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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCAATTTTGGGCGGGACAGTTCAGGTTCCAACTCTCTCTGGAGATGTAGTTCTAAAGgtacctccaaaatcagtttaccctcattttcaatcttctcctttgtttattatgtcggaattctccatctgccttgcatattacag

Basic information

species Oryza sativa
transcript LOC_Os06g02620.1
intron # 14
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os06g02620.1 (Oryza sativa), 5'ss of exon 14
lower sequence: GRMZM2G473367_T01 (Zea mays), 5'ss of exon 11
GCAATTTTGGGCGGGACAGTTCAGGTTCCAACTCTCTCTGGAGATGTAGTTCTAAAGgtacctccaaaatcagtttaccctcattttcaatcttctcctttgtttat-tatgtcggaattctccatctgccttgcatattacag
||||||||||| ||||||||||| || |||||||||  |||||| || ||||||||||||  |   |  |||| |  |  |||||| || || |    | | ||||| ||| |   ||||  || |||  |             
GCAATTTTGGGAGGGACAGTTCAAGTCCCAACTCTCAGTGGAGACGTTGTTCTAAAGgtatgt---atgtcagatagc--tcatttcca-tcatgcgttctctttatatatctgataattgaccttctcacag-----------

upper sequence: LOC_Os06g02620.1 (Oryza sativa), 5'ss of exon 14
lower sequence: GRMZM2G153068_T01 (Zea mays), 5'ss of exon 12
GCAATTTTGGGCGGGACAGTTCAGGTTCCAACTCTCTCTGGAGATGTAGTTCTAAAGgtacctccaaaatcagtttaccctcattttcaatcttctcctttgtttattatgtcggaattctccatctgccttgcatattacag
||||||||||| ||||||||||| || |||||||||  |||||| || ||||||||||||  |   |  |||| |  |    |  ||| ||| |    | | ||||| || || || |  |  | ||  ||| ||        
GCAATTTTGGGAGGGACAGTTCAAGTCCCAACTCTCAGTGGAGACGTTGTTCTAAAGgtatgt---atgtcagatagct---aacttccatcatacgttctctttat-atatctga-taattgacct-tcttacag-------

upper sequence: LOC_Os06g02620.1 (Oryza sativa), 5'ss of exon 14
lower sequence: GLYMA15G42640.1 (Glycine max), 5'ss of exon 15
GCAATTTTGGGCGGGACAGTTCAGGTTCCAACTCTCTCTGGAGATGTAGTTCTAAAGgt--acctccaaaatcagtttaccctcattttcaatcttctcctttgtttattatgtcggaattctccatctgccttgcatattacag
||||||||||| || ||  ||||||| ||||||||  |||||||||| |||||||||||     |   ||   | |||  | |    ||   |  | |   |   | |||| ||  ||        ||||  | |||        
GCAATTTTGGGTGGAACCATTCAGGTCCCAACTCTTACTGGAGATGTTGTTCTAAAGgtttgtattgcaacataatttctcatggcattt--tggttttagtaactgattaagtttgatgatgggttctgtttggcag-------

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|396941303|gb|HO188512.1|HO188512
EST:     TGGGCGGGACAGTTCAGGTTCCAACTCTCTCTGGAGATGTAGTTCTAAAG                         GTCAAGCCTGGTACTCAGCCTGGCCAAAAGGTGGTTCTGAGAGGAAAAG
genomic: TGGGCGGGACAGTTCAGGTTCCAACTCTCTCTGGAGATGTAGTTCTAAAGgtacctccaa ... catattacagGTCAAGCCTGGTACTCAGCCTGGCCAAAAGGTGGTTCTGAGAGGAAAAG
EST: gi|86525359|gb|CI165565.1|CI165565
EST:     TCTCTCTGGAGATGTAGTTCTAAAG                         GTCAAGCCTGGTACTCAGCCTGGCCAAAAGGTGTTTCTGAGAGGAAAAG
genomic: TCTCTCTGGAGATGTAGTTCTAAAGgtacctccaa ... catattacagGTCAAGCCTGGTACTCAGCCTGGCCAAAAGGTGGTTCTGAGAGGAAAAG
EST: gi|38477689|gb|CF961822.1|CF961822
EST:     TGGGCGGGACAGTTCAGGTTCCAACTCTCTCTGGAGATGTAGTTCTAAAG                         GTCAAGCCTGGTACTCAGCCTGGCCAAAAGGTGGTTCTGAGAGGAAAAG
genomic: TGGGCGGGACAGTTCAGGTTCCAACTCTCTCTGGAGATGTAGTTCTAAAGgtacctccaa ... catattacagGTCAAGCCTGGTACTCAGCCTGGCCAAAAGGTGGTTCTGAGAGGAAAAG
EST: gi|88832398|gb|CI019339.1|CI019339
EST:     TGGGCGGGACAGTTCAGGTTCCAACTCTCTCTGGAGATGTAGTTCTAAAG                         GTCAAGCCTGGTACTCAGCCTGGCCAAAAGGTGGTTCTGAGAGGAAAAG
genomic: TGGGCGGGACAGTTCAGGTTCCAACTCTCTCTGGAGATGTAGTTCTAAAGgtacctccaa ... catattacagGTCAAGCCTGGTACTCAGCCTGGCCAAAAGGTGGTTCTGAGAGGAAAAG
EST: gi|29614537|gb|CB619550.1|CB619550
EST:     TGGGCGGGACAGTTCAGGTTCCAACTCTCTCTGGAGATGTAGTTCTAAAG                         GTCAAGCCTGGTACTCAGCCTGGCCAAAAGGTGGTTTTGAGAGGAAAAG
genomic: TGGGCGGGACAGTTCAGGTTCCAACTCTCTCTGGAGATGTAGTTCTAAAGgtacctccaa ... catattacagGTCAAGCCTGGTACTCAGCCTGGCCAAAAGGTGGTTCTGAGAGGAAAAG
EST: gi|87018983|gb|CI256868.1|CI256868
EST:     TGGGCGGGACAGTTCAGGTTCCAACTCTCTCTGGAGATGTAGTTCTAAAG                         GTCAAGCCTGGTACTCAGCCTGGCCAAAAGGTGGTTCTGAGAGGAAAAG
genomic: TGGGCGGGACAGTTCAGGTTCCAACTCTCTCTGGAGATGTAGTTCTAAAGgtacctccaa ... catattacagGTCAAGCCTGGTACTCAGCCTGGCCAAAAGGTGGTTCTGAGAGGAAAAG
EST: gi|22304698|gb|BQ905920.1|BQ905920
EST:     GGCGGGACAGTTCAGGGTTCCAACTCTCTCTGGAGATTGTAGTTCTAAAG                         GTCAAGCCTGGTACTCAGCCTGGCCAAAAGGTGGTTCTGAGAGGAAAAG
genomic: GGCGGGACAGTTCA-GGTTCCAACTCTCTCTGGAGA-TGTAGTTCTAAAGgtacctccaa ... catattacagGTCAAGCCTGGTACTCAGCCTGGCCAAAAGGTGGTTCTGAGAGGAAAAG

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), 74 (downstream exon)
Score: 23

GCAATTTTGGGCGGGACAGTTCAGGTTCCAACTCTCTCTGGAGATGTAGTTCTAAAGgtacctccaa ... catattacagGTCAAGCCTGGTACTCAGCCTGGCCAAAAGGTGGTTCTGAGAGGAAAAG




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GCAATTTTGGGCGGGACAGTTCAGGTTCCAACTCTCTCTGGAGATGTAGTTCTAAAGgtacctccaaaatcagtttaccctcattttcaatcttctcctttgtttattatgtcggaattctccatctgccttgcatattacag

- - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - -  GGAGAT
- - - - - - - - - - - - - - - - - - - - GAGATG