGATCTCCAGgtaatccaaa ... tgtttatcagGAGAGGAACGAGAGGCTCTTCTACAAGCTTTTGATTGATAATGTGGAGGAG
EST: gi|58672135|gb|CK060821.1|CK060821
EST:     GCCAGTACAGTGTACCTTTGCAGCGTTACATGGCCATGATGGATCTCCAG                         GAGAGGAACGAGAGGCTCTTCTACAAGCTTTTGATTGATAATGTGGAGGAG
genomic: GCCAGTACAGTGTACCTTTGCAGCGTTACATGGCCATGATGGATCTCCAGgtaatccaaa ... tgtttatcagGAGAGGAACGAGAGGCTCTTCTACAAGCTTTTGATTGATAATGTGGAGGAG

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), 75 (downstream exon)
Score: 76

GTGAAGAAGATCATGCATAATCTTCGCCAGTACAGTGTACCTTTGCAGCGTTACATGGCCATGATGGATCTCCAGgtaatccaaa ... tgtttatcagGAGAGGAACGAGAGGCTCTTCTACAAGCTTTTGATTGATAATGTGGAGGAGCTTCTCCCTGTGGTGTATACACCAACAGTAGGTGAGGCCTGCCAGAAGT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aatgtggaggaacagcatgttgaagatatgataataatacctttgtgtttatcagGAGAGGAACGAGAGGCTCTTCTACAAGCTTTTGATTGATAATGTGGAGGAGCTTCTCCCTGTGGTGTATACACCAACAGTAGGTGAGGCCTGCCAGAAGT
                                       cctttgt  CT-rich tract
                      aagatatgataataat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaatccaaattaatcttttttacctgatgacttcttgaatgatttacaatttaacaaaaatgactgggcattgggcaatgtggaggaacagcatgttgaagatatgataataatacctttgtgtttatcagGAGAGGAACGAGAGGCTCTTCTACAAGCTTTTGATTGATAATGTGGAGGAGCTTCTCCCTGTGGTGTATACACCAACAGTAGGTGAGGCCTGCCAGAAGT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT