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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tcatattgctgctctcttttactcgatacctaagacaaagggtggtcaggtatttgttacgaaggagacctgtcttacctaggagaaaattcttttgcagATGCGTCTAAATCTGGTGTTGCGCAGGAAGCAATGCAAAATGGAGTACGTCAAGCAGGGAAAGCCATCACTGAGCAAGAGGCTAGGCAGATTCTTGGTGT

Basic information

species Arabidopsis thaliana
transcript AT3G59280.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT3G59280.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA02G08820.1 (Glycine max), 3'ss of exon 1
--tcata-ttgctgctctcttttactcgataccta-agaca-aagggtggtcaggtatttgttacgaaggagacctgtcttacctaggagaaaattcttttgcagATGCGTCTAAATCTGGTGTTGCGCAGGAAGCAATGCAAAATGGAGTACGTCAAGCAGGGAAAGCCATCACTGAGCAAGAGGCTAGGCAGATTCTTGGTGT
  || |      |  ||||| | ||||  |||  | ||||| ||   ||    |||  | | |            | ||||| | |  |    ||  | |||||||||| || |||  ||||||||| || ||  |||| ||||||    | ||   |||  | || |  || || |||||||||||||||||||||||||||||
tgtcttggccaattttctctctcactctgtacacatagacacaacaatgcagcggttctagatcttctca----ttttcttaac-attatgttatgttattgcagATGCCTCAAAAAATGGTGTTGCACAAGAGACAATTCAAAATACTATGCGCAGAGCTAGCAAGGTGATGACAGAGCAAGAGGCTAGGCAGATTCTTGGTGT
















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|86063868|gb|DR359625.1|DR359625
EST:     TGGGATCATTGGTCGTGCTGTCTTTCAAGCCTATCGTCAAGCACTTGCTA                         ATGCGTCTAAATCTGGTGTTGCGCAGGAAGCAATGCAAAATGGAGTACGTC
genomic: TGGGATCATTGGTCGTGCTGTCTTTCAAGCCTATCGTCAAGCACTTGCTAgtaagtttcc ... tcttttgcagATGCGTCTAAATCTGGTGTTGCGCAGGAAGCAATGCAAAATGGAGTACGTC
EST: gi|152038381|gb|AV821341.2|AV821341
EST:     TGGGATCATTGGTCGTGCTGTCTTTCAAGCCTATCGTCAAGCACTTGCTA                         ATGCGTCTAAATCTGGTGTTGCGCAGGAAGCAATGCAAAATGGAGTACGTC
genomic: TGGGATCATTGGTCGTGCTGTCTTTCAAGCCTATCGTCAAGCACTTGCTAgtaagtttcc ... tcttttgcagATGCGTCTAAATCTGGTGTTGCGCAGGAAGCAATGCAAAATGGAGTACGTC
EST: gi|86082243|gb|DR378002.1|DR378002
EST:     CTATCGTCAAGCACTTGCTA                         ATGCGTCTAAATCTGGTGTTGCGCAGGAAGCAATGCAAAATGGAGTACGTC
genomic: CTATCGTCAAGCACTTGCTAgtaagtttcc ... tcttttgcagATGCGTCTAAATCTGGTGTTGCGCAGGAAGCAATGCAAAATGGAGTACGTC
EST: gi|86084307|gb|DR380066.1|DR380066
EST:     TGGGATCATTGGTCGTGCTGTCTTTCAAGCCTATCGTCAAGCACTTGCTA                         ATGCGTCTAAATCTGGTGTTGCGCAGGAAGCAATGCAAAATGGAGTACGTC
genomic: TGGGATCATTGGTCGTGCTGTCTTTCAAGCCTATCGTCAAGCACTTGCTAgtaagtttcc ... tcttttgcagATGCGTCTAAATCTGGTGTTGCGCAGGAAGCAATGCAAAATGGAGTACGTC
EST: gi|116454644|gb|EG497236.1|EG497236
EST:     TGGGATCATTGGTCGTGCTGTCTTTCAAGCCTATCGTCAAGCACTTGCTA                         ATGCGTCTAAATCTGGTGTTGCGCAGGAAGCAATGCAAAATGGAGTACGTC
genomic: TGGGATCATTGGTCGTGCTGTCTTTCAAGCCTATCGTCAAGCACTTGCTAgtaagtttcc ... tcttttgcagATGCGTCTAAATCTGGTGTTGCGCAGGAAGCAATGCAAAATGGAGTACGTC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcaggtatttgttacgaaggagacctgtcttacctaggagaaaattcttttgcagATGCGTCTAAATCTGGTGTTGCGCAGGAAGCAATGCAAAATGGAGTACGTCAAGCAGGGAAAGCCATCACTGAGCAAGAGGCTAGGCAGATTCTTGGTGT
                          gtcttac  putative branch site (score: 3)
                                            ttcttttgc  putative PPT
                                        aaaattctttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tcatattgctgctctcttttactcgatacctaagacaaagggtggtcaggtatttgttacgaaggagacctgtcttacctaggagaaaattcttttgcagATGCGTCTAAATCTGGTGTTGCGCAGGAAGCAATGCAAAATGGAGTACGTCAAGCAGGGAAAGCCATCACTGAGCAAGAGGCTAGGCAGATTCTTGGTGT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGAT
- - - - ctgctct
- - - - - - - - - - - -cgatacc
- - - - - - - - - - - - - - - - agacaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aaggaga
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gagaaaa