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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtcagttcttcgcacatagtttccatcttatgttttagtgagaacaatgatcgtgtggttatcttttcaaagttatattttgctgttcaagaatgagagttctatatttttctttagATTTTGCAAGAGGAAATTGGTGGTGTTAAAGGCCATTTTGGACCAATTAACGCGCTGGCATTTAATCCTGATGGGCGGAG

Basic information

species Oryza sativa
transcript LOC_Os08g21660.2
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os08g21660.2 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G028834_T03 (Zea mays), 3'ss of exon 5
gtcagttcttcg-cacatagtttccatcttatgttttagtgagaaca-atgatcgtgtggttatcttttcaaagttatattttgctgttcaagaatgagagttctatatttttctttagATTTTGCAAGAGGAAATTGGTGGTGTTAAAGGCCATTTTGGACCAATTAACGCGCTGGCATTTAATCCTGATGGGCGGAG
|| | |||||   ||  || |         | |  ||| |         | |     | | || |||   | | ||| | |||  ||  |     |||        |  | |  ||||||||||||||||||||||||||||||||||||| |||||||| |||||||| ||  |||||||||||||||||||||||||
gtaatttctttttcagttaataaattatcaaggcattactccttttgtgttacttccttgctaacttggtatacttacaattt-ttgaactgttctgattaaaacttgctctcttttagATTTTGCAAGAGGAAATTGGTGGTGTTAAAGGACATTTTGGGCCAATTAATGCTTTGGCATTTAATCCTGATGGGCGGAG

upper sequence: LOC_Os08g21660.2 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G143330_T01 (Zea mays), 3'ss of exon 5
gtcagttcttcgcacatagtttccatcttatgttttagtgagaacaatgatcgtgtggttatcttttcaaagttatattttgctgttcaagaatgagagttctatatttttctttagATTTTGCAAGAGGAAATTGGTGGTGTTAAAGGCCATTTTGGACCAATTAACGCGCTGGCATTTAATCCTGATGGGCGGAG
|| | || |  |  || ||  |  |    |||  ||| |            | | | | || |||| ||   ||| | | |      ||  | |   |   ||   |  |  ||||||||||||||||||||||||||||||||||||| |||||||| |||||||| ||  |||||||||||||||||||||||||
gtgatttttcagttcacagaatataa---atgccttactctttttgtgttacatcttgctaactttgcatgcttacaatatttgaaccattattattaaaact---tgctcttttagATTTTGCAAGAGGAAATTGGTGGTGTTAAAGGGCATTTTGGGCCAATTAATGCTTTGGCATTTAATCCTGATGGGCGGAG

upper sequence: LOC_Os08g21660.2 (Oryza sativa), 3'ss of exon 5
lower sequence: GLYMA09G36870.2 (Glycine max), 3'ss of exon 3
gtcagttcttcgcacatagtttccatcttatgttttagtgagaacaatgatcgtgtggttatcttttcaaagttatattttgctgttcaagaatgagagttctatatttttctttagATTTTGCAAGAGGAAATTGGTGGTGTTAAAGGCCATTTTGGACCAATTAACGCGCTGGCATTTAATCCTGATGGGCGGAG----
                ||| ||   | ||   |  ||            |   | || | |  | |  || | |||   |   |||  |   ||     || | ||||  || ||||||| | ||||| |||||||| ||||| |||||||| |||||||||||||| ||  |||| ||||| ||||||||    ||    
---------------gtaggtttttttttccttcctat-----------actatatgttgagttctgtaatggtat---tgaatgtctacttatttcgcttttttatt--tcattagATTCTTCAAGAAGAAATTGGGGGTGTGAAAGGCCACTTTGGACCAATTAATGCATTGGCTTTTAACCCTGATGGAAAAAGGTAT

upper sequence: LOC_Os08g21660.2 (Oryza sativa), 3'ss of exon 5
lower sequence: GLYMA01G03610.2 (Glycine max), 3'ss of exon 6
gtcagttcttcgcacatagtttccatcttatgttttagtgagaacaatgatcgtgtggttatcttttcaaagttatattttgctgttcaagaatgagagttctatatttttctttagATTTTGCAAGAGGAAATTGGTGGTGTTAAAGGCCATTTTGGACCAATTAACGCGCTGGCATTTAATCCTGATGGGCGGAG
           |    |  |||   || | |  | |  | ||  |  | ||  | ||  || | | |     || |  |||    ||||    ||       |||   |||  ||||||| | ||||| |||||||| ||||| ||||| ||||||||||||||||| ||  |||| ||||| ||||||||    ||
-----------gttttttttttttttcctttactatgtttagttctctaatgatatg--taacatctacttattttgctttttatttcatatttg------ttattcatttgattagATTCTTCAAGAAGAAATTGGGGGTGTAAAAGGGCATTTTGGACCAATTAATGCATTGGCTTTTAACCCTGATGGAAAAAG

upper sequence: LOC_Os08g21660.2 (Oryza sativa), 3'ss of exon 5
lower sequence: GLYMA12G00510.1 (Glycine max), 3'ss of exon 3
gtcagttcttcgcacatagtttccatcttatgttttagtgagaacaatgatcgtgt-ggttatcttttcaaagttatattttgctgttcaagaatgagagttctatatttttctttagATTTTGCAAGAGGAAATTGGTGGTGTTAAAGGCCATTTTGGACCAATTAACGCGCTGGCATTTAATCCTGATGGGCGGAG
|| ||||  |      |  ||| | || ||   | |  || | ||  ||||  | | |  | |||  |        |||||||||               || | |   |||  ||||||| | ||||| |||||||| ||||| ||||||||||||||||||||||| ||  |||| ||||| ||||||||    ||
gtaagtttgtt-----tgcttttcttcctagactatgttgtgtactgtgatgatattgaatgtctact--------tattttgcttcctt---------ttttttttcatttgattagATTCTTCAAGAAGAAATTGGGGGTGTGAAAGGCCATTTTGGACCAATTAATGCATTGGCTTTTAACCCTGATGGAAAAAG

upper sequence: LOC_Os08g21660.2 (Oryza sativa), 3'ss of exon 5
lower sequence: GLYMA09G36870.1 (Glycine max), 3'ss of exon 3
gtcagttcttcgcacatagtttccatcttatgttttagtgagaacaatgatcgtgtggttatcttttcaaagttatattttgctgttcaagaatgagagttctatatttttctttagATTTTGCAAGAGGAAATTGGTGGTGTTAAAGGCCATTTTGGACCAATTAACGCGCTGGCATTTAATCCTGATGGGCGGAG
                ||| ||   | ||   |  ||            |   | || | |  | |  || | |||   |   |||  |   ||     || | ||||  || ||||||| | ||||| |||||||| ||||| |||||||| |||||||||||||| ||  |||| ||||| ||||||||    ||
---------------gtaggtttttttttccttcctat-----------actatatgttgagttctgtaatggtat---tgaatgtctacttatttcgcttttttatt--tcattagATTCTTCAAGAAGAAATTGGGGGTGTGAAAGGCCACTTTGGACCAATTAATGCATTGGCTTTTAACCCTGATGGAAAAAG

upper sequence: LOC_Os08g21660.2 (Oryza sativa), 3'ss of exon 5
lower sequence: GLYMA01G03610.1 (Glycine max), 3'ss of exon 6
gtcagttcttcgcacatagtttccatcttatgttttagtgagaacaatgatcgtgtggttatcttttcaaagttatattttgctgttcaagaatgagagttctatatttttctttagATTTTGCAAGAGGAAATTGGTGGTGTTAAAGGCCATTTTGGACCAATTAACGCGCTGGCATTTAATCCTGATGGGCGGAG
|| |||| ||      |  || |  |  |||||||   |      ||||||  |||    ||||  | |   || |  |||    ||||    ||       |||   |||  ||||||| | ||||| |||||||| ||||| ||||| ||||||||||||||||| ||  |||| ||||| ||||||||    ||
gtaagtttttttttttt--ttcctttactatgtttagttctc--taatgat-atgtaac-atctactta---ttttgctttttatttcatatttg------ttattcatttgattagATTCTTCAAGAAGAAATTGGGGGTGTAAAAGGGCATTTTGGACCAATTAATGCATTGGCTTTTAACCCTGATGGAAAAAG

upper sequence: LOC_Os08g21660.2 (Oryza sativa), 3'ss of exon 5
lower sequence: AT2G46290.1 (Arabidopsis thaliana), 3'ss of exon 7
gtcagttcttcgcacatagtttccatcttatgttttagtgagaacaatgatcgtgtggttatcttttcaaagttatattttgctgttcaagaatgagagttctatatttttctttagATTTTGCAAGAGGAAATTGGTGGTGTTAAAGGCCATTTTGGACCAATTAACGCGCTGGCATTTAATCCTGATGGGCGGAG
                           |  ||||  ||| | |||| |  |  | |    |  | |   ||  |  |    | | |  ||   ||    |  | |  |  | | |||||| ||||||||||||||||||| || ||||| ||||||||||| ||||| ||  ||||||| | ||||||||||  |||
-------------------------gttagtgttgcagt-aaaacagtt-ttatttaaaaacttgt---aacctggaaagagatatgtaactgtgtatttggtcttataatatatagATTCTGCAAGAGGAAATTGGTGGCGTGAAAGGTCATTTTGGACCTATTAATGCTTTGGCATTCAGTCCTGATGGGAAGAG

upper sequence: LOC_Os08g21660.2 (Oryza sativa), 3'ss of exon 5
lower sequence: AT2G46280.3 (Arabidopsis thaliana), 3'ss of exon 5
gtcagttcttcgcacatagtttccatctta-tgttttagtgagaacaatgatcgtgtggttatcttttcaaagttatattttgctgttcaagaatgagagttctatatttttctttagATTTTGCAAGAGGAAATTGGTGGTGTTAAAGGCCATTTTGGACCAATTAACGCGCTGGCATTTAATCCTGATGGGCGGAG
           |    |  ||   ||   | ||||||| |  |||  ||| |    |||  |    | || |  | ||  |  | ||  |  | || |  |  |||| | |    |||||| |||||||||||||||||||||| ||||| ||||||||||| || || ||  ||||||| ||||||||||||  |||
-----------gttagtgtttataataagagtgttttacttggaaacatg-taacctggaaa---atacacatatttaaataaccgtgtatcattgtgtttggtataatat---atagATTCTGCAAGAGGAAATTGGTGGTGTGAAAGGTCATTTTGGACCTATAAATGCTTTGGCATTCAATCCTGATGGGAAGAG

upper sequence: LOC_Os08g21660.2 (Oryza sativa), 3'ss of exon 5
lower sequence: PP1S28_21V6.2 (Physcomitrella patens), 3'ss of exon 1
gtcagttcttcgcacatagtttccatcttatgttttagtgagaacaatgatcgtgtggttatcttttcaaagttatattttgctgttcaagaatgagagttctatatttttctt--tagATTTTGCAAGAGGAAATTGGTGGTGTTAAAGGCCATTTTGGACCAATTAACGCGCTGGCATTTAATCCTGATGGGCGGAG
                    | || | |||   ||||      | | | |||    |  |     |   ||   |||    |    ||   | | |  ||    |  ||  | |   |||||||  ||||||||||||||||||| || |||||||||||||| ||||| || || |  ||||||||||| ||  ||||
------------------aatgcctttttaccatttatccgagatattcatcaca-gactgcaactcataaagcatagaaagagaatccttatttaccgtctcgtgattgacgtgccagATTTTCGAAGAGGAAATTGGTGGTGTGAAGGGCCATTTTGGACCTATTAATGCTCTAGTTTTTAATCCTGACGGAAGGAG

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|2797339|gb|AA750633.1|AA750633
EST:     CTATGACAGATCGTCGTGCAGGAAAATTTGAAGCGAAATTTTTTCACAAG                         ATTTTGCAAGAGGAAATTGGTGGTGTTAAAGGCCATTTTGGACCAATTAAC
genomic: CTATGACAGATCGTCGTGCAGGAAAATTTGAAGCGAAATTTTTTCACAAGgtcagttctt ... ttttctttagATTTTGCAAGAGGAAATTGGTGGTGTTAAAGGCCATTTTGGACCAATTAAC




















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: 74 (upstream exon), 61 (downstream exon)
Score: 22

GTGGTTATTGGAGGTGGTCAAGATGCGATGAATGTGACTATGACAGATCGTCGTGCAGGAAAATTTGAAGCGAAATTTTTTCACAAGgtcagttctt ... ttttctttagATTTTGCAAGAGGAAATTGGTGGTGTTAAAGGCCATTTTGGACCAATTAACGCGCTGGCATTTAATCCTGATGGGCGGAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cttttcaaagttatattttgctgttcaagaatgagagttctatatttttctttagATTTTGCAAGAGGAAATTGGTGGTGTTAAAGGCCATTTTGGACCAATTAACGCGCTGGCATTTAATCCTGATGGGCGGAG
                                     ttctatatttttcttt  CT-rich tract
                                     ttctatatttttcttt  TA-rich tract