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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GAAGAGGGCTCTTGAGATGGCGCAGGTTGATCCAGATGAAGTGGATCTGGTCTTGATGTGTACATCTACTCCAGAGGATCTTTTTGGTAGTGCTCCTCAGgtataagactaaatagctttggtaattgtcaccactcaagtgaaaagatcaatgtaacatcaatgtacttgcagttgagctgcatggatgtcttcaatac...

Basic information

species Vitis vinifera
transcript Vv02s0154g00140.t01
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv02s0154g00140.t01 (Vitis vinifera), 5'ss of exon 3
lower sequence: GRMZM2G022563_T01 (Zea mays), 5'ss of exon 3
GAAGAGGGCTCTTGAGATGGCGCAGGTTGATCCAGATGAAGTGGATCTGGTCTTGATGTGTACATCTACTCCAGAGGATCTTTTTGGTAGTGCTCCTCAGgtataagactaaatagctttggtaattgtcaccactcaagtgaaaagatcaatgtaacatcaatgtacttgcagttgagctgcatggatgtcttcaatac---
  | ||||| |||||||||||    ||  |  | || || || || || ||  |  | ||||||||||||||||| ||||| |||||  ||||| ||||||||| | |  | |||  |||     || | ||   |    |  | |  | |   |   |    |  | ||    || |  |   ||     | |||       
TCAAAGGGCACTTGAGATGGCCGGAGTAAAAGCTGAAGATGTCGACCTCGTTCTTCTTTGTACATCTACTCCAGATGATCTGTTTGGAGGTGCTGCTCAGgtatcataacatata--tttaagcgttatgacatttgtcattgatatgttagcctttgaaagttagaattttgtttcaa-tatgtgagaaccctcatggtttt

upper sequence: Vv02s0154g00140.t01 (Vitis vinifera), 5'ss of exon 3
lower sequence: GLYMA18G44350.1 (Glycine max), 5'ss of exon 3
GAAGAGGGCTCTTGAGATGGCGCAGGTTGATCCAGATGAAGTGGATCTGGTCTTGATGTGTACATCTACTCCAGAGGATCTTTTTGGTAGTGCTCCTCAGgtataagactaaatagc--tttggtaattgtcaccactca-agtgaaaagatcaatgtaacatcaatgtacttgcagttgagctgcatggatgtcttcaatac
 | ||  ||||||||||||||  |||| || || |||||  | || ||  | |||||||| |||||||| |||||||||||||||||||||||||| |||||||  |   |    |    ||| | |   | |    | | | |     | |   | |||| |   | ||       ||    |  |   ||      ||   
-AGGAAAGCTCTTGAGATGGCAAAGGTAGACCCTGATGATCTTGACCTAATATTGATGTGCACATCTACGCCAGAGGATCTTTTTGGTAGTGCTCCACAGGtatgggctcaggatgtatcttgttgagaataattctttacattctgctgttgtctttaacctttgtctagcaatcttttttttaaaaaaataaaaataaa--

upper sequence: Vv02s0154g00140.t01 (Vitis vinifera), 5'ss of exon 3
lower sequence: GLYMA09G41380.1 (Glycine max), 5'ss of exon 3
GAAGAGGGCTCTTGAGATGGCGCAGGTTGATCCAGATGAAGTGGATCTGGTCTTGATGTGTACATCTACTCCAGAGGATCTTTTTGGTAGTGCTCCTCAGgtataagactaaatagctt--tggtaattgtcaccactcaagtgaaaagatcaatgtaacatcaatgtacttgcagttgagctgcatggatgtcttcaatac-
 | ||  ||||||||||||||  |||| || || |||||  | || ||  | |||||||| |||||||| |||||||||||||||||||||||||| |||||||  |   |    |  |  || | |   | |    | |  |       |     | | | |  ||  || | | |     |   |  |  |  | |  || 
TAGGAAAGCTCTTGAGATGGCAAAGGTAGACCCTGATGATCTTGACCTAATATTGATGTGCACATCTACGCCAGAGGATCTTTTTGGTAGTGCTCCACAGgtatgggttcaggatgtatcatgttgagattaattctttacattctgctgttgtcttta-acctttgc-ctagtaatcctttttttttta-attattagcaca

upper sequence: Vv02s0154g00140.t01 (Vitis vinifera), 5'ss of exon 3
lower sequence: PP1S87_63V6.1 (Physcomitrella patens), 5'ss of exon 5
GAAGAGGGCTCTTGAGATGGCGCAGGTTGATCCAGATGAAGTGGATCTGGTCTTGATGTGTACATCTACTCCAGAGGATCTTTTTGGTAGTGCTCCTCAGgtataag--actaaatagctttggtaattgtcaccactcaagtgaaaagatcaa--tgtaacatcaatgtacttgcag-ttgagctgcatggatgtcttcaatac
 | || ||| ||||| |||||  | ||  ||||||| || || ||| || | ||  | || |||||||||||||| ||||| ||||| |||||||| ||||||| |   ||| ||     |      |||    ||   |  |  |  |||     |||||||| ||       |||  ||  ||  |||  | ||| |      
AAGGAAGGCCCTTGAAATGGCTAATGTGAATCCAGAGGATGTTGATTTGTTATTACTCTGCACATCTACTCCAGATGATCTATTTGGCAGTGCTCCGCAGgtatgacgtactgaaattgatgcacgtttgcgtgcaaagagatttagtgattgtcttgtaacatgaaacagaaagcatcttctgcaccattcaggtccta-----

upper sequence: Vv02s0154g00140.t01 (Vitis vinifera), 5'ss of exon 3
lower sequence: PP1S11_305V6.1 (Physcomitrella patens), 5'ss of exon 5
GAAGAGGGCTCTTGAGATGGCGCAGGTTGATCCAGATGAAGTGGATCTGGTCTTGATGTGTACATCTACTCCAGAGGATCTTTTTGGTAGTGCTCCTCAGgtata--agactaaatagctttggtaattgtcaccactcaagtgaaaagatcaatgtaacatcaatgtacttgcagttgagctgcatggatgtcttcaatac-
 | || ||| || || |||||  | ||  | ||||| || || ||| || | ||| ||||||||||||||||||| ||||| |||||||||||||| |||||||     | | ||    ||       ||| | |||  ||  ||     |   | |   || | | |     |    ||||  | |        | |     
AAGGAAGGCCCTCGAAATGGCTAACGTGAAACCAGAGGATGTTGATTTGTTGTTGCTGTGTACATCTACTCCAGACGATCTATTTGGTAGTGCTCCACAGgtatgccgtattgaagtaattgcacgtgtgtgatcacataacagagtgtgtattttttctataactatg---acgagggagcctcttttgcactattaggttc

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|71864497|gb|DT013552.1|DT013552
EST:     TCTTGATGTGTACATCTACTCCAGAGGATCTTTTTGGTAGTGCTCCTCAG                         ATCCAAAAAGCACTTGGCTGC
genomic: TCTTGATGTGTACATCTACTCCAGAGGATCTTTTTGGTAGTGCTCCTCAGgtataagact ... catatatcagATCCAAAAAGCACTTGGCTGC
EST: gi|110394481|gb|EC959504.1|EC959504
EST:     TCTTGATGTGTACATCTACTCCAGAGGATCTTTTCGGTAGTGCTCCTCAG                         ATCCAAAAAGCACTTGGCTGCNNNNNNNNTCCTTTGGCTTACGATATTACA
genomic: TCTTGATGTGTACATCTACTCCAGAGGATCTTTTTGGTAGTGCTCCTCAGgtataagact ... catatatcagATCCAAAAAGCACTTGGCTGCAAAAAAAATCCTTTGGCTTATGATATTACA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GAAGAGGGCTCTTGAGATGGCGCAGGTTGATCCAGATGAAGTGGATCTGGTCTTGATGTGTACATCTACTCCAGAGGATCTTTTTGGTAGTGCTCCTCAGgtataagactaaatagctttggtaattgtcaccactcaagtgaaaagatcaatgtaacatcaatgtacttgcagttgagctgcatggatgtcttcaatac

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTCCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -agactaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gaaaaga
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aacatcaa