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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacctgttctaattactgttacaaactattattaagtggtctaaattggaaacagcacacatagtctgttgattcatggcattcttcttttaaatcttgtagCTGCTATATTAAAACATCCTAGAACACCAACAACTGCCAATCCTTCTATGGATTATCCATCAGGAGATTCTGATCACGTCTCCAAGAGAACGAGACCAGT

Basic information

species Oryza sativa
transcript LOC_Os03g14980.1
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g14980.2 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G030422_T02 (Zea mays), 3'ss of exon 7
gtacctgttctaattactgttacaaactattattaagtggtctaaattggaaacagcacacatagtctgttgattcatggcattcttcttttaaatcttgtagCTGCTATATTAAAACATCCTAGAACACCAACAACTGCCAATCCTTCTATGGATTATCCATCAGGAGATTCTGATCACGTCTCCAAGAGAACGAGACCAGT
|||  | |   |  |  |||  ||||| || || || ||| || | |   |  |||  |   | ||||||| | | ||| |  |||   |||| || || |||| | | | || || |||||||||||||| |||||||  ||||||  ||||||||||||||||||||||||||| ||| | ||||||||||| ||||| ||
gtatttatgtcatct--tgtcgcaaacaataatgaaatggcctgattcaaagccagttcgtgt-gtctgtttactaatgtctatctgtctttacattttatagCCGTTTTGTTGAAGCATCCTAGAACACCCACAACTGGTAATCCTGGTATGGATTATCCATCAGGAGATTCTGACCACATTTCCAAGAGAACTAGACCGGT
















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|58653134|gb|CK041814.1|CK041814
EST:     TCCTGCTGTGTCTGGTGGAGCTATTGGATTTGGTACTCCTACAAATCCTG                         CTGCTATATTAAAACATCCTAGAACACCAACAACTGCCAATCCTTCTATGG
genomic: TCCTGCTGTGTCTGGTGGAGCTATTGGATTTGGTACTCCTACAAATCCTGgtacctgttc ... aatcttgtagCTGCTATATTAAAACATCCTAGAACACCAACAACTGCCAATCCTTCTATGG
EST: gi|88407882|gb|CI588911.1|CI588911
EST:     TCCTGGTGTGTCTGGTGGAGCTATTGGATTTGGTACTCCTAAAAATCCTG                         CTGCTATATTAAAACATCCTAGAACACCAACAACTGCCAATCCTTCTATGG
genomic: TCCTGCTGTGTCTGGTGGAGCTATTGGATTTGGTACTCCTACAAATCCTGgtacctgttc ... aatcttgtagCTGCTATATTAAAACATCCTAGAACACCAACAACTGCCAATCCTTCTATGG
EST: gi|58693082|gb|CK081769.1|CK081769
EST:     TCCTGCTGTGTCTGGTGGAGCTATTGGATTNGGTACTCCTACAAATCCTG                         CTGCTATATTAAAACATCCTAGAACACCAACAACTGCCAATCCTTCTATGG
genomic: TCCTGCTGTGTCTGGTGGAGCTATTGGATTTGGTACTCCTACAAATCCTGgtacctgttc ... aatcttgtagCTGCTATATTAAAACATCCTAGAACACCAACAACTGCCAATCCTTCTATGG
EST: gi|29656775|gb|CB653050.1|CB653050
EST:     TCCTGCTGTGTCTGGTGGAGCTATTGGATTTGGTACTCCTACAAATCCTG                         CTGCTATATTAAAACATCCTAGAACACCAACAACTGCCAATCCTTCTATGG
genomic: TCCTGCTGTGTCTGGTGGAGCTATTGGATTTGGTACTCCTACAAATCCTGgtacctgttc ... aatcttgtagCTGCTATATTAAAACATCCTAGAACACCAACAACTGCCAATCCTTCTATGG
EST: gi|58661312|gb|CK049992.1|CK049992
EST:     TCCTGCTGTGTCTGGTGGAGCTATTGGATTTGGTACTCCTACAAATCCTG                         CTGCTATATTAAAACATCCTAGAACACCAACAACTGCCAATCCTTCTATGG
genomic: TCCTGCTGTGTCTGGTGGAGCTATTGGATTTGGTACTCCTACAAATCCTGgtacctgttc ... aatcttgtagCTGCTATATTAAAACATCCTAGAACACCAACAACTGCCAATCCTTCTATGG
EST: gi|58673842|gb|CK062528.1|CK062528
EST:     CTCCTACAAATCCTG                         CTGCTATATTAAAACATCCTAGAACACCAACAACTGCCAATCCTTCTATGG
genomic: CTCCTACAAATCCTGgtacctgttc ... aatcttgtagCTGCTATATTAAAACATCCTAGAACACCAACAACTGCCAATCCTTCTATGG
EST: gi|29628402|gb|CB633413.1|CB633413
EST:     TCCTGCTGTGTCTGGTGGAGCTATTGGATTTGGTACTCCTACAAATCCTG                         CTGCTATATTAAAACATCCTAGAACACCAACAACTGCCAATCCTTCTATGG
genomic: TCCTGCTGTGTCTGGTGGAGCTATTGGATTTGGTACTCCTACAAATCCTGgtacctgttc ... aatcttgtagCTGCTATATTAAAACATCCTAGAACACCAACAACTGCCAATCCTTCTATGG
EST: gi|29625346|gb|CB630357.1|CB630357
EST:     TCCTGCTGTGTCTGGTGGAGCTATTGGATTTGGTACTCCTACAAATCCTG                         CTGCTATATTAAAACATCCTAGAACACCAACAACTGCCAATCCTTCTATGG
genomic: TCCTGCTGTGTCTGGTGGAGCTATTGGATTTGGTACTCCTACAAATCCTGgtacctgttc ... aatcttgtagCTGCTATATTAAAACATCCTAGAACACCAACAACTGCCAATCCTTCTATGG
EST: gi|29622174|gb|CB627185.1|CB627185
EST:     GTCTGGTGGAGCTATCGTATTTGGTACTCCTACAAATCCTG                         CTGCTATATTAAAACATCCTAGAACACCAACAACTGCCAATCCTTCTATGG
genomic: GTCTGGTGGAGCTATTGGATTTGGTACTCCTACAAATCCTGgtacctgttc ... aatcttgtagCTGCTATATTAAAACATCCTAGAACACCAACAACTGCCAATCCTTCTATGG
EST: gi|29656774|gb|CB653049.1|CB653049
EST:     TCCTGCTGTGTCTGGTGGAGCTATTGGATTTGGTACTCCTACAAATCCTG                         CTGCTATATTAAAACATCCTAGAACACCAACAACTGCCAATCCTTCTATGG
genomic: TCCTGCTGTGTCTGGTGGAGCTATTGGATTTGGTACTCCTACAAATCCTGgtacctgttc ... aatcttgtagCTGCTATATTAAAACATCCTAGAACACCAACAACTGCCAATCCTTCTATGG
EST: gi|87023591|gb|CI286342.1|CI286342
EST:     TCCTGCTGTGTCTGGTGGAGCTATTGGATTTGGTACTCCTACAAATCCTG                         CTGCTATATTAAAACATCCTAGAACACCAACAACTGCCAATCCTTCTATGG
genomic: TCCTGCTGTGTCTGGTGGAGCTATTGGATTTGGTACTCCTACAAATCCTGgtacctgttc ... aatcttgtagCTGCTATATTAAAACATCCTAGAACACCAACAACTGCCAATCCTTCTATGG

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: 73 (upstream exon), 75 (downstream exon)
Score: 75

CCTGTCCCACCTCTGGCTGGCTGGATGTCAAACCCTCCAGCAGTAACACATCCTGCTGTGTCTGGTGGAGCTATTGGATTTGGTACTCCTACAAATCCTGgtacctgttc ... aatcttgtagCTGCTATATTAAAACATCCTAGAACACCAACAACTGCCAATCCTTCTATGGATTATCCATCAGGAGATTCTGATCACGTCTCCAAGAGAACGAGACCAGT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ggaaacagcacacatagtctgttgattcatggcattcttcttttaaatcttgtagCTGCTATATTAAAACATCCTAGAACACCAACAACTGCCAATCCTTCTATGGATTATCCATCAGGAGATTCTGATCACGTCTCCAAGAGAACGAGACCAGT
                   tgttgat  putative branch site (score: 75)
                                 attcttcttttaaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtacctgttctaattactgttacaaactattattaagtggtctaaattggaaacagcacacatagtctgttgattcatggcattcttcttttaaatcttgtagCTGCTATATTAAAACATCCTAGAACACCAACAACTGCCAATCCTTCTATGGATTATCCATCAGGAGATTCTGATCACGTCTCCAAGAGAACGAGACCAGT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA