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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtagtgaacaatctccattgctgtttgtcagatgcagtttaagcagaaatcttgtcactttaaagtctgtaacttcatctgcaaatggtgcatctgtgtgtgcagGTTGGAGGATGGTCTGAGGTGTATGAAGGGCTCACATTTGCGTCAGTGAGAGGTGCTGGGCATGAGGTGCCACTGTTTCAGCCAAGGAGAGCATTCAGGA

Basic information

species Oryza sativa
transcript LOC_Os02g55130.4
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g55130.1 (Oryza sativa), 3'ss of exon 8
lower sequence: GRMZM5G879749_T01 (Zea mays), 3'ss of exon 9
gtagtgaacaatctccattgctgtttgtcagatgcagtttaagcagaaatcttgtcact-ttaaagtctgtaacttcatctgcaaatggtgcatctgtgtgtgcagGTTGGAGGATGGTCTGAGGTGTATGAAGGGCTCACATTTGCGTCAGTGAGAGGTGCTGGGCATGAGGTGCCACTGTTTCAGCCAAGGAGAGCATTCAGGA
                                    ||             |||   || ||   |  |||||| || || |    ||| ||    |  ||||||||| |||||||||||||||||||| ||||||||||| |||||||| |||||||| || ||||||||||||||  |||| ||||| ||||| || |||||||
------------------------------------gtacggaacttgccattgctgctgttgttgcttgtaacgtcttccgagtttggggc----gcatgtgcagGTAGGAGGATGGTCTGAGGTGTACGAAGGGCTCACGTTTGCGTCGGTGAGAGGCGCAGGGCATGAGGTGCCGTTGTTCCAGCCCAGGAGGGCGTTCAGGA

upper sequence: LOC_Os02g55130.1 (Oryza sativa), 3'ss of exon 8
lower sequence: Vv11s0037g00320.t01 (Vitis vinifera), 3'ss of exon 8
gtagtgaacaatctc--cattgctgtttgtcagatgcagtttaagcag-aaatcttgtcactttaaagtctgtaacttcatctgcaaatggtgcatctgtgtgtgcagGTTGGAGGATGGTCTGAGGTGTATGAAGGGCTCACATTTGCGTCAGTGAGAGGTGCTGGGCATGAGGTGCCACTGTTTCAGCCAAGGAGAGCATTCAGGA
   ||  || || |     ||| | ||| |    |  |  | ||   | |||| |  |   | ||| | || ||  |     |  || |    ||  |   ||  ||||| || || ||| | ||||||||||||||||| || |||||  | ||||||||||| ||||||||||| || ||||||||||| | | |||| |||    
---gtacaccattttattgttgttatttatttattaaaaataaaaaggtaaatgtgatttttctaaggactatatatgagcttaaaagt----caattaattgaacagGTAGGGGGGTGGACAGAGGTGTATGAAGGGCTAACCTTTGCCACTGTGAGAGGTGCCGGGCATGAGGTTCCTCTGTTTCAGCCGATGCGAGCTTTCCTTC
















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|29637027|gb|CB642036.1|CB642036
EST:     TTGGACTGAAGACGAAGATCCGCTGGTACCCTTGGTACTCAGCTGGACAG                         GTTGGAGGATGGTTTGAGGTGTATGAAGGGCTCACATTTGCGTCAGTGAGA
genomic: TTGGACTGAAGACGAAGATCCGCTGGTACCCTTGGTACTCAGCTGGACAGgtagtgaaca ... gtgtgtgcagGTTGGAGGATGGTCTGAGGTGTATGAAGGGCTCACATTTGCGTCAGTGAGA
EST: gi|88964246|gb|CI045439.1|CI045439
EST:     AGACGAAGATCCGCTGGTACCCTTGGTACTCAGCTGGACAG                         GTTGGAGGATGGTCTGAGGTGTATGAAGGGCTCACATTTGCGTCAGTGAGA
genomic: AGACGAAGATCCGCTGGTACCCTTGGTACTCAGCTGGACAGgtagtgaaca ... gtgtgtgcagGTTGGAGGATGGTCTGAGGTGTATGAAGGGCTCACATTTGCGTCAGTGAGA
EST: gi|86504237|gb|CI146870.1|CI146870
EST:     TTGGACTGAAGACGAAGATCCGCTGGTACCCTTGGTACTCAGCTGGACAG                         GTTGGAGGATGGTCTGAGGTGTATGAAGGGCTCACATTTGCGTCAGTGAGA
genomic: TTGGACTGAAGACGAAGATCCGCTGGTACCCTTGGTACTCAGCTGGACAGgtagtgaaca ... gtgtgtgcagGTTGGAGGATGGTCTGAGGTGTATGAAGGGCTCACATTTGCGTCAGTGAGA
EST: gi|86503050|gb|CI145683.1|CI145683
EST:     TTGGACTGAAGACGAAGATCCGCTGGTACCCTTGGTACTCAGCTGGACAG                         GTTGGAGGATGGTCTGAGGTGTATGAAGGGCTCACATTTGCGTCAGTGAGA
genomic: TTGGACTGAAGACGAAGATCCGCTGGTACCCTTGGTACTCAGCTGGACAGgtagtgaaca ... gtgtgtgcagGTTGGAGGATGGTCTGAGGTGTATGAAGGGCTCACATTTGCGTCAGTGAGA
EST: gi|86517525|gb|CI157731.1|CI157731
EST:     TTGGACTGAAGACGAAGATCCGCTGGTACCCTTGGTACTCAGCTGGACAG                         GTTGGAGGATGGTCTGAGGTGTATGAAGGGCTCACATTTGCGTCAGTGAGA
genomic: TTGGACTGAAGACGAAGATCCGCTGGTACCCTTGGTACTCAGCTGGACAGgtagtgaaca ... gtgtgtgcagGTTGGAGGATGGTCTGAGGTGTATGAAGGGCTCACATTTGCGTCAGTGAGA
EST: gi|29664011|gb|CB660286.1|CB660286
EST:     TTGGACTGAAGACGAAGATCCGCTGGTACCCTTGGTACTCAGCTGGACAG                         GTTGGAGGATGGTCTGAGGTGTATGAAGGGCTCACATTTGCGTCAGTGAGA
genomic: TTGGACTGAAGACGAAGATCCGCTGGTACCCTTGGTACTCAGCTGGACAGgtagtgaaca ... gtgtgtgcagGTTGGAGGATGGTCTGAGGTGTATGAAGGGCTCACATTTGCGTCAGTGAGA
EST: gi|88956207|gb|CI092495.1|CI092495
EST:     TTGGACTGAAGACGAAGATCCGCTGGTACCCTTGGTACTCAGCTGGACAG                         GTTGGAGGATGGTCTGAGGTGTATGAAGGGCTCACATTTGCGTCAGTGAGA
genomic: TTGGACTGAAGACGAAGATCCGCTGGTACCCTTGGTACTCAGCTGGACAGgtagtgaaca ... gtgtgtgcagGTTGGAGGATGGTCTGAGGTGTATGAAGGGCTCACATTTGCGTCAGTGAGA
EST: gi|29676175|gb|CB672450.1|CB672450
EST:     TTGGACTGAAGACGAAGATCCGCTGGTACCCTTGGTACTCAGCTGGACAG                         GTTGGAGGATGGTCTGAGGTGTATGAAGGGCTCACATTTGCGTCAGTGAGA
genomic: TTGGACTGAAGACGAAGATCCGCTGGTACCCTTGGTACTCAGCTGGACAGgtagtgaaca ... gtgtgtgcagGTTGGAGGATGGTCTGAGGTGTATGAAGGGCTCACATTTGCGTCAGTGAGA
EST: gi|88218970|gb|CI220530.1|CI220530
EST:     TTGGACTGAAGACGAAGATCCGCTGGTACCCTTGGTACTCAGCTGGACAG                         GTTGGAGGATGGTCTGAGGTGTATGAAGGGCTCACATTTGCGTCAGTGAGA
genomic: TTGGACTGAAGACGAAGATCCGCTGGTACCCTTGGTACTCAGCTGGACAGgtagtgaaca ... gtgtgtgcagGTTGGAGGATGGTCTGAGGTGTATGAAGGGCTCACATTTGCGTCAGTGAGA
EST: gi|86484761|gb|CI127394.1|CI127394
EST:     TTGGACTGAAGACGAAGATCCGCTGGTACCCTTGGTACTCAGCTGGACAG                         GTTGGAGGATGGTCTGAGGTGTATGAAGGGCTCACATTTGCGTCAGTGAGA
genomic: TTGGACTGAAGACGAAGATCCGCTGGTACCCTTGGTACTCAGCTGGACAGgtagtgaaca ... gtgtgtgcagGTTGGAGGATGGTCTGAGGTGTATGAAGGGCTCACATTTGCGTCAGTGAGA
EST: gi|5771050|gb|AU077939.1|AU077939
EST:     TTGNACTGAAGACGAAGATCCGCTGGTACCCTTGGTACTCAGCTGGACAG                         GTTGGAGGATGGTCTGAGGTGTATGAAGGGCTCACATTTGCGTCAGTGAGA
genomic: TTGGACTGAAGACGAAGATCCGCTGGTACCCTTGGTACTCAGCTGGACAGgtagtgaaca ... gtgtgtgcagGTTGGAGGATGGTCTGAGGTGTATGAAGGGCTCACATTTGCGTCAGTGAGA
EST: gi|88968080|gb|CI098322.1|CI098322
EST:     TTGGACTGAAGACGAAGATCCGCTGGTACCCTTGGTACTCAGCTGGACAG                         GTTGGAGGATGGTCTGAGGTGTATGAAGGGCTCACATTTGCGTCAGTGAGA
genomic: TTGGACTGAAGACGAAGATCCGCTGGTACCCTTGGTACTCAGCTGGACAGgtagtgaaca ... gtgtgtgcagGTTGGAGGATGGTCTGAGGTGTATGAAGGGCTCACATTTGCGTCAGTGAGA

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: 71 (upstream exon), 29 (downstream exon)
Score: 3

CACGGATTCAGTCGTTCCGGTTACTGCAACGAGGTTTGCGCTTAGCCATCTTGGACTGAAGACGAAGATCCGCTGGTACCCTTGGTACTCAGCTGGACAGgtagtgaaca ... gtgtgtgcagGTTGGAGGATGGTCTGAGGTGTATGAAGGGCTCACATTTGCGTCAGTGAGAGGTGCTGGGCATGAGGTGCCACTGTTTCAGCCAAGGAGAGCATTCAGGA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cttgtcactttaaagtctgtaacttcatctgcaaatggtgcatctgtgtgtgcagGTTGGAGGATGGTCTGAGGTGTATGAAGGGCTCACATTTGCGTCAGTGAGAGGTGCTGGGCATGAGGTGCCACTGTTTCAGCCAAGGAGAGCATTCAGGA
                ctgtaac  putative branch site (score: 3)
      actttaaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtagtgaacaatctccattgctgtttgtcagatgcagtttaagcagaaatcttgtcactttaaagtctgtaacttcatctgcaaatggtgcatctgtgtgtgcagGTTGGAGGATGGTCTGAGGTGTATGAAGGGCTCACATTTGCGTCAGTGAGAGGTGCTGGGCATGAGGTGCCACTGTTTCAGCCAAGGAGAGCATTCAGGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCA