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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATCTGCACAATCCAATATCGGGTTGTTAAGGAACATGCTGATGATGCATTCTATGAGTTGCAGAATCCCCAACAGCAAATTCAGGCCTACGTCTTTGATGgtaaaattattaatattgaacaattcagctgttgctcatagcaaattactgactcaaaaatctaaccactttttccttgaaatcag

Basic information

species Oryza sativa
transcript LOC_Os06g04460.1
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os06g04460.1 (Oryza sativa), 5'ss of exon 2
lower sequence: GRMZM2G026884_T01 (Zea mays), 5'ss of exon 1
ATCTGCACAATCCAATATCGGGTTGTTAAGGAACATGCTGATGATGCATTCTATGAGTTGCAGAATCCCCAACAGCAAATTCAGGCCTACGTCTTTGATGgtaaaattattaatattgaacaattcagctgttgctcatagcaaattactgactcaaaaatctaaccactttttccttgaaatcag
|||||||||||||| || || ||||| |||||| |||| |||||||| ||||||||||||||||||||||| |||||||| ||||||||||||||||||||| || ||||||  |  || |  |   | | |||| |     |      | ||   | | |  ||    |||||    |||||   
ATCTGCACAATCCAGTACCGTGTTGTCAAGGAAAATGCAGATGATGCTTTCTATGAGTTGCAGAATCCCCAGCAGCAAATCCAGGCCTACGTCTTTGATGgtgaa-ttattagcaccgagctttcttggttttgcacggcttatgagtataacctgacacttgaa----tttttatgagaaatag-

upper sequence: LOC_Os06g04460.1 (Oryza sativa), 5'ss of exon 2
lower sequence: GLYMA09G28170.1 (Glycine max), 5'ss of exon 2
ATCTGCACAATCCAATATCGGGTTGTTAAGGAACATGCTGATGATGCATTCTATGAGTTGCAGAATCCCCAACAGCAAATTCAGGCCTACGTCTTTGATGgtaaaatt--attaatattgaacaattcagctgttgctcatagcaaattactgactcaaaaatctaaccactttttccttgaaatcag-------------
 | ||  | || ||||| || ||  |||||||| | ||||||||||| |||||||||||||| || || ||  |||| || ||||| || || ||||||||||   ||   |||||  |      ||       |  | ||    | ||  ||  | ||   |   |     | ||   ||   |                
CTGTGTTCGATTCAATACCGAGTGATTAAGGAAAACGCTGATGATGCTTTCTATGAGTTGCAAAACCCTCAGGAGCAGATCCAGGCTTATGTTTTTGATGgtactgttttgttaatggttcttttttgtatcaattttgattttgatttcttgttttaattgtgacattgtgtgttgtgtggtttggttggtgcttttcag

upper sequence: LOC_Os06g04460.1 (Oryza sativa), 5'ss of exon 2
lower sequence: GLYMA16G32990.1 (Glycine max), 5'ss of exon 2
ATCTGCACAATCCAATATCGGGTTGTTAAGGAACATGCTGATGATGCATTCTATGAGTTGCAGAATCCCCAACAGCAAATTCAGGCCTACGTCTTTGATGgtaaaatt--attaatattgaacaatt-----cagctgttgctcatagcaaattactgactcaaaaatcta----accactttttccttgaaatcag
 | ||  | || ||||| || ||  |||||||| | ||||||||||| |||||||||||||| || || ||  |||| || ||||| || || ||||||||||   ||   ||||   |      ||     ||| | | ||  ||    | ||  ||  | ||  || |         |||  |  |     ||||
CTGTGTTCGATTCAATACCGAGTGATTAAGGAAAACGCTGATGATGCTTTCTATGAGTTGCAAAACCCTCAGGAGCAGATCCAGGCTTATGTTTTTGATGgtagtgttttgttaacgcttcttttttgtacacagttat-gccaattttgatttcttgttttaattatgtgttgtgtggcttggttttgtgtttcag

upper sequence: LOC_Os06g04460.1 (Oryza sativa), 5'ss of exon 2
lower sequence: Vv16s0022g01690.t01 (Vitis vinifera), 5'ss of exon 2
ATCTGCACAATCCAATATCGGGTTGTTAAGGAACATGCTGATGATGCATTCTATGAGTTGCAGAATCCCCAACAGCAAATTCAGGCCTACGTCTTTGATGgtaaaattatta-----atattgaacaattcagctgttgctcatagcaaatta-ctgactcaaaaatctaac-cactttt--tccttgaaatcag-------------------------------
 | ||| ||||||||||||| ||  |||| ||| |||| |||||||| || |||||||| ||||| ||| || |||| |||||||| |  || |||||||||||  ||   |     || | |||   || |||  |       || |||||  |||  |      | |    |||  ||  | |||||    |                                
CTTTGCTCAATCCAATATCGTGTGATTAAAGAAAATGCGGATGATGCCTTTTATGAGTTACAGAACCCCAAAGAGCAGATTCAGGCTTTTGTGTTTGATGgtaacttttgcatggttatctggaaatttttagccatattatgcagtaaattttctggttttttggtttctttcacccttgattcttgatgctattctgatgatgcattttgttgtgtgttgcaag

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|58592117|gb|CF990425.1|CF990425
EST:     CTATGAGTTGCAGAATCCCCAACAGCAAATTCAGGCCTACGTCTTTGATG                         TGGTCCGAGCTATAGTTCCGAGAATGAATCTTGATGATCTTTTTGAGCAAA
genomic: CTATGAGTTGCAGAATCCCCAACAGCAAATTCAGGCCTACGTCTTTGATGgtaaaattat ... ttgaaatcagTGGTCCGAGCTATAGTTCCGAGAATGAATCTTGATGATCTTTTTGAGCAAA
EST: gi|218489547|gb|FG966244.1|FG966244
EST:     CTATGAGTTGCAGAATCCCCAACAGCAAATTCAGGCCTACGTCTTTGATG                         TGGTCCGAGCTATAG-TCCGAGAATGAATCTTGATGATCTTTTTGAGCAAA
genomic: CTATGAGTTGCAGAATCCCCAACAGCAAATTCAGGCCTACGTCTTTGATGgtaaaattat ... ttgaaatcagTGGTCCGAGCTATAGTTCCGAGAATGAATCTTGATGATCTTTTTGAGCAAA
EST: gi|218496061|gb|FG945877.1|FG945877
EST:     CTATGAGTTGCAGAATCCCCAACAGCAAATTCAGGCCTACGTCTTTGATG                         TGGTCCGAGCTATAGTTCCGAGAATGAATCTTGATGATCTTTATGAGCAAA
genomic: CTATGAGTTGCAGAATCCCCAACAGCAAATTCAGGCCTACGTCTTTGATGgtaaaattat ... ttgaaatcagTGGTCCGAGCTATAGTTCCGAGAATGAATCTTGATGATCTTTTTGAGCAAA
EST: gi|218488749|gb|FG970419.1|FG970419
EST:     CTATGAGTTGCAGAATCCCCTACAGCTAATTCAGGCCTACGTCTTTGATG                         TGGTCCGAGCTATAGTTCCGAGAATGAATCTTGATGATCTTTTTGAGCAAA
genomic: CTATGAGTTGCAGAATCCCCAACAGCAAATTCAGGCCTACGTCTTTGATGgtaaaattat ... ttgaaatcagTGGTCCGAGCTATAGTTCCGAGAATGAATCTTGATGATCTTTTTGAGCAAA

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), 74 (downstream exon)
Score: 11

ATCTGCACAATCCAATATCGGGTTGTTAAGGAACATGCTGATGATGCATTCTATGAGTTGCAGAATCCCCAACAGCAAATTCAGGCCTACGTCTTTGATGgtaaaattat ... ttgaaatcagTGGTCCGAGCTATAGTTCCGAGAATGAATCTTGATGATCTTTTTGAGCAAAAGAATGATGTGGCGAAAGCTGTACTTCAGGAGCTAGAAAAG




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