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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...attaatcgttgaatgctgcattggtttggattgagttattggtaatttttgttcttattgattatccgtttctaaaactttgacaattggtgtattctagGGGACATTTATGAGCATGCTGTTGTTCTAAGCGTCAAAACCGAGGATCAAGATGCTTTTGAGAGAGATTTCTTCCAGCTGAAACCTTACTATGTGGATGC

Basic information

species Arabidopsis thaliana
transcript AT1G64520.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G64520.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GRMZM2G121452_T01 (Zea mays), 3'ss of exon 2
-----attaatcgttgaatgctgcattggtttggattgagttattggtaatttttgttcttattgattatccgtttctaaaactttgacaattggtgtattctagGGGACATTTATGAGCATGCTGTTGTTCTAAGCGTCAAAACCGAGGATCAAGATGCTTTTGAGAGAGATTTCTTCCAGCTGAAACCTTACTATGTGGATGC
     |  ||   |  |  | | | |    |   ||   ||| ||  || ||    ||| | |  |     |   | |  ||||  | | |       |||  |||||||||||||||||||||||||||| | || || |||   ||||| |||||||| |||||  | ||||||| ||||||||| ||||| ||  ||||| |
gtagcagaaaagatcaagaggtccttgaactgttatgctgttcttt-tagttacccttcct-tcaacagagcaagttttgaactcagccca---aaacatttcagGGGACATTTATGAGCATGCTGTTGTTTTGAGTGTGAAACTTGAGGACCAAGATGCGTTTGAACGCGATTTCTGCCAGCTGAAGCCTTATTACATGGATAC

upper sequence: AT1G64520.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GRMZM2G073077_T01 (Zea mays), 3'ss of exon 2
attaatcgttgaatgctgcattggtttggattgagttattg-gtaatttttgttcttattgattatccgtttctaaaactttga---caatt-ggtgtattctagGGGACATTTATGAGCATGCTGTTGTTCT-AAGCGTCAAAACCGAGGATCAAGATGCTTTTGAGAGAGATTTCTTCCAGCTGAAACCTTACTATGTGGATGC
 ||| |  | |||     ||   |       |||  ||||  | | |  |||| ||||    | | | |      ||  |||||   |||        |||  |||||||||||||||||||||||||||| |  || || |||   ||||| |||||||| |||||  | |||||||  ||||| || ||||| ||  |||||  
tttagtaatagaaaagatcaagaggccca--tgaactattatgcagtacttgtacttagccttcaacggagc---aagttttgaactcaacccaaaacatttcagGGGACATTTATGAGCATGCTGTTGTTTTTGAGTGTGAAACTTGAGGACCAAGATGCATTTGAACGTGATTTCTGTCAGCTAAAGCCTTATTACATGGATA-

upper sequence: AT1G64520.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GRMZM2G073077_T02 (Zea mays), 3'ss of exon 2
attaatcgttgaatgctgcattggtttggattgagttattg-gtaatttttgttcttattgattatccgtttctaaaactttga---caatt-ggtgtattctagGGGACATTTATGAGCATGCTGTTGTTCTAAGCGTCAAAACCGAGGATCAAGATGCTTTTGAGAGAGATTTCTTCCAGCTGAAACCTTACTATGTGGATGC
 ||| |  | |||     ||   |       |||  ||||  | | |  |||| ||||    | | | |      ||  |||||   |||        |||  ||||||||||||||||||||||||||||                                                                          
tttagtaatagaaaagatcaagaggccca--tgaactattatgcagtacttgtacttagccttcaacggagc---aagttttgaactcaacccaaaacatttcagGGGACATTTATGAGCATGCTGTTGTT--------------------------------------------------------------------------

upper sequence: AT1G64520.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA08G08690.1 (Glycine max), 3'ss of exon 2
-attaatcgttgaatgctgcattggtttggattgagttattggtaatttttgttcttattgattatccgtttctaaaactttgacaattggtgta-ttctagGGGACATTTATGAGCATGCTGTTGTTCTAAGCGTCAAAACCGAGGATCAAGATGCTTTTGAGAGAGATTTCTTCCAGCTGAAACCTTACTATGTGGATGC
 |  |    |   ||  |   |   | |  | |||     |   || | ||     | ||   | |  |||| |       ||    ||  |  | ||| |||||| || ||||||||||||||||| || || || ||||  ||||||||||||||||| || || |||||||||||| |||| ||||| |||   |||||
tagcatcaatgagataatatctacttattaaatgaaaaggtaaaaaatgttagaagttttatgtctaagttttttt--tcctgttggtttttaaacttccagGGGATATATATGAGCATGCTGTTGTCCTTAGTGTGAAAATTGAGGATCAAGATGCTTTCGAAAGGGATTTCTTCCAGTTGAAGCCTTATTATACAGATGC

upper sequence: AT1G64520.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA05G25730.1 (Glycine max), 3'ss of exon 2
-attaatcgttgaatgctgcattggtttggattgagttattg-gtaatttttgttcttattgattatccgtttctaaaactttgacaattggtgtattctagGGGACATTTATGAGCATGCTGTTGTTCTAAGCGTCAAAACCGAGGATCAAGATGCTTTTGAGAGAGATTTCTTCCAGCTGAAACCTTACTATGTGGATGC
 ||| |   |  |       || | |    ||| | | |    ||||    ||||   ||      |   ||| |     || |    ||    |  || |||||| || || |||||||||||||| || || || ||||  |||||||||||||||||||| || |||||||||||| |||| ||||| |||   |||||
tatttagtatcaataagattatagctacttattaaatgaaaaagtaaaaaatgttaagatatcaagtttattttttcctgttggttttttaaact--tccagGGGATATATACGAGCATGCTGTTGTCCTTAGTGTGAAAAATGAGGATCAAGATGCTTTTGAAAGGGATTTCTTCCAGTTGAAGCCTTATTATACAGATGC

upper sequence: AT1G64520.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: Vv02s0025g02010.t01 (Vitis vinifera), 3'ss of exon 2
attaatcgttgaat-gctgc-attggtttggatt---gagttattggtaatttttgttcttattgattatccgtttctaaaactttgacaattggtgtattctagGGGACATTTATGAGCATGCTGTTGTTCTAAGCGTCAAAACCGAGGATCAAGATGCTTTTGAGAGAGATTTCTTCCAGCTGAAACCTTACTATGTGGATGC
||     || |  | | | | |   |||||  ||   || ||     ||| | ||    |||  || | |||  |   | |||||   |  | | || |||  |||||| || ||||||||||||||||| ||||| ||||| || |||||||| ||||| |||||||| |||||||| ||| |||||||||| |||   ||| |
atagggtgtagggttgttactaaatgtttgatttagagaatttcccctaaatgtttgatttagagaatttccactc--acaactt---ctgtggctgaatttcagGGGATATATATGAGCATGCTGTTGTCCTAAGTGTCAAGACAGAGGATCAGGATGCGTTTGAGAGGGATTTCTTTCAGTTGAAACCTTATTATACAGATAC

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|116486366|gb|EG528958.1|EG528958
EST:     TCCATTGTTCGAGAATTCACCTAATGCAGCCAAGGAATTGACTATTGCAA                         GGGACATTTATGAGCATGCTGTTGTTCTAAGCGTCAAAACCGAGGATCAAG
genomic: TCCATTGTTCGAGAATTCACCTAATGCAGCCAAGGAATTGACTATTGCAAgtaagtttct ... tgtattctagGGGACATTTATGAGCATGCTGTTGTTCTAAGCGTCAAAACCGAGGATCAAG
EST: gi|116486373|gb|EG528965.1|EG528965
EST:     TCCATTGTTCGAGAATTCACCTAATGCAGCCAAGGAATTGACTATTGCAA                         GGGACATTTATGAGCATGCTGTTGTTCTAAGCGTCAAAACCGAGGATCAAG
genomic: TCCATTGTTCGAGAATTCACCTAATGCAGCCAAGGAATTGACTATTGCAAgtaagtttct ... tgtattctagGGGACATTTATGAGCATGCTGTTGTTCTAAGCGTCAAAACCGAGGATCAAG
EST: gi|116486364|gb|EG528956.1|EG528956
EST:     TCCATTGTTCGAGAATTCACCTAATGCAGCCAAGGAATTGACTATTGCAA                         GGGACATTTATGAGCATGCTGTTGTTCTAAGCGTCAAAACCGAGGATCAAG
genomic: TCCATTGTTCGAGAATTCACCTAATGCAGCCAAGGAATTGACTATTGCAAgtaagtttct ... tgtattctagGGGACATTTATGAGCATGCTGTTGTTCTAAGCGTCAAAACCGAGGATCAAG
EST: gi|116486368|gb|EG528960.1|EG528960
EST:     TCCATTGTTCGAGAATTCACCTAATGCAGCCAAGGAATTGACTATTGCAA                         GGGACATTTATGAGCATGCTGTTGTTCTAAGCGTCAAAACCGAGGATCAAG
genomic: TCCATTGTTCGAGAATTCACCTAATGCAGCCAAGGAATTGACTATTGCAAgtaagtttct ... tgtattctagGGGACATTTATGAGCATGCTGTTGTTCTAAGCGTCAAAACCGAGGATCAAG
EST: gi|116410781|gb|EG453373.1|EG453373
EST:     TCCATTGTTCGAGAATTCACCTAATGCAGCCAAGGAATTGACTATTGCAA                         GGGACATTTATGAGCATGCTGTTGTTCTAAGCGTCAAAACC
genomic: TCCATTGTTCGAGAATTCACCTAATGCAGCCAAGGAATTGACTATTGCAAgtaagtttct ... tgtattctagGGGACATTTATGAGCATGCTGTTGTTCTAAGCGTCAAAACC
EST: gi|116486371|gb|EG528963.1|EG528963
EST:     TCCATTGTTCGAGAATTCACCTAATGCAGCCAAGGAATTGACTATTGCAA                         GGGACATTTATGAGCATGCTGTTGTTCTAAGCGTCAAAACCGAGGATCAAG
genomic: TCCATTGTTCGAGAATTCACCTAATGCAGCCAAGGAATTGACTATTGCAAgtaagtttct ... tgtattctagGGGACATTTATGAGCATGCTGTTGTTCTAAGCGTCAAAACCGAGGATCAAG
EST: gi|116486376|gb|EG528968.1|EG528968
EST:     TCCATTGTTCGAGAATTCACCTAATGCAGCCAAGGAATTGACTATTGCAA                         GGGACATTTATGAGCATGCTGTTGTTCTAAGCGTCAAAACCGAGGATCAAG
genomic: TCCATTGTTCGAGAATTCACCTAATGCAGCCAAGGAATTGACTATTGCAAgtaagtttct ... tgtattctagGGGACATTTATGAGCATGCTGTTGTTCTAAGCGTCAAAACCGAGGATCAAG
EST: gi|116486365|gb|EG528957.1|EG528957
EST:     TCCATTGTTCGAGAATTCACCTAATGCAGCCAAGGAATTGACTATTGCAA                         GGGACATTTATGAGCATGCTGTTGTTCTAAGCGTCAAAACCGAGGATCAAG
genomic: TCCATTGTTCGAGAATTCACCTAATGCAGCCAAGGAATTGACTATTGCAAgtaagtttct ... tgtattctagGGGACATTTATGAGCATGCTGTTGTTCTAAGCGTCAAAACCGAGGATCAAG
EST: gi|116410784|gb|EG453376.1|EG453376
EST:     TCCATTGTTCGAGAATTCACCTAATGCAGCCAAGGAATTGACTATTGCAA                         GGGACATTTATGAGCATGCTGTTGTTCTAAGCGTCAAAACCGAGGATCAAG
genomic: TCCATTGTTCGAGAATTCACCTAATGCAGCCAAGGAATTGACTATTGCAAgtaagtttct ... tgtattctagGGGACATTTATGAGCATGCTGTTGTTCTAAGCGTCAAAACCGAGGATCAAG
EST: gi|116486359|gb|EG528951.1|EG528951
EST:     TCCATTGTTCGAGAATTCACCTAATGCAGCCAAGGAATTGACTATTGCAA                         GGGACATTTATGAGCATGCTGTTGTTCTAAGCGTCAAAACCGAGGATCAAG
genomic: TCCATTGTTCGAGAATTCACCTAATGCAGCCAAGGAATTGACTATTGCAAgtaagtttct ... tgtattctagGGGACATTTATGAGCATGCTGTTGTTCTAAGCGTCAAAACCGAGGATCAAG
EST: gi|125239192|gb|EL253277.1|EL253277
EST:     TTGTTCGAGAATTCACCTAATGCAGCCAAGGAATTGACTATTGCAA                         GGGACATTTATGAGCATGCTGTTGTTCTAAGCGTCAAAACCGAGGATC
genomic: TTGTTCGAGAATTCACCTAATGCAGCCAAGGAATTGACTATTGCAAgtaagtttct ... tgtattctagGGGACATTTATGAGCATGCTGTTGTTCTAAGCGTCAAAACCGAGGATC
EST: gi|116486357|gb|EG528949.1|EG528949
EST:     TCCATTGTTCGAGAATTCACCTAATGCAGCCAAGGAATTGACTATTGCAA                         GGGACATTTATGAGCATGCTGTTGTTCTAAGCGTCAAAACCGAGGATCAAG
genomic: TCCATTGTTCGAGAATTCACCTAATGCAGCCAAGGAATTGACTATTGCAAgtaagtttct ... tgtattctagGGGACATTTATGAGCATGCTGTTGTTCTAAGCGTCAAAACCGAGGATCAAG
EST: gi|116486361|gb|EG528953.1|EG528953
EST:     TCCATTGTCCGAGAATTCACCTAATGCAGCCAAGGAATTGACTATTGCAA                         GGGACATTTATGAGCATGCTGTTGTTCTAAGCGTCAAAACCGAGGATCAAG
genomic: TCCATTGTTCGAGAATTCACCTAATGCAGCCAAGGAATTGACTATTGCAAgtaagtttct ... tgtattctagGGGACATTTATGAGCATGCTGTTGTTCTAAGCGTCAAAACCGAGGATCAAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttttgttcttattgattatccgtttctaaaactttgacaattggtgtattctagGGGACATTTATGAGCATGCTGTTGTTCTAAGCGTCAAAACCGAGGATCAAGATGCTTTTGAGAGAGATTTCTTCCAGCTGAAACCTTACTATGTGGATGC
      ttcttattgattat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
attaatcgttgaatgctgcattggtttggattgagttattggtaatttttgttcttattgattatccgtttctaaaactttgacaattggtgtattctagGGGACATTTATGAGCATGCTGTTGTTCTAAGCGTCAAAACCGAGGATCAAGATGCTTTTGAGAGAGATTTCTTCCAGCTGAAACCTTACTATGTGGATGC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGA
- - - - - - - - - - - ggtttgg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ctaaaac