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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TCAGAACTAGCCCAGCTCACCAACCAGCTCATTCTATGAGATCCAGACGGACAGGTGGTACATGGGCTCGGCCACGTGGCTCTGATGATGGGTATTCAAGgtcagtggtagagactcttcgttgtctgtgttttgtgttcccgagatagtcgttatcgataagggaaaacgtgttacgcatgtcgattcatggatagggt...

Basic information

species Oryza sativa
transcript LOC_Os02g25580.1
intron # 18
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g25580.2 (Oryza sativa), 5'ss of exon 14
lower sequence: GRMZM2G052880_T01 (Zea mays), 5'ss of exon 18
TCAGAACTAGCCCAGCTC-ACCAA--CCAGCTCATTCTATGAGATCCAGACGGACAGGTGGTACATGGGCTCGGCCACGTGGCTCTGATGATGGGTATTCAAGgtcagtggtagagactcttcgttgtctgtgttttgtgttcccgagatagtcgttatcgataagggaaaacgtgttacgcatgtcg-attcatggatagggt
     | |||| | || | | |||  || ||||| || ||| |||||||||| |||||||| ||||||||  | || ||||||||||||||||| |||||||||| |||||| || |||| |   |   |   | ||  || | | ||  ||||  | |   || |   | ||   ||    |  |   |    |  ||  || 
---CCAGTAGCTCTGCCCGAACAAGCCCCGCTCACTCAATGCGATCCAGACGAACAGGTGGCACATGGGCAAGACCTCGTGGCTCTGATGATGGATATTCAAGgtgagtggtggatactcatttcttggttcatgttaagtactccagccagtccgttttcttaggcatatacacattttttaaataataccggtacattagg-

upper sequence: LOC_Os02g25580.2 (Oryza sativa), 5'ss of exon 14
lower sequence: Vv13s0019g05000.t01 (Vitis vinifera), 5'ss of exon 18
-----TCAGAACTAGCCCAGCTCA-CCAACCAGCTCATTCTATGAGATCCAGACGGACAGGTGGTACATGGGCTCGGCCACGTGGCTCTGATGATGGGTATTCAAGgt-cagtggtagagactcttcgttgtctgtgttttgtgttcccgagatagtcgttatcgataagggaaaacgtgtta--cgcatgtcgattcatggatagggt
     |||| || ||     |     ||| || | |||||  || || | |||||| |       |||||||||||||| || |||||||||||||| |||||||||| |  | || |    |||   || |  || | ||  ||   | | || |  |||||  ||       | | |   |  | ||||  |  |||||   |    
CTGCATCAGTACGAGGAAGTCAAGGTCAAGCACCCCATTCAGTGCGAGCAAGACGGTC------CACATGGGCTCGGCCTCGGGGCTCTGATGATGGTTATTCAAGgtactcttgtggctgttctcttttattggtatgtttagtcaaccatattgaggttatgcatgtatttgagcttcccagccacatgctgcctcatgtgaaa---
















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|84117192|gb|CD150959.1|CD150959
EST:     GGTACATGGGCTCGGCCACGTGGCTCTGATGATGGGTATTCAAG                         TGATTCAGTGCTGAAGCATTCGTGGAGTGACTTCAAAAAGCTTGGTCAGCG
genomic: GGTACATGGGCTCGGCCACGTGGCTCTGATGATGGGTATTCAAGgtcagtggta ... aaatttgcagTGATTCAGTGCTGAAGCATTCGTCGAGTGACTTCAAAAAGCTTGGTCAGCG
EST: gi|86502532|gb|CI145165.1|CI145165
EST:     ACAGGTGGTACATGGGCTCGGCCACGTGGCTCTGATGATGGGTATTCAAG                         TGATTCAGTGCTGAAGCATTCGTCGAGTGACTTCAAAAAGCTTGGTCAGCG
genomic: ACAGGTGGTACATGGGCTCGGCCACGTGGCTCTGATGATGGGTATTCAAGgtcagtggta ... aaatttgcagTGATTCAGTGCTGAAGCATTCGTCGAGTGACTTCAAAAAGCTTGGTCAGCG
EST: gi|218505032|gb|FG952958.1|FG952958
EST:     ACAGGTGGTACATGGGCTCGGCCACGTGGCTCTGATGATGGGTATTCAAG                         TGATTCAGTGCTGAAGCATTCGTCGAGTGACTTCAAAAAGCTTGGTCAGCG
genomic: ACAGGTGGTACATGGGCTCGGCCACGTGGCTCTGATGATGGGTATTCAAGgtcagtggta ... aaatttgcagTGATTCAGTGCTGAAGCATTCGTCGAGTGACTTCAAAAAGCTTGGTCAGCG
EST: gi|38481465|gb|CF965554.1|CF965554
EST:     ACAGGTGGTACATGGGCTCGGCCACGTGGCTCTGATGATGGGTATTCAAG                         TGATTCAGTGCTGAAGCATTCGTCGAGTGACTTCAAAAAGCTTGGTCAGCG
genomic: ACAGGTGGTACATGGGCTCGGCCACGTGGCTCTGATGATGGGTATTCAAGgtcagtggta ... aaatttgcagTGATTCAGTGCTGAAGCATTCGTCGAGTGACTTCAAAAAGCTTGGTCAGCG
EST: gi|163922673|gb|EG714174.1|EG714174
EST:     GGTGGTACATGGGCTCGGCCACGTGGCTCTGATGATGGGTATTCAAG                         TGATTCAGTGCTGAAGCATTCGTCGAGTGACTTCAAAAAGCTTGGTCAGCG
genomic: GGTGGTACATGGGCTCGGCCACGTGGCTCTGATGATGGGTATTCAAGgtcagtggta ... aaatttgcagTGATTCAGTGCTGAAGCATTCGTCGAGTGACTTCAAAAAGCTTGGTCAGCG
EST: gi|29626796|gb|CB631807.1|CB631807
EST:     ACAGGTGGTACATGGGCTCGGCCACGTGGCTCTGATGATGGGTATTCAAG                         TGATTCAGTGCTGAAGCATTCGTCGAGTGACTTCAAAAAGCTTGGTCAGCG
genomic: ACAGGTGGTACATGGGCTCGGCCACGTGGCTCTGATGATGGGTATTCAAGgtcagtggta ... aaatttgcagTGATTCAGTGCTGAAGCATTCGTCGAGTGACTTCAAAAAGCTTGGTCAGCG
EST: gi|29626758|gb|CB631769.1|CB631769
EST:     ACAGGTGGTACATGGGCTCGGCCACGTGGCTCTGATGATGGGTATTCAAG                         TGATTCAGTGCTGAAGCATTCGTCGAGTGACTTCAAAAAGCTTGGTCAGCG
genomic: ACAGGTGGTACATGGGCTCGGCCACGTGGCTCTGATGATGGGTATTCAAGgtcagtggta ... aaatttgcagTGATTCAGTGCTGAAGCATTCGTCGAGTGACTTCAAAAAGCTTGGTCAGCG
EST: gi|29689435|gb|CB685710.1|CB685710
EST:     ACAGGTGGTACATGGGCTCGGCCACGTGGCTCTGATGATGGGTATTCAAG                         TGATTCAGTGCTGAAGCATTCGTCGAGTGACTTCAAAAAGCTTGGTCAGCG
genomic: ACAGGTGGTACATGGGCTCGGCCACGTGGCTCTGATGATGGGTATTCAAGgtcagtggta ... aaatttgcagTGATTCAGTGCTGAAGCATTCGTCGAGTGACTTCAAAAAGCTTGGTCAGCG

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: 42 (upstream exon), 64 (downstream exon)
Score: 13

TCAGAACTAGCCCAGCTCACCAACCAGCTCATTCTATGAGATCCAGACGGACAGGTGGTACATGGGCTCGGCCACGTGGCTCTGATGATGGGTATTCAAGgtcagtggta ... aaatttgcagTGATTCAGTGCTGAAGCATTCGTCGAGTGACTTCAAAAAGCTTGGTCAGCGTATATTTGTGTTTGTCATTGGTGGCGCCACTCGGTCGGAG




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