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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgccattctgatctttaaccccaatctgttctatatgatactttagtatgttttcatttccttgatttaatgcatggtttacactgacaaccatatttctaatgcagATGATGTGGAGACTTAATTTTTTTGTGGCTTTCTGCTGCATTGTCCTTGACAATGATTACATGCTCTATTACATATGCCCAATGCACACTTTGTTTACTC

Basic information

species Oryza sativa
transcript LOC_Os01g44040.3
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g44040.2 (Oryza sativa), 3'ss of exon 7
lower sequence: GLYMA08G08730.1 (Glycine max), 3'ss of exon 8
gtgccattc--tgatctttaaccccaatctgttctatatgatac------tttagtatgttttcatttccttgatttaatgcatggtttacactgacaaccatatttctaatgcagATGATGTGGAGACTTAATTTTTTTGTGGCTTTCTGCTGCATTGTCCTTGACAATGATTACATGCTCTATTACATATGCCCAATGCACACTTTGTTTACTC
||   | ||  ||| ||| ||  ||| | || | ||  || ||       | ||   | ||   ||| |  |  ||  ||  |   | ||| || ||      |  | |  |||||||||||||| | ||||||||||||||||| ||||| || ||||| ||| ||||||| || |||||||| || |||||||||||||||||  | || ||| 
gtaagagtcattgaccttaaataccattttgctttacttggtatccattgtctatccttttcctattactctttttgcataaacaatatac-ctaactcgttaaaatttcttgcagATGATGTGGCGGCTTAATTTTTTTGTGGCCTTCTGTTGTATTGTGCTTAACAATGACTATATGCTCTACTATATATGCCCAATGCACACGCTTTTCACTT

upper sequence: LOC_Os01g44040.2 (Oryza sativa), 3'ss of exon 7
lower sequence: GLYMA05G25780.1 (Glycine max), 3'ss of exon 8
---gtgccattct-gatctttaaccccaatct-gttctatatgatac------tttagtatgttttcatttccttgatttaatgcatggtttacactgacaaccatatttctaatgcagATGATGTGGAGACTTAATTTTTTTGTGGCTTTCTGCTGCATTGTCCTTGACAATGATTACATGCTCTATTACATATGCCCAATGCACACTTTGTTTACTC
    |    | || || ||| ||  ||| | | | | ||  |  |        | ||   | ||    || |  |  ||  ||  |   | |||          | | |||   |||||||||||||| | ||||||||||||||||| ||||| || ||||| ||| ||||||| || |||||||| || |||||||||||||||||  | || ||| 
gtaatagagtccttgaccttaaataccatttttgctttactttgtgtccactgtctatccttttcctgttactctttttgcataaacaatatacctaactcgttaaaattcct-tgcagATGATGTGGCGGCTTAATTTTTTTGTGGCCTTCTGTTGTATTGTGCTTAACAATGACTATATGCTCTACTATATATGCCCAATGCACACGCTTTTCACTT

upper sequence: LOC_Os01g44040.2 (Oryza sativa), 3'ss of exon 7
lower sequence: AT2G34410.1 (Arabidopsis thaliana), 3'ss of exon 7
---gtgccattctgatctttaaccc-caatctgttctatatgatactttagtatgttttcatttccttgatttaatgcatggtttacactgacaaccatatttctaatgcagATGATGTGGAGACTTAATTTTTTTGTGGCTTTCTGCTGCATTGTCCTTGACAATGATTACATGCTCTATTACATATGCCCAATGCACACTTTGTTTACTC
    |  || |   |   ||||        |  |  |||||| | ||   | |  | ||  ||||  ||| | ||     | |   ||   | |    || ||||  | |||||||||||| | ||||| || |||||||| ||  |||||||| | ||  | |||||||| ||||| || ||||| || |||||||||||| |||| ||||
gtcatttcaattgcacagttaattagttgaccatgatatatgcttctaagggacatgttgttttcaatgactcaa-----gatgctcatgaaaacttttacttct--tccagATGATGTGGCGTCTTAACTTATTTGTGGCGTTTAGCTGCATTATTCTCAATAATGATTATATGCTGTACTACATCTGTCCAATGCACACTCTGTTCACTC

upper sequence: LOC_Os01g44040.2 (Oryza sativa), 3'ss of exon 7
lower sequence: AT1G29890.1 (Arabidopsis thaliana), 3'ss of exon 6
----gtgccattctgatctttaaccccaatctgttctatatgatactttagtatgttttcatttccttgatttaatgcatggtttacactgac-----aaccatatttctaatgcagATGATGTGGAGACTTAATTTTTTTGTGGCTTTCTGCTGCATTGTCCTTGACAATGATTACATGCTCTATTACATATGCCCAATGCACACTTTGTTTACTC
    |  | | | |  ||  | |||  | | |||||  | |   |  | |   | ||||      |   || |  | ||  | | |   |        || | | |   |||| |||||||||||| | ||||| ||||||||||| || || |||||| | ||  ||||||| || ||||| || ||||| || |||||||||||| | || || |
gtcagatcaactattttcgatcaccatagtttgttcagtttaccatgtgatgttcttttagagagcactatgtctttcaaagctcaagatttttatgaaagcttttacttaatccagATGATGTGGCGGCTTAACTTTTTTGTGGCGTTTTGTTGCATTATTCTCAACAATGACTATATGCTGTACTACATCTGTCCAATGCACACTCTATTCACGC

upper sequence: LOC_Os01g44040.2 (Oryza sativa), 3'ss of exon 7
lower sequence: Vv10s0003g02830.t01 (Vitis vinifera), 3'ss of exon 2
------gtgcca-ttctgatctttaaccccaatctgttctatatgatactttagtatgttttcatttccttgatttaa---tgcatggtttacactgacaaccata--tttctaatgcagATGATGTGGAGACTTAATTTTTTTGTGGCTTTCTGCTGCATTGTCCTTGACAATGATTACATGCTCTATTACATATGCCCAATGCACACTTTGTTTACTC
       ||  | |||||| || |  |  || |    | |      |  | | ||   ||||||||| ||  |||| |   |  ||  ||||   ||  || | |   ||||||||||||||||||||| | || ||||| |||||||| || ||||||||||| ||| ||||||| |||||||| || || || ||||| ||||||||  | || ||||
gtgaccttgttaattctgaactgtttcatcatttctctattagaagtgatattgttccttttcattttctatatttcaattttgataatttaggatgtgaatctttactttctaatgcagATGATGTGGCGGCTAAATTTCTTTGTGGCATTTTGCTGCATTGTTCTTAACAATGACTACATGCTATACTATATCTGCCCCATGCACACGCTTTTCACTC

upper sequence: LOC_Os01g44040.2 (Oryza sativa), 3'ss of exon 7
lower sequence: PP1S5_239V6.1 (Physcomitrella patens), 3'ss of exon 7
gtgccattctgatctttaaccccaatctgttctatatgatactttagtatgttttcatttccttgatttaatgcatggtttacactgac-aaccatatttctaatgcagATGATGTGGAGACTTAATTTTTTTGTGGCTTTCTGCTGCATTGTCCTTGACAATGATTACATGCTCTATTACATATGCCCAATGCACACTTTGTTTACTC
       |  |   | |      |   |||   ||    ||   |   || | ||  || | |     ||||    |   | |||||||         |  |   ||||||||||||| | || |||||  | ||    ||  |||||||||| ||  ||||||| ||||||||||| ||||| || |||||||||||| | || ||||
-------ttcgcgatctgctttgagggtgtggaatcaagtatcgtc-cat-tcttagttgcttctggataatcggagtcatgcactgactgggttcgatgatttggcagATGATGTGGCGGCTCAATTTCCTGGTCTTCTTTAGCTGCATTGTACTGAACAATGACTACATGCTCTACTACATCTGTCCAATGCACACTCTCTTCACTC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttcatttccttgatttaatgcatggtttacactgacaaccatatttctaatgcagATGATGTGGAGACTTAATTTTTTTGTGGCTTTCTGCTGCATTGTCCTTGACAATGATTACATGCTCTATTACATATGCCCAATGCACACTTTGTTTACTC
                                            ttctaat  putative branch site (score: 2)
                                         tatttct  CT-rich tract
                                        atatttctaat  TA-rich tract