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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aaagacgattcttgtatgtcatcattcacacgggagtagtttatatatctagccattgatgttgcatcctcgatgcctgtggtttttctgaatatttcagGGCAGATGATGAAGTTGTTGATCCAAAGAAGTACCTTGAGGAATCTTGCAAACCAAAATGTGTGAAGCCACTTCTCGAATATCAG

Basic information

species Arabidopsis thaliana
transcript AT1G15120.2
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G15120.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: LOC_Os11g06340.1 (Oryza sativa), 3'ss of exon 1
aaagacgattcttgtatgtcatcattcacacggga-gtagtttatatatctagccattgatgttgcatcctcgatgcctgtggtttttctgaa------tatttcagGGCAGATGATGAAGTTGTTGATCCAAAGAAGTACCTTGAGGAATCTTGCAAACCAAAATGTGTGAAGCCACTTCTCGAATATCAG
       || |  | | |   | ||   | |   | ||  |  | || ||| |   || |  ||   | ||| |   || |||||||            ||  | ||||| ||||| |||  |||||||||||||||||||||||||||    ||||| ||  | || || ||||||||    || ||| ||
------tataccagaaagatctaatgttctcaaaatgttatgcaaatgtct-gtttttaaccttaagttctcaacttctatggttttctaatgttgttttaccttagGGCGGATGAAGAACCTGTTGATCCAAAGAAGTACCTTGAGGAGCGCTGCAAGCCCCAGTGCGTAAAGCCACTCTATGAGTATGAG

upper sequence: AT1G15120.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: Vv18s0072g00810.t01 (Vitis vinifera), 3'ss of exon 2
aaagacgattcttgta----tgt-catcattcacacgggagtagttta-tatatctagccattgatgttgcatcctcgatgcctgtggtttttctgaatatttcagGGCAGATGATGAAGTTGTTGATCCAAAGAAGTACCTTGAGGAATCTTGCAAACCAAAATGTGTGAAGCCACTTCTCGAATATCAG
     | |||  ||||    ||| ||||||||    | |  ||| ||| || |  |||    || | |       |   ||  | |  |   | | |  | || ||||| || || ||   |||||||||||||||||| ||||| ||||||||||| || || |||||||      | |  | |||| ||
-----ctatttgtgtaaacctgtacatcattctttggagtttagattaatagacttagtttatg-tataaatatataactgtgtatcttgccttttatcaatttagGGCGGACGAAGAGCCTGTTGATCCAAAGAAGTATCTTGAAGAATCTTGCAAGCCTAAGTGTGTGAGATATTTGCGTGCATATGAG
















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|125254649|gb|EL268734.1|EL268734
EST:     TCTTCAGCTTCCAATTGACTTTCAACAT                         GGCAGATGATGAAGTTG
genomic: TCTTCAGCTTCCAATTGACTTTCAACATgtaagcttat ... aatatttcagGGCAGATGATGAAGTTG
EST: gi|125069741|gb|EL135410.1|EL135410
EST:     CAATCTCAGTCTTCAGCTTCCAATTGACTTTCAACAT                         GGCTGATGATGAAGTTGTTGATCCAAAGAAGTACCTTGAGGAATCTTGCAA
genomic: CAATCTCAGTCTTCAGCTTCCAATTGACTTTCAACATgtaagcttat ... aatatttcagGGCAGATGATGAAGTTGTTGATCCAAAGAAGTACCTTGAGGAATCTTGCAA
EST: gi|164150954|gb|ES064203.1|ES064203
EST:     TCAATCTCAGTCTTCAGCTTCCAATTGACTTTCAACAT                         GGCAGATGATGAAGTTGTTGATCCAAAGAAGTACCTTGAGGAATCTTGCAA
genomic: TCAATCTCAGTCTTCAGCTTCCAATTGACTTTCAACATgtaagcttat ... aatatttcagGGCAGATGATGAAGTTGTTGATCCAAAGAAGTACCTTGAGGAATCTTGCAA
EST: gi|125010309|gb|EL082578.1|EL082578
EST:     ACTTTCAACAT                         GGCAGATGATGAAGTTGTTGATCCAAAGAAGTACCTTGAGGAATCTTGCAA
genomic: ACTTTCAACATgtaagcttat ... aatatttcagGGCAGATGATGAAGTTGTTGATCCAAAGAAGTACCTTGAGGAATCTTGCAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tatctagccattgatgttgcatcctcgatgcctgtggtttttctgaatatttcagGGCAGATGATGAAGTTGTTGATCCAAAGAAGTACCTTGAGGAATCTTGCAAACCAAAATGTGTGAAGCCACTTCTCGAATATCAG
        cattgat  putative branch site (score: 4)
                                     tttttctgaatattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aaagacgattcttgtatgtcatcattcacacgggagtagtttatatatctagccattgatgttgcatcctcgatgcctgtggtttttctgaatatttcagGGCAGATGATGAAGTTGTTGATCCAAAGAAGTACCTTGAGGAATCTTGCAAACCAAAATGTGTGAAGCCACTTCTCGAATATCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC
-aagacga
- - - - - - - - - - - -attcaca
- - - - - - - - - - - - - - - - - - - - - - - - ctagcca