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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtattaaaaagtgaaactaaaaacataatgtgcaacccttgttgctattctgttactgctgttaaatgatgactcaccaagtggaatatttacttcagctatacatttattataatttcagGAAGGACAAAATAATGGGAATGGAACTACATTTCAACCCAATGTTATAATGCAAGGGCAGTCACCATCGGATTATGTTTTGAATGTAGTTTCAAATGTTC

Basic information

species Oryza sativa
transcript LOC_Os03g05720.1
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g05720.1 (Oryza sativa), 3'ss of exon 7
lower sequence: AC209858.4_FGT002 (Zea mays), 3'ss of exon 7
gtattaaaaagtgaaactaaaaacataatgtgcaacccttgttgctattctgttactgctgttaaatgatgactcaccaagtggaatatttacttcagctatacatttattataatttcagGAAGGACAAAATAATGGGAATGGAACTACATTTCAACCCAATGTTATAATGCAAGGGCAGTCACCATCGGATTATGTTTTGAATGTAGTTTCAAATGTTC
                             || ||  | |   |  ||   |||| |  |   ||||| ||            |||  |||| ||| | ||   | |||   | | ||||||||||  |||| || || ||| | | ||| ||||||||| |||||||||||||||||||| ||||| || ||||||||| |||||||||||||||   | |
-----------------------------gtacactcatatattataccttgtt-ccacccataaataat------------ggatcattttcttgatcttctcgtttcaca-attttcagGAAGAGCAAATTACTGCGAAGGCAGCTAAATTTCAACCTAATGTTATAATGCAAGGGCATTCACCTTCAGATTATGTTCTGAATGTAGTTTCAAGCATCC
















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|58612095|gb|CK039807.1|CK039807
EST:     ATGCACTTGACACTGGCGAGGAAGAAGTAAAACGCCTTGATCAGCACCAG                         GAAGGACAAAATAATGGGAATGGAACTACATTTCAACCCAATGTTATAATG
genomic: ATGCACTTGACACTGCCGAGGAAGAAGTAAAACGCCTTGATCAGCACCAGgtattaaaaa ... ataatttcagGAAGGACAAAATAATGGGAATGGAACTACATTTCAACCCAATGTTATAATG
EST: gi|86501444|gb|CI144077.1|CI144077
EST:     ATGCACTTGACACTGCCGAGGAAGAAGTAAAACGCCTTGATCAGCACCAG                         GAAGGACAAAATAATGGGAATGGAACTACATTTCAACCCAATGTTATAATG
genomic: ATGCACTTGACACTGCCGAGGAAGAAGTAAAACGCCTTGATCAGCACCAGgtattaaaaa ... ataatttcagGAAGGACAAAATAATGGGAATGGAACTACATTTCAACCCAATGTTATAATG
EST: gi|29634108|gb|CB639117.1|CB639117
EST:     ATGCACTTGACACTGCCGAGGAAGAAGTAAAACGCCTTGATCAGCCCCAG                         GAAGGACAAAATAATGGGAATGGAATTACATTTCAACCCAATGTTATAATG
genomic: ATGCACTTGACACTGCCGAGGAAGAAGTAAAACGCCTTGATCAGCACCAGgtattaaaaa ... ataatttcagGAAGGACAAAATAATGGGAATGGAACTACATTTCAACCCAATGTTATAATG
EST: gi|7332525|gb|AU085871.1|AU085871
EST:     ATGCACTTGACACTGCCGAGGAAGAAGTAAAACCCCTTGATCAGCACCAG                         G-AGGACAAAATAATGGGAATGGAACTACATTTCANCCCAATGTTATAATG
genomic: ATGCACTTGACACTGCCGAGGAAGAAGTAAAACGCCTTGATCAGCACCAGgtattaaaaa ... ataatttcagGAAGGACAAAATAATGGGAATGGAACTACATTTCAACCCAATGTTATAATG
EST: gi|218485889|gb|FG950181.1|FG950181
EST:     ATGCACTTGACACTGCCGAGGAAGAAGTAAAACGCCTTGATCAGCACCAG                         GAAGGACAAAATAATGGGAATGGAACTACATTTCAACCCAATGTTATAATG
genomic: ATGCACTTGACACTGCCGAGGAAGAAGTAAAACGCCTTGATCAGCACCAGgtattaaaaa ... ataatttcagGAAGGACAAAATAATGGGAATGGAACTACATTTCAACCCAATGTTATAATG
EST: gi|218482933|gb|FG946915.1|FG946915
EST:     ATGCACTTGACACTGCCGAGGAAGAAGTAAAACGCCTTGATCAGCACCAG                         GAAGGACAAAATAATGGGAATGGAACTACATTTCAACCCAATGTTATAATG
genomic: ATGCACTTGACACTGCCGAGGAAGAAGTAAAACGCCTTGATCAGCACCAGgtattaaaaa ... ataatttcagGAAGGACAAAATAATGGGAATGGAACTACATTTCAACCCAATGTTATAATG
EST: gi|218478499|gb|FG957068.1|FG957068
EST:     ATGCACTTGACACTGCCGAGGAAGAAGTAAAACGCCTTGATCAGCACCAG                         GAAGGACAAAATAATGGGAATGGAACTACATTTCAACCCAATGTTATAATG
genomic: ATGCACTTGACACTGCCGAGGAAGAAGTAAAACGCCTTGATCAGCACCAGgtattaaaaa ... ataatttcagGAAGGACAAAATAATGGGAATGGAACTACATTTCAACCCAATGTTATAATG
EST: gi|218482633|gb|FG949654.1|FG949654
EST:     CTTGACACTGCCGAGGAAGAAGTAAAACGCCTTGATCAGCACCAG                         GAAGGACAAAATAATGGGAATGGAACTACATTTCAACCCAATGTTATAATG
genomic: CTTGACACTGCCGAGGAAGAAGTAAAACGCCTTGATCAGCACCAGgtattaaaaa ... ataatttcagGAAGGACAAAATAATGGGAATGGAACTACATTTCAACCCAATGTTATAATG

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: 72 (upstream exon), 61 (downstream exon)
Score: 12

TCCTGGTAGGAAAACCAAAGAGACAGTAACTGCTGCTGATGCAATTATTGATGCACTTGACACTGCCGAGGAAGAAGTAAAACGCCTTGATCAGCACCAGgtattaaaaa ... ataatttcagGAAGGACAAAATAATGGGAATGGAACTACATTTCAACCCAATGTTATAATGCAAGGGCAGTCACCATCGGATTATGTTTTGAATGTAGTTTCAAATGTTC




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgatgactcaccaagtggaatatttacttcagctatacatttattataatttcagGAAGGACAAAATAATGGGAATGGAACTACATTTCAACCCAATGTTATAATGCAAGGGCAGTCACCATCGGATTATGTTTTGAATGTAGTTTCAAATGTTC
    gactcac  putative branch site (score: 12)
                  aatatttacttcagct  TA-rich tract