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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtcagttacatttggttaccatccttttggttgatgcatgatgaatttagataacaactgtactagcatactgtttttcccatataaagagtcaaataaactatctccagtgattctttgcttcaaaataagttaaattggtgtttctttcctaacagGAGCAATAGCAATTGCAGTCGCAAATCCTACTGATCTTGTAAAAGTTCGGCTTCAAGCTGAAGGAAAATTGCCACCTGGGGTTCCAAGGCGTTACACTGG

Basic information

species Vitis vinifera
transcript Vv06s0004g05940.t01
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv06s0004g05940.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GRMZM2G165629_T02 (Zea mays), 3'ss of exon 3
gtcagttacatttggttaccatccttttggttgatgcatgatgaatttagataacaactgtactagcatactgtttttcccatataaagagtcaaataaactatctccagtgattctttgcttcaaaataagttaaattggtgtttctttccta---acagGAGCAATAGCAATTGCAGTCGCAAATCCTACTGATCTTGTAAAAGTTCGGCTTCAAGCTGAAGGAAAATTGCCACCTGGGGTTCCAAGGCGTTACACTGG---
                                                      ||    || ||  ||   ||   | |  | |||||           | |    | |  ||     |   || |    |||||||     ||| ||  |||    |||| |  ||||||||||  || |||||||| ||||||||||| |||||| || | |||||||| |||||   || | |    ||    ||| ||||  ||||   
-----------------------------------------------------tcatagataataaaatcaggtcggttcactttaaaggt--------gccacgctcggcaatgtggagaaccatacattgttaaatgatctttttttgtctattttcagGTGTGATAGCAATTGTTGTGGCAAATCCAACTGATCTTGTTAAAGTTAGGTTGCAAGCTGATGGAAAG--GCTAAC-ACTGTCAAGAGGAGTTATTCTGGAGC

upper sequence: Vv06s0004g05940.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA18G07540.1 (Glycine max), 3'ss of exon 3
gtcagttacatttggttaccatccttttggttgatgcatgatgaatttagataacaactgtactagcatactgtttttcccatataaagagtcaaataaactatctccagtgattctttgcttcaaaataagttaaattggtgtttct--ttcctaacagGAGCAATAGCAATTGCAGTCGCAAATCCTACTGATCTTGTAAAAGTTCGGCTTCAAGCTGAAGGAAAATTGCCACCTGGGGTTCCAAGGCGTTACACTGG-
                                                       |  || |  | | ||  |  || |||||| | | | | | ||  | | | |    | ||  | |   ||| | | | || | |   | |||     |  | | ||| ||  | |||||  || | || ||||| |||||||| || |||||| ||||||||||||||||  |||||||| ||||||| || ||||||||  |||| 
-------------------------------------------------------aggtg-aggaactta--gcattccccatagatataat-atatgta-tgttttgtattatattatatgtcatagtca-ttgactcacttttttgaacttgtgataggTGCTTTGGCAATCACAATTGCTAATCCGACTGATCTAGTCAAAGTTAGGCTTCAAGCTGAAGGTCAATTGCCATCTGGGGTACCTAGGCGTTATTCTGGC

upper sequence: Vv06s0004g05940.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA08G45130.1 (Glycine max), 3'ss of exon 3
gtcagttacatttggttaccatccttttggttgatgcatgatgaatttagataacaactgtactagcatactgtttttcccatataaagagtcaaataaactatctccagtgattctttgcttcaaaataagttaaattggtgtttctttcctaacagGAGCAATAGCAATTGCAGTCGCAAATCCTACTGATCTTGTAAAAGTTCGGCTTCAAGCTGAAGGAAAATTGCCACCTGGGGTTCCAAGGCGTTACACTGG
                                                      |||  ||       |   |  || |||||  | | |     ||    | | |   || |||  ||  |    | | | | |  ||  ||    | |    | ||| ||  | |||||  || | || ||||| |||||||| || |||||| ||||||||||||||||  |||||||| ||||||| || | ||||||  ||||
------------------------------------------------------caaaggtgaggaagt-tagcattccccatggatatatatgtatgttttgtattatgttatttgttaatagtcattgactcacttttttgagcttgt---gatagGTGCTTTGGCAATCACAATTGCTAATCCAACTGATCTAGTCAAAGTTAGGCTTCAAGCTGAAGGTCAATTGCCAACTGGGGTACCTAAGCGTTATTCTGG

upper sequence: Vv06s0004g05940.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: AT5G58970.2 (Arabidopsis thaliana), 3'ss of exon 3
gtcagttacatttggttaccatccttttggttgatgcatgatgaatttagataacaactgtactagcatactgtttttcccatataaagagtcaaata-aactatctccagtgattctttg---cttcaaaataagttaaattggtgtttctttcctaacagGAGCAATAGCAATTGCAGTCGCAAATCCTACTGATCTTGTAAAAGTTCGGCTTCAAGCTGAAGGAAAATTGCCACCTGGGGTTCCAAGGCGTTACACTGG
                                                                 |    ||   ||    || |  | ||||   |  || || ||  ||||| |  |||    |  |||   | |||  ||  ||| | |  |  ||||||||| ||||| |||   || || ||||| ||||||||||| ||||||||||||||| | |||||||| || ||  |||||||||| ||||||||  | ||
-----------------------------------------------------------------gtgagctcagttcttaattttgatagtctcttggaagtaacttgagtgaatgattgagattataaagggaattattttattgtgtgtgacacaacagGAGCTATAGCTATTATTGTAGCTAATCCAACTGATCTTGTTAAAGTTCGGCTTCAATCAGAAGGAAAGTTACCGGCTGGGGTTCCTAGGCGTTATGCAGG

upper sequence: Vv06s0004g05940.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: EFJ24273 (Selaginella moellendorffii), 3'ss of exon 3
gtcagttacatttggttaccatccttttggttgatgcatgatgaatttagataacaactgtactagcatactgtttttcccatataaagagtcaaataaactatctccagtgattctttgcttcaaaataagttaaattggtgtt--tctttcctaacagGAGCAATAGCAATTGCAGTCGCAAATCCTACTGATCTTGTAAAAGTTCGGCTTCAAGCTGAAGGAAAATTGCCACCTGGGGTTCCAAGGCGTTACACTGG
                                                                                          |||   ||   |  |     |  ||| ||| ||     |   ||   ||    ||  ||| |  |  |||| ||  |||| ||  | || || ||||||||||||||||| || |||||||| || || ||||||||| || |||| || |||||  |||| ||| | ||
------------------------------------------------------------------------------------------gtctgctactttggcctgtttcgttccttggttttgg-tgtctttgcttacgattaatctcttttggcagGTGCTTTAGCCATAACTGTTGCGAATCCTACTGATCTTGTGAAGGTTCGGCTACAGGCCGAAGGAAAACTGGCACCCGGAGTTCCTCGGCGGTACTCCGG

upper sequence: Vv06s0004g05940.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: EFJ35536 (Selaginella moellendorffii), 3'ss of exon 3
gtcagttacatttggttaccatccttttggttgatgcatgatgaatttagataacaactgtactagcatactgtttttcccatataaagagtcaaataaactatctccagtgattctttgcttcaaaataagttaaattggtgtt--tctttcctaacagGAGCAATAGCAATTGCAGTCGCAAATCCTACTGATCTTGTAAAAGTTCGGCTTCAAGCTGAAGGAAAATTGCCACCTGGGGTTCCAAGGCGTTACACTGG
                                                                                          |||   ||   |  |     |  ||| ||| ||     |   ||   ||    ||  ||| |  |  |||| ||  |||| ||  | || || ||||||||||||||||| || |||||||| || || ||||||||| || |||| || |||||  |||| ||| | ||
------------------------------------------------------------------------------------------gtctgctactttggcctgtttcgttccttgattttgg-tgtctttgcttacgattaatctcttttggcagGTGCTTTAGCCATAACTGTTGCGAATCCTACTGATCTTGTGAAGGTTCGGCTACAGGCCGAAGGAAAACTGGCACCCGGAGTTCCTCGGCGGTACTCCGG

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|351045029|gb|FQ449283.1|FQ449283
EST:     TGTTGGTGATGTCCCTTTATTCAAGAAAGTACTTGCTGCACTGATAACTG                         GAGCAATAGCAATTGCAGTCGTAAATCCTACTGATCTTGTAAAAGTTCGGC
genomic: TGTTGGTGATGTCCCTTTATTCAAGAAAGTACTTGCTGCACTGATAACTGgtcagttaca ... ttcctaacagGAGCAATAGCAATTGCAGTCGCAAATCCTACTGATCTTGTAAAAGTTCGGC
EST: gi|349814387|gb|FQ398827.1|FQ398827
EST:     TGTTGGTGATGTCCCTTTATTCAAGAAAGTACTTGCTGCACTGATAACTG                         GAGCAATAGCAATTGCAGTCGCAAATCCTACTGATCTTGTAAAAGTTCGGC
genomic: TGTTGGTGATGTCCCTTTATTCAAGAAAGTACTTGCTGCACTGATAACTGgtcagttaca ... ttcctaacagGAGCAATAGCAATTGCAGTCGCAAATCCTACTGATCTTGTAAAAGTTCGGC
EST: gi|352793820|gb|FQ481974.1|FQ481974
EST:     TGTTGGTGATGTCCCTTTATTCAAGAAAGTACTTGCTGCACTGATAACTG                         GAGCAATAGCAATTGCAGTCGCAAATCCTACTGATCTTGTAAAAGCTCGGC
genomic: TGTTGGTGATGTCCCTTTATTCAAGAAAGTACTTGCTGCACTGATAACTGgtcagttaca ... ttcctaacagGAGCAATAGCAATTGCAGTCGCAAATCCTACTGATCTTGTAAAAGTTCGGC
EST: gi|351051586|gb|FQ450138.1|FQ450138
EST:     TGTTGGTGATGTCCCTTTATTCAAGAAAGTACTTGCTGCACTGATAACTG                         GAGCAATAGCAATTGCAGTCGCAAATCCTACTGATCTTGTAAAAGTTCGGC
genomic: TGTTGGTGATGTCCCTTTATTCAAGAAAGTACTTGCTGCACTGATAACTGgtcagttaca ... ttcctaacagGAGCAATAGCAATTGCAGTCGCAAATCCTACTGATCTTGTAAAAGTTCGGC
EST: gi|349821879|gb|FQ413050.1|FQ413050
EST:     TGTTGGTGATGTCCCTTTATTCAAGAAAGTACTTGCTGCACTGATAACTG                         GAGCAATAGCAATTGCAGTCGCAAATCCTACTGATCTTGTAAAAGTTCGGC
genomic: TGTTGGTGATGTCCCTTTATTCAAGAAAGTACTTGCTGCACTGATAACTGgtcagttaca ... ttcctaacagGAGCAATAGCAATTGCAGTCGCAAATCCTACTGATCTTGTAAAAGTTCGGC
EST: gi|351054855|gb|FQ462885.1|FQ462885
EST:     TGTTGGTGATGTCCCTTTATTCAAGAAAGTACTTGCTGCACTGATAACTG                         GAGCAATAGCAATTGCAGTCGCAAATCCTACTGATCTTGTAAAAGTTCGGC
genomic: TGTTGGTGATGTCCCTTTATTCAAGAAAGTACTTGCTGCACTGATAACTGgtcagttaca ... ttcctaacagGAGCAATAGCAATTGCAGTCGCAAATCCTACTGATCTTGTAAAAGTTCGGC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tctccagtgattctttgcttcaaaataagttaaattggtgtttctttcctaacagGAGCAATAGCAATTGCAGTCGCAAATCCTACTGATCTTGTAAAAGTTCGGCTTCAAGCTGAAGGAAAATTGCCACCTGGGGTTCCAAGGCGTTACACTGG
                                      tgtttctttcct  CT-rich tract
                  ttcaaaataagttaaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtcagttacatttggttaccatccttttggttgatgcatgatgaatttagataacaactgtactagcatactgtttttcccatataaagagtcaaataaactatctccagtgattctttgcttcaaaataagttaaattggtgtttctttcctaacagGAGCAATAGCAATTGCAGTCGCAAATCCTACTGATCTTGTAAAAGTTCGGCTTCAAGCTGAAGGAAAATTGCCACCTGGGGTTCCAAGGCGTTACACTGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA