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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CAGCAGATGCTGCTTTGCAGCATGAGTGGTTCCGTGAAGTTCCTCTACCTAAATCAAAGGATTTCATGCCAACATTCCCTGCTCTAAATGAATTAGACAGgtacttcttcgcaaccatttaatctacttgtagtgttgcttaaatatctttgtttcatgtagtgaaatttattttcctaaaattccacag

Basic information

species Oryza sativa
transcript LOC_Os04g41100.3
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os04g41100.6 (Oryza sativa), 5'ss of exon 7
lower sequence: GRMZM2G139038_T01 (Zea mays), 5'ss of exon 6
CAGCAGATGCTGCTTTGCAGCATGAGTGGTTCCGTGAAGTTCCTCTACCTAAATCAAAGGATTTCATGCCAACATTCCCTGCTCTAAATGAATTAGACAGgtacttcttcgcaaccatttaatctacttgtagtgttgc-ttaaatatctttgtttcatgta-gtgaaatttattttccta---------aaattccacag
||||||| | |||| || | ||  | ||||||  |||||||||||| ||||||||||| || |||||||||||||| |||||||| |||||| | |||||||| || ||   |||||| |  | |   | | ||       ||  |   | | ||||||  | |  ||||| |||| | ||         ||||| |||||
CAGCAGACGATGCTCTGAAACACAAATGGTTCTCTGAAGTTCCTCTGCCTAAATCAAAAGACTTCATGCCAACATTTCCTGCTCTTAATGAACTTGACAGgtattttttt--aaccatctcctttcactctggtccaatgctacgttgttctatttcataaatgcaaaattgatttccatatataatttgaaattacacag

upper sequence: LOC_Os04g41100.6 (Oryza sativa), 5'ss of exon 7
lower sequence: GRMZM2G179097_T03 (Zea mays), 5'ss of exon 6
CAGCAGATGCTGCTTTGCAGCATGAGTGGTTCCGTGAAGTTCCTCTACCTAAATCAAAGGATTTCATGCCAACATTCCCTGCTCTAAATGAATTAGACAGgtacttcttcgcaaccatttaatctacttgtagtgttgcttaaatatctttgtttcatgtagtgaaatttattttcctaaa--attccacag-------
||||||| | |||| |  ||||  | ||||||  |||||||||||| |||||||||||||| ||||||||||||||||||||||| |||||| | ||||||||  | ||   |||  | |   | ||||   |    | |||  |   | | ||||||  |   ||||| |||| | || |  |||  | |        
CAGCAGACGATGCTCTTAAGCACAAATGGTTCTCTGAAGTTCCTCTGCCTAAATCAAAGGACTTCATGCCAACATTCCCTGCTCTTAATGAACTTGACAGgtaaattttt--aactttctctcccactta-ggctcagtttacgtggttctatttcatacatccaaattgatttccatatataatttgaaaatacacag

upper sequence: LOC_Os04g41100.6 (Oryza sativa), 5'ss of exon 7
lower sequence: GLYMA08G10810.1 (Glycine max), 5'ss of exon 5
CAGCAGATGCTGCTTTGCAGCATGAGTGGTTCCGTGAAGTTCCTCTACCTAAATCAAAGGATTTCATGCCAACATTCCCTGCTCTAAATGAATTAGACAGgtacttcttcgcaaccatttaatctacttgtagtgttgcttaaatatctttgtttcatgtagtgaaatttattttcctaaaattccacag----------------------------------------------------------------------------------------
| || || | |||| |  | |||||||||||||||||||||||||| || |||   || || |||||||| ||||| ||||||| | |||     |||||||| ||   |  ||   ||  |  | || |     ||  |  || |  ||| |||  | ||       |  | |   |||||      ||                                                                                        
CTGCCGAAGATGCTCTAAATCATGAGTGGTTCCGTGAAGTTCCTCTCCCCAAAAGTAAAGAATTCATGCCTACATTTCCTGCTCAACATGCTCAGGACAGgtaatttgacctaa---ttggaaatgctggagcaatttttataagaatttttttttgtttatgttctctagtctggataaaagagggaagttgtgtaaaatatttgctgagtctatactatataacatttatcaacttttatttttgacaagttttcataatttcatcatataaatag

upper sequence: LOC_Os04g41100.6 (Oryza sativa), 5'ss of exon 7
lower sequence: AT1G67580.2 (Arabidopsis thaliana), 5'ss of exon 5
CAGCAGATGCTGCTTTGCAGCATGAGTGGTTCCGTGAAGTTCCTCTACCTAAATCAAAGGATTTCATGCCAACATTCCCTGCTCTAAATGAATTAGACAGgtacttcttcgcaaccatttaatctacttgtagtgttgcttaaatatctttgtttcatgtagtgaaatttattttcctaaaattccacag
| |   |||  ||| |  ||||||| |||||||| ||||| ||||| || ||||| || ||||||||||| || || ||||||| | |||    |||||||||||         | || ||| ||      |    || || | | |  || | ||   || |     || | | ||||           
CTGTTAATGAAGCTCTAAAGCATGATTGGTTCCGCGAAGTCCCTCTGCCAAAATCCAAAGATTTCATGCCTACTTTTCCTGCTCAACATGCCCAAGACAGgtactg----aggtctatctaaactgaaacgatcagtggttgactttaattctgtctcttactttttcttctatgcctag----------

upper sequence: LOC_Os04g41100.6 (Oryza sativa), 5'ss of exon 7
lower sequence: Vv01s0010g02550.t01 (Vitis vinifera), 5'ss of exon 5
CAGCAGATGCTGCTTTGCAGCATGAGTGGTTCCGTGAAGTTCCTCTACCTAAATCAAAGGATTTCATGCCAACATTCCCTGCTCTAAATGAATTAGACAGgtacttcttcgcaaccatttaatctacttgtagtgttgcttaaat----atctttgtttcatgtag-------tgaaatttattttcctaaaat--tccacag
|||| || |||||| |  | ||||| |||||||| ||||||||||| || ||||| || ||||||||||| || || |||||||   |||     ||||||||  |   | | |    | | | ||  ||     |   |   |      | ||| |||  | |||       | ||||  |||||  | |  |  |   |||
CAGCTGAAGCTGCTCTTAACCATGATTGGTTCCGCGAAGTTCCTCTTCCCAAATCTAAAGATTTCATGCCTACTTTTCCTGCTCAGCATGCCCAGGACAGgtatcttgaccctatacatgactttaaatgagagatgagtaggagtgcagtttttattttttatagcaatttctaaaataaattttgttcatttgattatcag

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|218494622|gb|FG958132.1|FG958132
EST:     AAATCAAAGGATTTCATGCCAACATTCCCTGCTCTAAATGAATTAGACAG                         GCGTTACCAA-CGGTATTTGAAGA
genomic: AAATCAAAGGATTTCATGCCAACATTCCCTGCTCTAAATGAATTAGACAGgtacttcttc ... aattccacagGCGT-ACCAAACGGTATTTGAAGA
EST: gi|29628989|gb|CB634000.1|CB634000
EST:     AAATCAAAGGATTTCATGCCAACATTCCCTGCTCTAAATGAATTAGACAG                         GCGTACCAAACGGTATTTGAAGAGTCCTGATCCTCTAGAAGAGCAACGATT
genomic: AAATCAAAGGATTTCATGCCAACATTCCCTGCTCTAAATGAATTAGACAGgtacttcttc ... aattccacagGCGTACCAAACGGTATTTGAAGAGTCCTGATCCTCTAGAAGAGCAACGATT
EST: gi|86910572|gb|CI294713.1|CI294713
EST:     AAATCAAAGGATTTCATGCCAACATTCCCTGCTCTAAATGAATTAGACAG                         GCGTACCAAACGGTATTTGAAGAGTCCTGATCCTCTAGAAGAGCAACGATT
genomic: AAATCAAAGGATTTCATGCCAACATTCCCTGCTCTAAATGAATTAGACAGgtacttcttc ... aattccacagGCGTACCAAACGGTATTTGAAGAGTCCTGATCCTCTAGAAGAGCAACGATT
EST: gi|58611941|gb|CK039653.1|CK039653
EST:     AAATCAAAGGATTTCATGCCAACATTCCCGGCTCTAAATGAATTAGACAG                         GCGTACCAAACGGTATTTGAAGAGTCCTG
genomic: AAATCAAAGGATTTCATGCCAACATTCCCTGCTCTAAATGAATTAGACAGgtacttcttc ... aattccacagGCGTACCAAACGGTATTTGAAGAGTCCTG

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: 68 (upstream exon), 75 (downstream exon)
Score: 32

CAGCAGATGCTGCTTTGCAGCATGAGTGGTTCCGTGAAGTTCCTCTACCTAAATCAAAGGATTTCATGCCAACATTCCCTGCTCTAAATGAATTAGACAGgtacttcttc ... aattccacagGCGTACCAAACGGTATTTGAAGAGTCCTGATCCTCTAGAAGAGCAACGATTGAAAGAACTACAAGGGAACATTGGCAACCGTGGTCTTTTTGGCTGAGCT




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