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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cctagtgttagaaaggccaaaaacaccttgtagaatcagtaccaaacgtactcttagtcactaatttgtacttggattaatccgatgttccctgtatcagATCAGTGTATATCGTTTACACGGTGCTCGGAGATGTCAGCATCTATGTTGTGGGCAAGGATGAGTATGATGAACTTGCTT

Basic information

species Vitis vinifera
transcript Vv09s0002g06730.t01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv09s0002g06730.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA07G03510.1 (Glycine max), 3'ss of exon 2
-------cctagtgttagaaaggccaaaaacaccttgtagaatcagtaccaaacgtactcttagtcactaatttgtacttggattaatccgatgttccctgtatcagATCAGTGTATATCGTTTACACGGTGCTCGGAGATGTCAGCATCTATGTTGTGGGCAAGGATGAGTATGATGAACTTGCTT
       |||| | ||    |  |  |   |    |||||||    | |    |  | |||||     ||   ||   | | | | || || | |||  || ||||| ||||| ||||| || ||||||||||| || ||||||||||||||||||||||||||||| || |||||||||||||| |
ctaactacctactattgttcattcatattccttgctgtagaaa-gttgcttgtctcattctta-----tatgatgctatagtactcattcgtt-ttctgtgcatcagGTCAGTTTATATTGTATACACGGTGCTTGGCGATGTCAGCATCTATGTTGTGGGCAAGGACGAATATGATGAACTTGCCT

upper sequence: Vv09s0002g06730.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA08G22580.2 (Glycine max), 3'ss of exon 1
cctagtgttagaaaggccaaaaacaccttgtagaatcagtaccaaacgtactcttagtcactaatttgtacttggattaatccgatgttccc--tgtatcagATCAGTGTATATCGTTTACACGGTGCTCGGAGATGTCAGCATCTATGTTGTGGGCAAGGATGAGTATGATGAACTTGCTT
  || |   |   |  ||  |  ||  ||      |  |||  ||      | |  |   || || ||    |  | || |   |  ||  |  || |||||||| || ||||| || ||||| ||||| || ||||||||||||||||| |||||||||||||||||||| |||||||| |
tttactaccaactattcctcattcatatttcttggt--gtagaaagttgcttgtctggttcttatatgattctaaagtacttgtacattttctttgcatcagATCGGTTTATATTGTATACACAGTGCTTGGCGATGTCAGCATCTATGTCGTGGGCAAGGATGAGTATGACGAACTTGCCT

upper sequence: Vv09s0002g06730.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA15G01150.1 (Glycine max), 3'ss of exon 3
-cctagtgttagaaaggccaaaaacaccttgtagaatcagtaccaaacgtactcttagtcactaatttgtacttggattaatccgatgttccctgtatcagATCAGTGTATATCGTTTACACGGTGCTCGGAGATGTCAGCATCTATGTTGTGGGCAAGGATGAGTATGATGAACTTGCTT
  ||  | ||    ||   |   |    || |    ||  |        |     ||    ||  | |    ||  | |  | | || ||  || |||||| ||||| || || || ||||| || || || ||||||||||| ||||||||||| ||||| |||||||||||||||||||
gtctcatctttatgagatgatgcaggttttcttttttcttttttccttttttgggtacatgctggtataatgttttacttgtac-attttatctctatcagGTCAGTTTACATTGTATACACAGTACTTGGGGATGTCAGCATATATGTTGTGGGGAAGGAAGAGTATGATGAACTTGCTT

upper sequence: Vv09s0002g06730.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: AT1G15370.1 (Arabidopsis thaliana), 3'ss of exon 2
cctagtgttagaaaggcca--aaaacaccttgtagaatcagtaccaaacgtactcttagtcactaatttgtacttggattaatccgatgttccctgtatcagATCAGTGTATATCGTTTACACGGTGCTCGGAGATGTCAGCATCTATGTTGTGGGCAAGGATGAGTATGATGAACTTGCTT
       | |      | |      ||  ||  ||||  | ||  ||||  |        || |  |  |   |   | |||      | |   |||  ||| || || |||||||| |||||  |||| || ||||| |||||||   |||| ||||| || |||||||||||||||||||
--gtacatcaatctacctattgtgtcattttcgagaaa-actatgaaaccaaactaacagcatttttggggtatataagtaacagagaggttgttgtg-cagGTCGGTTTATATCGTGTACACAATGCTAGGGGATGTTAGCATCTTCCTTGTTGGCAAAGACGAGTATGATGAACTTGCTT

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|37190396|gb|CF609745.1|CF609745
EST:     GACAATCTTAAAGGAGTAAAAAATGAGGAGCTTCTTGTTGCTTGCCACAA                         ATCAGTGTATATCGTTTACACGGTGCTCGGAGATGTCAGCATCTATGTTGT
genomic: GACAATCTTAAAGGCGTAAAAAATGAGGAGCTTCTTGTTGCTTGCCACAAgtacgggtgt ... cctgtatcagATCAGTGTATATCGTTTACACGGTGCTCGGAGATGTCAGCATCTATGTTGT
EST: gi|352777162|gb|FQ474469.1|FQ474469
EST:     GACAATCTTAAAGGCGTAAAAAATGAGGAGCTTCTTGTTGCTTGCCACAA                         ATCAGTGTATATCGTTTACACGGTGCTCGGAGATGTCAGCATCTATGTTGT
genomic: GACAATCTTAAAGGCGTAAAAAATGAGGAGCTTCTTGTTGCTTGCCACAAgtacgggtgt ... cctgtatcagATCAGTGTATATCGTTTACACGGTGCTCGGAGATGTCAGCATCTATGTTGT
EST: gi|37190163|gb|CF609512.1|CF609512
EST:     GACAATCTTAAAGGAGTAAAAAATGAGGAGCTTCTTGTTGCTTGCCACAA                         ATCAGTGTATATCGTTTACACGGTGCTCGGAGATGTCAGCATCTATGTTGT
genomic: GACAATCTTAAAGGCGTAAAAAATGAGGAGCTTCTTGTTGCTTGCCACAAgtacgggtgt ... cctgtatcagATCAGTGTATATCGTTTACACGGTGCTCGGAGATGTCAGCATCTATGTTGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

acgtactcttagtcactaatttgtacttggattaatccgatgttccctgtatcagATCAGTGTATATCGTTTACACGGTGCTCGGAGATGTCAGCATCTATGTTGTGGGCAAGGATGAGTATGATGAACTTGCTT
                                        tgttccct  CT-rich tract
                taatttgta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
cctagtgttagaaaggccaaaaacaccttgtagaatcagtaccaaacgtactcttagtcactaatttgtacttggattaatccgatgttccctgtatcagATCAGTGTATATCGTTTACACGGTGCTCGGAGATGTCAGCATCTATGTTGTGGGCAAGGATGAGTATGATGAACTTGCTT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG
- - - - - -aaaggcc
- - - - - - - - - aaaaaca
- - - - - - - - - - - - -ccttgta
- - - - - - - - - - - - - - - - - - - - accaaac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tacttgg