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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...caaataaataaataggtttttacatcttttgactttgtggctccttttttccaactctaagttctactctctaatgttttcatccctctggcctttacagACCATTAGTTACATGGCCGAACGTGTTGTTGGAACAGGATCATTCGGAATTGTATTCCAG

Basic information

species Arabidopsis thaliana
transcript AT2G30980.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT2G30980.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA13G36570.1 (Glycine max), 3'ss of exon 1
caaataaataaataggtttttacatctt---ttgactttgtggctccttttttccaactctaagttctactctcta-atgttttcatccctctggcctttacagACCATTAGTTACATGGCCGAACGTGTTGTTGGAACAGGATCATTCGGAATTGTATTCCAG
 | |    | ||||   ||  |    |    ||||   |      |     || ||| |     ||||| |||  | |  |||     |   || |  || |||||||| ||||||||||| |||||||||||||| || ||||||||||||||||| ||||||
-agaattttgaataaaattaaatgcttgagattgatgataacatccacgggtttcaatttc---ttctattcttcataaatttgtgctcgaatgccacttgcagACCATCAGTTACATGGCTGAACGTGTTGTTGGCACTGGATCATTCGGAATTGTTTTCCAG

upper sequence: AT2G30980.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA12G33950.1 (Glycine max), 3'ss of exon 2
----caaataaataaataggtttttacatcttttgactttgtggctccttttttccaactctaagttctactctcta-atgttttcatccctctggcctttacagACCATTAGTTACATGGCCGAACGTGTTGTTGGAACAGGATCATTCGGAATTGTATTCCAG
      ||||||  | |   |  |||    |  |||   ||     |     || ||| |     || || |||  | |  |||     |   || |  || |||||||| |||||||||||||||||||||||||| || |||||||| || ||||| ||||||
attttgaataaa--attgactgcttaagattgatgatgatggcatccacgggtttcaatttc---ttttattcttcataaatttgtgctctaatgcctcttgcagACCATCAGTTACATGGCCGAACGTGTTGTTGGCACTGGATCATTTGGCATTGTTTTCCAG

upper sequence: AT2G30980.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA06G42840.1 (Glycine max), 3'ss of exon 2
---caaataaataaataggtttttacatcttttgactttgtggctccttttttccaactctaagttctactctctaatgttttcatccctc-tggcctttacagACCATTAGTTACATGGCCGAACGTGTTGTTGGAACAGGATCATTCGGAATTGTATTCCAG
     ||||| |  | |  |  | | ||  | ||| |||    |    ||| | |  |   ||   ||  | | | ||| || | |||||  |  |   | |||||||| ||||||||||| |||||||||||||| || |||||||| ||| |||| ||||||
ggttcaataactttaaaattggtgatattgtctgagttt----cattatttgttcttcgtaaataacttatttgttatgattccttccctgataccacctgcagACCATCAGTTACATGGCAGAACGTGTTGTTGGCACTGGATCATTTGGAGTTGTTTTCCAG

upper sequence: AT2G30980.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA12G15470.2 (Glycine max), 3'ss of exon 2
-caaataaataaatag-gtttttacatcttttgactttgtggctccttttttccaactctaagttctactctctaatgttttcatccctctggcctttacagACCATTAGTTACATGGCCGAACGTGTTGTTGGAACAGGATCATTCGGAATTGTATTCCAG
    || |||| |||   | |||  |       |     |      | || | |     ||| || |    | | ||   |||  |    |  |   | |||||||| ||||||||||| |||||||||||||| || |||||||| ||| |||| || |||
atgcattaatatatattatctttggagtccaaaaaaaaataaaatttattcttcgtaaataacttatttgttatgattacttc--catgataccacctgcagACCATCAGTTACATGGCAGAACGTGTTGTTGGCACTGGATCATTTGGAGTTGTTTTTCAG

upper sequence: AT2G30980.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: PP1S306_43V6.2 (Physcomitrella patens), 3'ss of exon 3
caaataaataaataggtttttacatcttttgact--ttgtggctccttttttccaactctaagttctactctctaatgttttcatccctctggcctttacagACCATTAGTTACATGGCCGAACGTGTTGTTGGAACAGGATCATTCGGAATTGTATTCCAG
    |        || ||   | |     ||| |  |   | ||      | |  | | ||  | ||  | |    ||     | |    ||     | ||||| || || ||   ||| |||||||||||||| || ||||||||||| ||||| ||||||
--cttttcctggaagcttgccaaaggacatgaatggtgcagactatcagctacttattttatctacttattttctttggaacaaacgacatgaatggtgcagACGATCAGCTATTCGGCAGAACGTGTTGTTGGCACTGGATCATTCGGGATTGTCTTCCAG

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|86048154|gb|DR343909.1|DR343909
EST:     GTCACATAATTTCTACTACAATTGGAGGCAAAAATGGTGAACCTAAACAG                         ACCATTAGTTACANTGGCCGAACGTGTTGTTGGAACAGGATCATTCGGAA
genomic: GTCACATAATTTCTACTACAATTGGAGGCAAAAATGGTGAACCTAAACAGgttggattct ... gcctttacagACCATTAGTTACA-TGGCCGAACGTGTTGTTGGAACAGGATCATTCGGAA
EST: gi|86048164|gb|DR343919.1|DR343919
EST:     GTCACATAATTTCTACTACAATTGGAGGCAAAAATGGTGAACCTAAACAG                         ACCATTAGTTACATGGCCGAACATGTTGTTGGAACAGGATCATTCGGAATT
genomic: GTCACATAATTTCTACTACAATTGGAGGCAAAAATGGTGAACCTAAACAGgttggattct ... gcctttacagACCATTAGTTACATGGCCGAACGTGTTGTTGGAACAGGATCATTCGGAATT
EST: gi|86048152|gb|DR343907.1|DR343907
EST:     GTCACATAATTTCTACTACAATTGGAGGCAAAAATGGTGAACCTAAACAG                         ACCATTAGTTACATGGCCGAACGTGTTGTTGGAACAGGATCATTCGGAATT
genomic: GTCACATAATTTCTACTACAATTGGAGGCAAAAATGGTGAACCTAAACAGgttggattct ... gcctttacagACCATTAGTTACATGGCCGAACGTGTTGTTGGAACAGGATCATTCGGAATT
EST: gi|86048153|gb|DR343908.1|DR343908
EST:     GTCACATAATTTCTACTACAATTGGAGGCAAAAATGGTGAACCTAAACAG                         ACCATTAGTTACATGGCCGAACGTGTTGTTGGAACAGGATCATTCGGAATT
genomic: GTCACATAATTTCTACTACAATTGGAGGCAAAAATGGTGAACCTAAACAGgttggattct ... gcctttacagACCATTAGTTACATGGCCGAACGTGTTGTTGGAACAGGATCATTCGGAATT
EST: gi|86048158|gb|DR343913.1|DR343913
EST:     GTCACATAATTTCTACTACAATTGGAGGCAAAAATGGTGAACCTAAACAG                         ACCATTAGTTACATGGCCGAACGTGTTGTTGGAACAGGATCATTCGGAATT
genomic: GTCACATAATTTCTACTACAATTGGAGGCAAAAATGGTGAACCTAAACAGgttggattct ... gcctttacagACCATTAGTTACATGGCCGAACGTGTTGTTGGAACAGGATCATTCGGAATT
EST: gi|86048162|gb|DR343917.1|DR343917
EST:     GTCACATAATTTCTACTACAATTGGAGGCAAAAATGGTGAACCTAAACAG                         ACCATTAGTTACATGGCCGAACGTGTTGTTGGAACAGGATCATTCGGAATT
genomic: GTCACATAATTTCTACTACAATTGGAGGCAAAAATGGTGAACCTAAACAGgttggattct ... gcctttacagACCATTAGTTACATGGCCGAACGTGTTGTTGGAACAGGATCATTCGGAATT
EST: gi|86048161|gb|DR343916.1|DR343916
EST:     GTCACATAATTTCTACTACAATTGGAGGCAAAAATGGTGAACCTAAACAG                         ACCATTAGTTACATGGCCGAACGTGTTGTTGGAACAGGATCATTCGGAATT
genomic: GTCACATAATTTCTACTACAATTGGAGGCAAAAATGGTGAACCTAAACAGgttggattct ... gcctttacagACCATTAGTTACATGGCCGAACGTGTTGTTGGAACAGGATCATTCGGAATT
EST: gi|86048155|gb|DR343910.1|DR343910
EST:     GTCACATAATTTCTACTACAATTGGAGGCAAAAATGGTGAACCTAAACAG                         ACCATTAGTTACATGGCCGAACGTGTTGTTGGAACAGGATCATTCGGAATT
genomic: GTCACATAATTTCTACTACAATTGGAGGCAAAAATGGTGAACCTAAACAGgttggattct ... gcctttacagACCATTAGTTACATGGCCGAACGTGTTGTTGGAACAGGATCATTCGGAATT
EST: gi|86048167|gb|DR343922.1|DR343922
EST:     GTCACATAATTTCTACTACAATTGGAGGCAAAAATGGTGAACCTAAACAG                         ACCATTAGTTACATGGCCGAACGTGTTGTTGGAACAGGATCATTCGGAATT
genomic: GTCACATAATTTCTACTACAATTGGAGGCAAAAATGGTGAACCTAAACAGgttggattct ... gcctttacagACCATTAGTTACATGGCCGAACGTGTTGTTGGAACAGGATCATTCGGAATT
EST: gi|86048168|gb|DR343923.1|DR343923
EST:     GTCACATAATTTCTACTACAATTGGAGGCAAAAATGGTGAACCTAAACAG                         ACCATTAGTTACATGGCCGAACGTGTTGTTGGAACAGGATCATTCGGAATT
genomic: GTCACATAATTTCTACTACAATTGGAGGCAAAAATGGTGAACCTAAACAGgttggattct ... gcctttacagACCATTAGTTACATGGCCGAACGTGTTGTTGGAACAGGATCATTCGGAATT
EST: gi|86048165|gb|DR343920.1|DR343920
EST:     GTCACATAATTTCTACTACAATTGGAGGCAAAAATGGTGAACCTAAACAG                         ACCATTAGTTACATGGCCGAACGTGTTGTTGGAACAGGATCATTCGGAATT
genomic: GTCACATAATTTCTACTACAATTGGAGGCAAAAATGGTGAACCTAAACAGgttggattct ... gcctttacagACCATTAGTTACATGGCCGAACGTGTTGTTGGAACAGGATCATTCGGAATT
EST: gi|86048159|gb|DR343914.1|DR343914
EST:     GTCACATAATTTCTACTACAATTGGAGGCAAAAATGGTGAACCTAAACAG                         ACCATTAGTTACATGGCCGAACGTGTTGTTGGAACAGGATCATTCGGAATT
genomic: GTCACATAATTTCTACTACAATTGGAGGCAAAAATGGTGAACCTAAACAGgttggattct ... gcctttacagACCATTAGTTACATGGCCGAACGTGTTGTTGGAACAGGATCATTCGGAATT
EST: gi|86048163|gb|DR343918.1|DR343918
EST:     GNCACATAATTTCTACTACAATTGGAGGCAAAAATGGTGAACCTAAACAG                         ACCATTAGTTACATGGCCGAACGTGTTGTTGGAACAGGATCATTCGGAATT
genomic: GTCACATAATTTCTACTACAATTGGAGGCAAAAATGGTGAACCTAAACAGgttggattct ... gcctttacagACCATTAGTTACATGGCCGAACGTGTTGTTGGAACAGGATCATTCGGAATT
EST: gi|163975543|gb|ES130057.1|ES130057
EST:     TTGGAGGCAAAAATGGTGAACCTAAACAG                         ACCATTAGTTACATGGCCGAACGTGTTGTTTGGAACAGGATCATTCGGAAT
genomic: TTGGAGGCAAAAATGGTGAACCTAAACAGgttggattct ... gcctttacagACCATTAGTTACATGGCCGAACGTGTTGTT-GGAACAGGATCATTCGGAAT
EST: gi|86048160|gb|DR343915.1|DR343915
EST:     GTCACATAATTTCTACTACAATTGGAGGCAAAAATGGTGAACCTAAACAG                         ACCATTAGTTACATGGCCGAACGTGTTGTTGGAACAGGATCATTCGGAATT
genomic: GTCACATAATTTCTACTACAATTGGAGGCAAAAATGGTGAACCTAAACAGgttggattct ... gcctttacagACCATTAGTTACATGGCCGAACGTGTTGTTGGAACAGGATCATTCGGAATT
EST: gi|86048169|gb|DR343924.1|DR343924
EST:     GTCACATAATTTCTACTACAATTGGAGGCAAAAATGGTGAACCTAAACAG                         ACCATTAGTTACATGGCCGAACGTGTTGTTGGAACAGGATCATTCGGAATT
genomic: GTCACATAATTTCTACTACAATTGGAGGCAAAAATGGTGAACCTAAACAGgttggattct ... gcctttacagACCATTAGTTACATGGCCGAACGTGTTGTTGGAACAGGATCATTCGGAATT
EST: gi|152033639|gb|BP560678.2|BP560678
EST:     GTCACATAATTTCTACTACAATTGGAGGCAAAAATGGTGAACCTAAACAG                         ACCATTAGTTACATGGCCGAACGTGTTGTTGGAACAGGATCATTCGGAATT
genomic: GTCACATAATTTCTACTACAATTGGAGGCAAAAATGGTGAACCTAAACAGgttggattct ... gcctttacagACCATTAGTTACATGGCCGAACGTGTTGTTGGAACAGGATCATTCGGAATT
EST: gi|86048157|gb|DR343912.1|DR343912
EST:     GTCACATAATTTCTACTACAATTGGAGGCAAAAATGGTGAACCTAAACAG                         ACCATTAGTTACATGGCCGAACGTGTTGTTGGAACAGGATCATTCGGAATT
genomic: GTCACATAATTTCTACTACAATTGGAGGCAAAAATGGTGAACCTAAACAGgttggattct ... gcctttacagACCATTAGTTACATGGCCGAACGTGTTGTTGGAACAGGATCATTCGGAATT
EST: gi|125113455|gb|EL164266.1|EL164266
EST:     CAAAAATGGTGAACCTAAACAG                         ACCATTAGTTACATGGCCGAACGTGTTGTTGGAACAGGATCATTCGGAATT
genomic: CAAAAATGGTGAACCTAAACAGgttggattct ... gcctttacagACCATTAGTTACATGGCCGAACGTGTTGTTGGAACAGGATCATTCGGAATT
EST: gi|86048156|gb|DR343911.1|DR343911
EST:     GTCACATAATTTCTACTACAATTGGAGGCAAAAATGGTGAACCTAAACAG                         ACCATTAGTTACATGGCCGAACGTGTTGTTGGAACAGGATCATTCGGAATT
genomic: GTCACATAATTTCTACTACAATTGGAGGCAAAAATGGTGAACCTAAACAGgttggattct ... gcctttacagACCATTAGTTACATGGCCGAACGTGTTGTTGGAACAGGATCATTCGGAATT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttttccaactctaagttctactctctaatgttttcatccctctggcctttacagACCATTAGTTACATGGCCGAACGTGTTGTTGGAACAGGATCATTCGGAATTGTATTCCAG
                       ctctaat  putative branch site (score: 3)
                                     tccctctggccttt  putative PPT
                          taatgtttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
caaataaataaataggtttttacatcttttgactttgtggctccttttttccaactctaagttctactctctaatgttttcatccctctggcctttacagACCATTAGTTACATGGCCGAACGTGTTGTTGGAACAGGATCATTCGGAATTGTATTCCAG

-aaataaa
- - - - - - - ggttttt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -actctct