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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtcagtcttctctatttacctttataactaaataagtgaaaatggccgctgatgaagtatagtgatcgtaatgtattaccacaagttactccttttctcaattgatgattaactggttttcagGTTTTATGGGACCTTCCAAGGTTTGTGAAGATAGTTGAAGTTGGACCACGGGACGGTCTGCAAAATGAGAAGAATACTGTACCCACATCTGTAAAGATTG

Basic information

species Oryza sativa
transcript LOC_Os12g04020.2
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os12g04020.2 (Oryza sativa), 3'ss of exon 4
lower sequence: GLYMA07G36340.1 (Glycine max), 3'ss of exon 2
gtcagtcttctctatttacctttataactaaataagtgaaaatggccgctgatgaagtatagtgatcgtaatgtattacc--acaagttactccttttctcaattgatgattaactggttttcagGTTTTATGGGACCTTCCAAGGTTTGTGAAGATAGTTGAAGTTGGACCACGGGACGGTCTGCAAAATGAGAAGAATACTGTACCCACATCTGTAAAGATTG
              || || |||||      |||  |  | |    |  |  |    |    | ||| || |   ||  |    |||| ||         |||||  | |||      |   ||| || |    |   | ||||  ||||| ||||||||||||||||| ||| |||| ||  | ||||||||||| || | |||||| |||  |||||||||||
--------------ttgacatttatgtt---atacatttatactttctgtagttggttgattttatcatatttcgttgtctggtaagtaacat------acaatttttaattgggcaatg--cagTTTATGAAAGGTATACCAAAATTTGTAAAGATAGTTGAAGTTGGTCCAAGGGATGGATTACAAAATGAGAAAAACATTGTACCAACAGATGTAAAGATTG

upper sequence: LOC_Os12g04020.2 (Oryza sativa), 3'ss of exon 4
lower sequence: GLYMA14G04110.1 (Glycine max), 3'ss of exon 3
gtcagtcttctctatttacctttataactaaataagtgaaaatggccgctgatgaagtatagtgatcgtaatgtattaccacaagttactccttttctcaattgatgattaactggttttcagGTTTTATGGGACCTTCCAAGGTTTGTGAAGATAGTTGAAGTTGGACCACGGGACGGTCTGCAAAATGAGAAGAATACTGTACCCACATCTGTAAAGATTG
                      ||||  | || |  |   | ||   | | ||    |  |    || |  | || ||       |   | |  || | |||||   | |  ||    | ||| || |        | |||| |||||| |||||||| |||||||| ||| |||| ||  | |||||||||||||| | ||| || |||||||| |||||||
---------------------atatattttaa-actttctattgtttgtttattttat-cacatttctttgtctagtaattagcatgttttcaatttttaattggacaatggctatgatgcagTTTCTGAATAGTATACCAAAGTTTGTAAAGATAGTAGAAGTTGGTCCAAGGGATGGATTACAAAATGAGAAGAACATTGTGCCTACATCTGTGAAGATTG

upper sequence: LOC_Os12g04020.2 (Oryza sativa), 3'ss of exon 4
lower sequence: GLYMA20G08360.1 (Glycine max), 3'ss of exon 4
gtcagtcttctctatttacctttataactaaataagtgaaaatggccgctgatgaagtatagtgatcgtaatgtattaccacaagttactccttttctcaattgatgattaactggttttcagGTTTTATGGGACCTTCCAAGGTTTGTGAAGATAGTTGAAGTTGGACCACGGGACGGTCTGCAAAATGAGAAGAATACTGTACCCACATCTGTAAAGATTG----------
                                                                   |||   |||| |      |      |    |  | |  | |||      |   ||| || |    |   | ||||  ||||| ||||||||||||||||| ||| |||| ||  | ||||||||||| || | |||||| |||  |||||||||||          
-------------------------------------------------------------------gtatcatatttctttggctggtaagtaacatacaattttaattgggcaatg--cagtttatgaaagGTATACCAAACTTTGTAAAGATAGTTGAAGTTGGTCCAAGGGATGGATTACAAAATGAGAAAAACATTGTACCAACAGATGTAAAGATTGAATTGATTCA

upper sequence: LOC_Os12g04020.2 (Oryza sativa), 3'ss of exon 4
lower sequence: GLYMA02G44610.1 (Glycine max), 3'ss of exon 3
gtcagtcttctctatttacctttataactaaataagtgaaaatggccgctgatgaagtatagtgatcgtaatgtattacc-acaagttactccttttctcaattga--tgattaactggtt--ttcagGTTTTATGGGACCTTCCAAGGTTTGTGAAGATAGTTGAAGTTGGACCACGGGACGGTCTGCAAAATGAGAAGAATACTGTACCCACATCTGTAAAGATTG-----------
                             | |||  | ||| |    | ||  |   |||  | |||| | |   ||  |  | | |||     |||   | || |  ||  |||  |  |  | |||  | |        | |||| |||||| |||||||| |||||||| ||| |||| ||  | |||||||||||||| | |||||| ||  ||||||||||||           
--------------------------gtaatatattttaaactttttgttgtcgttttatt-ttatcgcatttccttttctgctaattaacatattttcaattttaattggataatggcatgatgcagtatctgaatagTATACCAAAGTTTGTAAAGATAGTAGAAGTTGGTCCAAGGGATGGATTACAAAATGAGAAGAACATTGTACCTACTGCTGTAAAGATTGAATTGATTCAC

upper sequence: LOC_Os12g04020.2 (Oryza sativa), 3'ss of exon 4
lower sequence: AT2G26800.3 (Arabidopsis thaliana), 3'ss of exon 3
-------------------------------------------------------------------gtcagtcttctctatttacctttataactaaataagtgaaaatggccgctgatgaagtatagtgatcgtaatgtattaccacaagttactccttttctcaattgatgattaactggttttcagGTTTTATGGGACCTTCCAAGGTTTGTGAAGATAGTTGAAGTTGGACCACGGGACGGTCTGCAAAATGAGAAGAATACTGTACCCACATCTGTAAAGATTG
                                                                     | ||||        ||  ||| ||     ||   |     |     ||| | ||   |    |    ||   |  |       ||    ||| |     ||  |   |   |||  || || | |     |   | |||| |||||||||||| || |||||||| ||| | || || ||||| |||||||| ||||  |||||||||||||||||| | |
gtaattgtctcgatggaggaaagtagtttttgacctctatataaaacatatccacagatacctcgttccccgtctatgtaggatagttttgtataatgattcatctttttcatttctgtttaaaatttcccactacaac-caccatttttttttctctcttattctgttttttttctgtttggaatttagATCTCTAAAGGTATACCAAAGTTTGTGAAGATTGTAGAAGTTGGTCCAAGAGATGGCCTGCAGAATGAGAAAAATATAGTACCCACATCTGTAAAGGTGG

upper sequence: LOC_Os12g04020.2 (Oryza sativa), 3'ss of exon 4
lower sequence: Vv06s0009g02640.t01 (Vitis vinifera), 3'ss of exon 2
gtcagtcttctctatttacctttataactaaataagtgaaaatggccgc--tgatgaagtatagtgatcgtaatgtattaccacaagttactccttttctcaattgatgattaactggttttcagGTTTTATGGGACCTTCCAAGGTTTGTGAAGATAGTTGAAGTTGGACCACGGGACGGTCTGCAAAATGAGAAGAATACTGTACCCACATCTGTAAAGATTG
                ||    ||||| |    |  | | |||    |   |  || |||    | |||    ||  |||    |  |||    || | |   |   |   |||  |     ||| ||||| | |   | |||| ||||||||||||||| |||||||| ||| |||| ||  |||||||||||||||||| |||||| ||| |||||||  | |
----------------taataatataattttgcattttacaatctttgtgttactggagttgtttcatc----tgatttattttattttatgttttatttttgtactttgataagag-----cagTTTTTAGGAGGTATACCAAAGTTTGTGAAGATAGTGGAAGTTGGTCCAAGGGATGGATTGCAAAATGAGAAGAATATTGTACCTACAGCTGTAAAAGTGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

taatgtattaccacaagttactccttttctcaattgatgattaactggttttcagGTTTTATGGGACCTTCCAAGGTTTGTGAAGATAGTTGAAGTTGGACCACGGGACGGTCTGCAAAATGAGAAGAATACTGTACCCACATCTGTAAAGATTG
                                      gattaac  putative branch site (score: 2)
                                                ttttc  putative PPT
                                    atgattaa  TA-rich tract