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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaagctttggagattgtttatccacattctttttgtggttatatatatatagtactcttttcagaattctgaccaaagaataattgtaaactggacatgtaataaactttgttaatcttttgttgttgaagGTTGATGAGAGAGGAATGAGGTGGTTTTACACCGGGGACATAGGGCAGTTTCATGCTGATGGTTGCCTTGAAATAATTGACCGTAGAAAGGACATAGTTA

Basic information

species Vitis vinifera
transcript Vv18s0001g02810.t01
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv18s0001g02810.t01 (Vitis vinifera), 3'ss of exon 10
lower sequence: LOC_Os11g06880.1 (Oryza sativa), 3'ss of exon 4
gtaaagctttggagattgtttatccacattctttttgtggttatatatatatagtactcttttcagaattctgaccaaagaataattgtaaactggacatgtaataaactttgttaatcttttgttgttgaagGTTGATGAGAGAGGAATGAGGTGGTTTTACACCGGGGACATAGGGCAGTTTCATGCTGATGGTTGCCTTGAAATAATTGACCGTAGAAAGGACATAGTTA
                                                 |||  |||  |    |  || |  |   ||       ||| ||    |     | |   ||||   ||       || ||||||| |||||| ||||| ||| ||||||| ||  | || ||||| || |  || ||| | ||||||||||||||||| ||||||||||  ||||||||||| |
------------------------------------------------gtatgttacgat----aatatgccaaagcaatctgtgctgtgaagcccatgataacttttctttaacaacaccaatttattgaagGATGATGAAAGAGGCATGCGGTGGTTCTATTCTGGTGACATTGGACGTTTGCATCCAGATGGTTGCCTTGAAATTATTGACCGTAAGAAGGACATAGTCA

upper sequence: Vv18s0001g02810.t01 (Vitis vinifera), 3'ss of exon 10
lower sequence: GLYMA13G03280.1 (Glycine max), 3'ss of exon 8
gtaaagctttggagattgtttatccacattctttttgtggttatatatatatagtactcttttcagaattctgaccaaagaataattgtaaactggacatgtaataaactttgttaatcttttgttgttgaagGTTGATGAGAGAGGAATGAGGTGGTTTTACACCGGGGACATAGGGCAGTTTCATGCTGATGGTTGCCTTGAAATAATTGACCGTAGAAAGGACATAGTTA
                                || |  | || | | | | || |  | ||||  |      ||  | ||||   |   ||  |  | ||  |||    ||  ||  |  ||| |   ||||||||||||| ||||||||||||||||||||||| || ||||| |||    ||||| | ||||| ||||||||||| ||||| |||| ||||||||| ||||
--------------------------------ttgtcagtttttgtgtttttatttttattttatgtggggggaggagagaa-gctaaaaaggtacaaattaaatgtttttactttgtactttttctgtgaagGTTGATGAAAGAGGAATGAGGTGGTTTTACACTGGTGACATTGGGAGAGTTCATCCAGATGGATGCCTTGAAATCATTGATCGTAAAAAGGACATTGTTA

upper sequence: Vv18s0001g02810.t01 (Vitis vinifera), 3'ss of exon 10
lower sequence: GLYMA14G23710.1 (Glycine max), 3'ss of exon 10
gtaaagctttggagattgtttatccacattctttttgtggttatatatatatagtactcttttcagaattctgaccaaagaataattgtaaactggacatgtaataaactttgttaatcttttgttgttgaagGTTGATGAGAGAGGAATGAGGTGGTTTTACACCGGGGACATAGGGCAGTTTCATGCTGATGGTTGCCTTGAAATAATTGACCGTAGAAAGGACATAGTTA
                            || ||| | |  || ||| ||| |  |  | | |  ||      ||  || | | ||  ||| |    ||||||  | |  |||  ||  ||||| |   ||||||||||||| || ||||||||||||||||||||||| ||||| |||    | ||| | ||||| ||||||||||| |||||  ||| ||||||||| ||||
----------------------------ttgtttgttttattttatttattttattttatgtggagggaggagag-aaggtaaaaaggtacaaattacatgtttttactttt--ta--cttttttccgtgaagGTTGATGAAAGGGGAATGAGGTGGTTTTACACCGGTGACATTGGGAGAGTGCATCCAGATGGATGCCTTGAAATCATTGATAGTAAAAAGGACATTGTTA

upper sequence: Vv18s0001g02810.t01 (Vitis vinifera), 3'ss of exon 10
lower sequence: GLYMA06G11860.1 (Glycine max), 3'ss of exon 8
gtaaagctttggagattgtttatccacattctttttgtggttatatatatatagtactcttttcagaattctgacc----aaagaataattgtaaactggacatgtaataaac-tttgttaatcttttgttgttgaagGTTGATGAGAGAGGAATGAGGTGGTTTTACACCGGGGACATAGGGCAGTTTCATGCTGATGGTTGCCTTGAAATAATTGACCGTAGAAAGGACATAGTTA
       | | |  ||  ||      |  | ||  ||    |  || ||  |  ||  |||||   |   ||   |      |  ||   | |    |    |  | ||| |  | |  |  |||| |||| |  ||||||||||| ||||||||||||||||| ||||| || |||||||||   || |||   |||||||||||||| || |||||  | | ||||||||||||||
------gtgttgttatatttctctttctctattaatgaaacttcatgtaactgttaagcttttagaagacctagtccttggcaatattgctcttttttttttaacttatatatatctacttttcttctgttat-aaagGTTGATGAAAGAGGAATGAGGTGGTTCTACACTGGTGACATAGGGAGATTCCATAAAGATGGTTGCCTTGAGATCATTGATAGGAAAAAGGACATAGTTA

upper sequence: Vv18s0001g02810.t01 (Vitis vinifera), 3'ss of exon 10
lower sequence: AT1G77590.1 (Arabidopsis thaliana), 3'ss of exon 9
gtaaagctttggagattgtttatccacattctttttgtggttatatatatatagtactcttttcagaattctgaccaaagaataattgtaaactggacatgtaataaactttgttaatcttttg--ttgttgaagGTTGATGAGAGAGGAATGAGGTGGTTTTACACCGGGGACATAGGGCAGTTTCATGCTGATGGTTGCCTTGAAATAATTGACCGTAGAAAGGACATAGTTA
                                       ||   | ||  | | || |  |||| | | | | |  |||||||   | |    |||   |      |||  | |||  |  |||  |  |  ||||||||||| |  |||||||||||||| ||||| || |||||||| |  |||||  ||||||| ||||| || ||||| ||||| | |||||| || ||||
---------------------------------------gtggcaaatcaacattattggtttcggcaatgtta--aaagaattggt-tggtttggttcttcctctaaccgttttatacacttgaatgttcaaagGTTGATGAAAAGGGAATGAGGTGGTTCTACACAGGAGACATAGGACGATTTCACCCTGATGGCTGCCTCGAGATAATAGACCGAAAAAAGGATATCGTTA

upper sequence: Vv18s0001g02810.t01 (Vitis vinifera), 3'ss of exon 10
lower sequence: EFJ27012 (Selaginella moellendorffii), 3'ss of exon 8
gtaaagctttggagattgtttatccacattctttttgtggttatatatatatagtactcttttcagaattctgaccaaagaataattgtaaactggacatgtaataaactttgttaatct--tttgttgttgaagGTTGATGAGAGAGGAATGAGGTGGTTTTACACCGGGGACATAGGGCAGTTTCATGCTGATGGTTGCCTTGAAATAATTGACCGTAGAAAGGACATAGTTA
                                                                               | | || | |  | |   | || |     | |  |||||    ||| ||  |||||||||| ||||| || ||||| ||||| ||||| || ||||| || ||||| ||| | ||||||||||| |||||  | ||||| |  |||||||| ||||
-------------------------------------------------------------------------------gtacaacttttcagtttccttgaagcgttcatgcttaattgggtttttttgtgaagGTTGACGAGAGGGGCATGAGATGGTTCTACACTGGTGACATTGGACAGTTCCATCCCGATGGTTGCCTGGAAATTGTAGACCGGAAGAAGGACATTGTTA

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|110385455|gb|EC949983.1|EC949983
EST:     TTACTGTTGGATATTTCAAAAATGAAGAGAAAACAAATGAAGTTTACAAG                         GTTGATGAGAGAGGAATGAGGTGGTTTTACACCGGGGACATAGGGCAGTTT
genomic: TTACTGTTGGATATTTCAAAAATGAAGAGAAAACAAATGAAGTTTACAAGgtaaagcttt ... gttgttgaagGTTGATGAGAGAGGAATGAGGTGGTTTTACACCGGGGACATAGGGCAGTTT
EST: gi|110418478|gb|EC984635.1|EC984635
EST:     TTACTGTTGGATATTTCAAAAATGAAGAGAAAACAAATGAAGTTTACAAG                         GTTGATGAGAGAGGAATGAGGTGGTTTTACACCGGGGACATAGGGCAGTTT
genomic: TTACTGTTGGATATTTCAAAAATGAAGAGAAAACAAATGAAGTTTACAAGgtaaagcttt ... gttgttgaagGTTGATGAGAGAGGAATGAGGTGGTTTTACACCGGGGACATAGGGCAGTTT
EST: gi|110389647|gb|EC954503.1|EC954503
EST:     TTACTGTTGGATATTTCAAAAATGAAGAGAAAACAAATGAAGTTTACAAG                         GTTGATGAGAGAGGAATGAGGTGGTTTTACACCGGGGACATAGGGCAGTTT
genomic: TTACTGTTGGATATTTCAAAAATGAAGAGAAAACAAATGAAGTTTACAAGgtaaagcttt ... gttgttgaagGTTGATGAGAGAGGAATGAGGTGGTTTTACACCGGGGACATAGGGCAGTTT
EST: gi|161716236|gb|FC065864.1|FC065864
EST:     TTACTGTTGGATATTTCAAAAATGAAGAGAAAACAAATGAAGTTTACAAG                         GTTGATGAGAGAGGAATGAGGTGGTTTTACACCGGGGACATAGGGCAGTTT
genomic: TTACTGTTGGATATTTCAAAAATGAAGAGAAAACAAATGAAGTTTACAAGgtaaagcttt ... gttgttgaagGTTGATGAGAGAGGAATGAGGTGGTTTTACACCGGGGACATAGGGCAGTTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agaataattgtaaactggacatgtaataaactttgttaatcttttgttgttgaagGTTGATGAGAGAGGAATGAGGTGGTTTTACACCGGGGACATAGGGCAGTTTCATGCTGATGGTTGCCTTGAAATAATTGACCGTAGAAAGGACATAGTTA
                                 tgttaat  putative branch site (score: 3)
                                       tcttttgtt  CT-rich tract
                       taataaactttgttaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaaagctttggagattgtttatccacattctttttgtggttatatatatatagtactcttttcagaattctgaccaaagaataattgtaaactggacatgtaataaactttgttaatcttttgttgttgaagGTTGATGAGAGAGGAATGAGGTGGTTTTACACCGGGGACATAGGGCAGTTTCATGCTGATGGTTGCCTTGAAATAATTGACCGTAGAAAGGACATAGTTA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGAT