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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagctcaagagaaagcatagcatcctttccaaacctcaaaagtagtttttttttaaaaaaaaaaactttcagaaaacacacattttttatatgttatattctcttccaattttcagGCTTTGGCTGATCCGTACTTCGCAAGTCTTGCTAATGTGGAACGTGAGCCCTCAAGACATCCAATCTCAAAACTTGAGTTTGAATTCGAGAGACGGAAGC

Basic information

species Oryza sativa
transcript LOC_Os06g49430.2
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os06g49430.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G135904_T01 (Zea mays), 3'ss of exon 6
gtaagctcaagagaaagcatagcatcctttccaaacctcaaaagtagtttttttttaaaaaaaaaaactttcagaaa-acacacattttttatatgttat-attctcttccaat-tttcagGCTTTGGCTGATCCGTACTTCGCAAGTCTTGCTAATGTGGAACGTGAGCCCTCAAGACATCCAATCTCAAAACTTGAGTTTGAATTCGAGAGACGGAAGC
|| | |||||   |||  ||    || ||| |   | | | |  | | |||   | |||| |    ||    | | | | |  ||||||| | ||  ||| ||| ||||    |  |||||||| | |||||||| ||||| |||   ||||||||||||||||||||||| |||||||| || || || ||||||||||||||||| || |||  |||||
gtgaactcaatt-aaaatatgttttctttttctttcattagatct-gctttccataaaaagatgtcacacgtatatatatatgcatttttgacattatattattatcttatcgtacttcagGCTCTAGCTGATCCATACTTTGCATCCCTTGCTAATGTGGAACGTGAGCCATCAAGACACCCGATTTCTAAACTTGAGTTTGAATTTGAAAGAAAGAAGC

upper sequence: LOC_Os06g49430.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G306028_T02 (Zea mays), 3'ss of exon 6
gtaagctcaagagaaagcatagcatcctttccaaacctcaaaagtagtttttttttaaaaaaaaaaactttcagaaaacacacattttttatatgttatattctcttccaattttcagGCTTTGGCTGATCCGTACTTCGCAAGTCTTGCTAATGTGGAACGTGAGCCCTCAAGACATCCAATCTCAAAACTTGAGTTTGAATTCGAGAGACGGAAGC
         | |  ||  | || |    ||  |    ||||    |    |        |||| ||| |||        |   |     ||||   |||| | |   |  |||| |||||| | |||||||| ||||| |||   ||||||||||||||||||||||| |||||||| ||||| || ||||||||||||||||| || ||| ||||||
---------aaaataaatacagtaattattgtatgaatcaactaaaaaggt--------aaaacaaattttattttggtatggagggggtataatatataattttaacttattt-cagGCTCTAGCTGATCCATACTTTGCATCCCTTGCTAATGTGGAACGTGAGCCATCAAGACACCCAATTTCTAAACTTGAGTTTGAATTTGAAAGAAGGAAGC
















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|33684106|gb|CF312345.1|CF312345
EST:     TAGAGCGTTTACTGGCATTTGATCCTAAAGATCGGTCTTCAGCTGAAGAA                         GCTTTGGCTGATCCGTACTTCGCAAGTCTTGCTAATGTGGAACGTGAGCCC
genomic: TAGAGCGTTTACTGGCATTTGATCCTAAAGATCGGTCTTCAGCTGAAGAAgtaagctcaa ... caattttcagGCTTTGGCTGATCCGTACTTCGCAAGTCTTGCTAATGTGGAACGTGAGCCC
EST: gi|88406114|gb|CI593894.1|CI593894
EST:     TAAAGATCGGTCTTCAGCTGAAGAA                         GCTTTGGCTGATCCGTACTTCGCAAGTCTTGCTAATGTGGAACGTGAGCCC
genomic: TAAAGATCGGTCTTCAGCTGAAGAAgtaagctcaa ... caattttcagGCTTTGGCTGATCCGTACTTCGCAAGTCTTGCTAATGTGGAACGTGAGCCC
EST: gi|33381883|gb|CF197226.1|CF197226
EST:     TAGAGCGTTTACTGGCATTTGATCCTAAAGATCGGCCTTCAGCTGAAGAA                         GCTTTGGCTGATCCGTACTTCGCAAGTCTTGCTAATGTGGAACGTGAGCCC
genomic: TAGAGCGTTTACTGGCATTTGATCCTAAAGATCGGTCTTCAGCTGAAGAAgtaagctcaa ... caattttcagGCTTTGGCTGATCCGTACTTCGCAAGTCTTGCTAATGTGGAACGTGAGCCC
EST: gi|58693904|gb|CK082591.1|CK082591
EST:     TAGAGCGTTTACTGGCATTTGATCCTAAAGATCGGCCTTCAGCTGAAGAA                         GCTTTGGCTGATCCGTACTTCGCAAGTCTTGCTAATGTGGAACGTGAGCCC
genomic: TAGAGCGTTTACTGGCATTTGATCCTAAAGATCGGTCTTCAGCTGAAGAAgtaagctcaa ... caattttcagGCTTTGGCTGATCCGTACTTCGCAAGTCTTGCTAATGTGGAACGTGAGCCC
EST: gi|58663177|gb|CK051863.1|CK051863
EST:     TAGAGCGTTTACTGGCATTTGATCCTAAAGATCGGCCTTCAGCTGAAGAA                         GCTTTGGCTGATCCGTACTTCGCAAGTCTTGCTAATGTGGAACGTGAGCCC
genomic: TAGAGCGTTTACTGGCATTTGATCCTAAAGATCGGTCTTCAGCTGAAGAAgtaagctcaa ... caattttcagGCTTTGGCTGATCCGTACTTCGCAAGTCTTGCTAATGTGGAACGTGAGCCC
EST: gi|218481672|gb|FG962985.1|FG962985
EST:     CATTTGATCCTAAAGATCGGCCTTCAGCTGAAGAA                         GCTTTGGCTGATCCGTACTTCGCAAGTCTTGCTAATGTGGAACGTGAGCCC
genomic: CATTTGATCCTAAAGATCGGTCTTCAGCTGAAGAAgtaagctcaa ... caattttcagGCTTTGGCTGATCCGTACTTCGCAAGTCTTGCTAATGTGGAACGTGAGCCC
EST: gi|218490968|gb|FG950249.1|FG950249
EST:     TAGAGCGTTTACTGGCATTTGATCCTAAAGATCGGCCTTCAGCTGAAGAA                         GCTTTGGCTGATCCGTACTTCGCAAGTCTTGCTAATGTGGAACGTGAGCCC
genomic: TAGAGCGTTTACTGGCATTTGATCCTAAAGATCGGTCTTCAGCTGAAGAAgtaagctcaa ... caattttcagGCTTTGGCTGATCCGTACTTCGCAAGTCTTGCTAATGTGGAACGTGAGCCC
EST: gi|58589575|gb|CF987883.1|CF987883
EST:     TAGAGCGTTTACTGGCATTTGATCCTAAAGATCGGCCTTCAGCTGAAGAA                         GCTTTGGCTGATCCGTACTTCGCAAGTCTTGCTAATGTGGAACGTGAGCCC
genomic: TAGAGCGTTTACTGGCATTTGATCCTAAAGATCGGTCTTCAGCTGAAGAAgtaagctcaa ... caattttcagGCTTTGGCTGATCCGTACTTCGCAAGTCTTGCTAATGTGGAACGTGAGCCC
EST: gi|58661035|gb|CK049715.1|CK049715
EST:     TAGAGCGTTTACTGGCATTTGATCCTCAAGATCGGACTTCAGCTGAAGAA                         GCTTTGGCTGATCCGTACTTCG
genomic: TAGAGCGTTTACTGGCATTTGATCCTAAAGATCGGTCTTCAGCTGAAGAAgtaagctcaa ... caattttcagGCTTTGGCTGATCCGTACTTCG

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: 67 (upstream exon), 48 (downstream exon)
Score: 21

CCCCTTCTCTCAGAAGTTCCGCAATACTGACCCCTTGGCTCTTCGTCTGCTAGAGCGTTTACTGGCATTTGATCCTAAAGATCGGTCTTCAGCTGAAGAAgtaagctcaa ... caattttcagGCTTTGGCTGATCCGTACTTCGCAAGTCTTGCTAATGTGGAACGTGAGCCCTCAAGACATCCAATCTCAAAACTTGAGTTTGAATTCGAGAGACGGAAGC




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aaaactttcagaaaacacacattttttatatgttatattctcttccaattttcagGCTTTGGCTGATCCGTACTTCGCAAGTCTTGCTAATGTGGAACGTGAGCCCTCAAGACATCCAATCTCAAAACTTGAGTTTGAATTCGAGAGACGGAAGC
                                     ttctcttccaattttc  CT-rich tract
           aaaacacacatttttt  TA-rich tract