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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCAGTCCATCGTGAGGTCGGCCATGGCGGCCGCCGTGCAGCAAGAGCCCCGCATGGGCGCCTCCATCCTCCGCCTCTTCTTCCACGACTGCTTCGTCAATgtaagtacaccatagctagctagctagcttgagagtggccagccatggcggctctgagaatgacggcggatggggatcgagctgatggtcgctcgccggcgttcatggcgattatatatgattgcag

Basic information

species Oryza sativa
transcript LOC_Os02g14160.1
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g14160.1 (Oryza sativa), 5'ss of exon 1
lower sequence: GRMZM2G405459_T01 (Zea mays), 5'ss of exon 1
GCAGTCCATCGTGAGGTCGGCCATGGCGGCCGCCGTGCAGCAAGAGCCCCGCATGGGCGCCTCCATCCTCCGCCTCTTCTTCCACGACTGCTTCGTCAATgtaagtacaccatagctagctagctagcttgagagtggccagccatggcggctctgagaatg-acggcggatggggatcgagctgatggtcgctcgccggcgttcatggcgattatatatgattgcag
|||| |||||||| || | |  ||||| |||||||||||||| ||||| || ||||| ||||||||||||||||||||||||||||||||||||||| | |||||     |||   |  |  |    ||||     |||  ||  ||  ||   | || |||    |||    |  ||| | |  |   ||  |        ||  |   |   ||  |         
GCAGGCCATCGTGCGGGCCGGGATGGCCGCCGCCGTGCAGCAGGAGCCGCGGATGGGGGCCTCCATCCTCCGCCTCTTCTTCCACGACTGCTTCGTCCAGgtaag-----catgcatgtcgtggcgccttg-----ggcttgc--tgctggtcgtcagtatgcgtcgcgccgcgccatccatccaacactccattattattattattattgcccatgcag--------
















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|88743568|gb|CI767076.1|CI767076
EST:     GCATGGGCGCCTCCATCCTCCGCCTCTTCTTCCACGACTGCTTCGTCAAT                         GGGTGCGACGCGTCGGTGCTGCTGGACGACTCG
genomic: GCATGGGCGCCTCCATCCTCCGCCTCTTCTTCCACGACTGCTTCGTCAATgtaagtacac ... atgattgcagGGGTGCGACGCGTCGGTGCTGCTGGACGACTCG
EST: gi|58656413|gb|CK045093.1|CK045093
EST:     GCATGGGCGCCTCCATCCTCCGCCTCTTCTTCCACGACTGCTTCGTCAAT                         GGGTGCGACGCGTCGGTGCTGCTGGACGACTCGTCGACGATCACCGGCGAG
genomic: GCATGGGCGCCTCCATCCTCCGCCTCTTCTTCCACGACTGCTTCGTCAATgtaagtacac ... atgattgcagGGGTGCGACGCGTCGGTGCTGCTGGACGACTCGTCGACGATCACCGGCGAG
EST: gi|58671450|gb|CK060136.1|CK060136
EST:     GCATGGGCGCCTCCATCCTCCGCCTCTTCTTCCACGACTGCTTCGTCAAT                         GGGTGCGACGCGTCGGTGCTGCTGGACGACTCGTCGACGATCACCGGCGAG
genomic: GCATGGGCGCCTCCATCCTCCGCCTCTTCTTCCACGACTGCTTCGTCAATgtaagtacac ... atgattgcagGGGTGCGACGCGTCGGTGCTGCTGGACGACTCGTCGACGATCACCGGCGAG
EST: gi|88745223|gb|CI768583.1|CI768583
EST:     GCATGGGCGCCTCCATCCTCCGCCTCTTCTTCCACGACTGCTTCGTCAAT                         GGGTGCGACGCGTCGGTGCTGCTGGACGACTCGTCGACGATCACCGGCG
genomic: GCATGGGCGCCTCCATCCTCCGCCTCTTCTTCCACGACTGCTTCGTCAATgtaagtacac ... atgattgcagGGGTGCGACGCGTCGGTGCTGCTGGACGACTCGTCGACGATCACCGGCG
EST: gi|58654371|gb|CK043051.1|CK043051
EST:     GCATGGGCGCCTCCATCCTCCGCCTCTTCTTCCACGACTGCTTCGTCAAT                         GGGTGCGACGCGTCGGTGCTGCTGGACGACTCGTCGACGATCACCGGCGAG
genomic: GCATGGGCGCCTCCATCCTCCGCCTCTTCTTCCACGACTGCTTCGTCAATgtaagtacac ... atgattgcagGGGTGCGACGCGTCGGTGCTGCTGGACGACTCGTCGACGATCACCGGCGAG
EST: gi|13447542|gb|AU181036.1|AU181036
EST:     GCGCCTCCATCCTCCGCCTCTTCTTCCACGACTGCTTCGTCAAT                         GGGTGCGACGCAGTCGGTGCTGCTGGACGACTCGTCGACGATCACCGGCGA
genomic: GCGCCTCCATCCTCCGCCTCTTCTTCCACGACTGCTTCGTCAATgtaagtacac ... atgattgcagGGGTGCGACGC-GTCGGTGCTGCTGGACGACTCGTCGACGATCACCGGCGA
EST: gi|58593599|gb|CF991907.1|CF991907
EST:     GCATGGGCGCCTCCATCCTCCGCCTCTTCTTCCACGACTGCTTCGTCAAT                         GGGTGCGACGCGTCGGTGCTGCTGGACGACTCGTCGACGATCACCGGCGAG
genomic: GCATGGGCGCCTCCATCCTCCGCCTCTTCTTCCACGACTGCTTCGTCAATgtaagtacac ... atgattgcagGGGTGCGACGCGTCGGTGCTGCTGGACGACTCGTCGACGATCACCGGCGAG

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: 73 (upstream exon), 58 (downstream exon)
Score: 3

GCAGTCCATCGTGAGGTCGGCCATGGCGGCCGCCGTGCAGCAAGAGCCCCGCATGGGCGCCTCCATCCTCCGCCTCTTCTTCCACGACTGCTTCGTCAATgtaagtacac ... atgattgcagGGGTGCGACGCGTCGGTGCTGCTGGACGACTCGTCGACGATCACCGGCGAGAAGAACGCCGGGCCGAACGCCAACTCGCTGCGCGGATTCGAGGTCATCG




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