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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AAAACTCTCAGGCAGCAGTTTTCCGACGCGACGGTCATCACAATCGCGCACCGGATCACCTCCGTCCTTGACAGCGACATGGTCTTGCTCCTTGACAACGgtgagtttagttcgccttccaagtcccaaaccaatcacagatgccactaatcaatctccgattttataacgacaataaccacagttccaactaaccaatcccaatttatcttacatattgtatgggtttgtcgcgtctgtctgacgaccgaaacaccgtgccaatgcttttgcag

Basic information

species Oryza sativa
transcript LOC_Os01g07870.1
intron # 9
splice site 5'
intron type U2

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|86504053|gb|CI146686.1|CI146686
EST:     CCGGATCACCTCCGTCCTTGACAGCGACATGGTCTTGCTCCTTGACAACG                         GTGTGGCCGTGGAGCGCGACACGCCGACCAGGCTACTGGAGGACAAGTCGT
genomic: CCGGATCACCTCCGTCCTTGACAGCGACATGGTCTTGCTCCTTGACAACGgtgagtttag ... gcttttgcagGTGTGGCCGTGGAGCGCGACACGCCGACCAGGCTACTGGAGGACAAGTCGT
EST: gi|87038101|gb|CI190725.1|CI190725
EST:     CCGGATCACCTCCGTCCTTGACAGCGACATGGTCTTGCTCCTTGACAACG                         GTGTGGCCGTGGAGCGCGACACGCCGACCAGGCTACTGGAGGACAAGTCGT
genomic: CCGGATCACCTCCGTCCTTGACAGCGACATGGTCTTGCTCCTTGACAACGgtgagtttag ... gcttttgcagGTGTGGCCGTGGAGCGCGACACGCCGACCAGGCTACTGGAGGACAAGTCGT
EST: gi|29638724|gb|CB643733.1|CB643733
EST:     CCGGATCACCTCCGTCCTTGACAGCGACATGGTCTTGCTCCTTGACAACG                         GTGTGGCCGTGGAGCGCGACACGCCGACCAGGCTACTGGAGGACAAGTCGT
genomic: CCGGATCACCTCCGTCCTTGACAGCGACATGGTCTTGCTCCTTGACAACGgtgagtttag ... gcttttgcagGTGTGGCCGTGGAGCGCGACACGCCGACCAGGCTACTGGAGGACAAGTCGT
EST: gi|86437514|gb|CI119236.1|CI119236
EST:     CCGGATCACCTCCGTCCTTGACAGCGACATGGTCTTGCTCCTTGACAACG                         GTGTGGCCGTGGAGCGCGACACGCCGACCAGGCTACTGGAGGACAAGTCGT
genomic: CCGGATCACCTCCGTCCTTGACAGCGACATGGTCTTGCTCCTTGACAACGgtgagtttag ... gcttttgcagGTGTGGCCGTGGAGCGCGACACGCCGACCAGGCTACTGGAGGACAAGTCGT
EST: gi|88575029|gb|CI666798.1|CI666798
EST:     CCGGATCACCTCCGTCCTTGACAGCGACATGGTCTTGCTCCTTGACAACG                         GTGTGGCCGTGGAGCGCGACACGCCGACCAGGCTACTGGAGGACAAGTCGT
genomic: CCGGATCACCTCCGTCCTTGACAGCGACATGGTCTTGCTCCTTGACAACGgtgagtttag ... gcttttgcagGTGTGGCCGTGGAGCGCGACACGCCGACCAGGCTACTGGAGGACAAGTCGT
EST: gi|33810075|gb|CF330925.1|CF330925
EST:     GACAGCGACATGGTCTTGCTCCTTGACAACG                         GTGTGGCCGTGGAGCGCGACACGCCGACCAGGCTACTGGAGGAGAAGTCGT
genomic: GACAGCGACATGGTCTTGCTCCTTGACAACGgtgagtttag ... gcttttgcagGTGTGGCCGTGGAGCGCGACACGCCGACCAGGCTACTGGAGGACAAGTCGT
EST: gi|29638723|gb|CB643732.1|CB643732
EST:     CCGGATCACCTCCGTCCTTGACAGCGACATGGTCTTGCTCCTTGACAACG                         GTGTGGCCGTGGAGCGCGACACGCCGACCAGGCTACTGGAGGACAAGTCGT
genomic: CCGGATCACCTCCGTCCTTGACAGCGACATGGTCTTGCTCCTTGACAACGgtgagtttag ... gcttttgcagGTGTGGCCGTGGAGCGCGACACGCCGACCAGGCTACTGGAGGACAAGTCGT

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: 75 (upstream exon), 68 (downstream exon)
Score: 8

AAAACTCTCAGGCAGCAGTTTTCCGACGCGACGGTCATCACAATCGCGCACCGGATCACCTCCGTCCTTGACAGCGACATGGTCTTGCTCCTTGACAACGgtgagtttag ... gcttttgcagGTGTGGCCGTGGAGCGCGACACGCCGACCAGGCTACTGGAGGACAAGTCGTCTCTCTTCTCCAAGCTCGTAGCGGAATACACGATGAGATCGACGCACAC




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