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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttactactttcacttcttgatcatactaagtttatgttttcttgatcttgggttgagtaaagctgattttgatgttttgtgtttaagGTTGGGATTTCGACGAATGAGACAGGAGAGAAAGTAGGAGCCTTTGCTTTGGCTTACGCAGCGCATAAAGCTGCATCTCCGATAAGGTTTCCGCCTACAG

Basic information

species Arabidopsis thaliana
transcript AT2G27290.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT2G27290.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA11G18410.1 (Glycine max), 3'ss of exon 2
gttactactttcacttcttgatcatactaagtttatgttttcttgatcttgggttgagtaaagctgattttgatgttttgtgttta-----agGTTGGGATTTCGACGAATGAGACAGGAGAGAAAGTAGGAGCCTTTGCTTTGGCTTACGCAGCGCATAAAGCTGCATCTCCGATAAGGTTTCCGCCTACAG
  | | ||    |||        |   ||  ||    |    ||||          | |    | ||||   |  ||  |||||||     ||||||| || || ||  ||| ||| ||||||||||| ||  ||||||| ||||| || || || ||||||||||||||||| || |||||||| || ||||
-gtgcaacacaaactaaac--ctaatgtagattgcaatcaaattgaaaacaaaacaattgcttcggattaataaattgcgtgtttatcctcagGTTGGAATCTCAACTGATGCGACTGGAGAGAAAGTTGGTACCTTTGCATTGGCATATGCTGCACATAAAGCTGCATCTCCAATTAGGTTTCCACCCACAG

upper sequence: AT2G27290.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA12G09850.1 (Glycine max), 3'ss of exon 2
gttactactttcacttcttgatcatactaagtttatgttttcttgatcttgggttgagtaaagctgattttgatgttttgtgttta-----agGTTGGGATTTCGACGAATGAGACAGGAGAGAAAGTAGGAGCCTTTGCTTTGGCTTACGCAGCGCATAAAGCTGCATCTCCGATAAGGTTTCCGCCTACAG
  | | ||  | |          |   ||  ||    |||  || |          | |    | | ||   |  ||  |||||||     ||||||| || || ||  ||| ||| || || ||||| ||  ||||||||||||| || || || ||||||||||||||||| || |||||||| || ||||
-gtgcaacactaaaactaaacctaatgtagattgcaatttaatttaaaacaaagcaattgcttcgggttaataaattgcgtgtttatcttcagGTTGGAATCTCAACTGATGCGACTGGCGAAAAAGTTGGTACCTTTGCTTTGGCATATGCTGCACATAAAGCTGCATCTCCAATTAGGTTTCCACCCACAG
















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|125201561|gb|EL216515.1|EL216515
EST:     GGTGTTGATGTTCAAGCTCTTCTTCTAAAG                         GTTGGGGAATTTCGACGAATGAGACAGGAGAGAAAGTAGGAGCCTTTGCTT
genomic: GGTGTTGATGTTCAAGCTCTTCTTCTAAAGgttactactt ... tgtgtttaagGTT-GGG-ATTTCGACGAATGAGACAGGAGAGAAAGTAGGAGCCTTTGCTT
EST: gi|86079229|gb|DR374986.1|DR374986
EST:     GCTATGTCCTTGTGACTTCCGGTGTTGATGTTCAAGCTCTTCTTCTAAAG                         GTTGGGATTTCGACGAATGAGACAGGAGAGAAAGTAGGAGCCTTTGCTTTG
genomic: GCTATGTCCTTGTGACTTCCGGTGTTGATGTTCAAGCTCTTCTTCTAAAGgttactactt ... tgtgtttaagGTTGGGATTTCGACGAATGAGACAGGAGAGAAAGTAGGAGCCTTTGCTTTG
EST: gi|125030323|gb|EL102592.1|EL102592
EST:     CCTTGTGACTTCCGGTGTTGATGTTCAAGCTCTTCTTCTAAAG                         GTTGGGATTTCGACGAATGAGACAGGAGAGAAAGTAGGAGCCTTTGCTTTG
genomic: CCTTGTGACTTCCGGTGTTGATGTTCAAGCTCTTCTTCTAAAGgttactactt ... tgtgtttaagGTTGGGATTTCGACGAATGAGACAGGAGAGAAAGTAGGAGCCTTTGCTTTG
EST: gi|124917861|gb|EH991735.1|EH991735
EST:     GCTATGTCCTTGTGACTTCCGGTGTTGATGTTCAAGCTCTTCTTCTAAAG                         GTTGGGATTTCGACGAA
genomic: GCTATGTCCTTGTGACTTCCGGTGTTGATGTTCAAGCTCTTCTTCTAAAGgttactactt ... tgtgtttaagGTTGGGATTTCGACGAA
EST: gi|125312299|gb|EL326384.1|EL326384
EST:     GCTATGTCCTTGTGACTTCCGGTGTTGATGTTCAAGCTCTTCTTCTAAAG                         GTTGGGATTTCGACGAATGAGAC
genomic: GCTATGTCCTTGTGACTTCCGGTGTTGATGTTCAAGCTCTTCTTCTAAAGgttactactt ... tgtgtttaagGTTGGGATTTCGACGAATGAGAC
EST: gi|125081741|gb|EL142849.1|EL142849
EST:     ATGTTCAAGCTCTTCTTCTAAAG                         GTTGGGATTTCGACGAATGAGACAGGAGAGAAAGTAGGAGCCTTTGCTTTG
genomic: ATGTTCAAGCTCTTCTTCTAAAGgttactactt ... tgtgtttaagGTTGGGATTTCGACGAATGAGACAGGAGAGAAAGTAGGAGCCTTTGCTTTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tatgttttcttgatcttgggttgagtaaagctgattttgatgttttgtgtttaagGTTGGGATTTCGACGAATGAGACAGGAGAGAAAGTAGGAGCCTTTGCTTTGGCTTACGCAGCGCATAAAGCTGCATCTCCGATAAGGTTTCCGCCTACAG
                                  ttttgat  putative branch site (score: 4)
                                 attttgat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttactactttcacttcttgatcatactaagtttatgttttcttgatcttgggttgagtaaagctgattttgatgttttgtgtttaagGTTGGGATTTCGACGAATGAGACAGGAGAGAAAGTAGGAGCCTTTGCTTTGGCTTACGCAGCGCATAAAGCTGCATCTCCGATAAGGTTTCCGCCTACAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC