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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...acttttgttactcctaatttttatgaaatgataattttgttatttttatctgaatctcccttttccctttcttctcttgtctttgttccttctgatgtagACACATTATGTTCTATTGCTGTGTTCATTTAAAGAACAATTGCAACAACACGTCCGTGTTCATGCTATGGAAGCCGTAATGGCTTGTTGGGAGCTTGAGC

Basic information

species Vitis vinifera
transcript Vv11s0118g00800.t01
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv11s0118g00800.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GLYMA15G24350.1 (Glycine max), 3'ss of exon 2
-acttttgttactcctaatttttatgaa-atgataattttgttatttttatctgaatctcccttttccctttcttctcttgtctttgttccttctgatgtagACACATTATGTTCTATTGCTGTGTTCATTTAAAGAACAATTGCAACAACACGTCCGTGTTCATGCTATGGAAGCCGTAATGGCTTGTTGGGAGCTTGAGC
 |||  |   |    | | |||  |  | | || |||    ||||||     ||   ||   ||| |   || | ||||| | |||  |  |  || ||||||| ||||||||| || |||| ||| | || |||||||||||||||||||| || |||||||||||||||||||| || ||||||||||||||||| || |
gactggttccatgattgagtttagtttacaggacaatgggcttatttcacattgctccttaatttacatgttttgctctttttttt--tgttgttgttgtagACGCATTATGTTATACTGCTCTGTGCTTTCAAAGAACAATTGCAACAACATGTACGTGTTCATGCTATGGAAGCTGTTATGGCTTGTTGGGAGCTGGAAC

upper sequence: Vv11s0118g00800.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GLYMA09G12820.1 (Glycine max), 3'ss of exon 1
--------acttttgttactcctaatttttatgaaatgataattttgttatttttatctgaatctcccttttccctttcttctcttgtctttgttccttctgatgtagACACATTATGTTCTATTGCTGTGTTCATTTAAAGAACAATTGCAACAACACGTCCGTGTTCATGCTATGGAAGCCGTAATGGCTTGTTGGGAGCTTGAGC
         |  |  ||     || |||| | || |  ||    |   |  ||| |  |||  |||| |  |   || |   | |||   || ||   |  | ||||||| ||||||||| || |||| ||| | || |||||||||||||||||||| |||||||||||||| |||||||| || ||||||||||||||| | || |
catgaattcccatgattgaatttagttttcaggaca--atgggctcaattatttcacatgatgctccttaat---ttacaagttttgctcttatt---ttcgttgtagACGCATTATGTTATACTGCTCTGTGCTTTCAAAGAACAATTGCAACAACATGTCCGTGTTCATGCCATGGAAGCTGTTATGGCTTGTTGGGAGTTGGAAC

upper sequence: Vv11s0118g00800.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GLYMA13G22530.1 (Glycine max), 3'ss of exon 1
--acttttgttactcctaatttttatgaaatgataattttgtt---atttttatctgaatctcccttttccctttcttctcttgtctttgttccttctgatgtagACACATTATGTTCTATTGCTGTGTTCATTTAAAGAACAATTGCAACAACACGTCCGTGTTCATGCTATGGAAGCCGTAATGGCTTGTTGGGAGCTTGAGC
   |||||| |     |  ||| |      | || | | || |   || || || ||||   |   |||    |   | |  |   ||||||     || || |||| ||||||||||| ||||| ||| | |||||||||||| |||| || || |||||||||||||| ||||| || || |||||||||||||| || ||||
gtccttttgatgggttttgtttctcattcttaattaatgtgcttaaatgttaatgtgaagagcttgttttttatgagttttgttattttgtt-----tgttgcagACCCATTATGTTCTGTTGCTCTGTGCCTTTAAAGAACAACTGCAGCAGCATGTCCGTGTTCATGCCATGGAGGCAGTGATGGCTTGTTGGGATCTGGAGC

upper sequence: Vv11s0118g00800.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GLYMA17G11330.2 (Glycine max), 3'ss of exon 1
--acttttgttactccta--atttttatgaaatgataattttgttatttttatctgaatctcccttttccctttcttctcttgtctttgttccttctgatgtagACACATTATGTTCTATTGCTGTGTTCATTTAAAGAACAATTGCAACAACACGTCCGTGTTCATGCTATGGAAGCCGTAATGGCTTGTTGGGAGCTTGAGC
    | ||||   | | |  ||  |||   ||||  | ||| ||| ||  | |    | ||   ||||       |   || || |||      | || || |||| ||||||||||| ||||| ||| | |||||||||||| |||| || || |||||||||||||| ||||| || || |||||||||||||| || ||||
cagttcttgtcgtttcaagaataattaatgaatgtgattttagttgttaatgtgaagagcttgtttttgatgagttatgctagtattt----tgtttgttgcagACCCATTATGTTCTGTTGCTCTGTGCCTTTAAAGAACAACTGCAGCAGCATGTCCGTGTTCATGCCATGGAGGCAGTGATGGCTTGTTGGGATCTGGAGC

upper sequence: Vv11s0118g00800.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: EFJ30264 (Selaginella moellendorffii), 3'ss of exon 1
acttttgttactcctaatttttatgaaatgataattttgttatttttatctgaatctcccttttccctttcttctcttgtctttgttcct-tctgatgtagACACATTATGTTCTATTGCTGTGTTCATTTAAAGAACAATTGCAACAACACGTCCGTGTTCATGCTATGGAAGCCGTAATGGCTTGTTGGGAGCTTGAGC
  |||| || ||  |  |||     || |    |||     |   || |  |  | |   ||||| |||| | || |  | ||| ||| | ||||||  || |||| |||||    |||||  | || || || || ||  | ||||||||||||||||| || || |||||||||||  |||| || |||||||| || |
ttttttttttctttttgtttcctgcaactttacattgaccgacacttttgcgtgttttttttttctctttttcctttacttttttttcttgtctgat-cagGCACACTATGTGACTTTGCTACGCTCGTTCAAGGATCAGCTCCAACAACACGTCCGTGTGCACGCCATGGAAGCCGTCGTGGCATGCTGGGAGCTAGAAC

upper sequence: Vv11s0118g00800.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: EFJ24869 (Selaginella moellendorffii), 3'ss of exon 1
-acttttgttactcctaatttt-tatgaaatgataattttgttatttttatctgaatctcccttttccctttcttctct-tgtctttgttccttctgatgtagACACATTATGTTCTATTGCTGTGTTCATTTAAAGAACAATTGCAACAACACGTCCGTGTTCATGCTATGGAAGCCGTAATGGCTTGTTGGGAGCTTGAGC
   ||||||| |    || |||  ||  |  || | |||||    |||| | |   | |   || || |||| | || | | | ||| |    ||||||  || |||| |||||    |||||  | || || || || ||  | ||||||||||||||||| || || |||||||||||  |||| || |||||||| || |
tctttttgtttcctgcaactttacattgaccgacacttttgcgtgttttcttt--tttttttttctctctttttcctttatatttttttcttgtctgat-cagGCACACTATGTGACTTTGCTACGCTCGTTCAAGGATCAGCTCCAACAACACGTCCGTGTGCACGCCATGGAAGCCGTCGTGGCATGCTGGGAGCTAGAAC

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|110732550|gb|EE107936.1|EE107936
EST:     GGTCCTTGGCAA-TCAGCCTTTGGATGATAAGGAGCTCGATCAGTTCATG                         ACACATTATGTTCTATTGCTGTGT
genomic: GGTCCTTG-CAAATCAGCCTTTGGATGATAAGGAGCTCGATCAGTTCATGgtgagaacat ... tctgatgtagACACATTATGTTCTATTGCTGTGT
EST: gi|110712932|gb|EE088409.1|EE088409
EST:     CGGTCCTTGCAAATCAGCCTTTGGATGATAAGGAGCTCGATCAGTTCATG                         ACACATTATGTTCTATTGCTGTGTTCATTTAAAGAACAATTGCAACAACAC
genomic: CGGTCCTTGCAAATCAGCCTTTGGATGATAAGGAGCTCGATCAGTTCATGgtgagaacat ... tctgatgtagACACATTATGTTCTATTGCTGTGTTCATTTAAAGAACAATTGCAACAACAC
EST: gi|110711490|gb|EE088027.1|EE088027
EST:     CGGTCCTTGCAAATCAGCCTTTGGATGATAAGGAGCTCGATCAGTTCATG                         ACACATTATGTTCTATTGCTGTGTTCATTTAAAGAACAATTGCAACAACAC
genomic: CGGTCCTTGCAAATCAGCCTTTGGATGATAAGGAGCTCGATCAGTTCATGgtgagaacat ... tctgatgtagACACATTATGTTCTATTGCTGTGTTCATTTAAAGAACAATTGCAACAACAC
EST: gi|110712547|gb|EE090292.1|EE090292
EST:     CGGTCCTTGCAAATCAGCCTTTGGATGATAAGGAGCTCGATCAGTTCATG                         ACACATTATGTTCTATTGCTGTGTTCATTTAAAGAACAATTGCAACAACAC
genomic: CGGTCCTTGCAAATCAGCCTTTGGATGATAAGGAGCTCGATCAGTTCATGgtgagaacat ... tctgatgtagACACATTATGTTCTATTGCTGTGTTCATTTAAAGAACAATTGCAACAACAC
EST: gi|110359310|gb|EC920596.1|EC920596
EST:     CGGTCCTTGCAAATCAGCCTTTGGATGATAAGGAGCTCGATCAGTTCATG                         ACACATTATGTTCTATTGCTGTGTTCATTTAAAGAACAATTGCAACAACAC
genomic: CGGTCCTTGCAAATCAGCCTTTGGATGATAAGGAGCTCGATCAGTTCATGgtgagaacat ... tctgatgtagACACATTATGTTCTATTGCTGTGTTCATTTAAAGAACAATTGCAACAACAC
EST: gi|352777777|gb|FQ466830.1|FQ466830
EST:     CGGTCCTTGCAAATCAGCCTTTGGATGATAAGGAGCTCGATCAGTTCATG                         ACACATTATGTTCTATTGCTGTGTTCATTTAAAGAACAATTGCAACAACAC
genomic: CGGTCCTTGCAAATCAGCCTTTGGATGATAAGGAGCTCGATCAGTTCATGgtgagaacat ... tctgatgtagACACATTATGTTCTATTGCTGTGTTCATTTAAAGAACAATTGCAACAACAC
EST: gi|37186487|gb|CF605840.1|CF605840
EST:     CGGTCCTTGCAAATCAGCCTTTGGATGATAAGGAGCTCGATCAGTTCATG                         ACACATTATGTTCTATTGCT
genomic: CGGTCCTTGCAAATCAGCCTTTGGATGATAAGGAGCTCGATCAGTTCATGgtgagaacat ... tctgatgtagACACATTATGTTCTATTGCT
EST: gi|32270192|gb|CD719351.1|CD719351
EST:     CGGTCCTTGCAAATCAGCCTTTGGATGATAAGGAGCTCGATCAGTTCATG                         ACACATTATGTTCTATTGCTGTGTTCATTTAAAGAACAATTGCAACAACAC
genomic: CGGTCCTTGCAAATCAGCCTTTGGATGATAAGGAGCTCGATCAGTTCATGgtgagaacat ... tctgatgtagACACATTATGTTCTATTGCTGTGTTCATTTAAAGAACAATTGCAACAACAC
EST: gi|110685038|gb|EE063001.1|EE063001
EST:     CGGTCCTTGCAAATCAGCCTTTGGATGATAAGGAGCTCGATCAGTTCATG                         ACACATTATGTTCTATTGCTGTGTTCATTTAAAGAACAATTGGCA-CAACA
genomic: CGGTCCTTGCAAATCAGCCTTTGGATGATAAGGAGCTCGATCAGTTCATGgtgagaacat ... tctgatgtagACACATTATGTTCTATTGCTGTGTTCATTTAAAGAACAATTG-CAACAACA
EST: gi|351021553|gb|FQ429657.1|FQ429657
EST:     CGGTCCTTGCAAATCAGCCTTTGGATGATAAGGAGCTCGATCAGTTCATG                         ACACATTATGTTCTATTGCTGTGTTCTTTTAA-GAACAATTGCAACAACAC
genomic: CGGTCCTTGCAAATCAGCCTTTGGATGATAAGGAGCTCGATCAGTTCATGgtgagaacat ... tctgatgtagACACATTATGTTCTATTGCTGTGTTCATTTAAAGAACAATTGCAACAACAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttatctgaatctcccttttccctttcttctcttgtctttgttccttctgatgtagACACATTATGTTCTATTGCTGTGTTCATTTAAAGAACAATTGCAACAACACGTCCGTGTTCATGCTATGGAAGCCGTAATGGCTTGTTGGGAGCTTGAGC
                                            ttctgat  putative branch site (score: 3)
         tctcccttttcccttt  CT-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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
acttttgttactcctaatttttatgaaatgataattttgttatttttatctgaatctcccttttccctttcttctcttgtctttgttccttctgatgtagACACATTATGTTCTATTGCTGTGTTCATTTAAAGAACAATTGCAACAACACGTCCGTGTTCATGCTATGGAAGCCGTAATGGCTTGTTGGGAGCTTGAGC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCTT
- - - - - ctcctaa
- - - - - - - - - - - - gaaatga