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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaatgttttctccaaatgctatcttgtaggatgtttgttagccaagtgaagttatatgctaagtgtggcaccactgatggttctgcataattttgcagCTTCAAGCTTATTTTCTTGTGCTTGATGATATTATGGACAACTCTCAAACACGACGTGGCCAGCCTTGCTGGTTTAGGGTGCCTCAG

Basic information

species Oryza sativa
transcript LOC_Os01g50760.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g50760.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G147721_T01 (Zea mays), 3'ss of exon 2
gtaatgttttctccaaatgctatcttgtaggatgttt---gttagccaagtgaagttatatgctaagtgtggcaccactgatggttctgcataattttgcagCTTCAAGCTTATTTTCTTGTGCTTGATGATATTATGGACAACTCTCAAACACGACGTGGCCAGCCTTGCTGGTTTAGGGTGCCTCAG
||| |  || || |   || |   ||  || || |||   |||| |  | |||| || | |||||| | ||  |      ||   | |   | || |||||||||||||||||||||||||||||||||||||||||||||||||| || ||||| |||||||| |||||||||||||| ||||| |||
gtactacttacttctg-tgttgctttcaagcattttttatgttaacagaatgaattt-tctgctaa-tatgaaattttaaatcactatttcttatcttgcagCTTCAAGCTTATTTTCTTGTGCTTGATGATATTATGGACAACTCCCAGACACGGCGTGGCCAACCTTGCTGGTTTAGAGTGCCACAG

upper sequence: LOC_Os01g50760.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G098569_T01 (Zea mays), 3'ss of exon 2
gtaatgttttctccaaatgctatcttgtaggatgtttgttagc--caagtgaagttatatgctaagtgtggcaccactgatggttctgcataattttgcagCTTCAAGCTTATTTTCTTGTGCTTGATGATATTATGGACAACTCTCAAACACGACGTGGCCAGCCTTGCTGGTTTAGGGTGCCTCAG
||| |  || || |   |  | | || ||  || |||  ||     |  |    || | |||||| | ||| |       |   | |   |  | || ||||||||||||||||||||||||||||||||||||||||||||||| || ||||| ||||||||||||||||||||||| ||||| |||
gtactagttccttctgtt--tgttttctatcatttttaatattaatagattgcattttctgctaa-tttggaattttaattcactatttcttgtcttacagCTTCAAGCTTATTTTCTTGTGCTTGATGATATTATGGACAACTCCCAGACACGGCGTGGCCAGCCTTGCTGGTTTAGAGTGCCACAG

upper sequence: LOC_Os01g50760.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GLYMA15G12780.1 (Glycine max), 3'ss of exon 3
--------------------gtaatgttttctccaaatgct--atcttgtaggatgtttgttagccaagtgaagttatatgctaagtgtggcaccactgatggttc--tgcataattttgcagCTTCAAGCTTATTTTCTTGTGCTTGATGATATTATGGACAACTCTCAAACACGACGTGGCCAGCCTTGCTGGTTTAGGGTGCCTCAG
                        | | || |   |||| |  | || ||   |    | | ||     |   || ||    |  | | ||  |   |||| ||    ||     ||||||||||||| || ||||||||||| |||||||| |||||||| |||||||| ||||| ||||| ||||| ||||||||||| |||||  ||
gtatggctgttgaaagcttttgcctttcttgtttgaatgattaaactagttctaatcgtttcagatgtttactgtgatggcattgggggggatcttatgattgtctgttgatgggttttgcagCTTCAGGCATATTTTCTTGTTCTTGATGACATTATGGATAACTCTCACACACGCCGTGGTCAGCCATGCTGGTTTAGAGTGCCCAAG

upper sequence: LOC_Os01g50760.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GLYMA09G01820.3 (Glycine max), 3'ss of exon 3
----------------gtaatgttttctccaaatgctatcttgtaggatgtttgttagccaagtgaagtta-tatgcta--agtgtggcaccac-tgatggt--tctgcataattttgcagCTTCAAGCTTATTTTCTTGTGCTTGATGATATTATGGACAACTCTCAAACACGACGTGGCCAGCCTTGCTGGTTTAGGGTGCCTCAG
                 | ||| |||       ||     || ||  |  | |  | |          ||| | || |   | || || | |   |||| ||  | ||     ||||||||||||| || ||||||||||| |||||||| |||||||| |||||||| ||||| || |||||||| ||||||||||| |||||  ||
gtatggaagttgaaagcttatgcttttcttgtttgaatgattatactagttctaatcgtttcagatgtttactgtgatggcattggggtatcttatgatcgtcttttgatgggttttgcagCTTCAGGCATATTTTCTTGTTCTTGATGACATTATGGATAACTCTCACACACGCCGCGGCCAGCCATGCTGGTTTAGAGTGCCCAAG

upper sequence: LOC_Os01g50760.1 (Oryza sativa), 3'ss of exon 2
lower sequence: AT4G17190.1 (Arabidopsis thaliana), 3'ss of exon 3
gtaatgttttctccaaatgctatcttgtaggatgtttgttagccaagtgaagttatatgctaagtgtggcaccactgatggttctgcataattttgcagCTTCAAGCTTATTTTCTTGTGCTTGATGATATTATGGACAACTCTCAAACACGACGTGGCCAGCCTTGCTGGTTTAGGGTGCCTCAG-------------
                          |||     | | |||  |   |    |||| |  | |        |   |  ||  | ||| |   ||||||||||||||||||||| |||||||||||||| || ||||||||||||   ||||| |||||||||||||| ||||||||   |||  ||             
--------------------------gtaattcctctttta--cttctcttcttatct-ttcatctcaatgctcattttgtatttgcttgcatttgcagCTTCAAGCTTATTTCCTTGTGCTTGATGACATCATGGACAACTCTGTCACACGCCGTGGCCAGCCTTGTTGGTTTAGAAAGCCAAAGGTTGGTATGATTG

upper sequence: LOC_Os01g50760.1 (Oryza sativa), 3'ss of exon 2
lower sequence: AT5G47770.1 (Arabidopsis thaliana), 3'ss of exon 3
gtaatgttttctccaaatgctatcttgtaggatgtttgttagccaagtgaagttatatg-------ctaagtgtggc-accactgatggttctgcataattttgcagCTTCAAGCTTATTTTCTTGTGCTTGATGATATTATGGACAACTCTCAAACACGACGTGGCCAGCCTTGCTGGTTTAGGGTGCCTCAG
||| |         |||  ||      |   || | | ||||  |     | |    |        ||   ||| || | |||| ||  |  |   ||  ||||||||| ||||||||||| ||||||||||||||||||||||| ||||||   || || ||||| || ||||||||||| || || ||||||
gta-taccaatgataaagacttatcctttcaatctctattagtaatagatactctcctctctctctctttatgtcgctatcactcatcatattcattatctttgcagCTCCAAGCTTATTTCCTTGTGCTTGATGATATTATGGATAACTCTGTCACTCGCCGTGGTCAACCTTGCTGGTTCAGAGTTCCTCAG

upper sequence: LOC_Os01g50760.1 (Oryza sativa), 3'ss of exon 2
lower sequence: Vv19s0015g01010.t01 (Vitis vinifera), 3'ss of exon 3
-----------------------gtaatgttttctc-caaatgctatcttgtaggatgtttgttagccaagtgaagt-tatatgctaagtgtggcaccactgatggttctgcataat-tttgcagCTTCAAGCTTATTTTCTTGTGCTTGATGATATTATGGACAACTCTCAAACACGACGTGGCCAGCCTTGCTGGTTTAGGGTGCCTCAG
                       ||| | | ||    |  | ||| | |   |||    |  | |  | |||| |     | || |   ||       |    |  || |  ||     |||||||||||||| ||||| ||||||||||||||||||||||| ||||| || ||||| || || || ||||||||||| ||||| ||  ||
gtaggcaacagaatacctcccctgtattttgttaaggctgaagctttttctcaggtccataatcataccagtgtatcgcttttgttgcatgacaatttatgccttcttttctatgccacttgcagCTTCAAGCATATTTCCTTGTGCTTGATGATATTATGGATAACTCGCATACACGTCGAGGTCAACCTTGCTGGTTCAGGGTTCCCAAG

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|88423214|gb|CI613515.1|CI613515
EST:     ATAAGGAGGAGACATTTCTTGCCTGCACCCTTGGTTGGTGCATTGAATGG                         CTTCAAGCTTATTTTCTTGTGCTTGATGATATTATGGACAACTCTCAAACA
genomic: ATAAGGAGGAGACATTTCTTGCCTGCACCCTTGGTTGGTGCATTGAATGGgtaatgtttt ... aattttgcagCTTCAAGCTTATTTTCTTGTGCTTGATGATATTATGGACAACTCTCAAACA
EST: gi|29684521|gb|CB680796.1|CB680796
EST:     ATAAGGAGGAGACATTTCTTGCCTGCACCCTTGGTTGGTGCATTGAATGG                         CTTCAAGCTTATTTTCTTGTGCTTGATGATATTATGGACAACTCTCAAACA
genomic: ATAAGGAGGAGACATTTCTTGCCTGCACCCTTGGTTGGTGCATTGAATGGgtaatgtttt ... aattttgcagCTTCAAGCTTATTTTCTTGTGCTTGATGATATTATGGACAACTCTCAAACA

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), 75 (downstream exon)
Score: 44

GATCTCTGTCATTGATAGTTTCAAGATGTTGAAGGGCACTGATGTTCTGAATAAGGAGGAGACATTTCTTGCCTGCACCCTTGGTTGGTGCATTGAATGGgtaatgtttt ... aattttgcagCTTCAAGCTTATTTTCTTGTGCTTGATGATATTATGGACAACTCTCAAACACGACGTGGCCAGCCTTGCTGGTTTAGGGTGCCTCAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aagtgaagttatatgctaagtgtggcaccactgatggttctgcataattttgcagCTTCAAGCTTATTTTCTTGTGCTTGATGATATTATGGACAACTCTCAAACACGACGTGGCCAGCCTTGCTGGTTTAGGGTGCCTCAG
                            cactgat  putative branch site (score: 44)
                                           ataatttt  TA-rich tract