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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...agcttgtaacttgaaacggttatgggatctagattactttagaatcaacaactgtggacttaactgttttgtcaaaacaatatctctttcaacattgcagACTGTACTGGAAGATTAAGTACGTGAGCAGGTTGCAGTACCTTTGGGAGGACATAAAGAAAGGCGAGGTGGAAATTCCCGACTTTGTGAAGAACCATGAC

Basic information

species Arabidopsis thaliana
transcript AT3G10210.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT3G10210.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA03G28460.2 (Glycine max), 3'ss of exon 3
----agcttgtaacttgaaacggttatgggatctagattactttagaat-caacaactgtggacttaactgttttgtcaaaacaatatctctttcaacattgcagACTGTACTGGAAGATTAAGTACGTGAGCAGGTTGCAGTACCTTTGGGAGGACATAAAGAAAGGCGAGGTGGAAATTCCCGACTTTGTGAAGAACCATGAC
| ||||| || || || | ||| | | || | || |||||| ||| | | || | | | ||| | || |||||||| ||||| || ||| || | |||||||||||||| |||||||||||||| ||| | || || || || |||||||| | |||||
caatacaaagtaacatgcgctaa--attggctgacaattgacccattgtatcacttttttgcacttaatcctttgggtttgttga---ctttgttgttggtttagATTATATTGGAAGATCAAGTATGTAAGCCGGCTTCAGTACCTTTGGGATGACATAAAGAAAGGAGAGATTGAGATACCGGATTTTGTGAAAAGTCATGAT
















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|86061743|gb|DR357500.1|DR357500
EST:     CGTTCAAGACTTGTCATTGCCACTCTTGGCCGCCTTCTTTTAAGTGGAGG                         ACTGTACTGGAAGATTAAGTACGTGAGCAGGTTGCAGTACCTTTNNNAGGA
genomic: CGTTCAAGACTTGTCATTGCCACTCTTGGCCGCCTTCTTTTAAGTGGAGGgtaatcattt ... aacattgcagACTGTACTGGAAGATTAAGTACGTGAGCAGGTTGCAGTACCTTTGGGAGGA






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

caacaactgtggacttaactgttttgtcaaaacaatatctctttcaacattgcagACTGTACTGGAAGATTAAGTACGTGAGCAGGTTGCAGTACCTTTGGGAGGACATAAAGAAAGGCGAGGTGGAAATTCCCGACTTTGTGAAGAACCATGAC
            acttaac  putative branch site (score: 3)
 tctctttca  putative PPT
 aaaacaatat  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
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---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
agcttgtaacttgaaacggttatgggatctagattactttagaatcaacaactgtggacttaactgttttgtcaaaacaatatctctttcaacattgcagACTGTACTGGAAGATTAAGTACGTGAGCAGGTTGCAGTACCTTTGGGAGGACATAAAGAAAGGCGAGGTGGAAATTCCCGACTTTGTGAAGAACCATGAC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC
- - - - - ttgaaac
- - - - - - - - - - - - - - - - - - - - - - -caacaac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - -acttaac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgttttg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aaaacaa