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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AATGAGATTGTCAAGCTTGAGAACTTCCCGTACTTGAATCGTCTTGGCACTCTGTTAGTTAACAATAACAGAATCACACGTATCAATCCCAATCTTGGTGgtaagattatatattttatcttgttatgatctgtttatcattttcataattttgctccagaacttaccttcagttgctcctgtttctag

Basic information

species Oryza sativa
transcript LOC_Os02g13990.1
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g13990.3 (Oryza sativa), 5'ss of exon 3
lower sequence: GRMZM2G021742_T01 (Zea mays), 5'ss of exon 3
AATGAGATTGTCAAGCTTGAGAACTTCCCGTACTTGAATCGTCTTGGCACTCTGTTAGTTAACAATAACAGAATCACACGTATCAATCCCAATCTTGGTGgtaagattatatattttatcttgttatgatctgtttatcattttcataattttgctccagaacttaccttcagttgctcctgtttctag----
|||||||||||||||||||| |||||||| |||||||||||||||||||||||  ||||||| ||||||||||||||||||||||||||||||||||| |||||||       |  | | || | |  |  ||||| ||    ||  |  |||||||||    | |||||   |      | |||| |     
AATGAGATTGTCAAGCTTGAAAACTTCCCATACTTGAATCGTCTTGGCACTCTACTAGTTAATAATAACAGAATCACACGTATCAATCCCAATCTTGGCGgtaagaac-----tcctgtattctcagcacttgttt-tctgactcccacatttgctccatgcttcaccttttttcttgtttttttccatgcag
















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|226698493|gb|GO497071.1|GO497071
EST:     TCTGTTAGTTAACAATAACAGAATCACACGTATCAATCCCAATCTTGGTG                         AGTTCTTGCCAAAGTTACATACATTGGTGCTTACAAACAATCGTCTTACAA
genomic: TCTGTTAGTTAACAATAACAGAATCACACGTATCAATCCCAATCTTGGTGgtaagattat ... ctgtttctagAGTTCTTGCCAAAGTTACATACATTGGTGCTTACAAACAATCGTCTTACAA
EST: gi|218492413|gb|FG947005.1|FG947005
EST:     TCTGTTAGTTAACAATAACAGAATCACACGTATCAATCCCAATCTTGGTG                         AGTTCTTGCCAAAGTTACATACATTGGTGCTTACAAACAATCGTCTTACAA
genomic: TCTGTTAGTTAACAATAACAGAATCACACGTATCAATCCCAATCTTGGTGgtaagattat ... ctgtttctagAGTTCTTGCCAAAGTTACATACATTGGTGCTTACAAACAATCGTCTTACAA
EST: gi|86904173|gb|CI306591.1|CI306591
EST:     TCTGTTAGTTAACAATAACAGAATCACACGTATCAATCCCAATCTTGGTG                         AGTTCTTGCCAAAGTTACATACATTGGTGCTTACA
genomic: TCTGTTAGTTAACAATAACAGAATCACACGTATCAATCCCAATCTTGGTGgtaagattat ... ctgtttctagAGTTCTTGCCAAAGTTACATACATTGGTGCTTACA
EST: gi|29660695|gb|CB656970.1|CB656970
EST:     TCTGTTAGTTAACAATAACAGAATCACACGTATCAATCCCAATCTTGGTG                         AGTTCTTGCCAAAGTTACATACATTGGTGCTTACAAACAATCGTCTTACAA
genomic: TCTGTTAGTTAACAATAACAGAATCACACGTATCAATCCCAATCTTGGTGgtaagattat ... ctgtttctagAGTTCTTGCCAAAGTTACATACATTGGTGCTTACAAACAATCGTCTTACAA
EST: gi|27553936|gb|CA997836.1|CA997836
EST:     TCTGTTAGTTAACAATAACAGAATCACACGTATCAATCCCAATCTTGGTG                         AGTTCTTGCCAAAGTTACATACATTGGTGCTTACAAACAATCGTCTTACAA
genomic: TCTGTTAGTTAACAATAACAGAATCACACGTATCAATCCCAATCTTGGTGgtaagattat ... ctgtttctagAGTTCTTGCCAAAGTTACATACATTGGTGCTTACAAACAATCGTCTTACAA
EST: gi|58602112|gb|CK012640.1|CK012640
EST:     TCTGTTAGTTAACAATAACAGAATCACACGTATCAATCCCAATCTTGGTG                         AGTTCTTGCCAAAGTTACATACATTGGTGCTTACAAACAATCGTCTTACAA
genomic: TCTGTTAGTTAACAATAACAGAATCACACGTATCAATCCCAATCTTGGTGgtaagattat ... ctgtttctagAGTTCTTGCCAAAGTTACATACATTGGTGCTTACAAACAATCGTCTTACAA
EST: gi|29663404|gb|CB659679.1|CB659679
EST:     TCTGTTAGTTAACAATAACAGAATCACACGTATCAATCCCAATCTTGGTG                         AGTTCTTGCCAAAGTTACATACATTGGTGCTTACAAACAATCGTCTTACAA
genomic: TCTGTTAGTTAACAATAACAGAATCACACGTATCAATCCCAATCTTGGTGgtaagattat ... ctgtttctagAGTTCTTGCCAAAGTTACATACATTGGTGCTTACAAACAATCGTCTTACAA
EST: gi|58662231|gb|CK050911.1|CK050911
EST:     TCTGTTAGTTAACAATAACAGAATCACACGTATCAATCCCAATCTTGGTG                         AGTTCTTGCCAAAGTTACATACATAGGTGCTTACAAACAATCGTCTTACAA
genomic: TCTGTTAGTTAACAATAACAGAATCACACGTATCAATCCCAATCTTGGTGgtaagattat ... ctgtttctagAGTTCTTGCCAAAGTTACATACATTGGTGCTTACAAACAATCGTCTTACAA

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: 51 (upstream exon), 75 (downstream exon)
Score: 30

AATGAGATTGTCAAGCTTGAGAACTTCCCGTACTTGAATCGTCTTGGCACTCTGTTAGTTAACAATAACAGAATCACACGTATCAATCCCAATCTTGGTGgtaagattat ... ctgtttctagAGTTCTTGCCAAAGTTACATACATTGGTGCTTACAAACAATCGTCTTACAAATCTTGCGGAGATCGATCCCCTGGCATCTCTTCCAAAGCTTCAGTTTCT




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