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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgaaatttctttactctaaaatttttgatcaatcgtctccctataatttttggtcagacgattagaagtttcaggtttccataaaaacctcgttactaattcatggaaagcttttctttcacagGTTTGACAAGAGAATCACTGAGTTTGCCGAAGAAAAGTTTAGCAGAGATGGAATTGATGTGAAACTTGGCTCGATGGTAACTAAAGTGAATGAGAAAGAT

Basic information

species Arabidopsis thaliana
transcript AT4G05020.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT4G05020.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: LOC_Os08g04630.1 (Oryza sativa), 3'ss of exon 4
---------------------gtgaaatttctttactctaaaatttt---tgatcaatcgtctccctataatttt--tggtcag--acgattagaagtttcaggtttccataaaaacct--cgttactaattca----tggaaagcttttctttc-acagGTTTGACAAGAGAATCACTGAGTTTGCCGAAGAAAAGTTTAGCAGAGATGGAATTGATGTGAAACTTGGCTCGATGGTAACTAAAGTGAATGAGAAAGAT
                     ||   ||||  ||  | | || || |   |  | | ||  ||   | | |||    || | ||  | |||   | | | | |     ||     |||   | ||   |||| |    ||   |  | | ||| | | |||||||||||||| || ||||| ||||| || || |||||| | || ||||| ||||||||||||  ||| |  |  ||    || ||   | || | |  
gtaaggccatactggatttctgttgcatttgattcatatgaagttatgactagtgattcacctttttctcattaccatgattagctatgatggaaggatgcggcaacgcaagcttaccctcccttgtaaatttaactttgattacatgtgcttcctatagGTTTGACAAGAGGATTACTGAATTTGCTGAGGATAAGTTTGGAAGGGATGGCATTGATGTGAAAACTGGATACAAAGTTGTGAAGGTTGCTAAGGATGCA

upper sequence: AT4G05020.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA13G32030.1 (Glycine max), 3'ss of exon 4
gtgaaatttctttactctaaaatttttgatcaatcgtctccctataatttttggtcagacgattagaagtttcaggtttccataaaaacctcgttactaattcatggaaagcttttctttcacagGTTTGACAAGAGAATCACTGAGTTTGCCGAAGAAAAGTTTAGCAGAGATGGAATTGATGTGAAACTTGGCTCGATGGTAACTAAAGTGAATGAGAAAGAT
                     |||||| |  | |  | |   | | |           || ||| |||  ||  | | |  |    | | |  ||  ||  |  |  |  ||| ||||  || ||||||||||||||||||||||  ||||| ||||| |||||| | |||||||| ||||||||||||   || || |||||   ||| ||   ||||||||| 
--------------------catttttaactatttatatttatctgaaaggaacattaac-atttgaatcttttgttatttagtttatcatacttgatatgt--tcaattgctcttct--catagGTTTGACAAGAGAATCACTGCTTTTGCTGAAGACAAGTTTCGAAGAGATGGGATTGATGTGAAAACAGGATCCATGGTTGTTAAGGTATCTGAGAAAGAA

upper sequence: AT4G05020.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA08G06380.1 (Glycine max), 3'ss of exon 4
gtgaaatttctttactctaaaatttttgat-caatcgtctccctataatttttggtcagacgattagaagtttcaggtttccataaaaacctcgttactaattcatggaaagcttttctttcacagGTTTGACAAGAGAATCACTGAGTTTGCCGAAGAAAAGTTTAGCAGAGATGGAATTGATGTGAAACTTGGCTCGATGGTAACTAAAGTGAATGAGAAAGAT
                    | | |||||| || || |     |   |  | ||||  |  | ||  || |   ||  | | || |     |   |  | |||| |   | |||    |||||  |||||||||| ||||||||||  ||||| ||||| |||||  | |||||||| ||||||||||||   || || |||||    || ||   | ||||||| 
--------------------agtatttgattcagtcatggattttatacgtgtggttgggtggtttaaaatag-agcatactatgagcttataagttttcattctt---atgctcacttttca--gGTTTGACAAAAGAATCACTGCTTTTGCTGAAGAGAAGTTCGGAAGAGATGGTATTGATGTGAAAACCGGATCCATGGTTGTGAAGGTTTCTCAGAAAGAA

upper sequence: AT4G05020.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA15G07290.1 (Glycine max), 3'ss of exon 4
gtgaaatttctttactctaaaatttttgatcaatcgtctccctataatttttggtcag-acgattagaagtttcaggtttccataaaaacctcgt--tactaattcatggaaagcttttctt-tcacagGTTTGACAAGAGAATCACTGAGTTTGCCGAAGAAAAGTTTAGCAGAGATGGAATTGATGTGAAACTTGGCTCGATGGTAACTAAAGTGAATGAGAAAGAT
                            ||  ||   || | |||| || |  |  || || ||||  | ||  |  |||   ||   |  |  |  ||||   | |||      |  |||| | | ||||||||||||||||| |||   ||||| ||||| |||||| | ||||| || ||||||||||||   || || |||||   ||| ||    |||||||| 
---------------------------catttataa-ctacttatagttatcagaaaggaccattaatatttgaatcttttgttatttagtttatcatactggat-atgttccattgctcttcttatagGTTTGACAAGAGAATTACTACTTTTGCTGAAGACAAGTTTCGAAGAGACGGGATTGATGTGAAAACAGGATCCATGGTTGTTAAGGTATCCGAGAAAGAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttcaggtttccataaaaacctcgttactaattcatggaaagcttttctttcacagGTTTGACAAGAGAATCACTGAGTTTGCCGAAGAAAAGTTTAGCAGAGATGGAATTGATGTGAAACTTGGCTCGATGGTAACTAAAGTGAATGAGAAAGAT
                        tactaat  putative branch site (score: 1)
                                         cttttctttcac  putative PPT
                       ttactaatt  TA-rich tract