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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaatttttgcaaacaaaaaacaaaaggtttcttaaggatagaatatataccgttgggagctatagaacacaggtcaattcgtacatttactttgttgcagGTGCTATACAATTTGCTAGGACAGAAGGATTAATACCAGCACCGGAGCCAACTCATGCCATTGCTGCTACCATCAGGGAAGCTCTCCATTGCAGAGAGAC

Basic information

species Vitis vinifera
transcript Vv14s0083g00460.t01
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv14s0083g00460.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA13G07130.1 (Glycine max), 3'ss of exon 5
gtaatttttgcaaacaaaaaac-aaaaggtttcttaaggatagaatatataccgttgggagctatagaacacaggtcaattcgtacatttactttgttgcagGTGCTATACAATTTGCTAGGACAGAAGGATTAATACCAGCACCGGAGCCAACTCATGCCATTGCTGCTACCATCAGGGAAGCTCTCCATTGCAGAGAGAC
|||||| |      | |   |    ||    | |  | | | | |||||||    |  ||   ||| |  |        |   |   | |  || ||| |||| |||||||| ||||| ||| | ||||| || |||||||| || || |||||||||||||| ||||| ||||| ||||||||| | | ||| |||||| |
gtaattctcattttccattcattggaaacaatatgcaagtttggatatatagaaattagaatcatataggatgaaattgtgt-tgtgtctttttggttacagGGGCTATACAGTTTGCCAGGTCTGAAGGGTTGATACCAGCTCCTGAACCAACTCATGCCATAGCTGCAACCATTAGGGAAGCTATTCGTTGTAGAGAGGC

upper sequence: Vv14s0083g00460.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA19G05630.1 (Glycine max), 3'ss of exon 2
gtaatt-----tttgcaaacaaaaaacaaaaggtttcttaaggatagaatatataccgttgggagctatagaacacaggtcaattcgtacatttactttgttgcagGTGCTATACAATTTGCTAGGACAGAAGGATTAATACCAGCACCGGAGCCAACTCATGCCATTGCTGCTACCATCAGGGAAGCTCTCCATTGCAGAGAGAC
||||||     ||| |   |     | | | |  || |  | | |   ||| |||       ||   ||| |  |         |  |   | |  || ||| |||| |||||||| ||||| ||| | ||||| || ||||||||  | || |||||||||||||| ||||| ||||| || |||||| | |  || ||||| ||
gtaattcacattttcctgtcgttggaaacatgcattatgcaagtttatataaatagaaactagaatcatatatgatcaaaattgtgttgtgtctttttggttacagGGGCTATACAGTTTGCCAGGTCTGAAGGGTTGATACCAGCTTCTGAACCAACTCATGCCATAGCTGCAACCATTAGAGAAGCTATTCGATGTAGAGAAAC

upper sequence: Vv14s0083g00460.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: EFJ24275 (Selaginella moellendorffii), 3'ss of exon 4
gtaatttttgcaaacaaaaaacaaaaggtttcttaaggatagaatatataccgttgggagctatagaacacaggtcaattcgtacatttactttgttgcagGTGCTATACAATTTGCTAGGACAGAAGGATTAATACCAGCACCGGAGCCAACTCATGCCATTGCTGCTACCATCAGGGAAGCTCTCCATTGCAGAGAGAC
                                       ||||| ||    | ||    | |||      | ||  ||          |  | |||  |||| ||| ||||||||||| | |  |||||| |||| |||||||| |||||||| || || || |||||||||||| | |||||    |  ||| |||||| 
--------------------------------------gtagaaaatcgctcttttactggtat----tcctggctaaa------gactggtatgtc-cagGAGCTCTACAATTTGCTCGAAGCGAAGGAATAATTCCAGCACCTGAGCCAACACACGCGATCGCTGCTACCATCCGTGAAGCGGAGCGATGCCGAGAGAG

upper sequence: Vv14s0083g00460.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: EFJ35538 (Selaginella moellendorffii), 3'ss of exon 4
gtaatttttgcaaacaaaaaacaaaaggtttcttaaggatagaatatataccgttgggagctatagaacacaggtcaattcgtacatttactttgttgcagGTGCTATACAATTTGCTAGGACAGAAGGATTAATACCAGCACCGGAGCCAACTCATGCCATTGCTGCTACCATCAGGGAAGCTCTCCATTGCAGAGAGAC
                                       ||||| |    |  ||     ||      | | | | ||          |  | |||  |||| ||| ||||||||||| | |  |||||| |||| |||||||| ||||||||||| || || |||||||| ||| | |||||    |  ||| |||||| 
--------------------------------------gtagaaaaatcgctctttt--actggtattcccggctaaa-------gactggtatgtc-cagGAGCTCTACAATTTGCTCGAAGCGAAGGAATAATTCCAGCACCTGAGCCAACTCACGCGATCGCTGCTACGATCCGTGAAGCGGAGCGATGCCGAGAGAG

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|110360953|gb|EC924398.1|EC924398
EST:     ACTGGGTTTCATGGAAGCAATCTCAATTCCTCAGATTGAATGCTTTCAAG                         GTGCTATACAATTTGCTAGGACAGAAGGATTAATACCAGCACCGGAGCCAA
genomic: ACTGGGTTTCATGGAAGCAATCTCAATTCCTCAGATTGAATGCTTTCAAGgtaatttttg ... tttgttgcagGTGCTATACAATTTGCTAGGACAGAAGGATTAATACCAGCACCGGAGCCAA
EST: gi|110362285|gb|EC925807.1|EC925807
EST:     ACTGGGTTTCATGGAAGCAATCTCAATTCCTCAGATTGAATGCTTTCAAG                         GTGCTATACAATTTGCTAGGACAGAAGGATTAATACCAGCACCGGAGCCAA
genomic: ACTGGGTTTCATGGAAGCAATCTCAATTCCTCAGATTGAATGCTTTCAAGgtaatttttg ... tttgttgcagGTGCTATACAATTTGCTAGGACAGAAGGATTAATACCAGCACCGGAGCCAA
EST: gi|26259789|gb|CA810852.1|CA810852
EST:     ACTGGGTTTCATGGAAGCAATCTCAATTCCTCAGATTGAATGCTTTCAAG                         GTGCTATACAATTTGCTAGGACAGAAGGATTAATACCAGCACCGGAGCCAA
genomic: ACTGGGTTTCATGGAAGCAATCTCAATTCCTCAGATTGAATGCTTTCAAGgtaatttttg ... tttgttgcagGTGCTATACAATTTGCTAGGACAGAAGGATTAATACCAGCACCGGAGCCAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tataccgttgggagctatagaacacaggtcaattcgtacatttactttgttgcagGTGCTATACAATTTGCTAGGACAGAAGGATTAATACCAGCACCGGAGCCAACTCATGCCATTGCTGCTACCATCAGGGAAGCTCTCCATTGCAGAGAGAC
                                        tttacttt  CT-rich tract
                                       atttacttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaatttttgcaaacaaaaaacaaaaggtttcttaaggatagaatatataccgttgggagctatagaacacaggtcaattcgtacatttactttgttgcagGTGCTATACAATTTGCTAGGACAGAAGGATTAATACCAGCACCGGAGCCAACTCATGCCATTGCTGCTACCATCAGGGAAGCTCTCCATTGCAGAGAGAC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGCT