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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ctgtgagtctttgatggttatagtgagaggaactttttattgattgatgtgtattggatgctgaagcttcatgttttgaattatgcaattgtgaattcagATGAACGTGTGCCTACTGAGCTAAAGAAAGCCATTATGCAAGCCAGGACAGACAAGAAGCTAACCCAGTCCCAACTTGCTCAA

Basic information

species Arabidopsis thaliana
transcript AT2G42680.1
intron # 2
splice site 3'
intron type U2

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|125257950|gb|EL272035.1|EL272035
EST:     CACTGAGAACCTTACTC                         ATGAACGTGTGCCTACTGAGCTAAAGAAA
genomic: CACTGAGAACCTTACTCgtaagtctta ... gtgaattcagATGAACGTGTGCCTACTGAGCTAAAGAAA
EST: gi|86081161|gb|DR376918.1|DR376918
EST:     CACATCTCTGAACACAAAAATGCTTGATGATGACACTGAGAACCTTACTC                         ATGAACGTGTGCCTACTGAGCTAAAGAAAGCCATTATGCAAGCCAGGACAG
genomic: CACATCTCTGAACACAAAAATGCTTGATGATGACACTGAGAACCTTACTCgtaagtctta ... gtgaattcagATGAACGTGTGCCTACTGAGCTAAAGAAAGCCATTATGCAAGCCAGGACAG
EST: gi|47829297|gb|CK118981.1|CK118981
EST:     CACATCTCTGAACACAAAAATGCTTGATGATGACACTGAGAACCTTACTC                         ATGAACGTGTGCCTACTGAGCTAAAGAAAGCCATTATGCAAGCCAGGACAG
genomic: CACATCTCTGAACACAAAAATGCTTGATGATGACACTGAGAACCTTACTCgtaagtctta ... gtgaattcagATGAACGTGTGCCTACTGAGCTAAAGAAAGCCATTATGCAAGCCAGGACAG
EST: gi|164182446|gb|ES115963.1|ES115963
EST:     CACATCTCTGAACACAAAAATGCTTGATGATGACACTGAGAACCTTACTC                         ATGAACGTGTG
genomic: CACATCTCTGAACACAAAAATGCTTGATGATGACACTGAGAACCTTACTCgtaagtctta ... gtgaattcagATGAACGTGTG
EST: gi|164217862|gb|ES103712.1|ES103712
EST:     CACATCTCTGAACACAAAAATGCTTGATGATGACACTGAGAACCTTACTC                         ATGAACGTGTGCCTACTG
genomic: CACATCTCTGAACACAAAAATGCTTGATGATGACACTGAGAACCTTACTCgtaagtctta ... gtgaattcagATGAACGTGTGCCTACTG
EST: gi|86086850|gb|DR382609.1|DR382609
EST:     TGAACACAAAAATGCTTGATGATGACACTGAGAACCTTACTC                         ATGAACGTGTGCCTACTGAGCTAAAGAAAGCCATTATGCAAGCCAGGACAG
genomic: TGAACACAAAAATGCTTGATGATGACACTGAGAACCTTACTCgtaagtctta ... gtgaattcagATGAACGTGTGCCTACTGAGCTAAAGAAAGCCATTATGCAAGCCAGGACAG
EST: gi|116455455|gb|EG498047.1|EG498047
EST:     CACATCTCTGAACACAAAAATGCTTGATGATGACACTGAGAACCTTACTC                         ATGAACGTGTGCCTACTGAGCTAAAGAAAGCCATTATGCAAGCCAGGACAG
genomic: CACATCTCTGAACACAAAAATGCTTGATGATGACACTGAGAACCTTACTCgtaagtctta ... gtgaattcagATGAACGTGTGCCTACTGAGCTAAAGAAAGCCATTATGCAAGCCAGGACAG
EST: gi|116455456|gb|EG498048.1|EG498048
EST:     CACATCTCTGAACACAAAAATGCTTGATGATGACACTGAGAACCTTACTC                         ATGAACGTGTGCCTACTGAGCTAAAGAAAGCCATTATGCAAGCCAGGACAG
genomic: CACATCTCTGAACACAAAAATGCTTGATGATGACACTGAGAACCTTACTCgtaagtctta ... gtgaattcagATGAACGTGTGCCTACTGAGCTAAAGAAAGCCATTATGCAAGCCAGGACAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gatgtgtattggatgctgaagcttcatgttttgaattatgcaattgtgaattcagATGAACGTGTGCCTACTGAGCTAAAGAAAGCCATTATGCAAGCCAGGACAGACAAGAAGCTAACCCAGTCCCAACTTGCTCAA
 gattgat  putative branch site (score: 4)
                         atgttttgaattat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ctgtgagtctttgatggttatagtgagaggaactttttattgattgatgtgtattggatgctgaagcttcatgttttgaattatgcaattgtgaattcagATGAACGTGTGCCTACTGAGCTAAAGAAAGCCATTATGCAAGCCAGGACAGACAAGAAGCTAACCCAGTCCCAACTTGCTCAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC
- - - - - - - - - - - - -agaggaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgttttg