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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttgtatctgcttataaatcaaaccaacctgaagtactgcgtcttgaattcttagctatagtgaaagagcatcttgtctggtatagGTTCATCGCTTGAGGCTGCTTGGAGACTATCATCACTCTACTCGAATTGCTTTTGTCGAGTTTGTAATG

Basic information

species Vitis vinifera
transcript Vv16s0098g01040.t01
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv16s0098g01040.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: GLYMA06G14050.1 (Glycine max), 3'ss of exon 9
----------------------------------------------------------------------gtttgtatctgcttataaatcaaaccaacctgaagtactgcgtcttg---aattcttagctatagtgaaaga---------gcatcttgtctg---gtatagGTTCATCGCTTGAGGCTGCTTGGAGACTATCATCACTCTACTCGAATTGCTTTTGTCGAGTTTGTAATG
                                                                       |||  ||    ||      |  | | |  |  | |||||  | |||     ||  |   |||  || || |            | || | |     | |||||||||||||||||||| ||||| || || ||||| || ||||||||||| ||||| ||||||| | ||
gtttgaagcttttaatggaactaggattatagtgttgattgctggttgagtttaagcatcatatgaaatatttttcattattttggtgtactcatctaggttcaatactgtttgttgttggtttaatgattatgttgtaaaattttacattattttttatttattcatctagGTTCATCGCTTGAGGCTTCTTGGGGATTACCATCATTCAACTCGAATTGCATTTGTTGAGTTTGCACTG

upper sequence: Vv16s0098g01040.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: GLYMA04G40750.1 (Glycine max), 3'ss of exon 8
---------------------------------------------------------------------------gtttgtatctgcttataaatcaaa--ccaacctgaagtactgcgtcttgaattctta-gctatagtgaa------agagcatcttgt---ctggtatagGTTCATCGCTTGAGGCTGCTTGGAGACTATCATCACTCTACTCGAATTGCTTTTGTCGAGTTTGTAATG
                                                                             || | |  |  |||  ||| |    |||       |  ||    || |||  ||| | | ||    |      |     | || |   ||  | |||||||||||||||||||| ||||| || || ||||| || ||||||||||| ||||| ||||| | | ||
gtttgtagcttttaatggaactaggattatagtgttcattgctggttgagtttaagcattatgtgaaatatttttcattattttggtgtattcatctaggttcaatactgtttgttgttggttaaatgattatgttgtaaaatattttccattattttttatttactcatctagGTTCATCGCTTGAGGCTTCTTGGGGATTACCATCATTCAACTCGAATTGCATTTGTTGAGTTCGCACTG

upper sequence: Vv16s0098g01040.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: GLYMA06G14030.1 (Glycine max), 3'ss of exon 9
--------------------------------------------------------------------------------------------gtttgtatctgcttataaatcaaaccaacctgaagtactgcgtcttgaattcttagctatagtgaaagagcatcttg-tctggtat--agGTTCATCGCTTGAGGCTGCTTGGAGACTATCATCACTCTACTCGAATTGCTTTTGTCGAGTTTGTAATG
                                                                                             ||  | |  | | |    |  |       | |     ||  | |     ||||    |  ||     | ||| ||| | || |||  ||||||| || |||||||| |||||||| || ||||| || ||||||||||||||||| |||||   | ||
gtttgtagcttttcatggaactaggcttttaacgtttattgttgattgaattttaagtatcatatgaggtatttcccactattttttggtgtattcatctgggttcaatgtttgagtttttgttattggttgaatttaattatcttgtaaaatgtttcccatcattttggtgtgttattcagGTTCAACGGTTGAGGCTTCTTGGAGATTACCATCATTCAACTCGAATTGCTTTTGTTGAGTTCACAGTG

upper sequence: Vv16s0098g01040.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: GLYMA04G40760.1 (Glycine max), 3'ss of exon 9
------------------------------------------------------------------------------------gtttgtatctgcttataaatcaaaccaacctgaagtactgcgt---cttgaattcttagctatagtgaaagag-------catcttg-tctggtat--agGTTCATCGCTTGAGGCTGCTTGGAGACTATCATCACTCTACTCGAATTGCTTTTGTCGAGTTTGTAATG
                                                                                     || || | | | | |   |  ||      |||  |  ||       |||||||      | | || ||| |        ||| ||| | || |||  ||||||| || |||||||| |||||||| || ||||| || ||||||||||||||||| |||||   | ||
gtttgtagcttttcatggaactagacctttaatgtttattgttgattgaattttaagtatcatttgaggtatttcccactattttttggtgtattcatctgggttcaat--gtttgagtttttgttattgtttgaatttaattatcttgtaaaatattttccatcattttggtgtgttatccagGTTCAACGGTTGAGGCTTCTTGGAGATTACCATCATTCAACTCGAATTGCTTTTGTTGAGTTCACAGTG

upper sequence: Vv16s0098g01040.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: PP1S62_224V6.1 (Physcomitrella patens), 3'ss of exon 7
-------------------------------------------------gtttgtatctgcttataaatcaaaccaacctgaagtactgc-gtcttgaattcttagctatagtgaaagagcatcttgtc------tggtat----agGTTCATCGCTTGAGGCTGCTTGGAGACTATCATCACTCTACTCGAATTGCTTTTGTCGAGTTTGTAATG
                                                    || |  | || ||   |||    | ||  |   | ||| ||  |    | |||  |  | |  | | | |||| | |      ||| ||    |||||  |||  | ||  || | || ||||||||||||||||||||||| || |||||||||||||| |||
gtaactaaacctgcggtcactttcgattttattcgtttatttattagctcgctgcaatttctaatgcttcacctgagccgtatacattgcagtggtttcgttttactttcatttgatgggaatctggacgtgtgatggaatgtgaagGTTGCTCGGCTAAGATTGTTGGGTGACTATCATCACTCTACTCGAATCGCATTTGTCGAGTTTGTGATG

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|110394549|gb|EC959681.1|EC959681
EST:     GTGACCCAGGCAGAAGTCAAACTTTTCTTTGAATCAATTTGTGGAGAG                         GTTCATCGCTTGAGGCTGCTTGGAGACTATCATCACTCTACTCGAATTGCT
genomic: GTGACCCAGGCAGAAGTCAAACTTTTCTTTGAATCAATTTGTGGAGAGgtttgtatct ... tctggtatagGTTCATCGCTTGAGGCTGCTTGGAGACTATCATCACTCTACTCGAATTGCT
EST: gi|254917332|gb|GR906158.1|GR906158
EST:     GTGACCCAGGCAGAAGTCAAACTTTTCTTTGAATCAATTTGTGGAGAG                         GTTCATCGCTTGAGGCTGCTTGGAGACTATCATCACTCTACTCGAATTGCT
genomic: GTGACCCAGGCAGAAGTCAAACTTTTCTTTGAATCAATTTGTGGAGAGgtttgtatct ... tctggtatagGTTCATCGCTTGAGGCTGCTTGGAGACTATCATCACTCTACTCGAATTGCT
EST: gi|110406292|gb|EC971861.1|EC971861
EST:     GTGACCCAGGCAGAAGTCAAACTTTTCTTTGAATCAATTTGTGGAGAG                         GTTCATCGCTTGAGGCTGCTTGGAGACTATCATCACTCTACTCGAATTGCT
genomic: GTGACCCAGGCAGAAGTCAAACTTTTCTTTGAATCAATTTGTGGAGAGgtttgtatct ... tctggtatagGTTCATCGCTTGAGGCTGCTTGGAGACTATCATCACTCTACTCGAATTGCT
EST: gi|110371491|gb|EC935557.1|EC935557
EST:     GTGACCCAGGCAGAAGTCAAACTTTTCTTTGAATCAATTTGTGGAGAG                         GTTCATCGCTTGAGGCTGCTTGGAGACTATCATCACTCTACTCGAATTGCT
genomic: GTGACCCAGGCAGAAGTCAAACTTTTCTTTGAATCAATTTGTGGAGAGgtttgtatct ... tctggtatagGTTCATCGCTTGAGGCTGCTTGGAGACTATCATCACTCTACTCGAATTGCT
EST: gi|110385680|gb|EC950225.1|EC950225
EST:     GTGACCCAGGCAGAAGTCAAACTTTTCTTTGAATCAATTTGTGGAGAG                         GTTCATCGCTTGAGGCTGCTTGGAGACTATCATCACTCTACTCGAATTGCT
genomic: GTGACCCAGGCAGAAGTCAAACTTTTCTTTGAATCAATTTGTGGAGAGgtttgtatct ... tctggtatagGTTCATCGCTTGAGGCTGCTTGGAGACTATCATCACTCTACTCGAATTGCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aagtactgcgtcttgaattcttagctatagtgaaagagcatcttgtctggtatagGTTCATCGCTTGAGGCTGCTTGGAGACTATCATCACTCTACTCGAATTGCTTTTGTCGAGTTTGTAATG
                                        tcttgtct  CT-rich tract
               aattctta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtttgtatctgcttataaatcaaaccaacctgaagtactgcgtcttgaattcttagctatagtgaaagagcatcttgtctggtatagGTTCATCGCTTGAGGCTGCTTGGAGACTATCATCACTCTACTCGAATTGCTTTTGTCGAGTTTGTAATG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGA