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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttttttgcactcaatattaagttttactgacttctgatgccaataatttcattgtttcccccattgacctaaatgttcatctttgtttttctttctctagAGTGGGCAACCTGAATTAATAGCTCTGGAGAAGGCAGTGAAAGAAGCCATGGTGCCTGCTGGAACTGCACTAGAG

Basic information

species Arabidopsis thaliana
transcript AT4G16180.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT4G16180.2 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: Vv05s0077g00820.t01 (Vitis vinifera), 3'ss of exon 2
ttttttgcactcaatattaagttt----tactgacttctgatgccaataatttcat-tgtttcccccattgacctaaatgttcatctttgtttttctttctctagAGTGGGCAACCTGAATTAATAGCTCTGGAGAAGGCAGTGAAAGAAGCCATGGTGCCTGCTGGAACTGCACTAGAG
    | ||| | ||    |||  |    | |    || |  |   | |   | ||  || | | ||  || |||   |  || || | | || | ||  ||  ||  ||||||||| ||  | ||||| |||||||||||| ||||||| |||||||| ||||||||||||||   ||||
---atggcaatgaagccaaagaatggaatgcaactttatcttttgagtcggtgcaagtgctactccttttaaccattacatt-atgtat-ttgtcctcactacagGCTGGGCAACCAGAGCTGATAGCACTGGAGAAGGCACTGAAAGAGGCCATGGTTCCTGCTGGAACTGCTAGAGAG

upper sequence: AT4G16180.2 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: Vv05s0077g00250.t01 (Vitis vinifera), 3'ss of exon 2
--ttttttgcactcaat--attaagttttactg-acttctgatgccaataatttcattgtttcccccattgacctaaatgttcatctttgtttttctttctctagAGTGGGCAACCTGAATTAATAGCTCTGGAGAAGGCAGTGAAAGAAGCCATGGTGCCTGCTGGAACTGCACTAGAG
       || |  |||   ||  |||   |||  |  | |   | |  |      | || | | ||  || |||  | |    |   |  || |     ||  ||  ||||||||| ||  | ||||| |||||||||||| ||||||| |||||||| ||||||||||||||   ||||
atggcaatgaagccaaagaatggagtgcaactttatcttttgagtcggtg---caagtgctactccttttaacc--attacataatgtatttgtctacactacagGCTGGGCAACCAGAGCTGATAGCACTGGAGAAGGCACTGAAAGAGGCCATGGTTCCTGCTGGAACTGCTAGAGAG

upper sequence: AT4G16180.2 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: Vv05s0077g00200.t01 (Vitis vinifera), 3'ss of exon 1
---ttttttgcactcaatattaagttttactgacttctgatgccaataatttcattgtttcccccattgacctaaatgttcatctttgtttttctttctctagAGTGGGCAACCTGAATTAATAGCTCTGGAGAAGGCAGTGAAAGAAGCCATGGTGCCTGCTGGAACTGCACTAGAG
       |    |  || | |    |  |      |||  ||       |   | || | | ||  || |||   |  || || | | || |     ||  ||  ||||||||| ||  | ||||| |||||||||||| ||||||| |||||||| ||||||||||||||   ||||
atggcaatgatgccaaagaatggagtgcaactttatcttttga-gtcggtgcaagtgctactccttttaaccattacatt-atgtat-ttgtctacactacagGCTGGGCAACCAGAGCTGATAGCACTGGAGAAGGCACTGAAAGAGGCCATGGTTCCTGCTGGAACTGCTAGAGAG

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|116426956|gb|EG469548.1|EG469548
EST:     CGGGCGAGCCACTTGATATTGAGCATCGAGTTGTTTATAATATCTTTCTT                         AGTGGGCAACCTGAATTAATAGCTCTGGAGAAGGCAGTGAAAGAAGCCATG
genomic: CGGGCGAGCCACTTGATATTGAGCATCGAGTTGTTTATAATATCTTTCCTgtgagtaatt ... ctttctctagAGTGGGCAACCTGAATTAATAGCTCTGGAGAAGGCAGTGAAAGAAGCCATG
EST: gi|116426954|gb|EG469546.1|EG469546
EST:     CGGGCGAGTCACTTGATATTGAGCATCGAGTTGTTTATAATATCTTTCCT                         AGTGGGCAACCTGAATTAATAGCTCTGGAGAAGGCAGTGAAAGAAGCCATG
genomic: CGGGCGAGCCACTTGATATTGAGCATCGAGTTGTTTATAATATCTTTCCTgtgagtaatt ... ctttctctagAGTGGGCAACCTGAATTAATAGCTCTGGAGAAGGCAGTGAAAGAAGCCATG
EST: gi|116426955|gb|EG469547.1|EG469547
EST:     CGGGCGAGCCACTTGATATTGAGCATCGAGTTGTTTATAATATCTTTCCT                         AGTGGGCAACCTGAATTAATAGCTCTGGAGAAGGCAGTGAAAGAAGCCATG
genomic: CGGGCGAGCCACTTGATATTGAGCATCGAGTTGTTTATAATATCTTTCCTgtgagtaatt ... ctttctctagAGTGGGCAACCTGAATTAATAGCTCTGGAGAAGGCAGTGAAAGAAGCCATG
EST: gi|116426974|gb|EG469566.1|EG469566
EST:     CGGGCGAGCCACTTGATATTGAGCATCGAGTTGTTTATAATATCTTTCCT                         AGTGGGCAACCTGAATTAATAGCTCTGGAGAAGGCAGTGAAAGAAGCCATG
genomic: CGGGCGAGCCACTTGATATTGAGCATCGAGTTGTTTATAATATCTTTCCTgtgagtaatt ... ctttctctagAGTGGGCAACCTGAATTAATAGCTCTGGAGAAGGCAGTGAAAGAAGCCATG
EST: gi|116426972|gb|EG469564.1|EG469564
EST:     CGGGCGAGCCACTTGATATTGAGCATCGAGTTGTTTATAATATCTTTCCT                         AGTGGGCAACCTGAATTAATAGCTCTGGAGAAGGCAGTGAAAGAAGCCATG
genomic: CGGGCGAGCCACTTGATATTGAGCATCGAGTTGTTTATAATATCTTTCCTgtgagtaatt ... ctttctctagAGTGGGCAACCTGAATTAATAGCTCTGGAGAAGGCAGTGAAAGAAGCCATG
EST: gi|116426950|gb|EG469542.1|EG469542
EST:     CGGGCGAGCCACTTGATATTGAGCATCGAGTTGTTTATAATATCTTTCCT                         AGTGGGCAACCTGAATTAATAGCTCTGGAGAAGGCAGTGAAAGAAGCCATG
genomic: CGGGCGAGCCACTTGATATTGAGCATCGAGTTGTTTATAATATCTTTCCTgtgagtaatt ... ctttctctagAGTGGGCAACCTGAATTAATAGCTCTGGAGAAGGCAGTGAAAGAAGCCATG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atttcattgtttcccccattgacctaaatgttcatctttgtttttctttctctagAGTGGGCAACCTGAATTAATAGCTCTGGAGAAGGCAGTGAAAGAAGCCATGGTGCCTGCTGGAACTGCACTAGAG
                     acctaaa  putative branch site (score: 3)
                            tgttcatctttgtttt  CT-rich tract
                                    tttgttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttttttgcactcaatattaagttttactgacttctgatgccaataatttcattgtttcccccattgacctaaatgttcatctttgtttttctttctctagAGTGGGCAACCTGAATTAATAGCTCTGGAGAAGGCAGTGAAAGAAGCCATGGTGCCTGCTGGAACTGCACTAGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGGA