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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...atcgttggacatgaattgtggctagctacttggttgattatttagtaaatatcagtttgttcatcacaatccctttgtcatgtttatgaggctgttgcagAATTCTGGACGTATGTGGAGAAATCTTTCACATGGACGGATCTTCCATCTAAATTTCCGACAAAATATGTACAGTTTCCT

Basic information

species Vitis vinifera
transcript Vv19s0014g05210.t01
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv19s0014g05210.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: LOC_Os08g04270.1 (Oryza sativa), 3'ss of exon 7
atcgttggacatgaattgtggctagctacttgg---ttgattatttagtaaatatcagtttgttcatcacaatccctttgtcatgtttatgaggctgttgcagAATTCTGGACGTATGTGGAGAAATCTTTCACATGGACGGATCTTCCATCTAAATTTCCGACAAAATATGTACAGTTTCCT
                  | || ||| |  |     | | || |||| |     ||| ||| | | |  || |  |  ||| | ||| ||     | |   |||||||||| | ||||| ||| |||| || |||||||| || |||||||| |||||||| ||||||||||| || ||||| 
----------------gttagcaagccatctcaacatagcttttttatttgcattcactttatgcttatcattgacactgtta-gttaata---ttatcatagAATTCTGGCCATATGTTGAGCAATCCTTTACATGGACTGACCTTCCATCAAAATTTCCAACAAAATATGTGCAATTTCCG

upper sequence: Vv19s0014g05210.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GRMZM2G148924_T03 (Zea mays), 3'ss of exon 6
atcgttggacatgaattgtggctagctacttggttgattatttagtaaatatcagtttgttcatcacaatccctttgtcat---gtttatgag-gctgttgcagAATTCTGGACGTATGTGGAGAAATCTTTCACATGGACGGATCTTCCATCTAAATTTCCGACAAAATATGTACAGTTTCCT
                                |||    |  || |  | |   | ||  |  |  ||       ||||||   ||| |  |  | ||| |||||||| |||   ||||| || ||||| |   ||||||| || |||||||| || ||||| ||||||||||| |||||||| 
--------------------------------gttagaaagctacttcaaagttgcttcatatttgcatgttgcgtgtcattgagttcaccaatgttgtcgcagAATTTTGGCTATATGTTGACAAATCATATTCATGGACTGACCTTCCATCAAAGTTTCCAACAAAATATGTCCAGTTTCCA

upper sequence: Vv19s0014g05210.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GLYMA10G02690.3 (Glycine max), 3'ss of exon 5
atcgttggacatgaattgtggctagctacttggttgattatttagtaaatatcagtttgttcatcacaatccctttgtcatgtttatgaggctgttgcagAATTCTGGACGTATGTGGAGAAATCTTTCACATGGACGGATCTTCCATCTAAATTTCCGACAAAATATGTACAGTTTCCT
| |     | |     | |    |  |  ||  ||  |  | ||  || | |    |||| | |  || |    |      |    | | | |  |||||| |||||||| ||||| || ||||| || |||||||| |||||||| ||||| ||||| ||||||||||| |||||||||
accaaaatataacccatttatgcatgtgatttttttttagtgtaccaattgtattattgtccttttcattttaatccatcaggccgttatgttactgcagAGTTCTGGACATATGTAGAAAAATCATTTACATGGACTGATCTTCCTTCTAAGTTTCCCACAAAATATGTCCAGTTTCCT

upper sequence: Vv19s0014g05210.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GLYMA02G17110.1 (Glycine max), 3'ss of exon 6
-atcgttggacatgaattgtggctagctacttggttgattatttagtaaatatcagtttgttcatcacaatccctttgtcatgtttatgaggctgttgcagAATTCTGGACGTATGTGGAGAAATCTTTCACATGGACGGATCTTCCATCTAAATTTCCGACAAAATATGTACAGTTTCCT
      |  |||  | || ||  |    | ||  || | | |        ||| | | |  |  |||   |   |   |||||||| | | | |  |||||| |||||||| ||||| || ||||| || |||||||| |||||||| ||||| ||||| ||||||||||| |||||||||
ccaaaatatacaccatttatgcatgtgaattttttttagtgtaccaattgtattattgtccttttcatt-ttaatccatcatgtttgttatgttactgcagAGTTCTGGACATATGTAGAAAAATCATTTACATGGACAGATCTTCCTTCTAAGTTTCCCACAAAATATGTCCAGTTTCCT

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|161719190|gb|FC065436.1|FC065436
EST:     CATTGCGAGTTGTGGTATGGACAACACCGTTAAGATTTGGTCAATGAAAG                         AATTCTGGACGTATGTGGAGAAATCTTTCACATGGACGGATCTTCCAATCT
genomic: CATTGCGAGTTGTGGTATGGACAACACCGTTAAGATTTGGTCAATGAAAGgtagcacatg ... gctgttgcagAATTCTGGACGTATGTGGAGAAATCTTTCACATGGACGGATCTTCCA-TCT
EST: gi|351053554|gb|FQ459301.1|FQ459301
EST:     CATTGCGAGTTGTGGTATGGACAACACCGTTAAGATTTGGTCAATGAAAG                         AATTCTGGACGTATGTGGAGAAATCTTTCACATGGACGGATCTTCCATCTA
genomic: CATTGCGAGTTGTGGTATGGACAACACCGTTAAGATTTGGTCAATGAAAGgtagcacatg ... gctgttgcagAATTCTGGACGTATGTGGAGAAATCTTTCACATGGACGGATCTTCCATCTA
EST: gi|351036699|gb|FQ457412.1|FQ457412
EST:     CATTGCGAGTTGTGGTATGGACAACACCGTTAAGATTTGGTCAATGAAAG                         AATTCTGGACGTATGTGGAGAAATCTTTCACATGGACGGATCTTCCATCTA
genomic: CATTGCGAGTTGTGGTATGGACAACACCGTTAAGATTTGGTCAATGAAAGgtagcacatg ... gctgttgcagAATTCTGGACGTATGTGGAGAAATCTTTCACATGGACGGATCTTCCATCTA
EST: gi|110378718|gb|EC943862.1|EC943862
EST:     GCGAGTTGT-GTATGGACAACACCGTTAAGATTTGGTCAATGAAAG                         AATTCTGGACGTATGTGGAGAAATCTTTCACATGGACGGATCTTCCATCTA
genomic: GCGAGTTGTGGTATGGACAACACCGTTAAGATTTGGTCAATGAAAGgtagcacatg ... gctgttgcagAATTCTGGACGTATGTGGAGAAATCTTTCACATGGACGGATCTTCCATCTA
EST: gi|351043856|gb|FQ452650.1|FQ452650
EST:     ATTGCGAGTTGTGGTAATGGACAACACCGTTAAGATTTGGTCAATGAAAG                         AATTCTGGACGTATGTGGAGAAATCTTTCACATGGACGGATCTTCCATCTA
genomic: ATTGCGAGTTGTGGTA-TGGACAACACCGTTAAGATTTGGTCAATGAAAGgtagcacatg ... gctgttgcagAATTCTGGACGTATGTGGAGAAATCTTTCACATGGACGGATCTTCCATCTA
EST: gi|352791431|gb|FQ481010.1|FQ481010
EST:     CATTGCGAGTTGTGGTATGGACAACACCGTTAAGATTTGGTCAATGAAAG                         AATTCTGGACGTATGTGGAGAAATCTTTCACATGGACGGATCTTCCATCTA
genomic: CATTGCGAGTTGTGGTATGGACAACACCGTTAAGATTTGGTCAATGAAAGgtagcacatg ... gctgttgcagAATTCTGGACGTATGTGGAGAAATCTTTCACATGGACGGATCTTCCATCTA
EST: gi|294965480|gb|GW839051.1|GW839051
EST:     CATTGCGAGTTGTGGTATGGACAACACCGTTAAGATTTGGTCAATGAAAG                         AATTCTGGACGTATGTGGA
genomic: CATTGCGAGTTGTGGTATGGACAACACCGTTAAGATTTGGTCAATGAAAGgtagcacatg ... gctgttgcagAATTCTGGACGTATGTGGA
EST: gi|351033874|gb|FQ447912.1|FQ447912
EST:     CATTGCGAGTTGTGGTATGGACAACACCGTTAAGATTTGGTCAATGAAAG                         AATTCTGGACGTATGTGGAGAAATCTTTCACATGGACGGATCTTCCATCTA
genomic: CATTGCGAGTTGTGGTATGGACAACACCGTTAAGATTTGGTCAATGAAAGgtagcacatg ... gctgttgcagAATTCTGGACGTATGTGGAGAAATCTTTCACATGGACGGATCTTCCATCTA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

taaatatcagtttgttcatcacaatccctttgtcatgtttatgaggctgttgcagAATTCTGGACGTATGTGGAGAAATCTTTCACATGGACGGATCTTCCATCTAAATTTCCGACAAAATATGTACAGTTTCCT
                                  atgtttat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
atcgttggacatgaattgtggctagctacttggttgattatttagtaaatatcagtttgttcatcacaatccctttgtcatgtttatgaggctgttgcagAATTCTGGACGTATGTGGAGAAATCTTTCACATGGACGGATCTTCCATCTAAATTTCCGACAAAATATGTACAGTTTCCT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA
- - - ggacatg
- - - - - - - - - tggctag
- - - - - - - - - - - - - tacttgg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tcatcac