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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cttcttcttctttttcttttgtgtctatcattttccttttattctttttcaacactttaccctgatctttgctgatttcttatcttactctgctttgcagACCCCAATATAATGAAAAAACTGCAAGTGGACAGGGGTGCAATTAAGTTTGTCCTTGCTGGAGCAAATATAATGTGTCCTGGCCTCACATCTCCTGGTGG

Basic information

species Vitis vinifera
transcript Vv14s0060g01920.t01
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv14s0060g01920.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA04G41130.2 (Glycine max), 3'ss of exon 4
----cttcttcttctttttcttttgtgtcta--tcattttccttttattctttttcaacactttaccctgatctttgctgatttcttatcttactctgctttgcagACCCCAATATAATGAAAAAACTGCAAGTGGACAGGGGTGCAATTAAGTTTGTCCTTGCTGGAGCAAATATAATGTGTCCTGGCCTCACATCTCCTGGTGG
      |    | |   |   |||| |||||   ||| |       ||  | ||  ||  | |||    ||   ||| |  || ||||| ||  |     ||| ||| || ||||||||||||||  | ||||| ||| | ||||||||||  |||||| | || || ||||| |||||||||||||| || ||||||||||| ||
ctattgtaggatgcagctgactttgggtctaacccatatgatgaaaatgatattgaaatgcattatatggaaaattg-tagttgcttattttttt-----ttgtagATCCAAATATAATGAAAAAGTTACAAGTTGACCGTGGTGCAATTAGATTTGTCTTGGCGGGTGCAAACATAATGTGTCCTGGTCTTACATCTCCTGGGGG

upper sequence: Vv14s0060g01920.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: AT1G09150.1 (Arabidopsis thaliana), 3'ss of exon 5
cttcttcttctttttcttttgtgtctatcattttccttttattctttttcaacactttaccctgatctttgctgatttcttatcttactct-----gctttgcagACCCCAATATAATGAAAAAACTGCAAGTGGACAGGGGTGCAATTAAGTTTGTCCTTGCTGGAGCAAATATAATGTGTCCTGGCCTCACATCTCCTGGTGG
    ||    |  ||   |  |   ||  |     |||  | | ||||    || ||  ||  ||   |     ||||   | || | | |     | ||||||||||| ||||||||||| |   | ||||| || || ||||| || |||||||| ||  |||| ||||| |||||||||||||| || ||||| || || ||
-acttttacatacttgaatgatacatagaaagaaacttggagtttttt----caattagccacgaatgtcaaaaatttggcagctgaatgtttggagttttgcagACCCAAATATAATGAAGAGGTTTCAAGTTGATAGAGGTGCCATAAAGTTTGTTCTGTCTGGTGCAAACATAATGTGTCCTGGTCTTACATCCCCGGGAGG

upper sequence: Vv14s0060g01920.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: EFJ21050 (Selaginella moellendorffii), 3'ss of exon 5
cttcttcttctttttcttttgtgtctatcattttccttttattctttttcaacactttaccctgatctttgctgatttcttatcttactctgctttgcagACCCCAATATAATGAAAAAACTGCAAGTGGACAGGGGTGCAATTAAGTTTGTCCTTGCTGGAGCAAATATAATGTGTCCTGGCCTCACATCTCCTGGTGG
       | |||           |  |   |  |||    || |   |||    | | |     |     ||| |    ||    |    || | | ||||||| |   | ||||| || || ||||| ||||| || || || ||||| ||||| || ||||||||||| |||||||| || || ||||||||||| ||
------gtccttacatgccaaccttgaggctcctccaccaatgcaagttcgtagcatgaggagaaaacgagctaacggttttcgctttcgtgatctccagACCCAACCGTGATGAAGAAGCTCCAAGTTGACAGAGGAGCCATCAAGTTCGTCCTCGCAGGAGCAAATATCATGTGTCCCGGACTGACATCTCCTGGAGG

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|30132447|gb|CB917786.1|CB917786
EST:     CAATGTTCGGGATGGACCTTACATGCCTACATTACGACTTCTTCACCAAT                         ACCCCAATATAATGAAAAAACTGCAAGTGGACAGGGGTGCAATTAAGTTTG
genomic: CAATGTTCGGGATGGACCTTACATGCCTACATTACGACTTCTTCACCAATgtaaagtatt ... tgctttgcagACCCCAATATAATGAAAAAACTGCAAGTGGACAGGGGTGCAATTAAGTTTG
EST: gi|110697600|gb|EE074740.1|EE074740
EST:     CAATGTTCGGGATGGACCTTACATGCCTACATTACGACTTCTTCACCAAT                         ACCCCAATATAATGAAAAAACTGCAAGTGGACAGGGGTGCAATTAAGTTTG
genomic: CAATGTTCGGGATGGACCTTACATGCCTACATTACGACTTCTTCACCAATgtaaagtatt ... tgctttgcagACCCCAATATAATGAAAAAACTGCAAGTGGACAGGGGTGCAATTAAGTTTG
EST: gi|110722653|gb|EE099067.1|EE099067
EST:     CAATGTTCGGGATGGACCTTACATGCCTACATTACGACTTCTTCACCAAT                         ACCCCAATATAATGAAAAAACTGCAAGTGGACAGGGGTGCAATTAAGTTTG
genomic: CAATGTTCGGGATGGACCTTACATGCCTACATTACGACTTCTTCACCAATgtaaagtatt ... tgctttgcagACCCCAATATAATGAAAAAACTGCAAGTGGACAGGGGTGCAATTAAGTTTG
EST: gi|45368131|gb|CK906490.1|CK906490
EST:     CAATGTTCGGGATGGACCTTACATGCCTACATTACGACTTCTTCACCAAT                         ACCCCAATATAATGAAAAAACTGCAAGTGGACAGGGGTGCAATTAAGTTTG
genomic: CAATGTTCGGGATGGACCTTACATGCCTACATTACGACTTCTTCACCAATgtaaagtatt ... tgctttgcagACCCCAATATAATGAAAAAACTGCAAGTGGACAGGGGTGCAATTAAGTTTG
EST: gi|110690622|gb|EE067882.1|EE067882
EST:     CAATGTTCGGGATGGACCTTACATGCCTACATTACGACTTCTTCACCAAT                         ACCCCAATATAATGAAAAAACTGCAAGTGGACAGGGGTGCAATTAAGTTTG
genomic: CAATGTTCGGGATGGACCTTACATGCCTACATTACGACTTCTTCACCAATgtaaagtatt ... tgctttgcagACCCCAATATAATGAAAAAACTGCAAGTGGACAGGGGTGCAATTAAGTTTG
EST: gi|32458352|gb|CD799526.1|CD799526
EST:     CAATGTTCGGGATGGACCTTACATGCCTACATTACGACTTCTTCACCAAT                         ACCCCAATATAATGAAAAAACTGCAAGTGGACAGGGGTGCAATTAAGTTTG
genomic: CAATGTTCGGGATGGACCTTACATGCCTACATTACGACTTCTTCACCAATgtaaagtatt ... tgctttgcagACCCCAATATAATGAAAAAACTGCAAGTGGACAGGGGTGCAATTAAGTTTG
EST: gi|30297956|gb|CB974750.1|CB974750
EST:     CAATGTTCGGGATGGACCTTACATGCCTACATTACGACTTCTTCACCAAT                         ACCCCAATATAATGAAAAAACTGCAAGTGGACAGGGGTGCAATTAAGTTTG
genomic: CAATGTTCGGGATGGACCTTACATGCCTACATTACGACTTCTTCACCAATgtaaagtatt ... tgctttgcagACCCCAATATAATGAAAAAACTGCAAGTGGACAGGGGTGCAATTAAGTTTG
EST: gi|110387074|gb|EC951714.1|EC951714
EST:     CAATGTTCGGGATGGACCTTACATGCCTACATTACGACTTCTTCACCAAT                         ACCCCAATATAATGAAAAAACTGCAAGTGGACAGGGGTGCAATTAAGTTTG
genomic: CAATGTTCGGGATGGACCTTACATGCCTACATTACGACTTCTTCACCAATgtaaagtatt ... tgctttgcagACCCCAATATAATGAAAAAACTGCAAGTGGACAGGGGTGCAATTAAGTTTG
EST: gi|51050864|gb|CO818767.1|CO818767
EST:     CAATGTTCGGGATGGACCTTACATGCCTACATTACGACTTCTTCACCAAT                         ACCCCAATATAATGAAAAAACTGCAAGTGGACAGGGGTGCAATTAAGTTTG
genomic: CAATGTTCGGGATGGACCTTACATGCCTACATTACGACTTCTTCACCAATgtaaagtatt ... tgctttgcagACCCCAATATAATGAAAAAACTGCAAGTGGACAGGGGTGCAATTAAGTTTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttttcaacactttaccctgatctttgctgatttcttatcttactctgctttgcagACCCCAATATAATGAAAAAACTGCAAGTGGACAGGGGTGCAATTAAGTTTGTCCTTGCTGGAGCAAATATAATGTGTCCTGGCCTCACATCTCCTGGTGG
                                    atcttac  putative branch site (score: 3)
                              tttcttatcttactct  CT-rich tract
                             atttcttat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
cttcttcttctttttcttttgtgtctatcattttccttttattctttttcaacactttaccctgatctttgctgatttcttatcttactctgctttgcagACCCCAATATAATGAAAAAACTGCAAGTGGACAGGGGTGCAATTAAGTTTGTCCTTGCTGGAGCAAATATAATGTGTCCTGGCCTCACATCTCCTGGTGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
cttcttc
- - - - - - - - - - - - - - - - - - - - - - - - -caacact
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - accctga
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ttgctga