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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTTCTTTCAATGAGGGGGAGCTGCTTCTTTTTTGCTTTTCCTCAGCATATATTGTTGCTTTGCTGCATGATACTCTAAAGGTCCCGCTGGATGATAAGAGgtgcgatcttttctgctgttctaatatttctatttcacattttgaacttcaggatttaaaatgttcattttgtttcag

Basic information

species Oryza sativa
transcript LOC_Os08g33850.2
intron # 7
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os08g33850.2 (Oryza sativa), 5'ss of exon 7
lower sequence: GRMZM2G152457_T03 (Zea mays), 5'ss of exon 7
GTTCTTTCAATGAGGGGGAGCTGCTTCTTTTTTGCTTTTCCTCAGCATATATTGTTGCTTTGCTGCATGATACTCTAAAGGTCCCGCTGGATGATAAGAGgtgcgatcttttctgctgttctaatatttctatttcacattttgaacttcaggatttaaaatgttcattttgtttcag
|||||||  |||| ||  | ||||||||||||||||||||||||||||||||| ||||| | ||||||||||| || ||  | || |||||| |||| |||||    |||||||        |  | |||||||     ||   ||| |    |||||  |      |||| | ||||
GTTCTTTTGATGACGGACAACTGCTTCTTTTTTGCTTTTCCTCAGCATATATTATTGCTCTACTGCATGATACGCTTAAAATGCCACTGGATCATAAAAGgtgaagccttttct--------ataagttctattctttgttg-aaacctggatatttatga-----gttttttctcag
















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|218485593|gb|FG957932.1|FG957932
EST:     ATTGTTGCTTTGCTGCATGATACTCTAAAGGTCCCGCTGGATGATAAGAT                         GATTGATGTTGCGACTCAAATTGGCGGTGTGCCTGTTGACTGGGCATTGGG
genomic: ATTGTTGCTTTGCTGCATGATACTCTAAAGGTCCCGCTGGATGATAAGAGgtgcgatctt ... tttgtttcagGATTGATGTTGCGAATCAAATTGGCGGTGTGCCTGTTGACTGGGCATTGGG
EST: gi|38482258|gb|CF966306.1|CF966306
EST:     ATTGTTGCTTTGCTGCATGATACTCTAAAGGTCCCGCTGGATGATAAGAT                         GATTGATGTTGCGAATCAAATTGGCGGTGTGCCTGTTGACTGGGCATTGGG
genomic: ATTGTTGCTTTGCTGCATGATACTCTAAAGGTCCCGCTGGATGATAAGAGgtgcgatctt ... tttgtttcagGATTGATGTTGCGAATCAAATTGGCGGTGTGCCTGTTGACTGGGCATTGGG
EST: gi|86418187|gb|CI032396.1|CI032396
EST:     ATTGTTGCTTTGCTGCATGATACTCTAAAGGTCCCGCTGGATGATAAGAG                         GATTGATGTTGCGAATCAAATTGGCGGTGTGCCTGTTGACTGGGCATTGGG
genomic: ATTGTTGCTTTGCTGCATGATACTCTAAAGGTCCCGCTGGATGATAAGAGgtgcgatctt ... tttgtttcagGATTGATGTTGCGAATCAAATTGGCGGTGTGCCTGTTGACTGGGCATTGGG
EST: gi|87016732|gb|CI275734.1|CI275734
EST:     ATTGTTGCTTTGCTGCATGATACTCTAAAGGTCCCGCTGGATGATAAGAG                         GATTGATGTTGCGAATCAAATTGGCGGTGTGCCTGTTGACTGGGCATTGGG
genomic: ATTGTTGCTTTGCTGCATGATACTCTAAAGGTCCCGCTGGATGATAAGAGgtgcgatctt ... tttgtttcagGATTGATGTTGCGAATCAAATTGGCGGTGTGCCTGTTGACTGGGCATTGGG
EST: gi|86902960|gb|CI312337.1|CI312337
EST:     ATTGTTGCTTTGCTGCATGATACTCTAAAGGTCCCGCTGGATGATAAGAG                         GATTGATGTTGCGAATCAAATTGGCGGTGTGCCTGTTGACTGGGCATTGGG
genomic: ATTGTTGCTTTGCTGCATGATACTCTAAAGGTCCCGCTGGATGATAAGAGgtgcgatctt ... tttgtttcagGATTGATGTTGCGAATCAAATTGGCGGTGTGCCTGTTGACTGGGCATTGGG
EST: gi|157650330|gb|EX449964.1|EX449964
EST:     ATTGTTGCTTTGCTGCATGATACTCTAAAGGTCCCGCTGGATGATAAGAG                         GATTGATGTTGCGAATCAAATTGGCGGTGTGCCTGTTGACTGGGCATTGGG
genomic: ATTGTTGCTTTGCTGCATGATACTCTAAAGGTCCCGCTGGATGATAAGAGgtgcgatctt ... tttgtttcagGATTGATGTTGCGAATCAAATTGGCGGTGTGCCTGTTGACTGGGCATTGGG
EST: gi|87019097|gb|CI297298.1|CI297298
EST:     ATTGTTGCTTTGCTGCATGATACTCTAAAGGTCCCGCTGGATGATAAGAG                         GATTGATGTTGCGAATCAAATTGGCGGTGTGCCTGTTGACTGGGCATTGGG
genomic: ATTGTTGCTTTGCTGCATGATACTCTAAAGGTCCCGCTGGATGATAAGAGgtgcgatctt ... tttgtttcagGATTGATGTTGCGAATCAAATTGGCGGTGTGCCTGTTGACTGGGCATTGGG
EST: gi|29688532|gb|CB684807.1|CB684807
EST:     ATTGTTGCTTTGCTGCATGATACTCTAAAGGTCCCGCTGGATGATAAGAG                         GATTGATGTTGCGAATCAAATTGGCGGTGTGCCTGTTGACTGGGCATTGGG
genomic: ATTGTTGCTTTGCTGCATGATACTCTAAAGGTCCCGCTGGATGATAAGAGgtgcgatctt ... tttgtttcagGATTGATGTTGCGAATCAAATTGGCGGTGTGCCTGTTGACTGGGCATTGGG
EST: gi|88968855|gb|CI098948.1|CI098948
EST:     AAGGTCCCGCTGGATGATAAGAG                         GATTGATGTTGCGAATCAAATTGGCGGTGTGCCTGTTGACTGGGCATTGGG
genomic: AAGGTCCCGCTGGATGATAAGAGgtgcgatctt ... tttgtttcagGATTGATGTTGCGAATCAAATTGGCGGTGTGCCTGTTGACTGGGCATTGGG
EST: gi|88198776|gb|CI198626.1|CI198626
EST:     CATGATACTCTAAAGGTCCCGCTGGATGATAAGAG                         GATTGATGTTGCGAATCAAATTGGCGGTGTGCCTGTTGACTGGGCATTGGG
genomic: CATGATACTCTAAAGGTCCCGCTGGATGATAAGAGgtgcgatctt ... tttgtttcagGATTGATGTTGCGAATCAAATTGGCGGTGTGCCTGTTGACTGGGCATTGGG
EST: gi|25806604|gb|CA762565.1|CA762565
EST:     ATTGTTGCTNTGCTGCATGATACTCTAAAGGTCCCGCTGGATGATAAGAT                         GATTGATGTTGCGAATCAAATNGGCGGTGTGCCTGTTGACTGGGCATTGGG
genomic: ATTGTTGCTTTGCTGCATGATACTCTAAAGGTCCCGCTGGATGATAAGAGgtgcgatctt ... tttgtttcagGATTGATGTTGCGAATCAAATTGGCGGTGTGCCTGTTGACTGGGCATTGGG

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: 57 (upstream exon), 57 (downstream exon)
Score: 13

GTTCTTTCAATGAGGGGGAGCTGCTTCTTTTTTGCTTTTCCTCAGCATATATTGTTGCTTTGCTGCATGATACTCTAAAGGTCCCGCTGGATGATAAGAGgtgcgatctt ... tttgtttcagGATTGATGTTGCGAATCAAATTGGCGGTGTGCCTGTTGACTGGGCATTGGGTGCTTTCATTGTGCAGAAGGCGTCAAACCAGACAGA




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTTCTTTCAATGAGGGGGAGCTGCTTCTTTTTTGCTTTTCCTCAGCATATATTGTTGCTTTGCTGCATGATACTCTAAAGGTCCCGCTGGATGATAAGAGgtgcgatcttttctgctgttctaatatttctatttcacattttgaacttcaggatttaaaatgttcattttgtttcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGGA