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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaggaaaaagaaccttcatcaaatgacttcttattgttatgcttgtatactgtctaatgcaaaagtataagtgttcttgaagaaattttgggatttccatgtgctttgtagatcagAAGGATGAGTCTTTTTACACTTTGAGTTGGGCATGCAGTATTGATGGCATCCCATTCTTGGTGGCTGGAGGAATCAATGGTATAATTCGTATCATTGATA

Basic information

species Vitis vinifera
transcript Vv19s0014g05210.t01
intron # 2
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 2
lower sequence: GLYMA10G02690.1 (Glycine max), 3'ss of exon 2
gtaaggaaaaagaaccttcatcaaatgacttcttattgttatgcttgtatactgtctaatgcaaaagtataagtgttcttgaagaa-attttgggatttccatgtgctt---tgtagatcagAAGGATGAGTCTTTTTACACTTTGAGTTGGGCATGCAGTATTGATGGCATCCCATTCTTGGTGGCTGGAGGAATCAATGGTATAATTCGTATCATTGATA
                      |  | ||| ||   | |    ||      || |     || |  || | | |  ||| ||| |    ||     ||| |||||  ||   |  |   |||||||||||||||||||||||  ||||||||||||||| | ||||||||| ||||||  | ||||||||||||||||||||  |||| ||  |||||||| 
--------------------gtatgtcactcctctctctctctctctctctctttagttagctagggtttcatttctctagaaaaccgcttctatttttacatgtttttatgtacacgccagAAGGATGAGTCTTTTTACACAGTGAGTTGGGCATGCAATGTTGATGGCACCCCATTTGTTGTGGCTGGAGGAATCAATGGGGTAATGCGAGTCATTGATG

upper sequence: Vv19s0014g05210.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA10G02690.3 (Glycine max), 3'ss of exon 1
gtaaggaaaaagaaccttcatcaaatgacttcttattgttatgcttgtatactgtctaatgcaaaagtataagtgttcttgaagaa-attttgggatttccatgtgctt---tgtagatcagAAGGATGAGTCTTTTTACACTTTGAGTTGGGCATGCAGTATTGATGGCATCCCATTCTTGGTGGCTGGAGGAATCAATGGTATAATTCGTATCATTGATA---
                      |  | ||| ||   | |    ||      || |     || |  || | | |  ||| ||| |    ||     ||| |||||  ||   |  |   |||||||||||||||||||||||  ||||||||||||||| | ||||||||| ||||||  | ||||||||||||||||||||  |||| ||  ||||||||    
--------------------gtatgtcactcctctctctctctctctctctctttagttagctagggtttcatttctctagaaaaccgcttctatttttacatgtttttatgtacacgccagaagGATGAGTCTTTTTACACAGTGAGTTGGGCATGCAATGTTGATGGCACCCCATTTGTTGTGGCTGGAGGAATCAATGGGGTAATGCGAGTCATTGATGTTG

upper sequence: Vv19s0014g05210.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA02G17110.1 (Glycine max), 3'ss of exon 2
gtaaggaaaaagaaccttcatcaaatgacttcttattgttatgcttgtatactgtctaatgcaaaagtataagtgttcttgaagaa-attttgggatttccatgtgctt-tgtag-atcagAAGGATGAGTCTTTTTACACTTTGAGTTGGGCATGCAGTATTGATGGCATCCCATTCTTGGTGGCTGGAGGAATCAATGGTATAATTCGTATCATTGATA
                                 | | | | | ||  ||  || | | | |  |  || | | |  ||| ||| |   |||  |  ||| |||||  || ||||  | |||||||||||||||||||||||  |||||||||| |||| | ||||||||| ||||||  | ||||||||||||||||||||  | || ||  |||||||| 
------------------------------gtatgtcggtctactc-taccctcttttaagttagggtttcatttctctagaaaattgtttctgtttttacatgtttttatgtaacaccagAAGGATGAGTCTTTTTACACAGTGAGTTGGGCGTGCAATGTTGATGGCACCCCATTTGTTGTGGCTGGAGGAATCAATGGGGTCATGCGAGTCATTGATG

upper sequence: Vv19s0014g05210.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA12G34240.1 (Glycine max), 3'ss of exon 2
gtaaggaaaaagaaccttcatcaaatgacttcttattgttatgcttgtatactgtctaatgcaaaagtataagtgttcttgaagaaattt--tgggatttccatgtgctt-tgtagatcagAAGGATGAGTCTTTTTACACTTTGAGTTGGGCATGCAGTATTGATGGCATCCCATTCTTGGTGGCTGGAGGAATCAATGGTATAATTCGTATCATTGATA
                         | | |   || ||  |      | |  | | | ||      |||||||| |   |  |||||| |  |   ||||  ||||  || |||| | |||||||||||||||||||||||| || |||||||||||| | || |||| | |||| |  | ||| |||||||| | |||||  |||||||  |||||||| 
------------------------gtaagtcaatagtgacacttcactctcttatttcattt----gtataagtatgtgtatagaaatgtgcttcaatttatatgtttttatgtaaaccagAAGGATGAGTCTTTTTACACTGTGGGTTGGGCATGCAATGTTAATGGGACCCCACTTGTTGTGACTGGAGGACTTAATGGGGTAATTCGAGTCATTGATG

upper sequence: Vv19s0014g05210.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA13G36310.1 (Glycine max), 3'ss of exon 2
gtaaggaaaaagaaccttcatcaaatgacttcttattgttatgcttgtatactgtctaatgcaaaagtataagtgttcttgaagaaattttgggatttccatgtgctt-tgtagatcagAAGGATGAGTCTTTTTACACTTTGAGTTGGGCATGCAGTATTGATGGCATCCCATTCTTGGTGGCTGGAGGAATCAATGGTATAATTCGTATCATTGATA
           | |  || ||  | ||||   | | | |  |  ||    | |      || ||||||||  || |    | | |  |  |   ||||  ||||  || |||| | |||||| ||||||||||||||||  || |||||||||||| | |||| || | |||| |  | |||||||||||| |||||||  |||| ||  |||||||| 
-----------gtaagttaat--agtgacccttcactctcttattt---catt------tgtaaaagtatgtgtat----ggaaatgtgcttcaatttatatgtttttatgtaaaccagAAGAATGAGTCTTTTTACACCGTGGGTTGGGCATGCAATGTTGACGGGACCCCACTTGTTGTGGCTGGAGGACTCAATGGGGTAATCCGAGTCATTGATG

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|71864778|gb|DT013833.1|DT013833
EST:     GTCTTGAAGGGGGCGTCATTGCTGTCTTGCAGTCTTACATTGATGAAGATAT                        
genomic: GTCTTGAAGGGGGCGTCATTGCTGTCTTGCAGTCTTACATTGATGAAG--ATgtaaggaaaa ... tgtagatca
EST: gi|71864778|gb|DT013833.1|DT013833
EST:     GTCTTGAAGGGGGCGTCATTGCTGTCTTGCAGTCTTACATTGATGAAGATAT                        
genomic: GTCTTGAAGGGGGCGTCATTGCTGTCTTGCAGTCTTACATTGATGAAG--ATgtaaggaaaa ... tgtagatca
EST: gi|71864778|gb|DT013833.1|DT013833
EST:     GTCTTGAAGGGGGCGTCATTGCTGTCTTGCAGTCTTACATTGATGAAGATAT                        
genomic: GTCTTGAAGGGGGCGTCATTGCTGTCTTGCAGTCTTACATTGATGAAG--ATgtaaggaaaa ... tgtagatca
EST: gi|71864778|gb|DT013833.1|DT013833
EST:     GTCTTGAAGGGGGCGTCATTGCTGTCTTGCAGTCTTACATTGATGAAGATAT                        
genomic: GTCTTGAAGGGGGCGTCATTGCTGTCTTGCAGTCTTACATTGATGAAG--ATgtaaggaaaa ... tgtagatca
EST: gi|161719190|gb|FC065436.1|FC065436
EST:     GTCTTGAAGGGGGCGTCATTGCTGTCTTGCAGTCTTACATTGATGAAGAT                         AAGGATGAGTCTTTTTACACTTTGAGTTGGGCATGCAGTATTGATGGCATC
genomic: GTCTTGAAGGGGGCGTCATTGCTGTCTTGCAGTCTTACATTGATGAAGATgtaaggaaaa ... tgtagatcagAAGGATGAGTCTTTTTACACTTTGAGTTGGGCATGCAGTATTGATGGCATC
EST: gi|351053554|gb|FQ459301.1|FQ459301
EST:     GTCTTGAAGGGGGCGTCATTGCTGTCTTGCAATCTTACATTGATGAAGAT                         AAGGATGAGTCTTTTTACACTTTGAGTTGGGCATGTAGTATTGATGGCATC
genomic: GTCTTGAAGGGGGCGTCATTGCTGTCTTGCAGTCTTACATTGATGAAGATgtaaggaaaa ... tgtagatcagAAGGATGAGTCTTTTTACACTTTGAGTTGGGCATGCAGTATTGATGGCATC
EST: gi|351036699|gb|FQ457412.1|FQ457412
EST:     GTCTTGAAGGGGGCGTCATTGCTGTCTTGCAATCTTACATTGATGAAGAT                         AAGGATGAGTCTTTTTACACTTTGAGTTGGGCATGTAGTATTGATGGCATC
genomic: GTCTTGAAGGGGGCGTCATTGCTGTCTTGCAGTCTTACATTGATGAAGATgtaaggaaaa ... tgtagatcagAAGGATGAGTCTTTTTACACTTTGAGTTGGGCATGCAGTATTGATGGCATC
EST: gi|351043856|gb|FQ452650.1|FQ452650
EST:     GTCTTGAAGGGGGCGTCATTGCTGTCTTGCAATCTTACATTGATGAAGAT                         AAGGATGAGTCTTTTTACACTTTGAGTTGGGCATGTAGTATTGATGGCATC
genomic: GTCTTGAAGGGGGCGTCATTGCTGTCTTGCAGTCTTACATTGATGAAGATgtaaggaaaa ... tgtagatcagAAGGATGAGTCTTTTTACACTTTGAGTTGGGCATGCAGTATTGATGGCATC
EST: gi|352791431|gb|FQ481010.1|FQ481010
EST:     GTCTTGAAGGGGGCGTCATTGCTGTCTTGCAATCTTACATTGATGAAGAT                         AAGGATGAGTCTTTTTACACTTTGAGTTGGGCATGTAGTATTGATGGCATC
genomic: GTCTTGAAGGGGGCGTCATTGCTGTCTTGCAGTCTTACATTGATGAAGATgtaaggaaaa ... tgtagatcagAAGGATGAGTCTTTTTACACTTTGAGTTGGGCATGCAGTATTGATGGCATC
EST: gi|161711022|gb|FC059448.1|FC059448
EST:     GTCTTGAAGGGGGCGTCATTGCTGTCTTGCAGTCTTACATTGATGAAGAT                         AAGGATGAGTCTTTTTACACTTTGAGTTGGGCATGCAGTATTGATGGCATC
genomic: GTCTTGAAGGGGGCGTCATTGCTGTCTTGCAGTCTTACATTGATGAAGATgtaaggaaaa ... tgtagatcagAAGGATGAGTCTTTTTACACTTTGAGTTGGGCATGCAGTATTGATGGCATC
EST: gi|294965480|gb|GW839051.1|GW839051
EST:     GTCTTGAAGGGGGCGTCATTGCTGTCTTGCAATCTTACATTGATGAAGAT                         AAGGATGAGTCTTTTTACACTTTGAGTTGGGCATGCAGTATTGATGGCATC
genomic: GTCTTGAAGGGGGCGTCATTGCTGTCTTGCAGTCTTACATTGATGAAGATgtaaggaaaa ... tgtagatcagAAGGATGAGTCTTTTTACACTTTGAGTTGGGCATGCAGTATTGATGGCATC
EST: gi|351033874|gb|FQ447912.1|FQ447912
EST:     GTCTTGAAGGGGGCGTCATTGCTGTCTTGCAATCTTACATTGATGAAGAT                         AAGGATGAGTCTTTTTACACTTTGAGTTGGGCATGCAGTATTGATGGCATC
genomic: GTCTTGAAGGGGGCGTCATTGCTGTCTTGCAGTCTTACATTGATGAAGATgtaaggaaaa ... tgtagatcagAAGGATGAGTCTTTTTACACTTTGAGTTGGGCATGCAGTATTGATGGCATC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aaagtataagtgttcttgaagaaattttgggatttccatgtgctttgtagatcagAAGGATGAGTCTTTTTACACTTTGAGTTGGGCATGCAGTATTGATGGCATCCCATTCTTGGTGGCTGGAGGAATCAATGGTATAATTCGTATCATTGATA
                  aagaaatttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaaggaaaaagaaccttcatcaaatgacttcttattgttatgcttgtatactgtctaatgcaaaagtataagtgttcttgaagaaattttgggatttccatgtgctttgtagatcagAAGGATGAGTCTTTTTACACTTTGAGTTGGGCATGCAGTATTGATGGCATCCCATTCTTGGTGGCTGGAGGAATCAATGGTATAATTCGTATCATTGATA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA