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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aatatgtatgcattaggaaagcacaagctagagaagtcaactgttgatcttatgcaataacatttttgttcttacagttttataaacttatttcaatcagGGTTGTTGCTGGTTAGCTCCCTTGCTATATGCACTATTGTAGAACTTCTGTCAATGTGGAACTTGACAAGGATAGAAGTTCAACTATGCAACATGTTATC

Basic information

species Vitis vinifera
transcript Vv11s0016g03130.t01
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv11s0016g03130.t01 (Vitis vinifera), 3'ss of exon 11
lower sequence: LOC_Os01g67870.1 (Oryza sativa), 3'ss of exon 11
-------aatatgtatgcattaggaaagcac--aagctag-agaagtcaactgttgatcttatgcaata-acatttttgttcttacagtttta---taaacttattt---caatcagGGTTGTTGCTGGTTAGCTCCCTTGCTATATGCACTATTGTAGAACTTCTGTCAATGTGGAACTTGACAAGGATAGAAGTTCAACTATGCAACATGTTATC
        ||   | | | |     |   |   |||||    ||  |  | |  |  |  ||   |||  || ||  | | | |   || |      | |||| |||      |||||  ||   || ||| ||| | |    ||||||||| |   ||||||| | ||||||||||| ||||||| | | ||| ||||||| ||||||||||| ||
gtcagtgcatgcctttccctctaagatctattaaagctgttggatatttatttctagttctaacaaatgcacgttcatctccctgtggtctctcatcagacttttttgtgtgttcagGTCTGAAACTAGTTTGCTGCTTGTTAATATGCACTCTCACAGAACTTGTTTCAATGTGGAATTTGACAAAGGTGGAAATTCAACTGTGCAACATGTTGTC

upper sequence: Vv11s0016g03130.t01 (Vitis vinifera), 3'ss of exon 11
lower sequence: GLYMA05G35860.1 (Glycine max), 3'ss of exon 10
aatatgtatgcattaggaaagcacaagctagagaagtcaactgttgatcttatgcaataacatttttgttcttacagttttataaac-ttatttcaatcagGGTTGTTGCTGGTTAGCTCCCTTGCTATATGCACTATTGTAGAACTTCTGTCAATGTGGAACTTGACAAGGATAGAAGTTCAACTATGCAACATGTTATC
|| |   |       | |  |||      |  ||    |||| || |  ||| ||  ||   |||  |||||| || ||| ||||      |||    ||||||| |   ||||   || ||| || ||||||||| |||| || ||||| |||||||||||||||||| |||||||||| ||||| ||||||||||||||
aaaacaaaaatgggtgtactgcattgttaactgagacgaacttttcaa-ttaagctttacattttcagttcttgcattttgataagtgccttttttcccagGGTTATCATTGGTGGCCTTCCTAGCCATATGCACTCTTGTTGAGCTTCTTTCAATGTGGAACTTGACACGGATAGAAGTCCAACTGTGCAACATGTTATC

upper sequence: Vv11s0016g03130.t01 (Vitis vinifera), 3'ss of exon 11
lower sequence: GLYMA08G03760.1 (Glycine max), 3'ss of exon 11
-aatatgtatgcattaggaaagcacaagctagagaagtcaactgttgatcttatgcaataacatttttgttcttacagttttataaa--cttatttcaatcagGGTTGTTGCTGGTTAGCTCCCTTGCTATATGCACTATTGTAGAACTTCTGTCAATGTGGAACTTGACAAGGATAGAAGTTCAACTATGCAACATGTTATC
 || |   |||  |  | |  |||      |  ||    |||| ||    ||| ||  ||   |||  |||||| || ||| ||||   | | |||    ||||||| |   |||| | || ||| || ||||||||| |||| || ||||| |||||||||||||||||| |||||||||| ||||| ||||||||||| ||
aaacaaaaatgggt--gtactgcattgttaactgagacgaacttttc-cattaagctttacattttcagttcttgcattttgataagtgcctttttttcccagGGTTATCATTGGTGACCTTCCTAGCCATATGCACTCTTGTTGAGCTTCTTTCAATGTGGAACTTGACACGGATAGAAGTCCAACTGTGCAACATGTTGTC

upper sequence: Vv11s0016g03130.t01 (Vitis vinifera), 3'ss of exon 11
lower sequence: GLYMA01G01130.1 (Glycine max), 3'ss of exon 11
--aatatgtatgcattaggaaagcacaagctagagaagtcaactgttgatcttatgcaataacatttttgttcttacagttttataaactta--tttcaatcagGGTTGTTGCTGGTTAGCTCCCTTGCTATATGCACTATTGTAGAACTTCTGTCAATGTGGAACTTGACAAGGATAGAAGTTCAACTATGCAACATGTTATC
  ||||   | |  ||  ||||    ||  || | | |  |     | || || || |  | |  | ||  |   |   ||| ||||  ||    ||   ||||| ||     ||||  |   ||| || | ||||||| || |   |||| | ||||||||||||||||||||||||||||||| ||| |||||||| || ||
agaatagtcaaggtttgtgaaaaggaaaa-taaaaatggaagaaactcattttttggatgagctatcttact---aagctttaataagatttgccttttctcagGTTTAACAATGGTGTGGATCCTAGCCACATGCACTCTTATTTCACTTTTCTCAATGTGGAACTTGACAAGGATAGAAGTTCTACTTTGCAACATATTGTC

upper sequence: Vv11s0016g03130.t01 (Vitis vinifera), 3'ss of exon 11
lower sequence: GLYMA16G08510.1 (Glycine max), 3'ss of exon 11
aatatgtatgcattaggaaagcacaagctagagaagtcaactgttgatcttatgcaataacatttttgttcttacagttttataaacttatttcaatcagGGTTGTTGCTGGTTAGCTCCCTTGCTATATGCACTATTGTAGAACTTCTGTCAATGTGGAACTTGACAAGGATAGAAGTTCAACTATGCAACATGTTATC------------------------
                                                                                       |   ||   ||||||||     ||||  |   ||| || | ||||||| || |   |||| | ||||||||||||||||||||||||||||||| ||| || ||||| || ||                        
------------------------------------------------------------------------------------gtttgccttttctcagggttaacaatggtgtggctcctagCCACATGCACTCTTATTTCACTTTTCTCAATGTGGAACTTGACAAGGATAGAAGTTCTACTTTGTAACATATTGTCCCCAGAGGCACCTCGACTTTCTCT

upper sequence: Vv11s0016g03130.t01 (Vitis vinifera), 3'ss of exon 11
lower sequence: AT2G19880.1 (Arabidopsis thaliana), 3'ss of exon 11
aatatgtatgcattaggaaagcacaagctagagaagtcaactgttgatcttatgcaataacatttttgttcttacagttttataaacttatttcaat-cagGGTTGTTGCTGGTTAGCTCCCTTGCTATATGCACTATTGTAGAACTTCTGTCAATGTGGAACTTGACAAGGATAGAAGTTCAACTATGCAACATGTTATC
  | |||| | |  |  |          |    || | || |  |    || |    |    || |  | | ||  |    |   |     ||| ||  |||  || |||| ||||   |  | || || |||||  |  | || ||||||||||||||||| ||||| ||   ||||||||| |||||||| ||||||||
gttgtgta-gaagcataatgatttgtcatcttcaacttaaattgtaggattgtctgtttttcttatgctacatattgaccgaaggatgaggttctatgtagGTATGATGCTTGTTATAACGTTGGCGATCTGCACCTTCATCGAGCTTCTGTCAATGTGGAATTTGACGAGACGAGAAGTTCAGCTATGCAATATGTTATC

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|294965468|gb|GW839039.1|GW839039
EST:     AGTTGCTTCTAAAGAGTACTCGCCTGAGGAAACAACCTCTGCTTCTGGTG                         GGTTGTTGCTGGTTAGCTCCCTTGCTATATGCACTATTGTAGAACTTCTGT
genomic: AGTTGCTTCTAAAGAGTACTCGCCTGAGGAAACAACCTTTGCTTCTGGTGgtgagcacac ... tttcaatcagGGTTGTTGCTGGTTAGCTCCCTTGCTATATGCACTATTGTAGAACTTCTGT






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gatcttatgcaataacatttttgttcttacagttttataaacttatttcaatcagGGTTGTTGCTGGTTAGCTCCCTTGCTATATGCACTATTGTAGAACTTCTGTCAATGTGGAACTTGACAAGGATAGAAGTTCAACTATGCAACATGTTATC
                       ttcttac  putative branch site (score: 2)
                                         cttatttc  putative PPT
                          ttacagttttataaac  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aatatgtatgcattaggaaagcacaagctagagaagtcaactgttgatcttatgcaataacatttttgttcttacagttttataaacttatttcaatcagGGTTGTTGCTGGTTAGCTCCCTTGCTATATGCACTATTGTAGAACTTCTGTCAATGTGGAACTTGACAAGGATAGAAGTTCAACTATGCAACATGTTATC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGT
- - -gtatgca
- - - - - - - aggaaag
- - - - - - - - - - -cacaagc
- - - - - - - - - - - - - - - - - - - - ctgttga
- - - - - - - - - - - - - - - - - - - - - - - - - - - caataac