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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtactttccattcattgttttgatcatctgcagagttcaatttactctcttatcccttagttacatgcatggaattctaccctaaaatcaactttatttcagttttctattggactgaaatctgtaactctgtttgcttgcaatgatgaacatgcttggatattgatactgtgattatagGACCCACTGGAGAAATTGTCGCAGCTGCTGATGATAAAGAGGAAGCTGTTGTTGTAGCACAATTTGATCTGGATAAAATCAAATCCAAGAGATATAGTTG

Basic information

species Vitis vinifera
transcript Vv06s0080g00560.t01
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv06s0080g00560.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: GLYMA13G39210.1 (Glycine max), 3'ss of exon 8
gtactttccattcattgttttgatcatctgcagagttcaatttactctcttatcccttagttacatgcatggaattctaccctaaaatcaactttat-ttcagttttctattggactgaaatctgtaactctgtttgcttg-caatgatgaacatgcttggatattgatactgtgattatagGACCCACTGGAGAAATTGTCGCAGCTGCTGATGATAAAGAGGAAGCTGTTGTTGTAGCACAATTTGATCTGGATAAAATCAAATCCAAGAGATATAGTTG
| || | || ||| | |||| | ||||| | ||| | || | | | || | | || | || | || | | ||||||| |||||||||||||| || ||||||||||||||||||||||||| || | || ||||||||| |||| || |||||||||| ||| || | ||
--------------------------------------------------------------------------------attgaattgaattttttcttcattcttctaacactagggaatatttagtt--gctggcataacttctctgtttctatttttgtcttttctatcaacatgtagGACCTACTGGAGAAATTGTTTCAATTGCTGATGATAAAGAGGAAGCTGTTCTTATTGCTCAATTTGATTTGGACAATATCAAATCCATGAGGCATTGCTG

upper sequence: Vv06s0080g00560.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: GLYMA12G31100.2 (Glycine max), 3'ss of exon 9
gtactttccattcattgttttgatcatctgcagagttcaatttactctcttatcccttagttacatgcatggaattctaccctaaaatcaactttatttcagttttctattggactgaaatctgtaac-tctgtttgcttgcaatgatgaacatgcttggatattgata----ctgtgattat--agGACCCACTGGAGAAATTGTCGCAGCTGCTGATGATAAAGAGGAAGCTGTTGTTGTAGCACAATTTGATCTGGATAAAATCAAATCCAAGAGATATAGTTG
|||| | ||| ||| | | | || || | | || || | | ||| ||| | | | || || || || | || | | ||| |||||| || ||||||||||| ||| ||||||||||||||||||||||||| || | || || ||||||||||| || |||||||| | ||| || ||||
-----------------------------------------------------------------------------------ttaatcgatttttttttcttcatttctt---ctaacacttggaaagtttagctgcaggca-taacttatctgtttatatttttgtcttctctatcaatatacagGACCTACAGGAGAAATTGTTTCAGTTGCTGATGATAAAGAGGAAGCTGTTCTTATTGCTCAGTTTGATCTGGACAAGATCAAATCAACGAGGCATTGTTG

upper sequence: Vv06s0080g00560.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: GLYMA08G07960.1 (Glycine max), 3'ss of exon 8
gtactttccattcattgttttgatcatctgcagagttcaatttactctcttatcccttagttacatgcatggaattctaccctaaaatcaactttatttcagttttctattggactgaaatctgtaactctgtttgcttgcaatgatgaac-atgcttggatattgata----ctgtgattat--agGACCCACTGGAGAAATTGTCGCAGCTGCTGATGATAAAGAGGAAGCTGTTGTTGTAGCACAATTTGATCTGGATAAAATCAAATCCAAGAGATATAGTTG
| ||| || ||| | | | | ||| | | | | || ||| ||||| |||| || || || || | || | | || |||||| ||||||||||| | || ||||||| |||||||| ||||||||| || | |||||||||||| |||| || |||||||||| |||| || ||||
----------------------------------------------------------------------------------tttaatgaatttttctct--tcatttgttgatatacacttggaaag---atttagctgcaagcatgagttgtgtttctatttttgtcttctctatcaacatgcagGACCTACTGGAGAAATCATTTCAACTGCTGACGATAAAGACGAAGCTGTTCTTATTGCACAATTTGATTTGGACAAGATCAAATCCATGAGACATTGTTG

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|30320849|gb|CD004111.1|CD004111
EST:     AGAGCATGGAAATACTGAAATCACATTCTATGGAAACTCTTTTATAGCAG                         GACCCACTGGAGAAATTGTCGCAGCTGCTGATGATAAAGAGGAAGCTGTTG
genomic: AGAGCATGGAAATACTGAAATCACATTCTATGGAAACTCTTTTATAGCAGgtactttcca ... gtgattatagGACCCACTGGAGAAATTGTCGCAGCTGCTGATGATAAAGAGGAAGCTGTTG
EST: gi|30321318|gb|CD004580.1|CD004580
EST:     AGAGCATGGAAATACTGAAATCACATTTTATGGAAACTCTTTTATAGCAG                         GACCCACTGGAGAAATTGTCGCAGCTGCTGATGATAAAGAGGAAGCTGTTG
genomic: AGAGCATGGAAATACTGAAATCACATTCTATGGAAACTCTTTTATAGCAGgtactttcca ... gtgattatagGACCCACTGGAGAAATTGTCGCAGCTGCTGATGATAAAGAGGAAGCTGTTG
EST: gi|22014795|gb|BQ799829.1|BQ799829
EST:     AGAGCATGGAAATACTGAAATCACATTCTATGGAAACTCTTTTATAGCAG                         GACCCACTGGAGAAATTGTCGCAGCTGCTGATGATAAAGAGGAAGCTGTTG
genomic: AGAGCATGGAAATACTGAAATCACATTCTATGGAAACTCTTTTATAGCAGgtactttcca ... gtgattatagGACCCACTGGAGAAATTGTCGCAGCTGCTGATGATAAAGAGGAAGCTGTTG
EST: gi|30134451|gb|CB919789.1|CB919789
EST:     AGAGCATGGAAATACTGAAATCACATTCTATGGAAACTCTTTTATAGCAG                         GACCCACTGGAGAAATTGTCGCAGCTGCTGATGATAAAGAGGAAGCTGTTG
genomic: AGAGCATGGAAATACTGAAATCACATTCTATGGAAACTCTTTTATAGCAGgtactttcca ... gtgattatagGACCCACTGGAGAAATTGTCGCAGCTGCTGATGATAAAGAGGAAGCTGTTG
EST: gi|26257496|gb|CA808559.1|CA808559
EST:     AGAGCATGGAAATACTGAAATCACATTCTATGGAAACTCTTTTATAGCAG                         GACCCACTGGAGAAATTGTCGCAGCTGCTGATGATAAAAAGGATGGCTGTT
genomic: AGAGCATGGAAATACTGAAATCACATTCTATGGAAACTCTTTTATAGCAGgtactttcca ... gtgattatagGACCCACTGGAGAAATTGTCGCAGCTGCTGATGATAAAGAGGAAG-CTGTT
EST: gi|110385570|gb|EC950109.1|EC950109
EST:     AGAGCATGGAAATACTGAAATCACATTCTATGGAAACTCTTTTATAGCAG                         GACCCACTGGAGAAATTGTCGCAGCTGCTGATGATAAAGAGGAAGCTGTTG
genomic: AGAGCATGGAAATACTGAAATCACATTCTATGGAAACTCTTTTATAGCAGgtactttcca ... gtgattatagGACCCACTGGAGAAATTGTCGCAGCTGCTGATGATAAAGAGGAAGCTGTTG
EST: gi|34543783|gb|CF512015.1|CF512015
EST:     AGAGCATGGAAATACTGAAATCACATTCTATGGAAACTCTTTTATAGCAG                         GACCCACTGGAGAAATTGTCGCAGCTGCTGATGATAAAGAGGAAGCTGTTG
genomic: AGAGCATGGAAATACTGAAATCACATTCTATGGAAACTCTTTTATAGCAGgtactttcca ... gtgattatagGACCCACTGGAGAAATTGTCGCAGCTGCTGATGATAAAGAGGAAGCTGTTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aactctgtttgcttgcaatgatgaacatgcttggatattgatactgtgattatagGACCCACTGGAGAAATTGTCGCAGCTGCTGATGATAAAGAGGAAGCTGTTGTTGTAGCACAATTTGATCTGGATAAAATCAAATCCAAGAGATATAGTTG
                                   tattgat  putative branch site (score: 3)
 atattgata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtactttccattcattgttttgatcatctgcagagttcaatttactctcttatcccttagttacatgcatggaattctaccctaaaatcaactttatttcagttttctattggactgaaatctgtaactctgtttgcttgcaatgatgaacatgcttggatattgatactgtgattatagGACCCACTGGAGAAATTGTCGCAGCTGCTGATGATAAAGAGGAAGCTGTTGTTGTAGCACAATTTGATCTGGATAAAATCAAATCCAAGAGATATAGTTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA