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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CCTCCTCCTCAATGCGATTGCCAACCAGCTGCGCTATCCAAACAACCACACACACTATTTTTCCTTCATAATTCTTTACTTGTTTTCTGAGGCAAACCAGgtatcggatgattacttactatgtggtctcctttttttgtttgtatgcaaatatacaccctttctgatgggaactaaatctgaaatcgcag

Basic information

species Oryza sativa
transcript LOC_Os10g40780.3
intron # 46
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os10g40780.3 (Oryza sativa), 5'ss of exon 46
lower sequence: GRMZM2G101007_T01 (Zea mays), 5'ss of exon 1
---------CCTCCTCCTCAATGCGATTGCCAACCAGCTGCGCTATCCAAACAACCACACACACTATTTTTCCTTCATAATTCTTTACTTGTTTTCTGAGGCAAACCAGgtatcggatgattacttactatgtggtctcctttttttgtttgtatgcaaatatacaccctttctgat---gggaactaaatctgaaatcgcag---------
         | |  | |||||||||||||| |||||||| ||||||||||| | ||| || |||||         ||| ||||| ||| ||||| | ||||||| ||||||||    |     ||    |         | |||   | | || ||  ||| |  |   | | ||||    | || ||| |     |||             
AGGCCGCTACATTATTCTCAATGCGATTGCTAACCAGCTTCGCTATCCAAATAGCCATACCCACTA---------CATCATTCTGTACCTGTTTGCCGAGGCAACCCAGgtatt---taggccctccagacacttcgctcctttagagctagtttgttaatttttagggtgtttgattttagaaattaactagtccatcatcttctaactcc

upper sequence: LOC_Os10g40780.3 (Oryza sativa), 5'ss of exon 46
lower sequence: EFJ17138 (Selaginella moellendorffii), 5'ss of exon 38
CCTCCTCCTCAATGCGATTGCCAACCAGCTGCGCTATCCAAACAACCACACACACTATTTTTCCTTCATAATTCTTTACTTGTTTTCTGAGGCAAACCAGgtatcggatgattacttactatgtggtctcctttttttgtttgtatgcaaatat-acaccctttctgatgggaactaaatctgaaatcgcag
| |  ||||||| || || ||||||||||| ||||||||||||||||| || || || || || | | |  | || ||||||||  | || || | |||||||       |    |   | |||| ||| || | |  | |      |||   |  | |  |   | |  | |                   
CTTGTTCCTCAACGCCATCGCCAACCAGCTCCGCTATCCAAACAACCATACGCATTACTTCTCGTGCGTGTTGCTCTACTTGTTCGCCGAAGCCAGCCAGgta-------agctttccttttgtgctcttctatgtaggctctagctcaatccttgcgctttgcttcaaagcag------------------

upper sequence: LOC_Os10g40780.3 (Oryza sativa), 5'ss of exon 46
lower sequence: EFJ31209 (Selaginella moellendorffii), 5'ss of exon 38
CCTCCTCCTCAATGCGATTGCCAACCAGCTGCGCTATCCAAACAACCACACACACTATTTTTCCTTCATAATTCTTTACTTGTTTTCTGAGGCAAACCAGgtatcggatgattacttactatgtggtctcctttttttgtttgtatgcaaatat-acaccctttctgatgggaactaaatctgaaatcgcag
| |  ||||||| || || ||||||||||| ||||||||||||||||| || || || || || | | |  | || ||||||||  | || || | |||||||       |    |   | |||| |||  | | |  | |      |||   |  | |  |   | |  | |                   
CTTGTTCCTCAACGCCATCGCCAACCAGCTCCGCTATCCAAACAACCATACGCATTACTTCTCGTGCGTGTTGCTCTACTTGTTCGCCGAAGCCAGCCAGgta-------agctttccttttgtgctcttttatgtaggctctagctcaatccttgcgctttgcttcaaagcag------------------

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|29644838|gb|CB649845.1|CB649845
EST:     CACACTATTTTTCCTTCATAATTCTTTACTTGTTTTCTGAGGCAAACCAG                         GAAATAGTCCAGGAGCAAATAACTAGGGTACTTCTGGAACGGCTAATAGTT
genomic: CACACTATTTTTCCTTCATAATTCTTTACTTGTTTTCTGAGGCAAACCAGgtatcggatg ... gaaatcgcagGAAATAGTCCAGGAGCAAATAACTAGGGTACTTCTGGAACGGCTAATAGTT
EST: gi|29686205|gb|CB682480.1|CB682480
EST:     CACACTATTTTTCCTTCATAATTCTTTACTTGTTTTCTGAGGCAAACCAG                         GAAATAGTCCAGGAGCAAATAACTAGGGTACTTCTGGAACGGTTAATAGTT
genomic: CACACTATTTTTCCTTCATAATTCTTTACTTGTTTTCTGAGGCAAACCAGgtatcggatg ... gaaatcgcagGAAATAGTCCAGGAGCAAATAACTAGGGTACTTCTGGAACGGCTAATAGTT
EST: gi|9886370|gb|BE607462.1|BE607462
EST:     CACACTATTTTTCCTTCATAATTCTTTACTTGTTTTCTGAGGCAAACCAG                         GAAATAGTCCAGGAGCAAATAACTAGGGTACTTCTGGAACGACTAATAGTT
genomic: CACACTATTTTTCCTTCATAATTCTTTACTTGTTTTCTGAGGCAAACCAGgtatcggatg ... gaaatcgcagGAAATAGTCCAGGAGCAAATAACTAGGGTACTTCTGGAACGGCTAATAGTT
EST: gi|29686204|gb|CB682479.1|CB682479
EST:     CACACTATTTTTCCTTCATAATTCTTTACTTGTTTTCTGAGGCAAACCAG                         GAAATAGTCCAGGAGCAAATAACTAGGGTACTTCTGGAACGGCTAATAGTT
genomic: CACACTATTTTTCCTTCATAATTCTTTACTTGTTTTCTGAGGCAAACCAGgtatcggatg ... gaaatcgcagGAAATAGTCCAGGAGCAAATAACTAGGGTACTTCTGGAACGGCTAATAGTT
EST: gi|29616068|gb|CB621080.1|CB621080
EST:     CACACTATTTTTCCTTCATAATTCTTTACTTGTTTTCTGAGGCAAACCAG                         GAAATAGTCCAGGAGCAAATAACTAGGGTACTTCTGGAACGGCTAATAGTT
genomic: CACACTATTTTTCCTTCATAATTCTTTACTTGTTTTCTGAGGCAAACCAGgtatcggatg ... gaaatcgcagGAAATAGTCCAGGAGCAAATAACTAGGGTACTTCTGGAACGGCTAATAGTT
EST: gi|58670528|gb|CK059214.1|CK059214
EST:     CACACTATTTTTCCTTCATAATTCTTTACTTGTTTTCTGAGGCAAACCAG                         GAAATAGTCCAGGAGCAAATAACTAGGGTACTTCTGGAACGGCTAATAGTT
genomic: CACACTATTTTTCCTTCATAATTCTTTACTTGTTTTCTGAGGCAAACCAGgtatcggatg ... gaaatcgcagGAAATAGTCCAGGAGCAAATAACTAGGGTACTTCTGGAACGGCTAATAGTT
EST: gi|29674319|gb|CB670594.1|CB670594
EST:     CACACTATTTTTCCTTCATAATTCTTTACTTGTTTTCTGAGGCAAACCAG                         GAAATAGTCCAGGAGCAAATAACTAGGGTACTTCTGGAACGGCTAATAGTT
genomic: CACACTATTTTTCCTTCATAATTCTTTACTTGTTTTCTGAGGCAAACCAGgtatcggatg ... gaaatcgcagGAAATAGTCCAGGAGCAAATAACTAGGGTACTTCTGGAACGGCTAATAGTT
EST: gi|89198422|gb|CI007482.1|CI007482
EST:     CACACTATTTTTCCTTCATAATTCTTTACTTGTTTTCTGAGGCAAACCAG                         GAAATAGTCCAGGAGCAAATAACTAGGGTACTTCTGGAACGGCTAATAGTT
genomic: CACACTATTTTTCCTTCATAATTCTTTACTTGTTTTCTGAGGCAAACCAGgtatcggatg ... gaaatcgcagGAAATAGTCCAGGAGCAAATAACTAGGGTACTTCTGGAACGGCTAATAGTT
EST: gi|29629738|gb|CB634747.1|CB634747
EST:     CACACTATTTTTCCTTCATAATTCTTTACTTGTTTTCTGAGGCAAACCAG                         GAAATAGTCCAGGAGCAAATAACTAGGGTACTTCTGGAACGGCTAATAGTT
genomic: CACACTATTTTTCCTTCATAATTCTTTACTTGTTTTCTGAGGCAAACCAGgtatcggatg ... gaaatcgcagGAAATAGTCCAGGAGCAAATAACTAGGGTACTTCTGGAACGGCTAATAGTT
EST: gi|29629914|gb|CB634923.1|CB634923
EST:     CACACTATTTTTCCTTCATAATTCTTTACTTGTTTTCTGAGGCAAACCAG                         GAAATAGTCCAGGAGCAAATAACTAGGGTACTTCTGGAACGGCTAATAGTT
genomic: CACACTATTTTTCCTTCATAATTCTTTACTTGTTTTCTGAGGCAAACCAGgtatcggatg ... gaaatcgcagGAAATAGTCCAGGAGCAAATAACTAGGGTACTTCTGGAACGGCTAATAGTT
EST: gi|88220672|gb|CI220232.1|CI220232
EST:     TTTCTGAGGCAAACCAG                         GAAATAGTCCAGGAGCAAATAACTAGGGTACTTCTGGAACGGCTAATAGTT
genomic: TTTCTGAGGCAAACCAGgtatcggatg ... gaaatcgcagGAAATAGTCCAGGAGCAAATAACTAGGGTACTTCTGGAACGGCTAATAGTT

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: 70 (upstream exon), 48 (downstream exon)
Score: 25

CCTCCTCCTCAATGCGATTGCCAACCAGCTGCGCTATCCAAACAACCACACACACTATTTTTCCTTCATAATTCTTTACTTGTTTTCTGAGGCAAACCAGgtatcggatg ... gaaatcgcagGAAATAGTCCAGGAGCAAATAACTAGGGTACTTCTGGAACGGCTAATAGTTAACCGCCCTCACCCGTGGGGGCTACTAATTACTTTCATTGAGCTTATAA




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