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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GATCAGGTAGAAGGAGATGGCGACTCTTGGTCTTGCCCCAAACATGAATCCAAACAAGTCATTTGAGgtgtgatgctttatgcaacaattgtcctccttttctatctgtgcttgtgttggtcctcacattctgtaaataataaatcatactagtatttactttgtaagttatttattatgtttaaattgtaaatgcag

Basic information

species Oryza sativa
transcript LOC_Os08g07960.1
intron # 2
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|88394469|gb|CI605810.1|CI605810
EST:     TGGCGACTCTTGGTCTTGCCCCAAACATGAATCCAAACAAGTCATTTGAG                         GTACTGCCTAATCCAGGTGACTCCGTATCGAGCCTCAGTTTTAGCCCAAAG
genomic: TGGCGACTCTTGGTCTTGCCCCAAACATGAATCCAAACAAGTCATTTGAGgtgtgatgct ... gtaaatgcagGTACTGCCTAATCCAGGTGACTCCGTATCGAGCCTCAGTTTTAGCCCAAAG
EST: gi|33793654|gb|CF322711.1|CF322711
EST:     TGGCGACTCTTGGTCTTGCCCCAAACATGAATCCAAACAAGTCATTTGAG                         GTACTGCCTAATCCAGGTGACTCCGTATCGAGCCTCAGTTTTAGCCCAAAG
genomic: TGGCGACTCTTGGTCTTGCCCCAAACATGAATCCAAACAAGTCATTTGAGgtgtgatgct ... gtaaatgcagGTACTGCCTAATCCAGGTGACTCCGTATCGAGCCTCAGTTTTAGCCCAAAG
EST: gi|88451540|gb|CI565593.1|CI565593
EST:     TGGCGACTCTTGGTCTTGCCCCAAACATGAATCCAAACAAGTCATTTGAG                         GTACTGCCTAATCCAGGTGACTCCGTATCGAGCCTCAGTTTTAGCCCAAAG
genomic: TGGCGACTCTTGGTCTTGCCCCAAACATGAATCCAAACAAGTCATTTGAGgtgtgatgct ... gtaaatgcagGTACTGCCTAATCCAGGTGACTCCGTATCGAGCCTCAGTTTTAGCCCAAAG
EST: gi|88357567|gb|CI623621.1|CI623621
EST:     TGGCGATTCTTGGTCTTGCCCCAAACATGAATCCAAACAAGTCATTTGAG                         GTACTGCCTAATCCAGGTGACTCCGTATCGAGCCTCAGTTTTAGCCCAAAG
genomic: TGGCGACTCTTGGTCTTGCCCCAAACATGAATCCAAACAAGTCATTTGAGgtgtgatgct ... gtaaatgcagGTACTGCCTAATCCAGGTGACTCCGTATCGAGCCTCAGTTTTAGCCCAAAG
EST: gi|29615879|gb|CB620891.1|CB620891
EST:     TGGCGACTCTTGGTCTTGCCCCAAACATGAATCCAAACAAGTCATTTGAG                         GTACTGCCTAATCCAGGTGACTCCGTATCGAGCCTCAGTTTTAGCCCAAAG
genomic: TGGCGACTCTTGGTCTTGCCCCAAACATGAATCCAAACAAGTCATTTGAGgtgtgatgct ... gtaaatgcagGTACTGCCTAATCCAGGTGACTCCGTATCGAGCCTCAGTTTTAGCCCAAAG
EST: gi|88356897|gb|CI620785.1|CI620785
EST:     TGGCGACTCTTGGTCTTGCCCCAAACATGAATCCAAACAAGTCATTTGAG                         GTACTGCCTAATCCAGGTGACTCCGTATCGAGCCTCAGTTTTAGCCCAAAG
genomic: TGGCGACTCTTGGTCTTGCCCCAAACATGAATCCAAACAAGTCATTTGAGgtgtgatgct ... gtaaatgcagGTACTGCCTAATCCAGGTGACTCCGTATCGAGCCTCAGTTTTAGCCCAAAG
EST: gi|88399681|gb|CI583415.1|CI583415
EST:     TGGCGACTCTTGGTCTTGCCCCAAACATGAATCCAAACAAGTCATTTGAG                         GTACTGCCTAATCCAGGTGACTCCGTATCGAGCCTCAGTTTTAGCCCAAAG
genomic: TGGCGACTCTTGGTCTTGCCCCAAACATGAATCCAAACAAGTCATTTGAGgtgtgatgct ... gtaaatgcagGTACTGCCTAATCCAGGTGACTCCGTATCGAGCCTCAGTTTTAGCCCAAAG
EST: gi|88314161|gb|CI602493.1|CI602493
EST:     TGGCGACTCTTGGTCTTGCCCCACACATGAATCCAAACAAGTCATTTGAG                         GTACTGCCTAATCCAGGTGACTCCGTATCGAGCCTCAGTTTTAGCCCAAAG
genomic: TGGCGACTCTTGGTCTTGCCCCAAACATGAATCCAAACAAGTCATTTGAGgtgtgatgct ... gtaaatgcagGTACTGCCTAATCCAGGTGACTCCGTATCGAGCCTCAGTTTTAGCCCAAAG
EST: gi|33795033|gb|CF323392.1|CF323392
EST:     TGGCGACTCTTGGTCTTGCCCCAAACATGAATCCAAACAAGTCATTTGAG                         GTACTGCCTAATCCAGGTGACTCCGTATCGAGCCTCAGTTTTAGCCCAAAG
genomic: TGGCGACTCTTGGTCTTGCCCCAAACATGAATCCAAACAAGTCATTTGAGgtgtgatgct ... gtaaatgcagGTACTGCCTAATCCAGGTGACTCCGTATCGAGCCTCAGTTTTAGCCCAAAG
EST: gi|29681300|gb|CB677575.1|CB677575
EST:     TGGCGACTCTTGGTCTTGCCCCAAACATGAATCCAAACAAGTCATTTGAG                         GTACTGCCTAATCCAGGTGACTCCGTATCGAGCCTCAGTTTTAGCCCAAAG
genomic: TGGCGACTCTTGGTCTTGCCCCAAACATGAATCCAAACAAGTCATTTGAGgtgtgatgct ... gtaaatgcagGTACTGCCTAATCCAGGTGACTCCGTATCGAGCCTCAGTTTTAGCCCAAAG
EST: gi|88397869|gb|CI583187.1|CI583187
EST:     TGGCGACTCTTGGTCTTGCCCCAAACATGAATCCAAACAAGTCATTTGAG                         GTACTGCCTAATCCAGGTGACTCCGTATCGAGCCTCAGTTTTAGCCCAAAG
genomic: TGGCGACTCTTGGTCTTGCCCCAAACATGAATCCAAACAAGTCATTTGAGgtgtgatgct ... gtaaatgcagGTACTGCCTAATCCAGGTGACTCCGTATCGAGCCTCAGTTTTAGCCCAAAG
EST: gi|88417412|gb|CI579073.1|CI579073
EST:     TGGCGACTCTTGGTCTTGCCCCAAACATGAATCCAAACAAGTCATTTGAG                         GTACTGCCTAATCCAGGTGACTCCGTATCGAGCCTCAGTTTTAGCCCAAAG
genomic: TGGCGACTCTTGGTCTTGCCCCAAACATGAATCCAAACAAGTCATTTGAGgtgtgatgct ... gtaaatgcagGTACTGCCTAATCCAGGTGACTCCGTATCGAGCCTCAGTTTTAGCCCAAAG
EST: gi|218492102|gb|FG950663.1|FG950663
EST:     TGGCGACTCTTGGTCTTGCCCCAAACATGAATCCAAACAAGTCATTTGAG                         GTACTGCCTAATCCAGGTGACTCCGTATCGAGCCTCAGTTTTAGCCCAAAG
genomic: TGGCGACTCTTGGTCTTGCCCCAAACATGAATCCAAACAAGTCATTTGAGgtgtgatgct ... gtaaatgcagGTACTGCCTAATCCAGGTGACTCCGTATCGAGCCTCAGTTTTAGCCCAAAG
EST: gi|88394449|gb|CI605790.1|CI605790
EST:     TGGCGACTCTTGGTCTTGCCCCAAACATGAATCCAAACAAGTCATTTGAG                         GTACTGCCTAATCCAGGTGACTCCGTATCGAGCCTCAGTTTTAGCCCAAAG
genomic: TGGCGACTCTTGGTCTTGCCCCAAACATGAATCCAAACAAGTCATTTGAGgtgtgatgct ... gtaaatgcagGTACTGCCTAATCCAGGTGACTCCGTATCGAGCCTCAGTTTTAGCCCAAAG
EST: gi|10794894|gb|AU108860.1|AU108860
EST:     TGGCGACTCTTGGTCTTGCCCCAAACATGAATCCAAACAAGTCATTTGAG                         GTACTGCCTAATCCAGGTGACTCCGTATCGAGCCTCAGTTTTAGCCCAAAG
genomic: TGGCGACTCTTGGTCTTGCCCCAAACATGAATCCAAACAAGTCATTTGAGgtgtgatgct ... gtaaatgcagGTACTGCCTAATCCAGGTGACTCCGTATCGAGCCTCAGTTTTAGCCCAAAG
EST: gi|25799251|gb|CA755212.1|CA755212
EST:     TGGCGACTCTTGGTCTTGCCCCAAACATGAATCCAAACAAGTCATTTGAG                         GTACTGCCTAATCCAGGTGACTCCGTATCGAGCCTCAGTTTTAGCCCAAAG
genomic: TGGCGACTCTTGGTCTTGCCCCAAACATGAATCCAAACAAGTCATTTGAGgtgtgatgct ... gtaaatgcagGTACTGCCTAATCCAGGTGACTCCGTATCGAGCCTCAGTTTTAGCCCAAAG
EST: gi|88417428|gb|CI579089.1|CI579089
EST:     TGGCGACTCTTGGTCTTGCCCCAAACATGAATCCAAACAAGTCATTTGAG                         GTACTGCCTAATCCAGGTGACTCCGTATCGAGCCTCAGTTTTAGCCCAAAG
genomic: TGGCGACTCTTGGTCTTGCCCCAAACATGAATCCAAACAAGTCATTTGAGgtgtgatgct ... gtaaatgcagGTACTGCCTAATCCAGGTGACTCCGTATCGAGCCTCAGTTTTAGCCCAAAG

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: 58 (upstream exon), 71 (downstream exon)
Score: 15

GATCAGGTAGAAGGAGATGGCGACTCTTGGTCTTGCCCCAAACATGAATCCAAACAAGTCATTTGAGgtgtgatgct ... gtaaatgcagGTACTGCCTAATCCAGGTGACTCCGTATCGAGCCTCAGTTTTAGCCCAAAGAGCAACCTTCTGGTGGCAACTTCCTGGGATAACCAG




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