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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TCTGCTATTGAGGAGAAAGTGATTGAAAGAGCTTACAAGAAGTTAGCACTTGATGCTCTGGTTATTCAACAAGGGAGATTGGCAGAACAGAAAAgtaagtgcgttatacagtgattgctttatgcattggttcatctctgacagaattggtatttatcttaactatgcag

Basic information

species Arabidopsis thaliana
transcript AT3G06400.1
intron # 13
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT3G06400.1 (Arabidopsis thaliana), 5'ss of exon 13
lower sequence: 13113.m00246 (Oryza sativa), 5'ss of exon 13
TCTGCTATTGAGGAGAAAGTGATTGAAAGAGCTTACAAGAAGTTAGCACTTGATGCTCTGGTTATTCAACAAGGGAGATTGGCAGAACAGAAAAgtaagtgcgttatacagtgattgc---tttatgcattggttcat-ctctgacagaattggtatttatcttaactatgcag---
| | | || ||||||||||||||||| || || ||||||||| | ||| | |||||| |||| |||||||||||  || ||||||| ||||| |||| ||   |  | |    |||     |||| | |    ||||| |  |   |  ||  | |||||| ||     |       
TATACCATCGAGGAGAAAGTGATTGAGAGGGCATACAAGAAGCTTGCATTGGATGCTTTGGTCATTCAACAAGGCCGACTGGCAGAGCAGAAGAgtatgtttttgctgcttgtattttatgtttaagaaggcattcatgcagtagtaagatatggatttattttgttcttctttcag

upper sequence: AT3G06400.1 (Arabidopsis thaliana), 5'ss of exon 13
lower sequence: GLYMA07G38050.2 (Glycine max), 5'ss of exon 13
TCTGCTATTGAGGAGAAAGTGATTGAAAGAGCTTACAAGAAGTTAGCACTTGATGCTCTGGTTATTCAACAAGGGAGATTGGCAGAACAGAAAAgtaagtgcgttatacagtgattgctttatgcattggttcatctctgacagaattggtat-ttatctta-actatgcag-----------------
| | | |||||||| ||||| |||||||| |||||||||||| | ||||||||||||||||| ||||| |||||| |||| || |||||||| |||||| |  || |   | | ||  | | ||  ||  ||  | | |  ||  |||| |   |||| | | |   | ||                  
TATACGATTGAGGAAAAAGTCATTGAAAGGGCTTACAAGAAGCTTGCACTTGATGCTCTGGTGATTCAGCAAGGGCGATTAGCTGAACAGAAGAgtaagggttttct---gggttttatctttgtttttattattttgttgcaagattgatggattatataacatggtacaatctatttgtgtatgcag

upper sequence: AT3G06400.1 (Arabidopsis thaliana), 5'ss of exon 13
lower sequence: GLYMA17G02640.1 (Glycine max), 5'ss of exon 13
TCTGCTATTGAGGAGAAAGTGATTGAAAGAGCTTACAAGAAGTTAGCACTTGATGCTCTGGTTATTCAACAAGGGAGATTGGCAGAACAGAAAAgtaag------tgcgttataca------gtgattgctttatgcattggttcatctctgacagaat-tggtatttatcttaactatgcag----
| | | |||||||| ||||| |||||||| |||||||| ||| | || |||||||||||||| ||||| |||||| |||| || |||||||| ||||||      ||  || ||         | |||  ||| |   | | || ||   | | | ||  |||||   |   ||  | || |     
TATACGATTGAGGAAAAAGTCATTGAAAGGGCTTACAAAAAGCTTGCTCTTGATGCTCTGGTGATTCAGCAAGGGCGATTAGCTGAACAGAAGAgtaagggtttctggattttatcttcgtttttattattttgttgctagatttatggattatataacatggtacacaatctatttgtgtatgcag

upper sequence: AT3G06400.1 (Arabidopsis thaliana), 5'ss of exon 13
lower sequence: GLYMA13G28720.1 (Glycine max), 5'ss of exon 13
TCTGCTATTGAGGAGAAAGTGATTGAAAGAGCTTACAAGAAGTTAGCACTTGATGCTCTGGTTATTCAACAAGGGAGATTGGCAGAACAGAAAAgtaagtgcgttatacagtgattgctttatgcattggttcatctctgacagaattg------gtatttatcttaact-----atgcag
| | | || || |||||||| |||||||| || ||||| ||| | ||||||||||||||||| ||||| |||||| ||||||| || ||||| |||| |      ||  |    ||   || |   || | | |    ||   | ||||      ||  ||   || | |      |||||
TATACAATAGAAGAGAAAGTCATTGAAAGGGCCTACAAAAAGCTTGCACTTGATGCTCTGGTGATTCAGCAAGGGCGATTGGCTGAGCAGAAGAgtatggattcaatgaataatttttcttgtttctttgctgaaagttgtgtggattgtctaatgtggttccattgatttttatgtgcag

upper sequence: AT3G06400.1 (Arabidopsis thaliana), 5'ss of exon 13
lower sequence: GLYMA15G10370.1 (Glycine max), 5'ss of exon 13
TCTGCTATTGAGGAGAAAGTGATTGAAAGAGCTTACAAGAAGTTAGCACTTGATGCTCTGGTTATTCAACAAGGGAGATTGGCAGAACAGAAAAgtaagtgcgttatacagtgattgctttatgcattggttcatctctgacagaattg----gtat-------ttatcttaactatgcag
| | | || || |||||||| |||||||| || ||||| ||| | ||||||||||||||||| ||||| |||||| ||||||| || ||||| |||| |      ||  |    ||   || |   || | | |    ||   | ||||     |||       ||  |||   | |||||
TATACAATAGAAGAGAAAGTCATTGAAAGGGCCTACAAAAAGCTTGCACTTGATGCTCTGGTGATTCAGCAAGGGCGATTGGCTGAGCAGAAGAgtaggaattcaatgaataacttttcttgtttctttgctgaaagttgtgtggattgtctaatatggttccattggcttttatgtgcag

upper sequence: AT3G06400.1 (Arabidopsis thaliana), 5'ss of exon 13
lower sequence: Vv05s0020g01780.t01 (Vitis vinifera), 5'ss of exon 13
TCTGCTATTGAGGAGAAAGTGATTGAAAGAGCTTACAAGAAGTTAGCACTTGATGCTCTGGTTATTCAACAAGGGAGATTGGCAGAACAGAAAAgtaagtgcgttatacagt----gattgctttatgcattggttcatct-ctgacagaattggtat--------ttatcttaactatgcag----------
| | | || ||||| || |||||||| |||||||| || || || ||||| |||||| |||| |||||||||||  | || ||||| ||||||||| ||    || | || |    | |||||||   |  ||          | | |||| | | |         || | ||   | ||  |          
TATACCATCGAGGAAAAGGTGATTGAGAGAGCTTATAAAAAATTGGCACTCGATGCTTTGGTGATTCAACAAGGACGGTTAGCAGAGCAGAAAAgtgagccatttctgcattacaagcttgctttgcactatgacatgctaattcatagaactagaaccactaacattttgttgtttttgtgggcttttgcag

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|116473628|gb|EG516220.1|EG516220
EST:     AGCACTTGATGCTCTGGTTATTCAACAAGGGAGATTGGCAGAACAGAAAA                         CTGTCAATAAGGATGAGTTGCTTCAAATGGTAAGATATGGTGCTGAGATGG
genomic: AGCACTTGATGCTCTGGTTATTCAACAAGGGAGATTGGCAGAACAGAAAAgtaagtgcgt ... aactatgcagCTGTCAATAAGGATGAGTTGCTTCAAATGGTAAGATATGGTGCTGAGATGG
EST: gi|116473629|gb|EG516221.1|EG516221
EST:     GTTATTCAACAAGGGAGATTGGCAGAACAGAAAA                         CTGTCAATAAGGATGAGTTGCTTCAAATGGTAAGATATGGTGCTGAGATGG
genomic: GTTATTCAACAAGGGAGATTGGCAGAACAGAAAAgtaagtgcgt ... aactatgcagCTGTCAATAAGGATGAGTTGCTTCAAATGGTAAGATATGGTGCTGAGATGG
EST: gi|125181844|gb|EL197762.1|EL197762
EST:     GCACTTGATGCTCTGGTTATTCAACAAGGGAGATTGGCAGAAACAGAAAA                         CTGTCAATAAGGATGAGTTG
genomic: GCACTTGATGCTCTGGTTATTCAACAAGGGAGATTGGCAGAA-CAGAAAAgtaagtgcgt ... aactatgcagCTGTCAATAAGGATGAGTTG

Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TCTGCTATTGAGGAGAAAGTGATTGAAAGAGCTTACAAGAAGTTAGCACTTGATGCTCTGGTTATTCAACAAGGGAGATTGGCAGAACAGAAAAgtaagtgcgttatacagtgattgctttatgcattggttcatctctgacagaattggtatttatcttaactatgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAT