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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TTGGTATTGCTTGGTGACTCTGGTGTAGGGAAAAGTTGCATTGTTCTTCGCTTTGTTCGTGGTCAGTTTGATCCCACTTCCAAGgtgattactgttttgagtctcttagtttcagttgataatgttattcttcaccttagatgcatgattcttactttcagaagttcgattgttttaaacttatttcctcaaataatttcag

Basic information

species Oryza sativa
transcript LOC_Os03g05740.1
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g05740.1 (Oryza sativa), 5'ss of exon 3
lower sequence: GRMZM2G362088_T02 (Zea mays), 5'ss of exon 4
TTGGTATTGCTTGGTGACTCTGGTGTAGGGAAAAGTTGCATTGTTCTTCGCTTTGTTCGTGGTCAGTTTGATCCCACTTCCAAGgtgatt-actgttttgagtctcttagtttcagttgataatgttattcttcaccttagatgcatgattcttactttcagaagttcgattgttttaaacttatttcctcaaataatttcag
||||||||||| || ||||| ||||| ||||||||||||||||||||||| ||||||||||||||||||||||| ||||||||||||||| ||||||||||     | || |  |      ||||  | | |                | | |   || ||| | ||| |||      ||||||| | |||||||  || |||
TTGGTATTGCTGGGAGACTCAGGTGTTGGGAAAAGTTGCATTGTTCTTCGTTTTGTTCGTGGTCAGTTTGATCCTACTTCCAAGgtgatttactgttttga-----tcagatcgacccatgaatgaaacttt----------------actttcggttgcagcatttccatt--ccccaacttatcttctcaaatggttacag

upper sequence: LOC_Os03g05740.1 (Oryza sativa), 5'ss of exon 3
lower sequence: GLYMA20G32320.1 (Glycine max), 5'ss of exon 3
TTGGTATTGCTTGGTGACTCTGGTGTAGGGAAAAGTTGCATTGTTCTTCGCTTTGTTCGTGGTCAGTTTGATCCCACTTCCAAGgtgattac-tgtt--ttgagtctcttagtttcagttgataatgttattcttcacctta--------gatgcatgattcttactttcagaagttcgattgttttaaacttatttcctcaaataatttcag--------------
 | ||  |  | ||||| |||||||| || ||||| || |||||||| || ||||||||||||||||||||||| || || ||||| | ||  ||||  ||  ||   ||  ||| | ||  |||| | ||| |||    ||        |||  |   || ||   ||   | |||  ||| ||  |     |||| || | ||  |||                 
CTTGTTCTCTTAGGTGATTCTGGTGTTGGCAAAAGCTGTATTGTTCTACGATTTGTTCGTGGTCAGTTTGATCCAACATCTAAGgtaaatatatgttgcttcggtacttttattttattttttaatataatttttcttaatatggtttatgatataaattttttgtctttttatgtt-aattattccatggaaattttcttatatgttttagactctgtaatgtaag

upper sequence: LOC_Os03g05740.1 (Oryza sativa), 5'ss of exon 3
lower sequence: GLYMA10G35230.3 (Glycine max), 5'ss of exon 3
TTGGTATTGCTTGGTGACTCTGGTGTAGGGAAAAGTTGCATTGTTCTTCGCTTTGTTCGTGGTCAGTTTGATCCCACTTCCAAGgtgattac-tgtt-ttgagt-ctcttagtttcagttgataatgttattcttcaccttaga-tgcatgattcttactttcagaagttcgattgttttaaacttatttcctcaaataatttcag-------------------------
 | ||  |  | ||||| |||||||| || ||||| || |||||||| || ||||||||||||||||||||||| || || ||||| | ||  |||| || ||| || ||| ||| | ||  |||||| ||| ||     || | |  ||||     |  |   |  ||     | | ||||  ||||| | |  |||  ||                             
CTTGTTCTCTTAGGTGATTCTGGTGTTGGTAAAAGCTGTATTGTTCTACGATTTGTTCGTGGTCAGTTTGATCCAACATCTAAGgtaaatatatgttatttagtacttttatttttattttttaatgtaattttttttaatatagtttatgacaaaaaaatattgtcgtcttgatatgttaa--ttattccatggaattgttcttatatgttttagactttgtaatgtaag

upper sequence: LOC_Os03g05740.1 (Oryza sativa), 5'ss of exon 3
lower sequence: AT3G54840.2 (Arabidopsis thaliana), 5'ss of exon 3
TTGGTATTGCTTGGTGACTCTGGTGTAGGGAAAAGTTGCATTGTTCTTCGCTTTGTTCGTGGTCAGTTTGATCCCACTTCCAAGgtgattactgttttga-gtctcttagtttcagttgataatgttattcttcaccttagatgcatgattct-tactttcagaagttcgattgttt---taaacttatttcctcaaataatttcag--------------------
|| ||  |  | || ||||||||||| || |||||||| ||||| ||||| ||||| ||||||||||||||  | || || ||||| | ||  |  |||   |||  | || |   ||||  || | |  | |      |    |||| |    |        |  || || | ||    || |||||| | | ||    || |||                     
TTAGTTCTATTAGGAGACTCTGGTGTTGGTAAAAGTTGTATTGTCCTTCGATTTGTACGTGGTCAGTTTGACGCTACATCTAAGgtaagtaaagccttgttatctaattgtctttattgaccatctgacacctttttagaacaccatgctctgatgtgagtgaatattagactattagagtatacttatctgc-cactagatctcaagactactagctatgtatcag

upper sequence: LOC_Os03g05740.1 (Oryza sativa), 5'ss of exon 3
lower sequence: Vv13s0019g04680.t01 (Vitis vinifera), 5'ss of exon 3
TTGGTATTGCTTGGTGACTCTGGTGTAGGGAAAAGTTGCATTGTTCTTCGCTTTGTTCGTGGTCAGTTTGATCCCACTTCCAAGgtgattactgttttgagtctcttagtttcagttgataatgttattcttcaccttagatgcatgattcttactttcagaagttcgattgttttaa-acttatttcctcaaataatttcag----------------------------------------------------------------
 |||| ||| | || || |||||||| || ||||| || ||||||||||| ||||||||||| |||||||| || || |||||||| |  | | |    ||     || | |  | ||   || || || ||| | ||   |  || |   |  || |   |  ||   ||||   ||    | ||  |   |||  | |||                                                                 
CTGGTTTTGTTGGGGGATTCTGGTGTTGGAAAAAGCTGTATTGTTCTTCGTTTTGTTCGTGGCCAGTTTGACCCTACATCCAAGgtaagaaatatacatagctatatattatgtgatgcacattttttttttcccttttattatattaaatt--ctgttcaaccttgttttgtgccaatggatgttagcatcaatcctctcatgcaaaatacatggatgttatttcatgatagatttacttagattggttgatcttaataacttcag

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|11565095|gb|AU165731.1|AU165731
EST:     GTTGCATTGTTCTTCGCTTTGTTCGTGGTCAGTTTGATCCCACTTCCAAG                         GTAACTG-CGGTGCATCATTTTTATCACAAACATTGGCTTTGGAGGACTCA
genomic: GTTGCATTGTTCTTCGCTTTGTTCGTGGTCAGTTTGATCCCACTTCCAAGgtgattactg ... ataatttcagGTAACTGTCGGTGCATCATTTTTATCACAAACATTGGCTTTGGAGGACTCA
EST: gi|3760086|gb|C97344.1|C97344
EST:     GTTGCATTGTTCTTCGCTTTGTTCGTGGTCAGTTTGATCCCACTTCCAAG                         GTAACTGTCGGTGCATCATTTTTATCACAAACATTGGCTTTGGAGGACTCA
genomic: GTTGCATTGTTCTTCGCTTTGTTCGTGGTCAGTTTGATCCCACTTCCAAGgtgattactg ... ataatttcagGTAACTGTCGGTGCATCATTTTTATCACAAACATTGGCTTTGGAGGACTCA
EST: gi|6782805|gb|C99985.1|C99985
EST:     GTTGCATTGTTCTTCGCTTTGTTCGTGGTCAGTTTGATCCCACTTCCAAG                         GTAACTGTCGGTGCATCATTTTTATCACAAACATTGGCTTTGGAGGACTCA
genomic: GTTGCATTGTTCTTCGCTTTGTTCGTGGTCAGTTTGATCCCACTTCCAAGgtgattactg ... ataatttcagGTAACTGTCGGTGCATCATTTTTATCACAAACATTGGCTTTGGAGGACTCA
EST: gi|300216317|gb|HO088102.1|HO088102
EST:     GTTGCATTGTTCTTCGCTTTGTTCGTGGTCAGTTTGATCCCACTTCCAAG                         GTAACTGTCGGTGCATCATTTTTATCACAAACATTGGCTTTGGAGGACTCA
genomic: GTTGCATTGTTCTTCGCTTTGTTCGTGGTCAGTTTGATCCCACTTCCAAGgtgattactg ... ataatttcagGTAACTGTCGGTGCATCATTTTTATCACAAACATTGGCTTTGGAGGACTCA

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: 74 (upstream exon), 64 (downstream exon)
Score: 20

TTGGTATTGCTTGGTGACTCTGGTGTAGGGAAAAGTTGCATTGTTCTTCGCTTTGTTCGTGGTCAGTTTGATCCCACTTCCAAGgtgattactg ... ataatttcagGTAACTGTCGGTGCATCATTTTTATCACAAACATTGGCTTTGGAGGACTCAACAATAGTGAAATTTGAAATATGGGATACCGCTGGACAAGAGAG




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