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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CAAGGATCGCCCCTCTTGGTACCGTGATTGCCGATGCGTAGATATCATCCATGTTATCCCTACGGGTAACGGCGGAACCATTGAGCTAATCTACATGCAGgtaaatatacccaatcgtgactcatgtgttgcatttttctcaagcatcactagctactctttgtttttggtaataaccattgcccttttcaattccttag

Basic information

species Oryza sativa
transcript LOC_Os12g41860.1
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os12g41860.1 (Oryza sativa), 5'ss of exon 6
lower sequence: GRMZM2G178102_T01 (Zea mays), 5'ss of exon 6
CAAGGATCGCCCCTCTTGGTACCGTGATTGCCGATGCGTAGATATCATCCATGTTATCCCTACGGGTAACGGCGGAACCATTGAGCTAATCTACATGCAGgtaaatatacccaatcgtgactca---------tgtgttgcatttttctcaagcatcactagctactctttgtttttggtaataaccattgcccttttcaattccttag
 ||||||||  | || ||||| || ||||| ||    || ||| || ||||||||||||||||||||||||| ||||| |||||||| ||||| ||||||||| || |   ||     |  |||          |||||   || |   | ||||  | || |||   ||| || | | || | |  |||    |||| |  ||  |||
TAAGGATCGTGCATCGTGGTATCGCGATTGTCGGCATGTTGATGTCCTCCATGTTATCCCTACGGGTAACGGTGGAACGATTGAGCTGATCTATATGCAGgtatatgtctgcacataaggttcagtctttttacgtgtttgtttatatactagcactagtaactatgtttt-ttgtggatagtgataatttatgttttaa--tctgtag

upper sequence: LOC_Os12g41860.1 (Oryza sativa), 5'ss of exon 6
lower sequence: GRMZM2G003509_T02 (Zea mays), 5'ss of exon 5
CAAGGATCGCCCCTCTTGGTACCGTGATTGCCGATGCGTAGATATCATCCATGTTATCCCTACGGGTAACGGCGGAACCATTGAGCTAATCTACATGCAGgtaaatat----acccaatcgtgactcatgtgttgcattt--ttctcaagcatcactagctactctttgtttttggtaataaccattgcccttttcaattccttag
 ||||||||| | || ||||| || ||||| ||  | || |||||| ||||||||||||||||||||||||| ||||| |||||||| ||||| |||||||||  | |    ||  ||          | |   |   ||  || |  |  |  |||||  ||| |   ||| | | |||||  |||  |||  |  | ||  |||
TAAGGATCGCGCATCGTGGTATCGCGATTGTCGGCGTGTTGATATCCTCCATGTTATCCCTACGGGTAACGGTGGAACGATTGAGCTGATCTATATGCAGgtatgtgtctgcacataagttcagtcttttttacgtgcttgattatgtactagtactagtaactgtgcttttgttgaaataaaaatt--cctgctttaatctgtag
















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|58656953|gb|CK045633.1|CK045633
EST:     ATGTTATCCCTACGGGTAACGGCGGAACCATTGAGCTAATCTACATGCAG                         ACTTATGCACCGACAACTTTGGCGGCACCACGCGACTTTTGGACTCTCCGC
genomic: ATGTTATCCCTACGGGTAACGGCGGAACCATTGAGCTAATCTACATGCAGgtaaatatac ... aattccttagACATATGCACCGACAACTTTGGCGGCACCACGCGACTTTTGGACTCTCCGC
EST: gi|58661675|gb|CK050355.1|CK050355
EST:     ATGTTATCCCTACGGGTAACGGCGGAACCATTGAGCTAATCTACATGCAG                         ACTTATGCACCGACAACTTTGGCGGCACCACGCGACTTTTGGACTCTCCGC
genomic: ATGTTATCCCTACGGGTAACGGCGGAACCATTGAGCTAATCTACATGCAGgtaaatatac ... aattccttagACATATGCACCGACAACTTTGGCGGCACCACGCGACTTTTGGACTCTCCGC
EST: gi|58654155|gb|CK042835.1|CK042835
EST:     ATGTTATCCCTACGGGTAACGGCGGAACCATTGAGCTAATCTACATGCAG                         ACTTATGCACCGACAACTTTGGCGGCACCACGCGACTTTTGGACTCTCCGC
genomic: ATGTTATCCCTACGGGTAACGGCGGAACCATTGAGCTAATCTACATGCAGgtaaatatac ... aattccttagACATATGCACCGACAACTTTGGCGGCACCACGCGACTTTTGGACTCTCCGC
EST: gi|58667004|gb|CK055690.1|CK055690
EST:     ATGTTATCCCTACGGGTAACGGCGGAACCATTGAGCTAATCTACATGCAG                         ACTTATGCACCGACAACTTTGGCGGCACCACGCGACTTTTGGACTCTCCGC
genomic: ATGTTATCCCTACGGGTAACGGCGGAACCATTGAGCTAATCTACATGCAGgtaaatatac ... aattccttagACATATGCACCGACAACTTTGGCGGCACCACGCGACTTTTGGACTCTCCGC
EST: gi|58675209|gb|CK063896.1|CK063896
EST:     ATGTTATCCCTACGGGTAACGGCGGAACCATTGAGCTAATCTACATGCAG                         ACTTATGCACCGACAACTTTGGCGGCACCACGCGACTTTTGGACTCTCCGC
genomic: ATGTTATCCCTACGGGTAACGGCGGAACCATTGAGCTAATCTACATGCAGgtaaatatac ... aattccttagACATATGCACCGACAACTTTGGCGGCACCACGCGACTTTTGGACTCTCCGC
EST: gi|58661332|gb|CK050012.1|CK050012
EST:     ATGTTATCCCTACGGGTAACGGCGGAACCATTGAGCTAATCTACATGCAG                         ACTTATGCACCGACAACTTTGGCGGCACCACGCGACTTTTGGACTCT
genomic: ATGTTATCCCTACGGGTAACGGCGGAACCATTGAGCTAATCTACATGCAGgtaaatatac ... aattccttagACATATGCACCGACAACTTTGGCGGCACCACGCGACTTTTGGACTCT
EST: gi|58675501|gb|CK064188.1|CK064188
EST:     ATGTTATCCCTACGGGTAACGGCGGAACCATTGAGCTAATCTACATGCAG                         ACTTATGCACCGACAACTTTGGCGGCACCACGCGACTTTTGGACTCTCCGC
genomic: ATGTTATCCCTACGGGTAACGGCGGAACCATTGAGCTAATCTACATGCAGgtaaatatac ... aattccttagACATATGCACCGACAACTTTGGCGGCACCACGCGACTTTTGGACTCTCCGC

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: 33 (upstream exon), 70 (downstream exon)
Score: 6

CAAGGATCGCCCCTCTTGGTACCGTGATTGCCGATGCGTAGATATCATCCATGTTATCCCTACGGGTAACGGCGGAACCATTGAGCTAATCTACATGCAGgtaaatatac ... aattccttagACATATGCACCGACAACTTTGGCGGCACCACGCGACTTTTGGACTCTCCGCTACACAAGTGGACTTGAAGATGGGAGTCTTGTG




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