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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tcaatctaattcaatcatggaacttaaaacttttgatcaatagaagtatttaaatatttaattttaatgttggtatttttctgtgtgcgcgctaatgcagGGGATTCAGAGAAGCTAGTTAAAGTTCTGTTTGAGCTTGCTAGACATCATGCACCATCGACAATATTTCTTGATGAAATTGATGCTATTATCAGCCAACG

Basic information

species Oryza sativa
transcript LOC_Os01g55260.2
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g55260.1 (Oryza sativa), 3'ss of exon 7
lower sequence: GRMZM2G022777_T01 (Zea mays), 3'ss of exon 7
tcaatctaattc--aatcatggaacttaaaacttttgatcaatagaagtatttaaatatttaattttaatgttggtatttttctgtgtgcgcgctaatgcagGGGATTCAGAGAAGCTAGTTAAAGTTCTGTTTGAGCTTGCTAGACATCATGCACCATCGACAATATTTCTTGATGAAATTGATGCTATTATCAGCCAACG
||  | |  |||  ||  || ||||| | |  |     |   ||     ||||   ||||     |  |   |  || | |  | |      |  | |||||| |||||||||||||| || ||||||||||||||||||||||| |||||||||||||| |||||||| ||||||||||| |||||||| |||||||| ||
tccttgttgttcttaagtatagaact-atatttcactctttttattcccatttctctattaggactggagaatc-taatgtctttttcatatgtgagtgcagGAGATTCAGAGAAGCTTGTCAAAGTTCTGTTTGAGCTTGCTAGGCATCATGCACCATCCACAATATTCCTTGATGAAATAGATGCTATCATCAGCCAGCG

upper sequence: LOC_Os01g55260.1 (Oryza sativa), 3'ss of exon 7
lower sequence: GLYMA05G26100.2 (Glycine max), 3'ss of exon 2
----------------tcaatctaat--tcaatcatggaacttaaaacttttgatcaatagaag-tatttaaatatttaattttaatgttg-gtatttttctg---tgtgcgcgctaatgcagGGGATTCAGAGAAGCTAGTTAAAGTTCTGTTTGAGCTTGCTAGACATCATGCACCATCGACAATATTTCTTGATGAAATTGATGCTATTATCAGCCAACG
                | | |  |||  | ||| |   |  |  ||  | |   | | |  | | |   | | | | | |||||     |  |||  |||      | |       | |||||| |||||||||||| |||| |||||  | ||||| ||||| || ||||||||||| || |||||||||||||||||||||||||| || || || |||||
gttagttagttacccattagttcaatagttaattacatatttacaatatatcagttagtttaggctgaattagtgtgttattttgtgaatacgtacatttacaaaatttattttggactgcagGTGATTCAGAGAAGTTAGTGAAAGTGTTATTTGAACTTGCAAGGCATCATGCACCCTCAACAATATTTCTTGATGAAATTGATGCAATCATTAGTCAACG

upper sequence: LOC_Os01g55260.1 (Oryza sativa), 3'ss of exon 7
lower sequence: GLYMA05G26100.1 (Glycine max), 3'ss of exon 7
tcaatctaattcaatcatggaacttaaaacttttgatcaatagaag-tatttaaatatttaattttaatgttg-gtatttttctg---tgtgcgcgctaatgcagGGGATTCAGAGAAGCTAGTTAAAGTTCTGTTTGAGCTTGCTAGACATCATGCACCATCGACAATATTTCTTGATGAAATTGATGCTATTATCAGCCAACG
  |||   | | ||| |   |  |  ||  | |   | | |  | | |   | | | | | |||||     |  |||  |||      | |       | |||||| |||||||||||| |||| |||||  | ||||| ||||| || ||||||||||| || |||||||||||||||||||||||||| || || || |||||
--aat---agttaattacatatttacaatatatcagttagtttaggctgaattagtgtgttattttgtgaatacgtacatttacaaaatttattttggactgcagGTGATTCAGAGAAGTTAGTGAAAGTGTTATTTGAACTTGCAAGGCATCATGCACCCTCAACAATATTTCTTGATGAAATTGATGCAATCATTAGTCAACG

upper sequence: LOC_Os01g55260.1 (Oryza sativa), 3'ss of exon 7
lower sequence: GLYMA08G09050.1 (Glycine max), 3'ss of exon 7
tcaatctaattcaatcatggaacttaaaacttttgatcaatagaagtatttaaatatttaattttaatgttggtatttttctgtgtgcgcgctaatgcagGGGATTCAGAGAAGCTAGTTAAAGTTCTGTTTGAGCTTGCTAGACATCATGCACCATCGACAATATTTCTTGATGAAATTGATGCTATTATCAGCCAACG
  | |  | | ||    |  ||  ||  | ||    |     ||| || ||   ||||   |    ||||   | |         |       | |||||| |||||||||||| |||| |||||  | ||||| ||||| || ||||||||||| || |||||||||||||| ||||||||||| || || || |||||
atagttaattacagatttacaatatatcagttagtttaggctgaattagtttgctattctgtgaatatgtacatttacaaaaaattcttttggactgcagGTGATTCAGAGAAGTTAGTGAAAGTGTTATTTGAACTTGCAAGGCATCATGCACCCTCAACAATATTTCTTGACGAAATTGATGCAATCATTAGTCAACG

upper sequence: LOC_Os01g55260.1 (Oryza sativa), 3'ss of exon 7
lower sequence: AT2G34560.1 (Arabidopsis thaliana), 3'ss of exon 7
----tcaatctaattcaatcatggaacttaaaacttttgatcaatagaagtatttaaatatttaattttaatgttggtatttttctgtgtgcgcgctaatgcagGGGATTCAGAGAAGCTAGTTAAAGTTCTGTTTGAGCTTGCTAGACATCATGCACCATCGACAATATTTCTTGATGAAATTGATGCTATTATCAGCCAACG
       || |  | |  | ||  |   | || | |   || |   | ||| ||||       |    |||  || |   |||||  |||         | |||| ||||| |||||| |  | | ||||||||| || || ||||| ||||||||||| |||||||||||||||||||| || || || || || ||||||||
gtgaaatattttgtacctttatttactcttaaccatgaaataagatgcagtctttagg-----agaaataaaatttgggcttttcaatgttt-------ttcagGTGATTCTGAGAAGTTGATAAGAGTTCTGTTCGATCTAGCTAGGCATCATGCACCTTCGACAATATTTCTTGATGAGATCGACGCGATCATAAGCCAACG

upper sequence: LOC_Os01g55260.1 (Oryza sativa), 3'ss of exon 7
lower sequence: Vv10s0003g03500.t01 (Vitis vinifera), 3'ss of exon 7
tcaatctaattcaatcatggaacttaaaacttttgatcaatagaagtatttaaatatttaattttaatgttgg--tatttttctgtgtgcgcgctaatgcagGGGATTCAGAGAAGCTAGTTAAAGTTCTGTTTGAGCTTGCTAGACATCATGCACCATCGACAATATTTCTTGATGAAATTGATGCTATTATCAGCCAACG
   ||    |   ||    ||  |  |  |||||  |  ||    |  | | |  |  | ||  |     ||    |||  | | |||    | | ||| ||| |||||||||||| |||| |||||  | |||||||||||||| || ||||| || || || |||||||||||||||||||||||  ||||||| |||||
--gatagtttatgatatctgatatgcatccttttcttagatgatggactgtcagcaagttatggtgggagtgtatcattcctttatgtttttgtttatgtagGTGATTCAGAGAAGTTAGTGAAAGTGTTATTTGAGCTTGCTAGGCACCATGCCCCTTCAACTATATTTCTTGATGAAATTGATGCGCTTATCAGTCAACG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtatttaaatatttaattttaatgttggtatttttctgtgtgcgcgctaatgcagGGGATTCAGAGAAGCTAGTTAAAGTTCTGTTTGAGCTTGCTAGACATCATGCACCATCGACAATATTTCTTGATGAAATTGATGCTATTATCAGCCAACG
                                            cgctaat  putative branch site (score: 3)
     taaatatttaatttta  TA-rich tract