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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttttaacttgagttatatctgccatttagtttattatgaaaactgtgcaaccttaatttgagtgtattggctctgtttatagGTTGTTGAAGATGGGTATGAGTTCTTTGCAGAAAGACAACTTGTTACAGTATTTTCAGCTCCCAACTATTGCGGGGAATTTGACAACGCTGGCGCAATGA

Basic information

species Arabidopsis thaliana
transcript AT2G29400.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT2G29400.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: LOC_Os03g16110.1 (Oryza sativa), 3'ss of exon 2
-----gttttaacttgagttatatctgccatttagtttattatgaaaactgtgcaaccttaatttgagtgtattggctctgtttatagGTTGTTGAAGATGGGTATGAGTTCTTTGCAGAAAGACAACTTGTTACAGTATTTTCAGCTCCCAACTATTGCGGGGAATTTGACAACGCTGGCGCAATGA
      ||||||    |   || | | || || ||| | || |     |      |  | |   |   | ||||   | || |   |||||||||| ||||| |||||||||||||| || ||||||||||| ||  |||| |||||||| |||||||| || |||||||| || || || |||||||
gtacaattttaatgcaa--catcttttcctttcagtattttttttggtcaac-tgaggtgatcatatttatatttcatgtgatgtcagGTTGTTGAGGATGGATATGAGTTCTTTGCCGACAGACAACTTGTCACCATATTCTCAGCTCCAAACTATTGTGGTGAATTTGATAATGCAGGTGCAATGA

upper sequence: AT2G29400.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GRMZM2G160237_T02 (Zea mays), 3'ss of exon 3
-----gttttaacttgagttatatctgccatttag-----tttattatgaaaactg-tgcaaccttaatttgagtgtattg-----gctctgtttatagGTTGTTGAAGATGGGTATGAGTTCTTTGCAGAAAGACAACTTGTTACAGTATTTTCAGCTCCCAACTATTGCGGGGAATTTGACAACGCTGGCGCAATGA
     |  ||| | |    |  | || |  ||| |     ||||||    |      || ||  | ||  ||  | |||||     | | || |   ||||||| || ||||||||||| || ||||| || ||||| ||||| ||  |||| || || ||||| ||||| || |||||||| || ||||| |||||||
gtaccgccttagcatttagtgcagcttctgttttgatctttttatttcacagttaactggaaattgaaggtgtttatattgcatgcgatgtgatgtcagGTTGTCGAGGATGGGTATGAATTTTTTGCTGACAGACAGCTTGTCACCATATTCTCGGCCCCCAATTATTGTGGTGAATTTGATAATGCTGGTGCAATGA

upper sequence: AT2G29400.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: Vv06s0004g05530.t01 (Vitis vinifera), 3'ss of exon 2
gttttaacttgagttatatctgccatttagtttattatgaaaactgtgcaaccttaatttgagtgtattggctctgtttatagGTTGTTGAAGATGGGTATGAGTTCTTTGCAGAAAGACAACTTGTTACAGTATTTTCAGCTCCCAACTATTGCGGGGAATTTGACAACGCTGGCGCAATGA
   |||  |||   |     |    ||   ||| ||||  ||    |||| |              || |  ||| |||  ||||||| |||||||| ||||| ||||||||||| ||||| ||||||||| ||||||| |||||||||||||| || |||||||| || ||||| |||||||
--gtta--ttgccattcccttattgttccattttttat--aactcatgcagctc--------acagatagcttctttttccagGTTGTGGAAGATGGATATGAATTCTTTGCAGACAGACAGCTTGTTACAATATTTTCTGCTCCCAACTATTGTGGTGAATTTGATAATGCTGGTGCAATGA

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|164108263|gb|ES159089.1|ES159089
EST:     GAGTTCTTGGAGAAACATGACATGGACCTTATCTGTCGTGCCCACCAG                         GTTGTTGAAGATGGGTATGAGTTCTTTGCAGAAAGACAACTTGTTAC
genomic: GAGTTCTTGGAGAAACATGACATGGACCTTATCTGTCGTGCCCACCAGgttttaactt ... ctgtttatagGTTGTTGAAGATGGGTATGAGTTCTTTGCAGAAAGACAACTTGTTAC
EST: gi|86075183|gb|DR370940.1|DR370940
EST:     CAGAGTTCTTGGAGAAACATGACATGGACCTTATCTGTCGTGCCCACCAG                         GTTGTTGAAGATGGGTATGAGTTCTTTGCAGAAAGACAACTTGTTACAGTA
genomic: CAGAGTTCTTGGAGAAACATGACATGGACCTTATCTGTCGTGCCCACCAGgttttaactt ... ctgtttatagGTTGTTGAAGATGGGTATGAGTTCTTTGCAGAAAGACAACTTGTTACAGTA
EST: gi|164210547|gb|ES046973.1|ES046973
EST:     GAGTTCTTGGAGAAACATGACATGGACCTTATCTGTCGTGCCCACCAG                         GTTGTTGAAGATGGGTATGAGTTCTTTGCAGAAAGACAACTTGTTACAGTA
genomic: GAGTTCTTGGAGAAACATGACATGGACCTTATCTGTCGTGCCCACCAGgttttaactt ... ctgtttatagGTTGTTGAAGATGGGTATGAGTTCTTTGCAGAAAGACAACTTGTTACAGTA
EST: gi|164060156|gb|ES186386.1|ES186386
EST:     CAGAGTTCTTGGAGAAACATGACATGGACCTTATCTGTCGTGCCCACCAG                         GTTGTTGAAGATGGGTATGAGTTCTTTGC
genomic: CAGAGTTCTTGGAGAAACATGACATGGACCTTATCTGTCGTGCCCACCAGgttttaactt ... ctgtttatagGTTGTTGAAGATGGGTATGAGTTCTTTGC
EST: gi|125320505|gb|EL334590.1|EL334590
EST:     CTGTCGTGCCCACCAG                         GTTGTTGAAGATGGGTATGAGTTCTTTGCAGAAAGACAACTTGTTACAGTA
genomic: CTGTCGTGCCCACCAGgttttaactt ... ctgtttatagGTTGTTGAAGATGGGTATGAGTTCTTTGCAGAAAGACAACTTGTTACAGTA
EST: gi|164163190|gb|ES206230.1|ES206230
EST:     CAGAGTTCTTGGAGAAACATGACATGGACCTTATCTGTCGTGCCCACCAG                         GTTGTTGAAGATGGGTA
genomic: CAGAGTTCTTGGAGAAACATGACATGGACCTTATCTGTCGTGCCCACCAGgttttaactt ... ctgtttatagGTTGTTGAAGATGGGTA
EST: gi|164214858|gb|ES018731.1|ES018731
EST:     GAGTTCTTGGAGAAACATTGACATGGACCTTATCTGTCGTGCCCACCAG                         GTTGTTGAAGATGGGTATGAGTTCTTTGCAGAAAGACAACTTGTTACAGTA
genomic: GAGTTCTTGGAGAAACA-TGACATGGACCTTATCTGTCGTGCCCACCAGgttttaactt ... ctgtttatagGTTGTTGAAGATGGGTATGAGTTCTTTGCAGAAAGACAACTTGTTACAGTA
EST: gi|116434806|gb|EG477398.1|EG477398
EST:     CAGAGTTCTTGGAGAA-CATGACATGGACCTTATCTGTCGTGCCCACCAG                         GTTGTTGAAGATGGGTATGAGTTCTTTGCAGAAAGAC
genomic: CAGAGTTCTTGGAGAAACATGACATGGACCTTATCTGTCGTGCCCACCAGgttttaactt ... ctgtttatagGTTGTTGAAGATGGGTATGAGTTCTTTGCAGAAAGAC
EST: gi|125250669|gb|EL264754.1|EL264754
EST:     TTATCTGTCGTGCCCACCAG                         GTTGTTGAAGATGGGTATGAGTTCTTTGCAGAAAGACAACTTGTTACAGTA
genomic: TTATCTGTCGTGCCCACCAGgttttaactt ... ctgtttatagGTTGTTGAAGATGGGTATGAGTTCTTTGCAGAAAGACAACTTGTTACAGTA
EST: gi|164231709|gb|ES002467.1|ES002467
EST:     GAGTTCTTGGAGAAACATGACATGGACCTTATCTGTCGTGCCCACCAG                         GTTGTTGAAGATGGGTATGAGTTCTTTGCAGAAAGACAACTTGTTACAGTA
genomic: GAGTTCTTGGAGAAACATGACATGGACCTTATCTGTCGTGCCCACCAGgttttaactt ... ctgtttatagGTTGTTGAAGATGGGTATGAGTTCTTTGCAGAAAGACAACTTGTTACAGTA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agtttattatgaaaactgtgcaaccttaatttgagtgtattggctctgtttatagGTTGTTGAAGATGGGTATGAGTTCTTTGCAGAAAGACAACTTGTTACAGTATTTTCAGCTCCCAACTATTGCGGGGAATTTGACAACGCTGGCGCAATGA
                       ccttaat  putative branch site (score: 4)
                                           ctctgttt  putative PPT
     attatgaaaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttttaacttgagttatatctgccatttagtttattatgaaaactgtgcaaccttaatttgagtgtattggctctgtttatagGTTGTTGAAGATGGGTATGAGTTCTTTGCAGAAAGACAACTTGTTACAGTATTTTCAGCTCCCAACTATTGCGGGGAATTTGACAACGCTGGCGCAATGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTC