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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttggtaattggtttgattctgcggatcttttcaatacgccggttctgattccgatcatatttcatgctaatatgtgtttcaatgttgtgggggacatgaaaacagGTACAAAGAGAGCATCACTTACCTAAAGGAGATTTCCCAAATGTGGATCATTTCAGGGAGGTGCTAAGTGGTTACAACATCGACAAGTTTGAGAAGCTAA

Basic information

species Arabidopsis thaliana
transcript AT3G20290.2
intron # 15
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT3G20290.2 (Arabidopsis thaliana), 3'ss of exon 15
lower sequence: GLYMA18G10150.1 (Glycine max), 3'ss of exon 15
gttggtaattggtttgattctgcggatcttttcaatacgccggttctgattccgatcatatttcatgctaatatgtgtttcaatgttgtgggggacatgaaaacagGTACAAAGAGAGCATCACTTACCTAAAGGAGATTTCCCAAATGTGGATCATTTCAGGGAGGTGCTAAGTGGTTACAACATCGACAAGTTTGAGAAGCTAA
||  | | ||   || ||  |   |  |  ||  || |    ||      |  ||| ||  || |   | | |  || ||   |||           ||  ||||| ||||||  |||   ||  ||||    || || || |||||||| || |||||||  |||    | |||||||||||||| ||||||||||||||  | |
gtatgaattttactttatatta--gtccagtttcatgcatgtgt---agctatgataattctttaaaattaaaaatgcttatgtgtaacaaaaat--tgctaacagATACAAAAGGAGTTCCATCTACCACCTGGTGACTTTCCAAATGTTGAACATTTCAAAGAGACCTTGAGTGGTTACAACATTGACAAGTTTGAGAAATTGA

upper sequence: AT3G20290.2 (Arabidopsis thaliana), 3'ss of exon 15
lower sequence: Vv19s0090g01130.t01 (Vitis vinifera), 3'ss of exon 15
gttggtaattggtttgattctgcggatcttttcaatacgccggttctgattccgatcatatttcatgctaatatgtgtttcaatgttgtgggggacatgaaaacagGTACAAAGAGAGCATCACTTACCTAAAGGAGATTTCCCAAATGTGGATCATTTCAGGGAGGTGCTAAGTGGTTACAACATCGACAAGTTTGAGAAGCTAA
   | |       |   | ||||  ||    |   ||  ||    |  ||||   |||   ||||| |    ||     ||| | |||      | ||  | |||||| || || |||   ||  | ||   ||| |||||||| || || || |||||||||||||| || |||||||||| ||| ||||| ||||||| | | |
---gttccacatctctctcctgcaaataaccttg-taaaccaacac--attcaattcaccattcatacattaatcgtactcattcttggttaatatatatatacagGTCCAGAGGGAGTTCCATCTGCCGGCAGGGGATTTCCCGAACGTTGACCATTTCAGGGAGGTACTGAGTGGTTACAGCATAGACAAATTTGAGAGGTTGA
















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|86078386|gb|DR374143.1|DR374143
EST:     CCAAAGCTCAACAGAAACTGATAGATAACTTGGAAGACGAGTTTGGAAAG                         GTACAAAGAGAGCATCACTTACCTAAAGGAGATTTCCCAAATGTGGATCAT
genomic: CCAAAGCTCAACAGAAACTGATAGATAACTTGGAAGACGAGTTTGGAAAGgttggtaatt ... atgaaaacagGTACAAAGAGAGCATCACTTACCTAAAGGAGATTTCCCAAATGTGGATCAT
EST: gi|116430167|gb|EG472759.1|EG472759
EST:     CCAAAGCTCAACAGAAACTGATAGATAACTTGGAAGACGAGTTTGGAAAG                         GTACAAAGAGAGCATCACTTACCTAAAGGAGATTTCCCAAATGTGGATCAT
genomic: CCAAAGCTCAACAGAAACTGATAGATAACTTGGAAGACGAGTTTGGAAAGgttggtaatt ... atgaaaacagGTACAAAGAGAGCATCACTTACCTAAAGGAGATTTCCCAAATGTGGATCAT
EST: gi|125077777|gb|EL140439.1|EL140439
EST:     CCAAAGCTCAACAGAAACTGATAGATAACTTGGAAGACGAGTTTGGAAAG                         GTACAAAGAGAGCATCACTTACCTAAAGGAGATTTCCCAAATGTGG
genomic: CCAAAGCTCAACAGAAACTGATAGATAACTTGGAAGACGAGTTTGGAAAGgttggtaatt ... atgaaaacagGTACAAAGAGAGCATCACTTACCTAAAGGAGATTTCCCAAATGTGG
EST: gi|124881562|gb|EH960464.1|EH960464
EST:     CCAAAGCTCAACAGAAACTGATAGATAACTTGGAAGACGAGTTTGGAAAG                         GTACAAAGAGAGCATCACTTACCTAAAGGAGATTTCCCAAATGTGGATCAT
genomic: CCAAAGCTCAACAGAAACTGATAGATAACTTGGAAGACGAGTTTGGAAAGgttggtaatt ... atgaaaacagGTACAAAGAGAGCATCACTTACCTAAAGGAGATTTCCCAAATGTGGATCAT
EST: gi|125247923|gb|EL262008.1|EL262008
EST:     AAGCTCAACAGAAACTGATAGATAACTTGGAAGACGAGTTTGGAAAG                         GTACAAAGAGAGCATCACTTACCTAAAGGAGATTTCCCAAATGTGGATCAT
genomic: AAGCTCAACAGAAACTGATAGATAACTTGGAAGACGAGTTTGGAAAGgttggtaatt ... atgaaaacagGTACAAAGAGAGCATCACTTACCTAAAGGAGATTTCCCAAATGTGGATCAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ccgatcatatttcatgctaatatgtgtttcaatgttgtgggggacatgaaaacagGTACAAAGAGAGCATCACTTACCTAAAGGAGATTTCCCAAATGTGGATCATTTCAGGGAGGTGCTAAGTGGTTACAACATCGACAAGTTTGAGAAGCTAA
              tgctaat  putative branch site (score: 2)
      atatttcat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttggtaattggtttgattctgcggatcttttcaatacgccggttctgattccgatcatatttcatgctaatatgtgtttcaatgttgtgggggacatgaaaacagGTACAAAGAGAGCATCACTTACCTAAAGGAGATTTCCCAAATGTGGATCATTTCAGGGAGGTGCTAAGTGGTTACAACATCGACAAGTTTGAGAAGCTAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGC