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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AAGGACCCAGCTAGGGTATTACACATGAACACAAGGCGCATATTGCATGAAGTATGGAGgtatggtattacaaatttatttagtaatcctttgctgtattttgtgtatagcaatagcaaacgttgcccataggaacagttgctcttgtggaatataggt...

Basic information

species Oryza sativa
transcript LOC_Os01g12470.1
intron # 9
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g12470.1 (Oryza sativa), 5'ss of exon 9
lower sequence: GRMZM2G177213_T02 (Zea mays), 5'ss of exon 9
AAGGACCCAGCTAGGGTATTACACATGAACACAAGGCGCATATTGCATGAAGTATGGAGgtatggtattacaaatttatttagtaatcctttgctgtattttgtgtatagcaatagcaaacgttgcccataggaacagttgctcttgtggaatataggt--------------------------------------------------------------------------------
||||| || |  ||||||||   ||||||||||||||||||||||| ||| || |||||||||| ||    ||  || |||  |          || || |    |  |    | |            | |||    | |    |  |||| | ||  |                                                                                
AAGGATCCTGAAAGGGTATTGAGCATGAACACAAGGCGCATATTGCTTGAGGTTTGGAGgtatg-tacc-taacctttttttttgggttagaattggatataagattgataggtggtctgttcataatagaggtttggctaagatattggagtgtacattctggaagtcctagcttggttgcatctcagtgccattgttgtcatggtattggagaataacactttgggtaccgttgcag
















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|58599725|gb|CK010253.1|CK010253
EST:     CACATGAACACAAGGCGCATATTGCATGAAGTATGGAG                         TAAGGAAGGCATCAGCGGGATATTCAGAGGTGCAGGTCCTCGAATGGCACG
genomic: CACATGAACACAAGGCGCATATTGCATGAAGTATGGAGgtatggtatt ... cttgttgcagTAAGGAAGGCATCAGCGGGATATTCAGAGGTGCAGGTCCTCGAATGGCACG
EST: gi|33799145|gb|CF325430.1|CF325430
EST:     GCTAGGGTATTACACATGAACACAAGGCGCATATTGCATGAAGTATGGAG                         TAAGGAAGGCATCAGCGGGATATTCAGAGGTGCAGGTCCTCGAATGGCACG
genomic: GCTAGGGTATTACACATGAACACAAGGCGCATATTGCATGAAGTATGGAGgtatggtatt ... cttgttgcagTAAGGAAGGCATCAGCGGGATATTCAGAGGTGCAGGTCCTCGAATGGCACG
EST: gi|66920313|gb|CX107161.1|CX107161
EST:     GCTAGGGTATTACACATGAACACAAGGCGCATATTGCATGAAGTATGGAG                         TAAGGAAGGCATCAGCGGGATATTCAGAGGTGCAGGTCCTCGAATGGCACG
genomic: GCTAGGGTATTACACATGAACACAAGGCGCATATTGCATGAAGTATGGAGgtatggtatt ... cttgttgcagTAAGGAAGGCATCAGCGGGATATTCAGAGGTGCAGGTCCTCGAATGGCACG
EST: gi|86534758|gb|CI174964.1|CI174964
EST:     GCTAGGGTATTACACATGAACACAAGGCGCATATTGCATGAAGTATGGAG                         TAAGGAAGGCATCAGCGGGATATTCAGAGGTGCAGGTCCTCGAATGGCACG
genomic: GCTAGGGTATTACACATGAACACAAGGCGCATATTGCATGAAGTATGGAGgtatggtatt ... cttgttgcagTAAGGAAGGCATCAGCGGGATATTCAGAGGTGCAGGTCCTCGAATGGCACG
EST: gi|218490164|gb|FG951467.1|FG951467
EST:     GCTAGGGTATTACACATGAACACAAGGCGCATATTGCATGAAGTATGGAG                         TAAGGAAGGCATCAGCGGGATATTCAGAGGTGCAGGTCCTCGAATGGCACG
genomic: GCTAGGGTATTACACATGAACACAAGGCGCATATTGCATGAAGTATGGAGgtatggtatt ... cttgttgcagTAAGGAAGGCATCAGCGGGATATTCAGAGGTGCAGGTCCTCGAATGGCACG
EST: gi|88531800|gb|CI460312.1|CI460312
EST:     CTA-GGTNATTACACATGAACACAAGGCGCATAGTGCATGAAGTATGGAG                         TAAGGAAGGGCATCAGCGGGATATTCAGAGGTGCGGGTCCTCGAATGGCAC
genomic: CTAGGGT-ATTACACATGAACACAAGGCGCATATTGCATGAAGTATGGAGgtatggtatt ... cttgttgcagTAAGGAA-GGCATCAGCGGGATATTCAGAGGTGCAGGTCCTCGAATGGCAC
EST: gi|88286726|gb|CI517837.1|CI517837
EST:     AACACAAGGCGCATATTGCATGAANTATGGAG                         TAAGGAAGGCATCAGCGGGATATTCAGAGGTGCAGGTCCTCGAATGGCACG
genomic: AACACAAGGCGCATATTGCATGAAGTATGGAGgtatggtatt ... cttgttgcagTAAGGAAGGCATCAGCGGGATATTCAGAGGTGCAGGTCCTCGAATGGCACG
EST: gi|29646721|gb|CB651728.1|CB651728
EST:     GCTAGGGTATTACACATGAACACAAGGCGCATATTGCATGAAGTATGGAG                         TAAGGAAGGCATCAGCGGGATATTCAGAGGTGCAGGTCCTCGAATGGCACG
genomic: GCTAGGGTATTACACATGAACACAAGGCGCATATTGCATGAAGTATGGAGgtatggtatt ... cttgttgcagTAAGGAAGGCATCAGCGGGATATTCAGAGGTGCAGGTCCTCGAATGGCACG
EST: gi|88722567|gb|CI746077.1|CI746077
EST:     GCTAGGGTATTACACATGAACACAAGGCGCATATTGCATGAACTATGGAG                         TAAGGAAGGCATCAGCGGGATATTCAGAGGTGCAGGTCCTCGAATGGCACG
genomic: GCTAGGGTATTACACATGAACACAAGGCGCATATTGCATGAAGTATGGAGgtatggtatt ... cttgttgcagTAAGGAAGGCATCAGCGGGATATTCAGAGGTGCAGGTCCTCGAATGGCACG
EST: gi|88840814|gb|CI080268.1|CI080268
EST:     GCTAGGGTATTACACATGAACACAAGGCGCATATTGCATGAAGTATGGAG                         TAAGGAAGGCATCAGCGGGATATTCAGAGGTGCAGGTCCTCGAATGGCACG
genomic: GCTAGGGTATTACACATGAACACAAGGCGCATATTGCATGAAGTATGGAGgtatggtatt ... cttgttgcagTAAGGAAGGCATCAGCGGGATATTCAGAGGTGCAGGTCCTCGAATGGCACG
EST: gi|2442709|gb|C74480.1|C74480
EST:     TACACATGGACACAAGGCGCAT-TTGCATGAAGTATGGAG                         TAAGGAAGGCATCAGCGGNATATTCAGAGGTGCAGGTCCTCGANTGGCACG
genomic: TACACATGAACACAAGGCGCATATTGCATGAAGTATGGAGgtatggtatt ... cttgttgcagTAAGGAAGGCATCAGCGGGATATTCAGAGGTGCAGGTCCTCGAATGGCACG

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: 59 (upstream exon), 54 (downstream exon)
Score: 10

AAGGACCCAGCTAGGGTATTACACATGAACACAAGGCGCATATTGCATGAAGTATGGAGgtatggtatt ... cttgttgcagTAAGGAAGGCATCAGCGGGATATTCAGAGGTGCAGGTCCTCGAATGGCACGGGCAGGGCCTTCAGTGGGCATCGTCGTCTCGTCATATGAAGTTGTGAAG




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