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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagcctaagccttattattgcgttcttacttgccttggccaatattaaactttgacttaatgtgctttctctactacatcctaaagcaacacaggataaccatatttttttactgtccccaaaagttagacataatcatatgataatatttctgtctaaatataatatgtcttcagGTGAAGAAAGTGAGGCCACATGTTCTTCTTGGTTTATCTGGAGTTGGTGGTATCTTTAATGAAGAA

Basic information

species Arabidopsis thaliana
transcript AT4G00570.1
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT4G00570.1 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: GLYMA07G08110.1 (Glycine max), 3'ss of exon 11
gtaagcctaagccttattattgcgttcttacttgccttggccaatattaaactttgacttaatgtgctttctctactacatcctaaagcaacacaggataaccatatttttttactgtccccaaaagttagacataatcatatgataatatttctgt--ctaaatataatatgtcttcagGTGAAGAAAGTGAGGCCACATGTTCTTCTTGGTTTATCTGGAGTTGGTGGTATCTTTAATGAAGAA
||||   | |      | ||   |     | |||  | |  ||||  |  |||||     | ||       | ||||      ||||   ||  |   | ||  || ||     ||      |||  |||  |||| |  |||    ||  ||   |   ||||  || | | |||| |||| |||||  | ||||||||||| || |||||||| ||||| ||||||||||| || ||||| || 
gtaaatgttacaggattcatcaaggaaa-atttgtttggctcaatgatctactttatgacattgaaaagaat-tactttgatataaaaggac-taaactcactttacttgaa-gctaattttaaagattatgcatacttttatagccatcctttaattcttaaacctattgt-tctttagGTTAAGAAGATTAGGCCACATGTGCTCCTTGGTTTGTCTGGCGTTGGTGGTATTTTCAATGAGGAG

upper sequence: AT4G00570.1 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: GLYMA03G01680.1 (Glycine max), 3'ss of exon 12
gtaagcctaagccttattattgcgttcttacttgccttggccaatattaaactttgacttaatgtgctttctctactacatcctaaagcaacacaggataaccatattttttta-ctgtccccaaaagttagacataatcatatgataatatttctgt-ctaaatataatatgtcttcagGTGAAGAAAGTGAGGCCACATGTTCTTCTTGGTTTATCTGGAGTTGGTGGTATCTTTAATGAAGAA
||||   | |      | ||   |     | | |  | |  ||||  |  |||||     | ||       |    |  ||   |||| |  | |   |    |  || ||  | ||      |||  |||  || | |  |||    ||  ||   | || ||   |||   |||| |||| |||||  | ||||||||||| || |||||||| ||||| ||||||||||| || ||||| || 
gtaaatgttataggattcatcaaggaaa-attcgtttggctcaatgatctactttatggcattgaaaagaattactttgatataaaaggactaaaccctctttactttattgaagctaattttaaagattatgcacacttttatagccatcctttaattcttaaaccaattgttctttagGTTAAGAAGATTAGGCCACATGTGCTCCTTGGTTTGTCTGGCGTTGGTGGTATTTTCAATGAGGAG

upper sequence: AT4G00570.1 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: Vv15s0046g03670.t01 (Vitis vinifera), 3'ss of exon 11
gtaagcctaagccttattattgcgttcttacttgccttggccaatattaaactttgacttaatgtgctttctctactacatcctaaagcaacacaggataaccatatttttttactgtccccaaaagttagacataatcatatgataatatttctgtctaaatataatatgt-cttcagGTGAAGAAAGTGAGGCCACATGTTCTTCTTGGTTTATCTGGAGTTGGTGGTATCTTTAATGAAGAA
       |||  | |||||    | | | |  ||||||   || ||| ||  |||   |||| |               ||  || |       |||| ||  | |||   |  ||| |    ||  ||| | || |||||     |  | || |   |    | || |  |  ||||||| || || || |  || ||||| ||||||||||| ||||||||||||||| |||| ||||| || 
------gtaaatcatattagattgatttaagctgcctttatcagtat-aagtttta--ttaagg---------------atgatagaatgtggaaggaaaa--agattgactagctgac----aattttacatatcatcattactcaggaattgtaattgctgaaaacaaatgtttcagGTTAAAAAGGTTAAACCCCATGTGCTTCTTGGTTTGTCTGGAGTTGGTGGTGTCTTCAATGAGGAG

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|164168279|gb|ES006850.1|ES006850
EST:     TTGCCAAAAATCCAGCTGAGATACGCGAGGGAGCAAGTATCGTTGAAGTG                         GTGAAGAAAGTGAGGCCACATGTTCTTCTTGGTTTATCTGGAGTTGGTGGT
genomic: TTGCCAAAAATCCAGCTGAGATACGCGAGGGAGCAAGTATCGTTGAAGTGgtaagcctaa ... atgtcttcagGTGAAGAAAGTGAGGCCACATGTTCTTCTTGGTTTATCTGGAGTTGGTGGT
EST: gi|116463393|gb|EG505985.1|EG505985
EST:     TTGCCAAAAATCCAGCTGAGATACGCGAGGGAGCAAGTATCGTTGAAGTG                         GTGAAGAAAGTGAGGCCACATGCTCTTCTTGGTTTATCTGGAGTTGGTGGT
genomic: TTGCCAAAAATCCAGCTGAGATACGCGAGGGAGCAAGTATCGTTGAAGTGgtaagcctaa ... atgtcttcagGTGAAGAAAGTGAGGCCACATGTTCTTCTTGGTTTATCTGGAGTTGGTGGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aaagttagacataatcatatgataatatttctgtctaaatataatatgtcttcagGTGAAGAAAGTGAGGCCACATGTTCTTCTTGGTTTATCTGGAGTTGGTGGTATCTTTAATGAAGAA
                                gtctaaa  putative branch site (score: 3)
                                              tgtcttc  putative PPT
          ataatcatatgataat  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagcctaagccttattattgcgttcttacttgccttggccaatattaaactttgacttaatgtgctttctctactacatcctaaagcaacacaggataaccatatttttttactgtccccaaaagttagacataatcatatgataatatttctgtctaaatataatatgtcttcagGTGAAGAAAGTGAGGCCACATGTTCTTCTTGGTTTATCTGGAGTTGGTGGTATCTTTAATGAAGAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA