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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagctttttcttcttccttttgctccttttatattgagtctattgacacaatcttgcttagttttcttgaattggttcttactttggtgtttgtggtagCTGGTGTGCCGATTGACAATGTCCTGTATCTTGGTGGACCAAACATTGCTGCTGAAATTTACAACAAGGAATATGCCAATGCTAGAATCTGTGGAGCTGC

Basic information

species Arabidopsis thaliana
transcript AT2G41540.2
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT2G41540.2 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: LOC_Os01g58740.1 (Oryza sativa), 3'ss of exon 2
------gtaagctttttcttcttccttttgctccttttatattgagtctattgacacaatcttgcttagttttcttgaattggttcttactttggtgtttgtggtagCTGGTGTGCCGATTGACAATGTCCTGTATCTTGGTGGACCAAACATTGCTGCTGAAATTTACAACAAGGAATATGCCAATGCTAGAATCTGTGGAGCTGC
      |     | ||  | |||  |||| || |||   | ||  |   |||    |  ||    |||  |||||  ||||  |  ||  |||| | | ||    ||| || || ||  | || ||  | || |||||||| || || ||||||||| | ||||||||||| || |||||||| |||||| | || |||||||||| 
ttaacggccgagtgttcatgcttggttttacttcttaactgttttga--attatatccttccaattta--tttctgcaatttatatttgttttgttttctgc---agCGGGGGTTCCATTGGAAAACATTCTTTATCTTGGAGGCCCTAACATTGCTTCAGAAATTTACAATAAAGAATATGCAAATGCTCGTATATGTGGAGCTGA

upper sequence: AT2G41540.2 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: LOC_Os01g71280.1 (Oryza sativa), 3'ss of exon 2
gtaagctttttcttcttccttttgctccttttatattgagtctattgacacaatcttgcttagtttt--cttgaattggttct-tactttggtgtttgtggtagCTGGTGTGCCGATTGACAATGTCCTGTATCTTGGTGGACCAAACATTGCTGCTGAAATTTACAACAAGGAATATGCCAATGCTAGAATCTGTGGAGCTGC
   |  |   | |   |  | ||     |  |  |   |  |||||    |   |||| ||  ||     |  || |  |||   | |||    |   | | |||||| || || | ||| ||| | || |||||||| || |||||||||||  | || ||||| ||||| |||||||| |||||| ||||||||||  |   
--gacatgcatttatgtgatattaactttcgttgacccaacctattccttc--ccttgttttattcaaattacaactaattcagcattttaaaataaattgcagCTGGAGTTCCAACTGAGAATATACTATATCTTGGAGGCCCAAACATTGCCTCAGAGATTTATAACAAAGAATATGCAAATGCTCGAATCTGTGGGTCCAA

upper sequence: AT2G41540.2 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GRMZM2G090747_T02 (Zea mays), 3'ss of exon 2
gtaagctttttcttcttccttttgctccttttatattgagtctattgacacaatcttgcttagttttcttgaattggttcttactttggtgtttgtggtagCTGGTGTGCCGATTGACAATGTCCTGTATCTTGGTGGACCAAACATTGCTGCTGAAATTTACAACAAGGAATATGCCAATGCTAGAATCTGTGGAGCTGC
  |  | | |   |  ||  |     |   | || |  |     |||       ||   | | |||   ||| ||  |    ||| | | || |   | |||||| || ||    || ||| | || |||||||| ||||| || |||||| |||||||||||||||| |||||||| |||||  | || |||||||||| 
agatacatatatatgctcaatgcttcctcctaatctccaagtatttgttgtcccctctttgattttgtatgatttattatggactattg-gtataatgcagCTGGAGTTCCATCAGAGAATATTCTTTATCTTGGCGGACCTAATATTGCTTCTGAAATTTACAACAAAGAATATGCAAATGCACGTATTTGTGGAGCTGA

upper sequence: AT2G41540.2 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GRMZM2G173195_T01 (Zea mays), 3'ss of exon 1
-gtaagctttttcttcttccttttgctccttttatattgagtctattgacacaatcttgcttagttttcttgaattggttcttactttgg-tgtttgtggtagCTGGTGTGCCGATTGACAATGTCCTGTATCTTGGTGGACCAAACATTGCTGCTGAAATTTACAACAAGGAATATGCCAATGCTAGAATCTGTGGAGCTGC
  | | |    |  |  |         |  ||||| |  | ||| |  | || ||  || || |||| |||   | | |  | |   ||| |  ||   | |||||| || ||  | || ||  | || |||||||| || |||||||||||| |||| ||||| ||||| |||||||| |||||| | || |||||||||| 
ttttaccgaactgatactaacaccctgctctttatctcaattctgt--atactatactg-ttggtttgcttttgtggttgttgatcatggattcttactgcagCTGGAGTTCCCTTGGAGAACATTCTATATCTTGGAGGCCCAAACATTGCTTCTGAGATTTATAACAAAGAATATGCGAATGCTCGCATATGTGGAGCTGA

upper sequence: AT2G41540.2 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GRMZM2G155348_T01 (Zea mays), 3'ss of exon 2
--------gtaagctttttcttcttccttttgctccttttatattgagtctattgacacaatcttgcttagttttcttgaattggttcttactttggtgtttgtggtagCTGGTGTGCCGATTGACAATGTCCTGTATCTTGGTGGACCAAACATTGCTGCTGAAATTTACAACAAGGAATATGCCAATGCTAGAATCTGTGGAGCTGC
         | |    | |   |    |||| || |||  ||  |  | ||  | |    |    | | ||   |   ||  || || |||    ||  |   | | |||||| || || | ||| ||| | || |||||||| ||||||||||| ||  | |||||||| ||||| |||||||| || ||| ||||||||||| |   
gcatctggttgaaacgtataaacagtttttttctgctta-atgcttggcctgcttatttga----gatcagcagtacaga-ctgatttttaa---ggaatgcattgcagCTGGAGTTCCAACTGAAAATATACTCTATCTTGGAGGACCAAACATCGCCTCGGAAATTTATAACAAAGAATATGCAAACGCTCGAATCTGTGGATCCAA

upper sequence: AT2G41540.2 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA03G28970.1 (Glycine max), 3'ss of exon 1
gtaagctttttcttcttccttttg-ctccttttatattgagtctattgacacaatcttgcttagttttc--ttgaattggttcttactttggtgtttgtggtagCTGGTGTGCCGATTGACAATGTCCTGTATCTTGGTGGACCAAACATTGCTGCTGAAATTTACAACAAGGAATATGCCAATGCTAGAATCTGTGGAGCTGC
  |  || ||| || ||  |||   ||  |||| ||||   ||    | || |  ||| ||||   | |  |   ||   |||||    | |      || ||||| | ||||| || || ||  | || ||||||||||| ||||| |||||  | ||||| ||||||||||| ||||||||||| |||||||||||||||| 
-aatactcttttttatttatttcatctgattttgtatta--tcataggtcatagcctt-cttaccatgcaataatatctattctttgcattgcaaacttgatagCTAGAGTGCCTATGGAGAACATACTCTATCTTGGTGGTCCAAATATTGCCTCAGAAATCTACAACAAGGAGTATGCCAATGCAAGAATCTGTGGAGCTGA

upper sequence: AT2G41540.2 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA19G31730.1 (Glycine max), 3'ss of exon 1
gtaagctttttcttcttccttttgctccttttatattg-agtctattgac---acaat--cttgcttagtt-ttcttgaattggttcttactttggtgtt--tgtggtagCTGGTGTGCCGATTGACAATGTCCTGTATCTTGGTGGACCAAACATTGCTGCTGAAATTTACAACAAGGAATATGCCAATGCTAGAATCTGTGGAGCTGC
          || |||   |||| ||  |   | ||   || ||  | ||    ||||    || |||||  |||   ||||  ||  |  ||  |        ||  |||| | ||||| || || ||  | || ||||||||||| ||||| |||||  | ||||| ||||||||||| ||||||||||| ||||| |||||||||| 
----------tcatctgattttttcttatcagagatcatagccttctaactatgcaataatatgtttagtccttccctaattctttactctttgcgcccaaacttgacagCTAGAGTGCCTATGGAGAACATACTTTATCTTGGTGGTCCAAATATTGCCTCAGAAATCTACAACAAGGAGTATGCCAATGCAAGAATATGTGGAGCTGA

upper sequence: AT2G41540.2 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA02G33340.1 (Glycine max), 3'ss of exon 1
gtaagctttttcttcttccttttgctccttttatattg--agtctattgacacaatcttgcttagttttcttgaatt---ggttcttactttggtgtttgtggtagCTGGTGTGCCGATTGACAATGTCCTGTATCTTGGTGGACCAAACATTGCTGCTGAAATTTACAACAAGGAATATGCCAATGCTAGAATCTGTGGAGCTGC
  |   ||| | |  |  |    |  |  |  |   ||  | | |  |   | |    |  |||  |||| | | |      |  ||||  ||     | ||  |||||| ||||| || || ||  | |||||||||||||| ||||| |||||  | ||||| ||||||||||| |||||||||||  |||| || |||| || 
--agaatttgtttgataac----gaccaatggaagctggtaatttggtagtatatctatttttatctttcctcattctcaactctttacaatgcatactttgacagCTGGAGTGCCTATGGAGAACATACTGTATCTTGGTGGTCCAAATATTGCCTCAGAAATATACAACAAGGAGTATGCCAATGCCCGAATTTGCGGAGATGA

upper sequence: AT2G41540.2 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA10G15900.1 (Glycine max), 3'ss of exon 1
gtaagctttttcttcttccttttgctccttttatattgagtctattgacacaatcttgcttagttttcttgaatt---ggttcttact-ttggtgtttgtggtagCTGGTGTGCCGATTGACAATGTCCTGTATCTTGGTGGACCAAACATTGCTGCTGAAATTTACAACAAGGAATATGCCAATGCTAGAATCTGTGGAGCTGC
  |   ||| | |  | ||      |        ||  | | || |   | |    |   ||  |||  | | |      |  ||||  ||  |  || ||  |||||| ||||| || || ||  | || ||||||||||| ||||| |||||  | ||||| ||||||||||| |||||||||||| |||| || ||||| | 
--agaatttatttgataccaaccaatagaagctgat--aatttagtagtatatctatttctatattttctcattctcaactctttacaattcatactt-tgacagCTGGAGTGCCTATGGAGAACATACTTTATCTTGGTGGTCCAAATATTGCCTCAGAAATATACAACAAGGAGTATGCCAATGCTCGAATATGCGGAGCAGA

upper sequence: AT2G41540.2 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: Vv08s0007g09000.t01 (Vitis vinifera), 3'ss of exon 1
--------------------------------gtaagctttttcttcttccttttgctccttttatattgag----------tctattgacacaat---cttg--------cttagttttcttgaattggttcttactttggtgtttgtg----gtagCTGGTGTGCCGATTGACAATGTCCTGTATCTTGGTGGACCAAACATTGCTGCTGAAATTTACAACAAGGAATATGCCAATGCTAGAATCTGTGGAGCTGC
                                 | |  | ||   |||   ||||| | ||| |  ||| |           | | |||  ||| |   |||          ||  |||   |||  |    |||  ||   | |   ||    | |||||||||  | || || ||  | || || ||||| ||||||||||||||  | || |||||||||||||| ||||| |||||| |||| |||||||||| 
gtaagggcctttgttttactatttattggtttctcaaatcttggctctatgttttgtttcttgtgaattaaaagtccatatatttcttggaacatttgccttaagaagagcttttatttctatgatctaagccttttttatatatccttgctgggcagCTGGTGTAGCTATGGAAAACATTCTTTACCTTGGAGGACCAAACATTGCCTCAGAGATTTACAACAAGGAGTATGCGAATGCTCGAATATGTGGAGCTGA

upper sequence: AT2G41540.2 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: PP1S114_190V6.1 (Physcomitrella patens), 3'ss of exon 3
-gtaagctttttcttcttccttttgctccttttatattgagtctattgacacaatcttgcttagttttcttgaattggttcttactttggtgt--ttgtggt--agCTGGTGTGCCGATTGACAATGTCCTGTATCTTGGTGGACCAAACATTGCTGCTGAAATTTACAACAAGGAATATGCCAATGCTAGAATCTGTGGAGCTGC
 ||  |  | |   | |  | |         |  | |   ||    ||| |   | |   ||| | |    |  ||||  || | | | ||||  ||||| |  ||| || |||||   ||| |||||  |||| || || || || ||||||||| ||||| ||||||||||||| ||||| |||||  | ||||| ||  ||| 
tgtgtgtgtgtaaatgtgtcctccagctggctcttgtcaggt----tgaaatggtatgaattaatatga--gggttgggactgaatattgtgtaattgtgattcagCCGGCGTGCCTTCTGAAAATGTTTTGTACCTGGGAGGTCCGAACATTGCTTCTGAAGTTTACAACAAGGAGTATGCTAATGCACGGATCTGCGGGTCTGA

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|124884546|gb|EH963448.1|EH963448
EST:     TCCACATATCATAACTCCAACAAAGATGATTCATCAAGCAA                         CTGGTGTGCCGATTGACAATGTCCTGTATCTTGGTGGACCAAACATTG
genomic: TCCACATATCATAACTCCAACAAAGATGATTCATCAAGCAAgtaagctttt ... tttgtggtagCTGGTGTGCCGATTGACAATGTCCTGTATCTTGGTGGACCAAACATTG
EST: gi|124834176|gb|EH918615.1|EH918615
EST:     TGAACCAGTTCCACATATCATAACTCCAACAAAGATGATTCATCAAGCAA                         CTGGTGTGACCGATTGACAATGTCCTGTATCT
genomic: TGAACCAGTTCCACATATCATAACTCCAACAAAGATGATTCATCAAGCAAgtaagctttt ... tttgtggtagCTGGTGTG-CCGATTGACAATGTCCTGTATCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gacacaatcttgcttagttttcttgaattggttcttactttggtgtttgtggtagCTGGTGTGCCGATTGACAATGTCCTGTATCTTGGTGGACCAAACATTGCTGCTGAAATTTACAACAAGGAATATGCCAATGCTAGAATCTGTGGAGCTGC
                               ttcttac  putative branch site (score: 2)
             ttagtttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagctttttcttcttccttttgctccttttatattgagtctattgacacaatcttgcttagttttcttgaattggttcttactttggtgtttgtggtagCTGGTGTGCCGATTGACAATGTCCTGTATCTTGGTGGACCAAACATTGCTGCTGAAATTTACAACAAGGAATATGCCAATGCTAGAATCTGTGGAGCTGC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGC