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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CTTGCATGATCCTTCTAAAGATACAGGGTATGTTGGGAGTGCTTTGTCTAGTAATATGATAAGGTTTTTCAAGAACAGTGATGACACGTGGAGCCATGAGgcaagtgaagtttctaaatctttttcttttgtcttatctcaaatctatgattaacttgtgatttaaactggtgttgttttag

Basic information

species Arabidopsis thaliana
transcript AT4G14040.1
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT4G14040.1 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: GLYMA05G28400.1 (Glycine max), 5'ss of exon 5
CTTGCATGATCCTTCTAAAGATACAGGGTATGTTGGGAGTGCTTTGTCTAGTAATATGATAAGGTTTTTCAAGAACAGTGATGACACGTGGAGCCATGAGgcaagtgaagtttcta------------aatctttttcttttgtcttatctcaaatctatgattaacttgtgatttaaactggtgttgttttag------
  ||||||||||||||||||||||||| |  |||||| |||| ||||| ||||| ||| || | ||||||||||     |||||  | ||||| ||||||| |  | ||   | ||            ||||  |   || |     |     ||  | | |||||   |    || |  |   | | || ||       
TCTGCATGATCCTTCTAAAGATACAGGTTTCGTTGGGTGTGCATTGTCAAGTAACATGGTACGCTTTTTCAAGACTGAAGATGAATCATGGAGTCATGAGgtacataaaaagtatatagtcaaaaatcaatccctaaattataggagaatcacaacatctcattaatcggaaggtttacattcagctattctatttttat

upper sequence: AT4G14040.1 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: GLYMA08G11400.1 (Glycine max), 5'ss of exon 5
CTTGCATGATCCTTCTAAAGATACAGGGTATGTTGGGAGTGCTTTGTCTAGTAATATGATAAGGTTTTTCAAGAACAGTGATGACACGTGGAGCCATGAGgca-----agtgaagtttctaaatctttttcttttgtcttatctcaaatctatgattaacttgtgatttaaactggtgttgttttag---------------
  ||||||||||||||||||||||||| |  || ||| |||| ||||| ||||| ||| || |||||||||||| |   |||||  | ||||| ||||||| |     |  | |  |  ||||   |       |   || |   | |   ||||  | ||  | | | | |  ||| |   || ||               
TCTGCATGATCCTTCTAAAGATACAGGTTTCGTGGGGTGTGCATTGTCAAGTAACATGGTACGGTTTTTCAAGACCGAGGATGAATCATGGAGTCATGAGgtacacaaaaaggatatagtaaaaaatcaatgcctaaattttaggagaatcatgac-atctcattaatcagaa-ggtttacattcagctattctatttttat

upper sequence: AT4G14040.1 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: GLYMA11G36670.1 (Glycine max), 5'ss of exon 5
CTTGCATGATCCTTCTAAAGATACAGGGTATGTTGGGAGTGCTTTGTCTAGTAATATGATAAGGTTTTTCAAGAACAGTGATGACACGTGGAGCCATGAGgcaagt--gaagtttctaaatctttttcttttgtcttatctcaaatctatgattaacttgtgatt-taaactggtgttgttttag--
||||||||||||| ||||||||||||| | ||| |||||||| ||| | ||||| |||||| | ||||| |||| |   |||||  | ||||||||||||| |  |   | | |  | ||| | | |      | |   ||   || |||   | | |  |  ||  | |||    ||  |||    
CTTGCATGATCCTGCTAAAGATACAGGTTTTGTCGGGAGTGCATTGACAAGTAACATGATACGATTTTTTAAGACCCAAGATGAATCATGGAGCCATGAGgtatatcaaaggatatttaatatctattcagcatatgtacttgtatatatatatcaatgatacttacagactaaacttactttgcag

upper sequence: AT4G14040.1 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: GLYMA18G00590.1 (Glycine max), 5'ss of exon 5
CTTGCATGATCCTTCTAAAGATACAGGGTATGTTGGGAGTGCTTTGTCTAGTAATATGATAAGGTTTTTCAAGAACAGTGATGACACGTGGAGCCATGAGg-----caagtgaagtttctaaatct-ttttcttttgtcttatctcaaatctatgattaacttgtg-atttaaactggtgttgttt-tag-------------------
 |||||||||||| ||||||||||||| | ||| || ||||| ||| | ||||| |||||| | ||||| |||| |   |||||  | |||||||||||||     |||  | |  ||  | |||| || | |||||     | |     ||   |  ||  |||   | || |    || |  || |||                   
TTTGCATGATCCTGCTAAAGATACAGGTTTTGTCGGCAGTGCATTGACAAGTAACATGATACGATTTTTTAAGACCCAAGATGAATCATGGAGCCATGAGgtatatcaaaaggatatttaatatctattctgttttggtcagtatatgtacttcaaccaaggtgtatgtatatatcaatgatacttatagactaagcttacttttgcag

upper sequence: AT4G14040.1 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: Vv05s0029g00240.t01 (Vitis vinifera), 5'ss of exon 5
CTTGCATGATCCTTCTAAAGATACAGGGTATGTTGGGAGTGCTTTGTCTAGTAATATGATAAGGTTTTTCAAGAACAGTGATGACACGTGGAGCCATGAGgcaagtgaagtttctaaatctttttcttttgtcttatctcaaatctatgattaacttgtgatttaaactggtgttgttttag-----------------------------------------------
| ||||||||||||||||||||||||||| ||| ||  |||| ||  | || || ||| |  | |||||||||| |   ||||   | |||||||| |||| | | | |   | |   | || |||  ||   || | | ||| ||     |   || ||| ||  | | || |   || ||                                               
CCTGCATGATCCTTCTAAAGATACAGGGTTTGTAGGTTGTGCCTTAACAAGCAACATGGTGCGATTTTTCAAGACCCCAGATGGGTCATGGAGCCACGAGgtatgcggataatatgtgt-ttcttcaattcctttgtttgaaacct-----tgcattttgaattgtattagtctctattaaggcatgacaatccacaatatataatcactccctaatttacttatgaag

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|124708347|gb|EH799749.1|EH799749
EST:     ATAAGGTTTTTCAAGAACAGTGATGACACGTGGAGCCATGAG                         GTTGTTATATCGGTTAAACCGTTGAAAGTCGAAAACTG
genomic: ATAAGGTTTTTCAAGAACAGTGATGACACGTGGAGCCATGAGgcaagtgaag ... gttgttttagGTTGTTATATCGGTTAAACCGTTGAAAGTCGAAAACTG
EST: gi|124944570|gb|EL020658.1|EL020658
EST:     TTTTCAAGAACAGTGATGACGCGTGGAGCCATGAG                         GTTGTTATATCGGTTAAACCGTTGAAAGTCGAAAACTGGATACTTCCAGAA
genomic: TTTTCAAGAACAGTGATGACACGTGGAGCCATGAGgcaagtgaag ... gttgttttagGTTGTTATATCGGTTAAACCGTTGAAAGTCGAAAACTGGATACTTCCAGAA
EST: gi|124997803|gb|EL070072.1|EL070072
EST:     CACGTGGAGCCATGAG                         GTTGTTATATCGGTTAAACCGTTGAAAGTCGAAAACTGGATACTTCCAGAA
genomic: CACGTGGAGCCATGAGgcaagtgaag ... gttgttttagGTTGTTATATCGGTTAAACCGTTGAAAGTCGAAAACTGGATACTTCCAGAA
EST: gi|124825490|gb|EH910356.1|EH910356
EST:     TAATATGATAAGGTTTTTCAAGAACAGTGATGACACGTGGAGCCATGAAG                         GTTGTTATATCGGTTAAACCGTTGAAAGTCGAAAA
genomic: TAATATGATAAGGTTTTTCAAGAACAGTGATGACACGTGGAGCCATGA-Ggcaagtgaag ... gttgttttagGTTGTTATATCGGTTAAACCGTTGAAAGTCGAAAA
EST: gi|124920101|gb|EH993839.1|EH993839
EST:     ACACGTGGAGCCATGAG                         GTTGTTATATCGGTTAAACCGTTGAAAGTCGAAAACTGGATACTTCCAGAA
genomic: ACACGTGGAGCCATGAGgcaagtgaag ... gttgttttagGTTGTTATATCGGTTAAACCGTTGAAAGTCGAAAACTGGATACTTCCAGAA
EST: gi|124762209|gb|EH852339.1|EH852339
EST:     CGTGGAGCCATGAG                         GTTGTTATATCGGTTAAACCGTTGAAAGTCGAAAACTGGATACTTCCAGAA
genomic: CGTGGAGCCATGAGgcaagtgaag ... gttgttttagGTTGTTATATCGGTTAAACCGTTGAAAGTCGAAAACTGGATACTTCCAGAA
EST: gi|125267566|gb|EL281651.1|EL281651
EST:     TGACACGTGGAGCCATGAG                         GTTGTTATATCGGTTAAACCGTTGAAAGTCGAAAACTGGATACTTCCAGAA
genomic: TGACACGTGGAGCCATGAGgcaagtgaag ... gttgttttagGTTGTTATATCGGTTAAACCGTTGAAAGTCGAAAACTGGATACTTCCAGAA
EST: gi|125174157|gb|EL195240.1|EL195240
EST:     TGACACGTGGAGCCATGAG                         GTTGTTATATCGGTTAAACCGTTGAAAGTCGAAAAACTGGATACTTCCAGA
genomic: TGACACGTGGAGCCATGAGgcaagtgaag ... gttgttttagGTTGTTATATCGGTTAAACCGTTGAAAGTCGAAAA-CTGGATACTTCCAGA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CTTGCATGATCCTTCTAAAGATACAGGGTATGTTGGGAGTGCTTTGTCTAGTAATATGATAAGGTTTTTCAAGAACAGTGATGACACGTGGAGCCATGAGgcaagtgaagtttctaaatctttttcttttgtcttatctcaaatctatgattaacttgtgatttaaactggtgttgttttag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GTGGAG