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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATCGATTCCCAAAATTGGGAATATTGGTCACATGACAAGAATAACCAACAAGCTTATTCAGTTGGGAAGCAGTAACGGCACAATCCAGATTCACTTGCAGgtgatatttcctttctttccattgactcaacagtctttaattttttgaactatgaagtacctgagttctctgctcactgtctcgaattattttttaacaatag

Basic information

species Oryza sativa
transcript LOC_Os01g40340.1
intron # 12
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g40340.1 (Oryza sativa), 5'ss of exon 12
lower sequence: GRMZM2G149321_T01 (Zea mays), 5'ss of exon 5
ATCGATTCCCAAAATTGGGAATATTGGTCACATGACAAGAATAACCAACAAGCTTATTCAGTTGGGAAGCAGTAACGGCACAATCCAGATTCACTTGCAGgtgatatttcctttctt---tccattgactcaacagtctttaattttttgaactatgaagtacctgagttctctgctcactgtctcgaattattttttaacaatag
| |   ||| | |||||| ||| |||||||||||||||||||| |||| || |||||||||||||| |  ||||||  ||||||||||  |||||| |||||    |||||||| |    ||  ||| || |  |||   |  |||| ||     |   ||   ||  |  |    |   | |                       
AACCCCTCCAAGAATTGGAAATGTTGGTCACATGACAAGAATAGCCAATAAACTTATTCAGTTGGGCAATAGTAACAACACAATCCAGGCTCACTTACAGgttcgctttcctttgtcaaatcttttggcttacgagtgcctggttttctgctgactattgtgtttggttgtttcttttgttttaatag------------------
















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|58691100|gb|CK079787.1|CK079787
EST:     AGCTTATTCAGTTGGGAAGCAGTAACGGCACAATCCAGATTCACTTGCAG                         GAAAATAGTGAGTGGGTTGACTGGCAAACAGATGTTCTAGTCAAGCGTAAT
genomic: AGCTTATTCAGTTGGGAAGCAGTAACGGCACAATCCAGATTCACTTGCAGgtgatatttc ... ttaacaatagGAAAATAGTGAGTGGGTTGACTGGCAAACAGATGTTCTAGTCAAGCGTAAT
EST: gi|29612947|gb|CB617960.1|CB617960
EST:     AGCTTATTCAGTTGGGAAGCAGTAACGGCACAATCCAGATTCACTTGCAG                         GAAAATAGTGAGTGGGTTGACTGGCAAACAGATGTTCTAGTCAAGCGTAAT
genomic: AGCTTATTCAGTTGGGAAGCAGTAACGGCACAATCCAGATTCACTTGCAGgtgatatttc ... ttaacaatagGAAAATAGTGAGTGGGTTGACTGGCAAACAGATGTTCTAGTCAAGCGTAAT
EST: gi|29680806|gb|CB677081.1|CB677081
EST:     AGCTTATTCAGTTGGGAAGCAGTAACGGCACAATCCAGATTCACTTGCAG                         GAAAATAGTGAGTGGGTTGACTGGCAAACAGATGTTCTAGTCAAGCGTAAT
genomic: AGCTTATTCAGTTGGGAAGCAGTAACGGCACAATCCAGATTCACTTGCAGgtgatatttc ... ttaacaatagGAAAATAGTGAGTGGGTTGACTGGCAAACAGATGTTCTAGTCAAGCGTAAT
EST: gi|24208348|gb|AU225375.1|AU225375
EST:     AGCTTATTCAGTTGGGAAGCAGTAACGGCACAATCCAGATTCACTTGCAG                         GAAAATAGTGAGTGGGTTGACTGGCAAACAGATGTTCTAGTCAAGCGTAAT
genomic: AGCTTATTCAGTTGGGAAGCAGTAACGGCACAATCCAGATTCACTTGCAGgtgatatttc ... ttaacaatagGAAAATAGTGAGTGGGTTGACTGGCAAACAGATGTTCTAGTCAAGCGTAAT
EST: gi|88717309|gb|CI740819.1|CI740819
EST:     AGCTTATTCAGTTGGGAAGCAGTAACGGCACAATCCAGATTCACTTGCAG                         GAAAATAGTGAGTGGGTTGACTGGCAAACAGATGTTCTAGTCAAGCGTAAT
genomic: AGCTTATTCAGTTGGGAAGCAGTAACGGCACAATCCAGATTCACTTGCAGgtgatatttc ... ttaacaatagGAAAATAGTGAGTGGGTTGACTGGCAAACAGATGTTCTAGTCAAGCGTAAT
EST: gi|58679221|gb|CK067908.1|CK067908
EST:     AGCTTATTCAGTTGGGAAGCAGTAACGGCACAATCCAGATTCACTTGCAG                         GAAAATAGTGAGTGGGTTGACTGGCAAACAGATGTTCTAGTCAAGCGTAAT
genomic: AGCTTATTCAGTTGGGAAGCAGTAACGGCACAATCCAGATTCACTTGCAGgtgatatttc ... ttaacaatagGAAAATAGTGAGTGGGTTGACTGGCAAACAGATGTTCTAGTCAAGCGTAAT
EST: gi|29680847|gb|CB677122.1|CB677122
EST:     AGCTTATTCAGTTGGGAAGCAGTAACGGCACAATCCAGATTCACTTGCAG                         GAAAATAGTGAGTGGGTTGACTGGCAAACAGATGTTCTAGTCAAGCGTAAT
genomic: AGCTTATTCAGTTGGGAAGCAGTAACGGCACAATCCAGATTCACTTGCAGgtgatatttc ... ttaacaatagGAAAATAGTGAGTGGGTTGACTGGCAAACAGATGTTCTAGTCAAGCGTAAT
EST: gi|58689270|gb|CK077957.1|CK077957
EST:     AGCTTATTCAGTTGGGAAGCAGTAACGGCACAATCCAGATTCACTTGCAG                         GAAAATAGTGAGTGGGTTGACTGGCAAACAGATGTTCTAGTCAAGCGTAAT
genomic: AGCTTATTCAGTTGGGAAGCAGTAACGGCACAATCCAGATTCACTTGCAGgtgatatttc ... ttaacaatagGAAAATAGTGAGTGGGTTGACTGGCAAACAGATGTTCTAGTCAAGCGTAAT

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: 60 (upstream exon), 59 (downstream exon)
Score: 30

ATCGATTCCCAAAATTGGGAATATTGGTCACATGACAAGAATAACCAACAAGCTTATTCAGTTGGGAAGCAGTAACGGCACAATCCAGATTCACTTGCAGgtgatatttc ... ttaacaatagGAAAATAGTGAGTGGGTTGACTGGCAAACAGATGTTCTAGTCAAGCGTAATGAGGTGGAGAATGTTTATCATTGGGCTTGTGG




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