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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaggcctgcctatttcatatgtacaacattagatggtgtttgtttttggcagcatcttattcatatgcttgtccatggaatcaaccagGTCCATCCTAAAAGCTGGCTGCTGATTATGAGCGTCCGGAGTACAACTTGTAGTCCGAGAAAAGTGCCTCACATCTGAAGCACGGCATCAGGTACTGGAT

Basic information

species Oryza sativa
transcript LOC_Os07g07974.1
intron # 10
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|38483294|gb|CF967096.1|CF967096
EST:     AATGAACAGTTCCGAGAGCGCATTCAACACTGCATCGCCTCTTGCTTTAG                         GTCCATCCTAAAAGCTGGCTGCTGATTATGAGCGTCCGGAGTACAACTTGT
genomic: AATGAACAGTTCCGAGAGCGCATTCAACACTGCATCGCCTCTTGCTTTAGgtaaggcctg ... aatcaaccagGTCCATCCTAAAAGCTGGCTGCTGATTATGAGCGTCCGGAGTACAACTTGT
EST: gi|86876040|gb|CI325564.1|CI325564
EST:     AATGAACAGTTCCGAGAGCGCATTCAACACTGCATCGCCTCTTGCTTTAG                         GTCCATCCTAAAAGCTGGCTGCTGATTATGAGCGTCCGGAGTACAACTTGT
genomic: AATGAACAGTTCCGAGAGCGCATTCAACACTGCATCGCCTCTTGCTTTAGgtaaggcctg ... aatcaaccagGTCCATCCTAAAAGCTGGCTGCTGATTATGAGCGTCCGGAGTACAACTTGT
EST: gi|88515857|gb|CI443511.1|CI443511
EST:     AATGAACAGTTCCGAGAGCGCATTCAACACTGCATCGCCTCTTGCTTTAG                         GTCCATCCTAAAAGCTGGCTGCTGATTATGAGCGTCCGGAGTACAACTTGT
genomic: AATGAACAGTTCCGAGAGCGCATTCAACACTGCATCGCCTCTTGCTTTAGgtaaggcctg ... aatcaaccagGTCCATCCTAAAAGCTGGCTGCTGATTATGAGCGTCCGGAGTACAACTTGT
EST: gi|88249583|gb|CI249432.1|CI249432
EST:     AATGAACAGTTCCGAGAGCGCATTCAACACTGCATCGCCTCTTGCTTTAG                         GTCCATCCTAAAAGCTGGCTGCTGATTATGAGCGTCCGGAGTACAACTTGT
genomic: AATGAACAGTTCCGAGAGCGCATTCAACACTGCATCGCCTCTTGCTTTAGgtaaggcctg ... aatcaaccagGTCCATCCTAAAAGCTGGCTGCTGATTATGAGCGTCCGGAGTACAACTTGT
EST: gi|88380595|gb|CI521164.1|CI521164
EST:     AATGAACAGTTCCGAGAGCGCATTCAACACTGCATCGCCTCTTGCTTTAG                         GTCCATCCTAAAAGCTGGCTGCTGATTATGAGCGTCCGGAGTACAACTTGT
genomic: AATGAACAGTTCCGAGAGCGCATTCAACACTGCATCGCCTCTTGCTTTAGgtaaggcctg ... aatcaaccagGTCCATCCTAAAAGCTGGCTGCTGATTATGAGCGTCCGGAGTACAACTTGT
EST: gi|88841281|gb|CI080735.1|CI080735
EST:     AATGAACAGTTCCGAGAGCGCATTCAACACTGCATCGCCTCTTGCTTTAG                         GTCCATCCTAAAAGCTGGCTGCTGATTATGAGCGTCCGGAGTACAACTTGT
genomic: AATGAACAGTTCCGAGAGCGCATTCAACACTGCATCGCCTCTTGCTTTAGgtaaggcctg ... aatcaaccagGTCCATCCTAAAAGCTGGCTGCTGATTATGAGCGTCCGGAGTACAACTTGT
EST: gi|86831705|gb|CI301555.1|CI301555
EST:     AATGAACAGTTCCGAGAGCGCATTCAACACTGCATCGCCTCTTGCTTTAG                         GTCCATCCTAAAAGCTGGCTGCTGATTATGAGCGTCCGGAGTACAACTTGT
genomic: AATGAACAGTTCCGAGAGCGCATTCAACACTGCATCGCCTCTTGCTTTAGgtaaggcctg ... aatcaaccagGTCCATCCTAAAAGCTGGCTGCTGATTATGAGCGTCCGGAGTACAACTTGT
EST: gi|88849352|gb|CI087874.1|CI087874
EST:     AATGAACAGTTCCGAGAGCGCATTCAACACTGCATCGCCTCTTGCTTTAG                         GTCCATCCTAAAAGCTGGCTGTTGATTATGAGCGTCCGGAGTACAACTTGT
genomic: AATGAACAGTTCCGAGAGCGCATTCAACACTGCATCGCCTCTTGCTTTAGgtaaggcctg ... aatcaaccagGTCCATCCTAAAAGCTGGCTGCTGATTATGAGCGTCCGGAGTACAACTTGT
EST: gi|5607306|gb|AU075978.1|AU075978
EST:     AATGAACAGTTCCGAGAGCGCATTCAACACTGCATCGCCTCTTGCTTTAG                         GTCCATCCTAAAAGCTGGCTGCTGATTATGAGCGTCCGGAGTACAACTTGT
genomic: AATGAACAGTTCCGAGAGCGCATTCAACACTGCATCGCCTCTTGCTTTAGgtaaggcctg ... aatcaaccagGTCCATCCTAAAAGCTGGCTGCTGATTATGAGCGTCCGGAGTACAACTTGT
EST: gi|89173031|gb|CI040924.1|CI040924
EST:     AATGGACAGTTCCGAGAGCGCATTCAACACTGCATCGCCTCTTGCTTTAG                         GTCCATCCTAAAAGCTGGCTGCTGATTATGAGCGTCCGGAGTACAACTTGT
genomic: AATGAACAGTTCCGAGAGCGCATTCAACACTGCATCGCCTCTTGCTTTAGgtaaggcctg ... aatcaaccagGTCCATCCTAAAAGCTGGCTGCTGATTATGAGCGTCCGGAGTACAACTTGT
EST: gi|88272738|gb|CI386593.1|CI386593
EST:     AATGAACAGTTCCGAGAACGCATTCAACACTGCATCGCCTCTTGCTTTAG                         GTCCATCCTAAAAGCTGGCTGCTGATTATGAGCGTCCGGAGTACAACTTGT
genomic: AATGAACAGTTCCGAGAGCGCATTCAACACTGCATCGCCTCTTGCTTTAGgtaaggcctg ... aatcaaccagGTCCATCCTAAAAGCTGGCTGCTGATTATGAGCGTCCGGAGTACAACTTGT
EST: gi|88253925|gb|CI352551.1|CI352551
EST:     AATGAACAGTTCCGAGAGCGCATTCAACACTGCATCGCCTCTTGCTTTAG                         GTCCATCCTAAAAGCTGGCTGCTGATTATGAGCGTCCGGAGTACAACTTGT
genomic: AATGAACAGTTCCGAGAGCGCATTCAACACTGCATCGCCTCTTGCTTTAGgtaaggcctg ... aatcaaccagGTCCATCCTAAAAGCTGGCTGCTGATTATGAGCGTCCGGAGTACAACTTGT
EST: gi|88286557|gb|CI525056.1|CI525056
EST:     TCAACACTGCATCGCCTCTTGCTTTAG                         GTCCATCCTAAAAGCTGGCTGCTGATTATGAGCGTCCGGAGTACAACTTGT
genomic: TCAACACTGCATCGCCTCTTGCTTTAGgtaaggcctg ... aatcaaccagGTCCATCCTAAAAGCTGGCTGCTGATTATGAGCGTCCGGAGTACAACTTGT
EST: gi|163928715|gb|EG711228.1|EG711228
EST:     AATGAACAGTTCCGAGAGCGCATTCAACACTGCATCGCCTCTTGCTTTAG                         GTCCATCCTAAAAGCTGGCTGCTGATTATGAGCGTCCGGAGTACAACTTGT
genomic: AATGAACAGTTCCGAGAGCGCATTCAACACTGCATCGCCTCTTGCTTTAGgtaaggcctg ... aatcaaccagGTCCATCCTAAAAGCTGGCTGCTGATTATGAGCGTCCGGAGTACAACTTGT
EST: gi|88989889|gb|CI018766.1|CI018766
EST:     AATGAACAGTTCCGAGAGCGCATTCAACACTGCATCGCCTCTTGCTTTAG                         GTCCATCCTAAAAGCTGGCTGCTGATTATGAGCGTCCGGAGTACAACTTGT
genomic: AATGAACAGTTCCGAGAGCGCATTCAACACTGCATCGCCTCTTGCTTTAGgtaaggcctg ... aatcaaccagGTCCATCCTAAAAGCTGGCTGCTGATTATGAGCGTCCGGAGTACAACTTGT
EST: gi|40492746|gb|BX900424.1|BX900424
EST:     AATGAACAGTTCCGAGAGCGCATTCAACACTGCATCGCCTCTTGCTTTAG                         GTCCATCCTAAAAGCTGGATGCTGATTATGAGCGTCCGGAGTACAACTTGT
genomic: AATGAACAGTTCCGAGAGCGCATTCAACACTGCATCGCCTCTTGCTTTAGgtaaggcctg ... aatcaaccagGTCCATCCTAAAAGCTGGCTGCTGATTATGAGCGTCCGGAGTACAACTTGT
EST: gi|88845509|gb|CI084434.1|CI084434
EST:     AATGAACAGTTCCGAGAGCGCATTCAACACTGCATCGCCTCTTGCTTTAG                         GTCCATCCTAAAAGCTGGCTGCTGATTATGAGCGTCCGGAGTACAACTTGT
genomic: AATGAACAGTTCCGAGAGCGCATTCAACACTGCATCGCCTCTTGCTTTAGgtaaggcctg ... aatcaaccagGTCCATCCTAAAAGCTGGCTGCTGATTATGAGCGTCCGGAGTACAACTTGT
EST: gi|88411402|gb|CI518926.1|CI518926
EST:     GAGAGCGCATTCAACACTGCATCGCCTCTTGCTTTAG                         GTCCATCCTAAAAGCTGGCTGCTGATTATGAGCGTCCGGAGTACAACTTGT
genomic: GAGAGCGCATTCAACACTGCATCGCCTCTTGCTTTAGgtaaggcctg ... aatcaaccagGTCCATCCTAAAAGCTGGCTGCTGATTATGAGCGTCCGGAGTACAACTTGT
EST: gi|88506008|gb|CI433514.1|CI433514
EST:     AATGAACAGTTCCGAGAGCGCATTCAACACTGCATCGCCTCTTGCTTTAG                         GTCCATCCTAAAAGCTGGCTGCTGATTATGAGCGTCCGGAGTACAACTTGT
genomic: AATGAACAGTTCCGAGAGCGCATTCAACACTGCATCGCCTCTTGCTTTAGgtaaggcctg ... aatcaaccagGTCCATCCTAAAAGCTGGCTGCTGATTATGAGCGTCCGGAGTACAACTTGT
EST: gi|86495658|gb|CI138291.1|CI138291
EST:     AATGAACAGTTCCGAGAGCGCATTCAACACTGCATCGCCTCTTGCTTTAG                         GTCCATCCTAAAAGCTGGCTGCTGATTATGAGCGTCCGGAGTACAACTTGT
genomic: AATGAACAGTTCCGAGAGCGCATTCAACACTGCATCGCCTCTTGCTTTAGgtaaggcctg ... aatcaaccagGTCCATCCTAAAAGCTGGCTGCTGATTATGAGCGTCCGGAGTACAACTTGT
EST: gi|88413579|gb|CI526141.1|CI526141
EST:     GAGAGCGCATTCAACACTGCATCGCCTCTTGCTTTAG                         GTCCATCCTAAAAGCTGGCTGCTGATTATGGAGGGCGGTTCCGGAGTACAA
genomic: GAGAGCGCATTCAACACTGCATCGCCTCTTGCTTTAGgtaaggcctg ... aatcaaccagGTCCATCCTAAAAGCTGGCTGCTGATTAT-GA--GC-G-TCCGGAGTACAA
EST: gi|86864415|gb|CI334138.1|CI334138
EST:     AATGAACAGTTCCGAGAGCGCATTCAACACTGCATCGCCTCTTGCTTTAG                         GTCCATCCTAAAAGCTGGCTGCTGATTATGAGCGTCCGGAGTACAACTTGT
genomic: AATGAACAGTTCCGAGAGCGCATTCAACACTGCATCGCCTCTTGCTTTAGgtaaggcctg ... aatcaaccagGTCCATCCTAAAAGCTGGCTGCTGATTATGAGCGTCCGGAGTACAACTTGT
EST: gi|86886843|gb|CI324264.1|CI324264
EST:     AATGAACAGTTCCGAGAGCGCATTCAACACTGCATCGCCTCTTGCTTTAG                         GTCCATCCTAAAAGCTGGCTGCTGATTATGAGCGTCCGGAGTACAACTTGT
genomic: AATGAACAGTTCCGAGAGCGCATTCAACACTGCATCGCCTCTTGCTTTAGgtaaggcctg ... aatcaaccagGTCCATCCTAAAAGCTGGCTGCTGATTATGAGCGTCCGGAGTACAACTTGT
EST: gi|86513770|gb|CI156403.1|CI156403
EST:     AATGAACAGTTCCGAGAGCGCATTCAACACTGCATCGCCTCTTGCTTTAG                         GTCCATCCTAAAAGCTGGCTGCTGATTATGAGCGTCCGGAGTACAACTTGT
genomic: AATGAACAGTTCCGAGAGCGCATTCAACACTGCATCGCCTCTTGCTTTAGgtaaggcctg ... aatcaaccagGTCCATCCTAAAAGCTGGCTGCTGATTATGAGCGTCCGGAGTACAACTTGT
EST: gi|88408818|gb|CI554140.1|CI554140
EST:     AATGAACAGTTCCGAGAGCGCATTCAACACTGCATCGCCTCTTGCTTTAG                         GTCCATCCTAAAAGCTGGCTGCTGATTATGAGCGTCCGGAGTACAACTTGT
genomic: AATGAACAGTTCCGAGAGCGCATTCAACACTGCATCGCCTCTTGCTTTAGgtaaggcctg ... aatcaaccagGTCCATCCTAAAAGCTGGCTGCTGATTATGAGCGTCCGGAGTACAACTTGT
EST: gi|88263386|gb|CI367160.1|CI367160
EST:     AATGAACAGTTCCGAGAGCGCATTCAACACTGCATCGCCTCTTGCTTTAG                         GTCCATCCTAAAAGCTGGCTGCTGATTATGAGCGTCCGGAGTACAACTTGT
genomic: AATGAACAGTTCCGAGAGCGCATTCAACACTGCATCGCCTCTTGCTTTAGgtaaggcctg ... aatcaaccagGTCCATCCTAAAAGCTGGCTGCTGATTATGAGCGTCCGGAGTACAACTTGT
EST: gi|88259704|gb|CI363997.1|CI363997
EST:     AATGAACAGTTCCGAGAGCGCATTCAACACTGCATCGCCTCTTGCTTTAG                         GTCCATCCTAAAAGCTGGCTGCTGATTATGAGCGTCCGGAGTACAACTTGT
genomic: AATGAACAGTTCCGAGAGCGCATTCAACACTGCATCGCCTCTTGCTTTAGgtaaggcctg ... aatcaaccagGTCCATCCTAAAAGCTGGCTGCTGATTATGAGCGTCCGGAGTACAACTTGT
EST: gi|88833693|gb|CI077174.1|CI077174
EST:     AATGAACAGTTCCGAGAGCGCATTCAACACTGCATCGCCTCTTGCTTTAG                         GTCCATCCTAAAAGCTGGCTGCTGATTATGAGCGTCCGGAGTACAACTTGT
genomic: AATGAACAGTTCCGAGAGCGCATTCAACACTGCATCGCCTCTTGCTTTAGgtaaggcctg ... aatcaaccagGTCCATCCTAAAAGCTGGCTGCTGATTATGAGCGTCCGGAGTACAACTTGT
EST: gi|218494145|gb|FG953174.1|FG953174
EST:     AATGAACAGTTCCGAGAGCGCATTCAACACTGCATCGCCTCTTGCTTTAG                         GTCCATCCTAAAAGCTGGCTGCTGATTATGAGCGTCCGGAGTACAACTTGT
genomic: AATGAACAGTTCCGAGAGCGCATTCAACACTGCATCGCCTCTTGCTTTAGgtaaggcctg ... aatcaaccagGTCCATCCTAAAAGCTGGCTGCTGATTATGAGCGTCCGGAGTACAACTTGT
EST: gi|88846245|gb|CI373013.1|CI373013
EST:     AATGAACAGTTCCGAGAGCGCATTCAACACTGCATCGCCTCTTGCTTTAG                         GTCCATCCTAAAAGCTGGCTGCTGATTATGAGCGTCCGGAGTACAACTTGT
genomic: AATGAACAGTTCCGAGAGCGCATTCAACACTGCATCGCCTCTTGCTTTAGgtaaggcctg ... aatcaaccagGTCCATCCTAAAAGCTGGCTGCTGATTATGAGCGTCCGGAGTACAACTTGT
EST: gi|88455376|gb|CI519397.1|CI519397
EST:     AATGAACAGTTCCGAGAGCGCATTCAACACTGCATCGCCTCTTGCTTTAGG                         GTCCATCCTAAAAGGTGGCTGCTNATTATGAGCGTCCGGAGTACAACTTT
genomic: AATGAACAGTTCCGAGAGCGCATTCAACACTGCATCGCCTCTTGCTTTA-Ggtaaggcctg ... aatcaaccagGTCCATCCTAAAAGCTGGCTGCTGATTATGAGCGTCCGGAGTACAACTTG
EST: gi|86482134|gb|CI124767.1|CI124767
EST:     AATGAACAGTTCCGAGAGCGCATTCAACACTGCATCGCCTCTTGCTTTAG                         GTCCATCCTAAAAGCTGGCTGCTGATTATGAGCGTCCGGAGTACAACTTGT
genomic: AATGAACAGTTCCGAGAGCGCATTCAACACTGCATCGCCTCTTGCTTTAGgtaaggcctg ... aatcaaccagGTCCATCCTAAAAGCTGGCTGCTGATTATGAGCGTCCGGAGTACAACTTGT
EST: gi|38476909|gb|CF961042.1|CF961042
EST:     AATGAACAGTTCCGAGAGCGCATTCAACACTGCATCGCCTCTTGCTTTAG                         GTCCATCCTAAAAGCTGGCTGCTGATTATGAGCGTCCGGAGTACAACTTGT
genomic: AATGAACAGTTCCGAGAGCGCATTCAACACTGCATCGCCTCTTGCTTTAGgtaaggcctg ... aatcaaccagGTCCATCCTAAAAGCTGGCTGCTGATTATGAGCGTCCGGAGTACAACTTGT
EST: gi|88444407|gb|CI557708.1|CI557708
EST:     AATGAACAGTTCCGAGAGCGCATTCAACACTGCATCGCCTCTTGCTTTAG                         GTCCATCCTAAAAGCTGGCTGCTGATTATGAGCGTCCGGAGTACAACTTGT
genomic: AATGAACAGTTCCGAGAGCGCATTCAACACTGCATCGCCTCTTGCTTTAGgtaaggcctg ... aatcaaccagGTCCATCCTAAAAGCTGGCTGCTGATTATGAGCGTCCGGAGTACAACTTGT
EST: gi|29622131|gb|CB627142.1|CB627142
EST:     AATGAACAGTTCCGAGAGCGCATTCAACACTGCATCGCCTCTTGCTTTAG                         GTCCATCCTAAAAGCTGGCTGCTGATTATGAGCGTCCGGAGTACAACTTGT
genomic: AATGAACAGTTCCGAGAGCGCATTCAACACTGCATCGCCTCTTGCTTTAGgtaaggcctg ... aatcaaccagGTCCATCCTAAAAGCTGGCTGCTGATTATGAGCGTCCGGAGTACAACTTGT

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: 62 (upstream exon), 65 (downstream exon)
Score: 13

TCCATCCCCTCATTTCCATCACTCATTGGAGACGCAAGCAGCGGTTCATCAATGAACAGTTCCGAGAGCGCATTCAACACTGCATCGCCTCTTGCTTTAGgtaaggcctg ... aatcaaccagGTCCATCCTAAAAGCTGGCTGCTGATTATGAGCGTCCGGAGTACAACTTGTAGTCCGAGAAAAGTGCCTCACATCTGAAGCACGGCATCAGGTACTGGAT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tggtgtttgtttttggcagcatcttattcatatgcttgtccatggaatcaaccagGTCCATCCTAAAAGCTGGCTGCTGATTATGAGCGTCCGGAGTACAACTTGTAGTCCGAGAAAAGTGCCTCACATCTGAAGCACGGCATCAGGTACTGGAT
                       ttattcatat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaaggcctgcctatttcatatgtacaacattagatggtgtttgtttttggcagcatcttattcatatgcttgtccatggaatcaaccagGTCCATCCTAAAAGCTGGCTGCTGATTATGAGCGTCCGGAGTACAACTTGTAGTCCGAGAAAAGTGCCTCACATCTGAAGCACGGCATCAGGTACTGGAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGC