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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TCCTTCGAGTTTAAAGATATAGTGAAAATCGGAAGAACTCATACTCAAGATGCTACACCTTTGACATTAGGACAAGAATTTGGTGGCTATGCTACTCAAgtaaattatttgttctgttttctatccttatataacaaaagtgaaaattacatgtcattaagaaataacttataaatttttggatttcatgattgtag

Basic information

species Arabidopsis thaliana
transcript AT5G50950.3
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT5G50950.3 (Arabidopsis thaliana), 5'ss of exon 5
lower sequence: GLYMA02G01930.2 (Glycine max), 5'ss of exon 6
TCCTTCGAGTTTAAAGATATAGTGAAAATCGGAAGAACTCATACTCAAGATGCTACACCTTTGACATTAGGACAAGAATTTGGTGGCTATGCTACTCAAgtaaat-------tatttg--ttctgttttctatccttatataacaaaagtgaaaattacatgtcattaagaaataacttataaatttttggatttcatgattgtag----------------------
||  | || ||||||||||| || || || ||| | ||||||||||||||||| |||||||||||  | |||||||| ||| |||| ||| |||| |||||||         | ||||  || ||  || | |  || | ||     ||| |  |||  ||||      | |||| | | |   |  |  ||||||    | ||                        
TCAGTTGAATTTAAAGATATTGTCAAGATTGGACGCACTCATACTCAAGATGCAACACCTTTGACTCTTGGACAAGAGTTTAGTGGATATACTACACAAgtaagccttcttatgtttggcttatgccttatgttgttctgtattttcagt-atcattg-atgttggatggtaatatcctgtgggtagt--gatttctcattagtcactactttttcctctatctacag

upper sequence: AT5G50950.3 (Arabidopsis thaliana), 5'ss of exon 5
lower sequence: GLYMA02G01920.1 (Glycine max), 5'ss of exon 6
TCCTTCGAGTTTAAAGATATAGTGAAAATCGGAAGAACTCATACTCAAGATGCTACACCTTTGACATTAGGACAAGAATTTGGTGGCTATGCTACTCAAgtaaatt------------atttgttctgttttctatcctta-tataacaaaag--------tgaaaattacat-gtcattaagaaataacttataaatttttggatttcatgattgtag
||  | || || |||||||| || || || ||| | ||||||||||||||||| |||||||||||  | |||||||| ||| |||| ||| |||| |||||||  |              |||| ||||||| |||  ||  |||||   | |        | |||     |  ||   |  |   | | || | | |  ||   |    |   || ||
TCAATTGAATTCAAAGATATTGTCAAGATTGGACGCACTCATACTCAAGATGCAACACCTTTGACTCTTGGACAAGAGTTTAGTGGGTATACTACACAAgtaagcttgcttatgtttggcttgtgctgttttgtatttttgctataatggatgctgcattgtaaaatcctgacagttcgtggggtgtgatttctcattacttttttcctttatctgcag

upper sequence: AT5G50950.3 (Arabidopsis thaliana), 5'ss of exon 5
lower sequence: GLYMA10G02040.2 (Glycine max), 5'ss of exon 6
TCCTTCGAGTTTAAAGATATAGTGAAAATCGGAAGAACTCATACTCAAGATGCTACACCTTTGACATTAGGACAAGAATTTGGTGGCTATGCTACTCAAgtaaa-ttatttgt-tctgttttctatccttatataacaaaagtgaaaattacatgtcattaagaaat------aacttataaatttttggatttcatgattgtag-------------
||  | || || |||||||| || || || ||| | ||||||||||||||||| |||||||||||  | || ||||| ||| |||| ||| |||| |||||||  ||  || | | ||  || |    || | ||       |   | |    |  ||||   ||||      |  | ||      | |  | |||| | | |               
TCAATTGAATTCAAAGATATTGTCAAGATTGGACGCACTCATACTCAAGATGCAACACCTTTGACTCTTGGGCAAGAGTTTAGTGGGTATACTACACAAgtaagcttgcttatgtttggcttttgctgttttgtattttctctatcattggtgttgcattgtaaaatcctggcagttcatggggagtggtttatcattactttttcctttatctgcag

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|125184030|gb|EL198984.1|EL198984
EST:     ATGCTACACCTTTGACATTAGGACAAGAATTTGGTGGCTATGCTACTCAA                         GTTGAGTATGGACTTAATAG
genomic: ATGCTACACCTTTGACATTAGGACAAGAATTTGGTGGCTATGCTACTCAAgtaaattatt ... atgattgtagGTTGAGTATGGACTTAATAG
EST: gi|125070433|gb|EL135844.1|EL135844
EST:     ATGCTACACCTTTGACATTAGGACAAGAATTTGGTGGCTATGCTACTCAA                         GTTGAGTATGGACTTAATAGAGTCGCA
genomic: ATGCTACACCTTTGACATTAGGACAAGAATTTGGTGGCTATGCTACTCAAgtaaattatt ... atgattgtagGTTGAGTATGGACTTAATAGAGTCGCA
EST: gi|116422670|gb|EG465262.1|EG465262
EST:     ATGCTACACCTTTGACATTAGGACAAGAATTTGGTGGCTATGCTACTCAA                         GTTGAGTATGGACTTAATAGAGTCGCATGTACTCTACCCCGCATCTATCAG
genomic: ATGCTACACCTTTGACATTAGGACAAGAATTTGGTGGCTATGCTACTCAAgtaaattatt ... atgattgtagGTTGAGTATGGACTTAATAGAGTCGCATGTACTCTACCCCGCATCTATCAG
EST: gi|125311122|gb|EL325207.1|EL325207
EST:     CAAGAATTTGGTGGCTATGCTACTCAA                         GTTGAGTATGGACTTAATAGAGTCGCATGTACTCTACCCCGCATCTATCAG
genomic: CAAGAATTTGGTGGCTATGCTACTCAAgtaaattatt ... atgattgtagGTTGAGTATGGACTTAATAGAGTCGCATGTACTCTACCCCGCATCTATCAG
EST: gi|116467405|gb|EG509997.1|EG509997
EST:     ATGCTACACCTTTGACATTAGGACAAGAATTTGGTGGCTATGCTACTCAA                         GTTGAGTATGGACTTAATAGAGTCGCATGTACTCTACCCCGCATCTATCAG
genomic: ATGCTACACCTTTGACATTAGGACAAGAATTTGGTGGCTATGCTACTCAAgtaaattatt ... atgattgtagGTTGAGTATGGACTTAATAGAGTCGCATGTACTCTACCCCGCATCTATCAG
EST: gi|116443356|gb|EG485948.1|EG485948
EST:     ATGCTACACCTTTGACATTAGGACAAGAATTTGGTGGCTATGCTACTCAA                         GTTGAGTATGGACTTAATAGAGTCGCATGTACTCTACCCCGCATCTATCAG
genomic: ATGCTACACCTTTGACATTAGGACAAGAATTTGGTGGCTATGCTACTCAAgtaaattatt ... atgattgtagGTTGAGTATGGACTTAATAGAGTCGCATGTACTCTACCCCGCATCTATCAG
EST: gi|116456305|gb|EG498897.1|EG498897
EST:     ATGCTACACCTTTGACATTAGGACAAGAATTTGGTGGCTATGCTACTCAA                         GTTGAGTATGGACTTAATAGAGTCGCATGTACTCTACCCCGCATCTATCAG
genomic: ATGCTACACCTTTGACATTAGGACAAGAATTTGGTGGCTATGCTACTCAAgtaaattatt ... atgattgtagGTTGAGTATGGACTTAATAGAGTCGCATGTACTCTACCCCGCATCTATCAG
EST: gi|125087477|gb|EL146591.1|EL146591
EST:     CTATGCTACTCAA                         GTTGAGTATGGACTTAATAGAGTCGCATGTACTCTACCCCGCATCTATCAG
genomic: CTATGCTACTCAAgtaaattatt ... atgattgtagGTTGAGTATGGACTTAATAGAGTCGCATGTACTCTACCCCGCATCTATCAG
EST: gi|116428316|gb|EG470908.1|EG470908
EST:     ATGCTACACCTTTGACATTAGGACAAGAATTTGGTGGCTATGCTACTCAA                         GTTGAGTATGGACTTAATAGAGTCGCATGTACTCTACCCCGCATCTATCAG
genomic: ATGCTACACCTTTGACATTAGGACAAGAATTTGGTGGCTATGCTACTCAAgtaaattatt ... atgattgtagGTTGAGTATGGACTTAATAGAGTCGCATGTACTCTACCCCGCATCTATCAG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TCCTTCGAGTTTAAAGATATAGTGAAAATCGGAAGAACTCATACTCAAGATGCTACACCTTTGACATTAGGACAAGAATTTGGTGGCTATGCTACTCAAgtaaattatttgttctgttttctatccttatataacaaaagtgaaaattacatgtcattaagaaataacttataaatttttggatttcatgattgtag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG