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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtagaagttgcctattgtcacccctctagtccttctcttttgtcttttaagatgcttacattaggtttacttctaacaatgttgaagttttatatccctccagCCATTAGGATTTCAGGTGGATGATGCAAAACTGAAGCGTGCTGGGTTGGATTATTGGCC

Basic information

species Vitis vinifera
transcript Vv13s0064g01270.t01
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv13s0064g01270.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: LOC_Os08g39600.1 (Oryza sativa), 3'ss of exon 2
-------------gtagaagttgcctattgtcacccctctagtccttctcttttgtcttttaagatgcttacattaggtttacttctaacaatgttgaagttttatatccctccagCCATTAGGATTTCAGGTGGATGATGCAAAACTGAAGCGTGCTGGGTTGGATTATTGGCC
              ||    | |   ||||       |||  ||||| |  ||  ||| |||     |    | || || |  | || | ||| |||     |   |    ||||||||||||| ||| |||| |||||  | || |||||||||||||| |||||||| |||||
gtaaggttagtgcttattgatagaacattgaatggtttctcttccttttacttgttctgttattcatcgggtactatgtgtgat-ctgaaaattttgtttgctgcaacgtttccagCCATTAGGTTTTAAGGTAGATGACACGAAGCTGAAGCGTGCTGGATTGGATTACTGGCC

upper sequence: Vv13s0064g01270.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA08G16210.1 (Glycine max), 3'ss of exon 3
gtagaagttgcctattgtcacccctctagtccttctcttttgtcttttaagatgc---------ttacattaggtttac--ttctaacaatg----ttgaagttttatatccctccagCCATTAGGATTTCAGGTGGATGATGCAAAACTGAAGCGTGCTGGGTTGGATTATTGGCC
     ||||     || | |  | | |  |  ||  | ||||    | |   ||          | |  || | | |||  | ||||   |     ||| | || | ||||  | ||||||||||||||||||||||||||| | ||||| |||||||||||||||||||| |||||
--gtgagttttactttctaaatcttattattttttacatttgatgataagattgtcatgtattttcatgtttgttgtacaatactaatggtagcctttgtatttctttatcttttcagCCATTAGGATTTCAGGTGGATGATACTAAACTAAAGCGTGCTGGGTTGGATTACTGGCC

upper sequence: Vv13s0064g01270.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: AT5G26880.2 (Arabidopsis thaliana), 3'ss of exon 2
gtagaagttgcctattgtcacccctctagtccttctcttttgtcttttaagatgcttacattaggtttacttctaacaatgttgaagttttatatccctccagCCATTAGGATTTCAGGTGGATGATGCAAAACTGAAGCGTGCTGGGTTGGATTATTGGCC
                           |      |      | ||| |    |  || || |  ||| |   || |   |||     |||  |    || ||||||||||| ||||| |||||||| || | | | ||||| ||||| ||||||||||||||
------------------------gtaaagtaaccaaacacgacttgttcattatttccagt--gttgatgacttaatctgtca---tttgttcctgcttcagCCATTAGGTTTTCAAGTGGATGACGCCAGAGTTAAGCGAGCTGGTTTGGATTATTGGCC

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|351022623|gb|FQ447145.1|FQ447145
EST:     CCATTGCCAGAACATGTGCAGCATCAGCTGTTGGACTGCACCTAATCGAG                         CCATTAGGATTTCAGGTGGATGATGCAAAACTGAAGCGTGCTGGGTTGGAT
genomic: CCATTGCCAGAACATGTGCAGCATCAGCTGTTGGACTTCACCTAATCGAGgtagaagttg ... atccctccagCCATTAGGATTTCAGGTGGATGATGCAAAACTGAAGCGTGCTGGGTTGGAT
EST: gi|26257252|gb|CA808315.1|CA808315
EST:     CCATTGCCAGAACATGTGCAGCATCAGCTGTTGGACTTCACCTAATCGAG                         CCATTAGGATTTCAGGTGGATGATGCAAAACTGAAGCGTGCTGGGTTGGAT
genomic: CCATTGCCAGAACATGTGCAGCATCAGCTGTTGGACTTCACCTAATCGAGgtagaagttg ... atccctccagCCATTAGGATTTCAGGTGGATGATGCAAAACTGAAGCGTGCTGGGTTGGAT
EST: gi|351015543|gb|FQ447372.1|FQ447372
EST:     CCATTGCCAGAACATGTGCAGCATCAGCTGTTGGACTTCACCTAATCGAG                         CCATTAGGATTTCAGGTGGATGATGCAAAACTGAAGCGTGCTGGGTTGGAT
genomic: CCATTGCCAGAACATGTGCAGCATCAGCTGTTGGACTTCACCTAATCGAGgtagaagttg ... atccctccagCCATTAGGATTTCAGGTGGATGATGCAAAACTGAAGCGTGCTGGGTTGGAT
EST: gi|349825487|gb|FQ419404.1|FQ419404
EST:     CCATTGCCAGAACATGTGCAGCATCAGCTGTTGGACTTCACCTAATCGAG                         CCATTAGGATTTCAGGTGGATGATGCAAAACTGAAGCGTGCTGGGTTGGAT
genomic: CCATTGCCAGAACATGTGCAGCATCAGCTGTTGGACTTCACCTAATCGAGgtagaagttg ... atccctccagCCATTAGGATTTCAGGTGGATGATGCAAAACTGAAGCGTGCTGGGTTGGAT
EST: gi|349831115|gb|FQ420785.1|FQ420785
EST:     CCATTGCCAGAACATGTGCAGCATCAGCTGTTGGACTTCACCTAATCGAG                         CCATTAGGATTTCAGGTGGATGATGCAAAACTGAAGCGTGCTGGGTTGGAT
genomic: CCATTGCCAGAACATGTGCAGCATCAGCTGTTGGACTTCACCTAATCGAGgtagaagttg ... atccctccagCCATTAGGATTTCAGGTGGATGATGCAAAACTGAAGCGTGCTGGGTTGGAT
EST: gi|26257522|gb|CA808585.1|CA808585
EST:     CCATTGCCAGAACATGTGCAGCATCAGCTGTTGGACTTCACCTAATCGAG                         CCATTAGGATTTCAGGTGGATGATGCAAAACTGAAGCGTGCTGGGTTGGAT
genomic: CCATTGCCAGAACATGTGCAGCATCAGCTGTTGGACTTCACCTAATCGAGgtagaagttg ... atccctccagCCATTAGGATTTCAGGTGGATGATGCAAAACTGAAGCGTGCTGGGTTGGAT
EST: gi|349825184|gb|FQ415731.1|FQ415731
EST:     CCATTGCCAGAACATGTGCAGCATCAGCTGTTGGACTGCATCTAATCGAG                         CCATTAGGATTTCAGGTGGATGATGCAAAACTGAAGCGTGCTGGGTTGGAT
genomic: CCATTGCCAGAACATGTGCAGCATCAGCTGTTGGACTTCACCTAATCGAGgtagaagttg ... atccctccagCCATTAGGATTTCAGGTGGATGATGCAAAACTGAAGCGTGCTGGGTTGGAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aagatgcttacattaggtttacttctaacaatgttgaagttttatatccctccagCCATTAGGATTTCAGGTGGATGATGCAAAACTGAAGCGTGCTGGGTTGGATTATTGGCC
                      ttctaac  putative branch site (score: 1)
                                       ttttatatccctcc  putative PPT
                                 ttgaagttttatat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtagaagttgcctattgtcacccctctagtccttctcttttgtcttttaagatgcttacattaggtttacttctaacaatgttgaagttttatatccctccagCCATTAGGATTTCAGGTGGATGATGCAAAACTGAAGCGTGCTGGGTTGGATTATTGGCC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC