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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...actactgcttttagacaacttatttccttctaaactctactgtcaccctttaaaagagtggaaagtgattccttacttagcaattactgctgcttgccagACCGTTCATGAAGGGCGCATCTACCAGTTGAAACTGTTCTGTGGTCAGGACTATCCGGATAATCCACCAACTGTGAAGTTCCAGACTCGGATAAATATGA

Basic information

species Vitis vinifera
transcript Vv01s0011g05630.t01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv01s0011g05630.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA08G04710.1 (Glycine max), 3'ss of exon 2
actactgct-tttagacaacttatttccttctaaactctactgtcaccctttaaaagagtggaaagtgattccttacttagcaattactg-ctgcttgccagACCGTTCATGAAGGGCGCATCTACCAGTTGAAACTGTTCTGTGGTCAGGACTATCCGGATAATCCACCAACTGTGAAGTTCCAGACTCGGATAAATATGA
|| |  |   | |  ||  |||  |   |  ||      ||   |    | |   | ||   ||  |  |    |  | |    ||  || |    |   ||  ||||||||||||||| ||||||||| ||||| | || |||||  |||| ||||| || |||||||||||||| |  || |||||| |||| || ||||
acaaaggaagtatgtactgctttctagttgttaggtgtaaccagctgtgtctgccaaagc--aatatattgatatgatgaatttttcttgtccatcttgaagGGCGTTCATGAAGGGCGTATCTACCAGCTGAAATTATTTTGTGGCAAGGATTATCCAGACAATCCACCAACTGTTAGATTTCAGACTAGGATTAACATGA

upper sequence: Vv01s0011g05630.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA07G24950.5 (Glycine max), 3'ss of exon 2
actactgcttttagacaacttatttccttctaaactctactgtcaccctttaaaagagtggaaagtgattccttacttagcaattactgctgcttgccagACCGTTCATGAAGGGCGCATCTACCAGTTGAAACTGTTCTGTGGTCAGGACTATCCGGATAATCCACCAACTGTGAAGTTCCAGACTCGGATAAATATGA--------------------------
                             |||||      |   ||    ||| | | ||  | |   |   || | |  | || |       || |||||| |||||||||||||| ||||||||||||||| |||| ||  |   ||| ||||| || ||||| ||| |||| |  || || ||  |||| || ||||                          
---------------------------aactaaaactagtttctactaaataatatattgatatggcctgtttttcctgtccatcatgttattttaccagactgttcatgaagggcgtatctaccagTTGAAATTGTTTTGCAGCAGGGATTATCCAGACAATCCTCCATCTGTTAGATTTCAAACAAGGATTAACATGACATGTGTCAATCAAGAAACTGGAGTG

upper sequence: Vv01s0011g05630.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA07G24950.3 (Glycine max), 3'ss of exon 2
actactgcttttagacaacttatttccttctaaactctactgtcaccctttaaaagagtggaaagtgattccttacttagcaattactgctgcttgccagACCGTTCATGAAGGGCGCATCTACCAGTTGAAACTGTTCTGTGGTCAGGACTATCCGGATAATCCACCAACTGTGAAGTTCCAGACTCGGATAAATATGA--------------------------
                                            ||    ||| | | ||  | |   |   || | |  | || |       || |||||| |||||||||||||| ||||||||||||||| |||| ||  |   ||| ||||| || ||||| ||| |||| |  || || ||  |||| || ||||                          
--------------------------------------------actaaataatatattgatatggcctgtttttcctgtccatcatgttattttaccagactgttcatgaagggcgtatctaccagttgaaattgttttgcagCAGGGATTATCCAGACAATCCTCCATCTGTTAGATTTCAAACAAGGATTAACATGACATGTGTCAATCAAGAAACTGGAGTG

upper sequence: Vv01s0011g05630.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA09G22600.1 (Glycine max), 3'ss of exon 2
actactgcttttagacaacttatttccttctaaactctactgtc-accctttaaaagagtggaaagtgattccttacttagcaattac-tgctgcttgccagACCGTTCATGAAGGGCGCATCTACCAGTTGAAACTGTTCTGTGGTCAGGACTATCCGGATAATCCACCAACTGTGAAGTTCCAGACTCGGATAAATATGA
  |   |||  ||  |||        ||  || | |  | | || |||   ||| | | ||  | |   |   |  | |  | || |  |  |  || |||||| |||||||||||||| ||| ||||||||||| |||| |||||  |||| ||||| || ||||| ||| |||| |  || || ||  |||| || ||||
tttctagctgctaagcaaaactaaaactagtatagt--agtatctaccaaataatatattgacatggcttgtttctcctgcccatcatgttatttttaccagACTGTTCATGAAGGGCGTATCCACCAGTTGAAATTGTTTTGTGGCAAGGATTATCCAGACAATCCTCCATCTGTTAGATTTCAAACAAGGATTAACATGA

upper sequence: Vv01s0011g05630.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA07G24950.4 (Glycine max), 3'ss of exon 2
-actactgcttttagacaacttatttccttctaaactctactgtcaccctttaaaagagtggaaagtgattccttacttagcaattactgctgcttgccagACCGTTCATGAAGGGCGCATCTACCAGTTGAAACTGTTCTGTGGTCAGGACTATCCGGATAATCCACCAACTGTGAAGTTCCAGACTCGGATAAATATGA
   |    ||||    |  || |         |||||    |   ||    ||| | | ||  | |   |   || | |  | || |       || |||||| |||||||||||||| ||||||||||||||| |||| ||  |   ||| ||||| || ||||| ||| |||| |  || || ||  |||| || ||||
gtgtctcactttctagctgctaagcaaaactaaaacta-gtttctactaaataatatattgatatggcctgtttttcctgtccatcatgttattttaccagACTGTTCATGAAGGGCGTATCTACCAGTTGAAATTGTTTTGCAGCAGGGATTATCCAGACAATCCTCCATCTGTTAGATTTCAAACAAGGATTAACATGA

upper sequence: Vv01s0011g05630.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA05G35000.1 (Glycine max), 3'ss of exon 2
---actactgcttttagacaacttatttccttctaaactctactgtcaccctttaaaagagtggaaagtgat--tccttacttagcaattactgctgcttgccagACCGTTCATGAAGGGCGCATCTACCAGTTGAAACTGTTCTGTGGTCAGGACTATCCGGATAATCCACCAACTGTGAAGTTCCAGACTCGGATAAATATGA
     |||||||||        | | |       || |  || ||||  ||   | || |     |  ||||  |  || |||  | |         ||| |||||| |||||||||||||| || |||||| ||||| | || |||||  |||| ||||| || |||||||||||||| |  || |||||| |||| || ||||
gtatgtactgctttctagttgttaagtgg-----aaccagtagtgtctgccaaaacaatatgcagatatgatgattttttcttgtccaccttgttctcttaccagACTGTTCATGAAGGGCGTATATACCAGCTGAAATTATTTTGTGGCAAGGATTATCCAGACAATCCACCAACTGTTAGATTTCAGACTAGGATTAACATGA

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|34550762|gb|CF518980.1|CF518980
EST:     ATGATATATACATGCAGTCGTGGACTGGGACTATCATTGGTCCTCCTAAT                         ACCGTTCATGAAGGGCGCATCTACCAGTTGAAACTGTTCTGTGGCCAGGAC
genomic: ATGATATATACATGCAGTCGTGGACTGGGACTATCATTGGTCCTCCTAATgtgagttttt ... tgcttgccagACCGTTCATGAAGGGCGCATCTACCAGTTGAAACTGTTCTGTGGTCAGGAC
EST: gi|32249291|gb|CD715110.1|CD715110
EST:     ATGATATATACATGCAGTCGTGGACTGGGACTATCATTGGTCCTCCTAAT                         ACCGTTCATGAAGGGCGCATCTACCAGTTGAAACTGTTCTGTGGCCAGGAC
genomic: ATGATATATACATGCAGTCGTGGACTGGGACTATCATTGGTCCTCCTAATgtgagttttt ... tgcttgccagACCGTTCATGAAGGGCGCATCTACCAGTTGAAACTGTTCTGTGGTCAGGAC
EST: gi|110399220|gb|EC965717.1|EC965717
EST:     ATGATATATACATGCAGTCGTGGACTGGGACTATCATTGGTCCTCCTAAT                         ACCGTTCATGAAGGGCGCATCTACCAGTTGAAACTGTTCTGTGGCCAGGAC
genomic: ATGATATATACATGCAGTCGTGGACTGGGACTATCATTGGTCCTCCTAATgtgagttttt ... tgcttgccagACCGTTCATGAAGGGCGCATCTACCAGTTGAAACTGTTCTGTGGTCAGGAC
EST: gi|161717210|gb|FC067216.1|FC067216
EST:     ATGATATATACATGCAGTCGTGGACTGGGACTATCATTGGTCCTCCTAAT                         ACCGTTCATGAAGGGCGCATCTACCAGTTGAAACTGTTCTGTGGCCAGGAC
genomic: ATGATATATACATGCAGTCGTGGACTGGGACTATCATTGGTCCTCCTAATgtgagttttt ... tgcttgccagACCGTTCATGAAGGGCGCATCTACCAGTTGAAACTGTTCTGTGGTCAGGAC
EST: gi|26266147|gb|CA817210.1|CA817210
EST:     ATGATATATACATGCAGTCGTGGACTGGGACTATCATTGGTCCTCCTAAT                         ACCGTTCATGAAGGGCGCATCTACCAGTTGAAACTGTTCTGTGGCCAGGAC
genomic: ATGATATATACATGCAGTCGTGGACTGGGACTATCATTGGTCCTCCTAATgtgagttttt ... tgcttgccagACCGTTCATGAAGGGCGCATCTACCAGTTGAAACTGTTCTGTGGTCAGGAC
EST: gi|37190155|gb|CF609504.1|CF609504
EST:     ATGATATATACATGCAGTCGTGGACTGGGACTATCATTGGTCCTCCTAAT                         ACCGTTCATGAAGGGCGCATCTACCAGTTGAAACTGTTCTGTGGCCAGGAC
genomic: ATGATATATACATGCAGTCGTGGACTGGGACTATCATTGGTCCTCCTAATgtgagttttt ... tgcttgccagACCGTTCATGAAGGGCGCATCTACCAGTTGAAACTGTTCTGTGGTCAGGAC
EST: gi|34548114|gb|CF516346.1|CF516346
EST:     ATGATATATACATGCAGTCGTGGACTGGGACTATCATTGGTCCTCCTAAT                         ACCGTTCATGAAAGGCGCATCTACCAGTTGAAACTGTTCTGTGGCCAGGAC
genomic: ATGATATATACATGCAGTCGTGGACTGGGACTATCATTGGTCCTCCTAATgtgagttttt ... tgcttgccagACCGTTCATGAAGGGCGCATCTACCAGTTGAAACTGTTCTGTGGTCAGGAC
EST: gi|30137020|gb|CB922358.1|CB922358
EST:     ATGATATATACATGCAGTCGTGGACTGGGACTATCATTGGTCCTCCTAAT                         ACCGTTCATGAAGGGCGCATCTACCAGTTGAAACTGTTCTGTGGCCAGGAC
genomic: ATGATATATACATGCAGTCGTGGACTGGGACTATCATTGGTCCTCCTAATgtgagttttt ... tgcttgccagACCGTTCATGAAGGGCGCATCTACCAGTTGAAACTGTTCTGTGGTCAGGAC
EST: gi|30298336|gb|CB975130.1|CB975130
EST:     ATGATATATACATGCAGTCGTGGACTGGGACTATCATTGGTCCTCCTAAT                         ACCGTTCATGAAGGGCGCATTTACCAGTTGAAACTGTTCCGTGGCCAGGAC
genomic: ATGATATATACATGCAGTCGTGGACTGGGACTATCATTGGTCCTCCTAATgtgagttttt ... tgcttgccagACCGTTCATGAAGGGCGCATCTACCAGTTGAAACTGTTCTGTGGTCAGGAC
EST: gi|349830853|gb|FQ418161.1|FQ418161
EST:     ATGATATATACATGCAGTCGTGGACTGGGACTATCATTGGTCCTCCTAAT                         ACCGTTCATGAAGGGCGCATCTACCAGTTGAAACTGTTCTGTGGCCAGGAC
genomic: ATGATATATACATGCAGTCGTGGACTGGGACTATCATTGGTCCTCCTAATgtgagttttt ... tgcttgccagACCGTTCATGAAGGGCGCATCTACCAGTTGAAACTGTTCTGTGGTCAGGAC
EST: gi|34361563|gb|CF403148.1|CF403148
EST:     TATCATTGGTCCTCCTAAT                         ACCGTTCATGAAGGGCGCATCTACCAGTTGAAACTGTTCTGTGGCCAGGAC
genomic: TATCATTGGTCCTCCTAATgtgagttttt ... tgcttgccagACCGTTCATGAAGGGCGCATCTACCAGTTGAAACTGTTCTGTGGTCAGGAC
EST: gi|34549812|gb|CF518044.1|CF518044
EST:     ATGATATATACATGCAGTCGTGGACTGGGACTATCATTGGTCCTCCTAAT                         ACCGTTCATGAAGGGCGCATCTACCAGTTGAAACTGTTCTGTGGCCAGGAC
genomic: ATGATATATACATGCAGTCGTGGACTGGGACTATCATTGGTCCTCCTAATgtgagttttt ... tgcttgccagACCGTTCATGAAGGGCGCATCTACCAGTTGAAACTGTTCTGTGGTCAGGAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ccctttaaaagagtggaaagtgattccttacttagcaattactgctgcttgccagACCGTTCATGAAGGGCGCATCTACCAGTTGAAACTGTTCTGTGGTCAGGACTATCCGGATAATCCACCAACTGTGAAGTTCCAGACTCGGATAAATATGA
                        tccttac  putative branch site (score: 2)
     taaaaga  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
actactgcttttagacaacttatttccttctaaactctactgtcaccctttaaaagagtggaaagtgattccttacttagcaattactgctgcttgccagACCGTTCATGAAGGGCGCATCTACCAGTTGAAACTGTTCTGTGGTCAGGACTATCCGGATAATCCACCAACTGTGAAGTTCCAGACTCGGATAAATATGA

-ctactgc
- - - - - - agacaac
- - - - - - - - - - - - tccttct
- - - - - - - - - - - - - - - - - - ctactgt
- - - - - - - - - - - - - - - - - - - - - -caccctt
- - - - - - - - - - - - - - - - - - - - - - - - - -aaaagag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aaagtga
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ttactgc