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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtataacatatttgatgcccatacaactcaaagctgaaagaaattttaattgattattcccttgtcttgaatcttcatgggtcaaatgtatatggtttgtagGTTGGCCCACTCCGCTGCTGGCCTGGTGGATTATGTCTCTCCAGGTCAATTGGTGACACAGATGTGGGAGAATTCATTGTCCCAATACCACATGTTAAGC

Basic information

species Vitis vinifera
transcript Vv14s0060g01580.t01
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv14s0060g01580.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GRMZM5G836628_T02 (Zea mays), 3'ss of exon 3
gtataacatatttgatgcccatacaactcaaagctgaaagaaattttaattgattattcccttgtcttgaatcttcatgggt-caaatgtatatggtttgtagGTTGGCCCACTCCGCTGCTGGCCTGGTGGATTATGTCTCTCCAGGTCAATTGGTGACACAGATGTGGGAGAATTCATTGTCCCAATACCACATGTTAAGC
                    | || |||  |    ||  |||    ||| |   |  |||    ||      || ||||  | |  ||||    ||  | ||||| ||||| ||||| |||||||||||||| || || ||||| || || || || ||||  ||||| ||||| |||||||| || || |||||||| ||||
------------------gtaaaccacttcagttcgagtgaatcagtaacttgcttatcctcaatca-attcctgcatgaatgcttatgttgggggactttagGTCGGCCCTCTCCGGTGCTGGCCTGGTGGCTTGTGCCTCTCAAGATCCATCGGGGACATGGATGTTGGAGAGTTCATTGTGCCCATTCCACATGTCAAGC

upper sequence: Vv14s0060g01580.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GRMZM2G006429_T01 (Zea mays), 3'ss of exon 3
gtataacatatttgatgcccatacaactcaaagctgaaagaaattttaattgattat---tcccttgtcttgaa------tcttcatggg-----tcaa---atgtatatggtttgtagGTTGGCCCACTCCGCTGCTGGCCTGGTGGATTATGTCTCTCCAGGTCAATTGGTGACACAGATGTGGGAGAATTCATTGTCCCAATACCACATGTTAAGC
        |  |   ||| ||  ||  |  | |  ||| ||   |   ||  | |||     |  ||  ||| |      ||| ||||||     | ||   || | |    ||| ||||| || || ||||| |||||||| |||||||| || || || ||||||||||| || || ||||| || || |||||||| || || |||||||| ||||
----gtagtgctcactgctcagtcattttgatgaagaaggattctaggatacaatatgagctctatgctttggaaacatttctgcatgggattttttaattaatttctcccttttttagGTGGGTCCTCTCCGATGCTGGCCAGGTGGATTGTGCCTTTCAAGGTCAATTGGGGATACTGATGTCGGCGAGTTCATTGTACCGATTCCACATGTCAAGC

upper sequence: Vv14s0060g01580.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA20G38270.1 (Glycine max), 3'ss of exon 4
gtataacatatttgatgcccatacaactcaaagctgaaagaaattttaattgattattcccttgtcttgaatcttcatgggtcaaatgtatatggtttgtagGTTGGCCCACTCCGCTGCTGGCCTGGTGGATTATGTCTCTCCAGGTCAATTGGTGACACAGATGTGGGAGAATTCATTGTCCCAATACCACATGTTAAGC
||||    || |   |    || |   || || |   | ||  |||||| |         | ||| |||  || | |        ||  ||     || ||||| || || || |||||||||||||||||||| || || || || |||||||||||||| || ||||||||||| ||||| |||||||||||||||||||
gtatggtgtaatctttat--attcctttctaatc---aggactttttaactag-------cctgttttggttcctta--------atacat-----ttatagGTAGGGCCTCTTCGCTGCTGGCCTGGTGGATTGTGCCTTTCTAGATCAATTGGTGACACGGACGTGGGAGAATTTATTGTGCCAATACCACATGTTAAGC

upper sequence: Vv14s0060g01580.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA10G29060.1 (Glycine max), 3'ss of exon 4
gtataacatatttgatgcccatacaactcaaagctgaaagaaattttaattgattattcccttgtcttgaatcttcatgggtcaaatgtatatggtttgtagGTTGGCCCACTCCGCTGCTGGCCTGGTGGATTATGTCTCTCCAGGTCAATTGGTGACACAGATGTGGGAGAATTCATTGTCCCAATACCACATGTTAAGC
||| ||  || |   |  | || |   || || |    || | ||||      | | |  | ||| |||  || | |        ||  ||      | ||||| || || || ||||| |||||||||||||| || || || || ||||||||||||||||| ||||||||||| |||||||||||||||||||| ||||
gtacaatgtaatc--tttctattcctttctaatc----aggactttt------tcactagcctgttttggttcctta--------atacat-----ctatagGTAGGGCCTCTTCGCTGTTGGCCTGGTGGATTGTGCCTTTCTAGATCAATTGGTGACACAGACGTGGGAGAATTTATTGTCCCAATACCACATGTCAAGC

upper sequence: Vv14s0060g01580.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA03G39260.1 (Glycine max), 3'ss of exon 4
gtataacatatttgatgcccatacaactcaaagctgaaagaaattttaattgattattcccttgtcttgaatcttcatgggtcaaatgtatatggtttgtagGTTGGCCCACTCCGCTGCTGGCCTGGTGGATTATGTCTCTCCAGGTCAATTGGTGACACAGATGTGGGAGAATTCATTGTCCCAATACCACATGTTAAGC
          | ||||||    ||   |    ||| |      |||  | | |  |||   |   ||| | |  |  ||| |    ||  |   |||| |||||||| || || ||||||||||| |||||||| || || ||||| ||||| || ||||| |||||||||||||| ||||| |||||||||||||| ||||
---------gtatgatgcaatcaccttttgc-gctcatgc---tttctaataaagattgtttaaactt-agtagttttggtt----tgcgttatgtttatagGTTGGGCCTCTTCGCTGCTGGCCAGGTGGATTGTGCCTATCCAGATCAATAGGCGACACGGATGTGGGAGAATTTATTGTGCCAATACCACATGTAAAGC

upper sequence: Vv14s0060g01580.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA19G41810.2 (Glycine max), 3'ss of exon 4
gtataacatatttgatgcccatacaactcaaagctgaaagaaattttaattgattattcccttgtcttgaatcttcatgggtcaaatgtatatggtttgtagGTTGGCCCACTCCGCTGCTGGCCTGGTGGATTATGTCTCTCCAGGTCAATTGGTGACACAGATGTGGGAGAATTCATTGTCCCAATACCACATGTTAAGC
                     ||  |  |||     |  |   |||  | | |  ||| | |   |||     ||  | |||    | |||   |||| |||||||| || || ||||||||||| |||||||| || || || || || || ||||||||||| ||||||||||| ||||| |||||||||||||||||||
--------------------gtatgatgcaatcaccattgtgctttctaataaagattgcttaaacttagtagtt--ttggtttgctttat---gtttatagGTTGGGCCTCTTCGCTGCTGGCCAGGTGGATTGTGCCTATCTAGATCTATAGGTGACACAGACGTGGGAGAATTTATTGTGCCAATACCACATGTTAAGC

upper sequence: Vv14s0060g01580.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: AT1G09160.2 (Arabidopsis thaliana), 3'ss of exon 4
---------------gtataacatatttgatgcccatacaactcaaagctgaaagaaattt-taat---tgattattcccttgtctt----gaatcttcatggg--tcaaatgtatatggtttgtagGTTGGCCCACTCCGCTGCTGGCCTGGTGGATTATGTCTCTCCAGGTCAATTGGTGACACAGATGTGGGAGAATTCATTGTCCCAATACCACATGTTAAGC
               ||  |    | ||  ||          |    ||||       ||| ||||   | |  | ||| | |  ||      || || ||| |  |  | | |          ||||| |||||||| || |||||||||||||| |||||||| || ||||| |||||||| || |||||||||||||| |||||||| |||||||| |||||||
gtatgatcatttccagtgaatttaagttactgtttcattgtgttttggctgtggtgggtttgtaatgtgtaagaagtccttggattttcaatgatattaatgtgctttgattatgccaatgcaatagGTCGGCCCACTACGATGCTGGCCTGGTGGTTTATGTCTTTCGAGGTCCATTGGTGATACGGATGTGGGAGAATTTATTGTCCCTATACCACACGTTAAGC

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|110687767|gb|EE065551.1|EE065551
EST:     TGCAAGTGGGGGTGAATTTGGAAAGCTGAATGTTTTTGGGGGCAATTGAG                         -TTGGCCC-CTTCCGCTG
genomic: TGCAAGTGGGGGTGAAGTTGGAAGGCTGAATGTTTTTGGGGGCAAT-GAGgtataacata ... tggtttgtagGTTGGCCCACT-CCGCTG
EST: gi|37189043|gb|CF608392.1|CF608392
EST:     CTGCAAGTGGGGGTGAAGTTGGAAGGCTGAATGTTTTTGGGGGCAATGAG                         GTTGGCCCACTCCGCTGCTGGCCTGGTGGATTATGTCTCTCCAGGTCAATT
genomic: CTGCAAGTGGGGGTGAAGTTGGAAGGCTGAATGTTTTTGGGGGCAATGAGgtataacata ... tggtttgtagGTTGGCCCACTCCGCTGCTGGCCTGGTGGATTATGTCTCTCCAGGTCAATT
EST: gi|110687916|gb|EE065868.1|EE065868
EST:     CTGCAAGTGGGGGTGAAGTTGGAAGGCTGAATGTTTTTGGGGGCAATGAG                         GTTGGCCCACTCCGCTGCTGGCCTGGTGGATTATGTCTCTCCAGATCAATT
genomic: CTGCAAGTGGGGGTGAAGTTGGAAGGCTGAATGTTTTTGGGGGCAATGAGgtataacata ... tggtttgtagGTTGGCCCACTCCGCTGCTGGCCTGGTGGATTATGTCTCTCCAGGTCAATT
EST: gi|110730227|gb|EE107063.1|EE107063
EST:     CTGCAAGTGGGGGTGAAGTTGGAAGGCTGAATGTTTTTGGGGGCAATGAG                         GTTGGCCCACTCCGCTGCTGGCCTGGTGGATTA
genomic: CTGCAAGTGGGGGTGAAGTTGGAAGGCTGAATGTTTTTGGGGGCAATGAGgtataacata ... tggtttgtagGTTGGCCCACTCCGCTGCTGGCCTGGTGGATTA
EST: gi|110699523|gb|EE076606.1|EE076606
EST:     CTGCAAGTGGGGGTGAAGTTGGAAGGCTGAATGTTTTTGGGGGCAATGAN                         GNTGGCCCACTCCGCTGCCTGGC-TGGTGGATTATGTCTCTCCAGATCAAT
genomic: CTGCAAGTGGGGGTGAAGTTGGAAGGCTGAATGTTTTTGGGGGCAATGAGgtataacata ... tggtttgtagGTTGGCCCACTCCGCTGC-TGGCCTGGTGGATTATGTCTCTCCAGGTCAAT
EST: gi|71890427|gb|DT039482.1|DT039482
EST:     CTGCAAGTGGGGGTGAAGTTGGAAGGCTGAATGTTTTTGGGGGCAATGAG                         GTTGGCCCACTCCGCTGCTGGCCTGGTGGATTATGTCTCTCCAGGTCAATT
genomic: CTGCAAGTGGGGGTGAAGTTGGAAGGCTGAATGTTTTTGGGGGCAATGAGgtataacata ... tggtttgtagGTTGGCCCACTCCGCTGCTGGCCTGGTGGATTATGTCTCTCCAGGTCAATT
EST: gi|254914412|gb|GR906513.1|GR906513
EST:     GGAAGGCTGAATGTTTTTGGGGGCAATGAG                         GTTGGCCCACTCCGCTGCTGGCCTGGTGGATTATGTCTCTCCAGATCAATT
genomic: GGAAGGCTGAATGTTTTTGGGGGCAATGAGgtataacata ... tggtttgtagGTTGGCCCACTCCGCTGCTGGCCTGGTGGATTATGTCTCTCCAGGTCAATT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aattgattattcccttgtcttgaatcttcatgggtcaaatgtatatggtttgtagGTTGGCCCACTCCGCTGCTGGCCTGGTGGATTATGTCTCTCCAGGTCAATTGGTGACACAGATGTGGGAGAATTCATTGTCCCAATACCACATGTTAAGC
                                    aaatgtatat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtataacatatttgatgcccatacaactcaaagctgaaagaaattttaattgattattcccttgtcttgaatcttcatgggtcaaatgtatatggtttgtagGTTGGCCCACTCCGCTGCTGGCCTGGTGGATTATGTCTCTCCAGGTCAATTGGTGACACAGATGTGGGAGAATTCATTGTCCCAATACCACATGTTAAGC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA