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 5'  3'   		2  
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 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ACCAAGCTGCGGAGAGGTGGTTGCATCACATGCAACAAGCACTGGATAGTGTCACAGAAATTGATGCAGATTCAAAAACCAAAATGATGAATTTTTTCAGgtaaattaaactcccccccccccctaattagcctctcattggttgctttctcaattgatacctaaacagcatctttcatttcaaaattagaacacattgcatatctggttttgtttttccag

Basic information

species Vitis vinifera
transcript Vv04s0008g04210.t01
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv04s0008g04210.t01 (Vitis vinifera), 5'ss of exon 3
lower sequence: LOC_Os06g39140.1 (Oryza sativa), 5'ss of exon 3
ACCAAGCTGCGGAGAGGTGGTTGCATCACATGCAACAAGCACTGGATAGTGTCACAGAAATTGATGCAGATTCAAAAACCAAAATGATGAATTTTTTCAGgtaaattaaactcccccccccccctaattagcctctcattggttgctttctcaattgatacctaaacagcatctttcatttcaaaattagaacacattgcatatctggttttgtttttccag
|||| ||||| ||| | ||| |||| || ||||| |||||  |||||| |         || || || |   ||||||||||||||||| ||||||||||||    |   || |  |      ||    |||      ||      ||| ||    |||    | || || ||| |   | ||                                       
ACCAGGCTGCAGAGCGATGGCTGCACCATATGCAGCAAGCTGTGGATACTACTGACAGCATAGACGCTGCCACAAAAACCAAAATGATGTATTTTTTCAGgt---ctgtgctacagctgaattcttgcaagc------ttacacattttgtcctaggatcttaatactgc-tctcttcctccag--------------------------------------

upper sequence: Vv04s0008g04210.t01 (Vitis vinifera), 5'ss of exon 3
lower sequence: GLYMA14G20380.1 (Glycine max), 5'ss of exon 3
ACCAAGCTGCGGAGAGGTGGTTGCATCACATGCAACAAGCACTGGATAGTGTCACAGAAATTGATGCAGATTCAAAAACCAAAATGATGAATTTTTTCAGgtaaattaaactcccccccccccctaattagcctctcattggttgct--ttctca-attgatacctaaacagcatctttcatttcaaaattagaacacattgcatatctggttttgtttttccag
| |||||||| ||||||||||| |||||||||||||| ||| | || |||   ||||| || ||||  || ||||| |||||||||||||| ||||||||||  |||   || ||||     || | ||  |     || ||||| |  |  | | |||||  | |  || | |   ||  |||  |                                      
ATCAAGCTGCAGAGAGGTGGTTACATCACATGCAACATGCATTAGACAGTACTACAGATATAGATGATGACTCAAAGACCAAAATGATGAACTTTTTCAGgtttatttt-ctaccccaaggtcccacttcacggaaaat-ggttgttcatgataacattgagtcattgactgtactcttgtttttcag-------------------------------------
















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|26258545|gb|CA809608.1|CA809608
EST:     GTCACAGAAATTGATGCAGATTCAAAAACCAAAATGATGAATTTTTTCAG                         GCACACTGCTTTCTTCCTTGTGGCTGGAGATGAGTTGAAGAATCGTAACCA
genomic: GTCACAGAAATTGATGCAGATTCAAAAACCAAAATGATGAATTTTTTCAGgtaaattaaa ... gtttttccagGCACACTGCTTTCTTCCTTGTGGCTGGAGATGAGTTGAAGAATCGTAACCA
EST: gi|110380155|gb|EC945400.1|EC945400
EST:     GTCACAGAAATTGATGCAGATTCAAAAACCAAAATGATGAATTTTTTCAG                         GCACACTGCTTTTTTCCTTGTGGCTGGAGATGAGTTGAAGAATCGTAGCCA
genomic: GTCACAGAAATTGATGCAGATTCAAAAACCAAAATGATGAATTTTTTCAGgtaaattaaa ... gtttttccagGCACACTGCTTTCTTCCTTGTGGCTGGAGATGAGTTGAAGAATCGTAACCA
EST: gi|110417416|gb|EC983468.1|EC983468
EST:     GTCACAGAAATTGATGCAGATTCAAAAACCAAAATGATGAATTTTTTCAG                         GCACACTGCTTTCTTCCTTGTGGCTGGAGATGAGTTGAAGAATCGTAACCA
genomic: GTCACAGAAATTGATGCAGATTCAAAAACCAAAATGATGAATTTTTTCAGgtaaattaaa ... gtttttccagGCACACTGCTTTCTTCCTTGTGGCTGGAGATGAGTTGAAGAATCGTAACCA
EST: gi|110370974|gb|EC934642.1|EC934642
EST:     GTCACAGAAATTGATGCAGATTCAAAAACCAAAATGATGAATTTTTTCAG                         GCACACTGCTTTCTTCCTTGTGGCTGGAGATGAGTTGAAGAATCGTAGCCA
genomic: GTCACAGAAATTGATGCAGATTCAAAAACCAAAATGATGAATTTTTTCAGgtaaattaaa ... gtttttccagGCACACTGCTTTCTTCCTTGTGGCTGGAGATGAGTTGAAGAATCGTAACCA
EST: gi|46919572|gb|CN548901.1|CN548901
EST:     GTCACAGAAATTGATGCAGATTCAAAAACCAAAATGATGAATTTTTTCGG                         GCACACTGCTTTCTTCCTTGTGGCTGGAGATGAGTTGAAGAATCGTAACCA
genomic: GTCACAGAAATTGATGCAGATTCAAAAACCAAAATGATGAATTTTTTCAGgtaaattaaa ... gtttttccagGCACACTGCTTTCTTCCTTGTGGCTGGAGATGAGTTGAAGAATCGTAACCA
EST: gi|32244919|gb|CD710738.1|CD710738
EST:     GTCACAGAAATTGATGCAGATTCAAAAACCAAAATGATGAATTTTTTCAG                         GCACACTGCTTTCTTCCTTGTGGCTGGAGATGAGTTGAAGAATCGTAACCA
genomic: GTCACAGAAATTGATGCAGATTCAAAAACCAAAATGATGAATTTTTTCAGgtaaattaaa ... gtttttccagGCACACTGCTTTCTTCCTTGTGGCTGGAGATGAGTTGAAGAATCGTAACCA
EST: gi|18458302|gb|BM436580.1|BM436580
EST:     GTCACAGAAATTGATGCAGATTCAAAAACCAAAATGATGAATTTTTTCAG                         GCACACTGCTTTCTTCCTTGTGGCTGGAGATGAGTTGAAGAATCGTAACCA
genomic: GTCACAGAAATTGATGCAGATTCAAAAACCAAAATGATGAATTTTTTCAGgtaaattaaa ... gtttttccagGCACACTGCTTTCTTCCTTGTGGCTGGAGATGAGTTGAAGAATCGTAACCA
EST: gi|22007494|gb|BQ792528.1|BQ792528
EST:     GTCACAGAAATTGATGCGGATTCAAAAACCAAAATGATGAATTTTTTCAG                         GCACACTGCTTTCTTCCTTGTGGCTGGAGATGAGTTGAAGAATCGTAACCA
genomic: GTCACAGAAATTGATGCAGATTCAAAAACCAAAATGATGAATTTTTTCAGgtaaattaaa ... gtttttccagGCACACTGCTTTCTTCCTTGTGGCTGGAGATGAGTTGAAGAATCGTAACCA
EST: gi|32457132|gb|CD798306.1|CD798306
EST:     GTCACAGAAATTGATGCAGATTCAAAAACCAAAATGATGAATTTTTTCAG                         GCACACTGCTTTCTTCCTTGTGGCTGGAGATGAGTTGAAGAATCGTAACCA
genomic: GTCACAGAAATTGATGCAGATTCAAAAACCAAAATGATGAATTTTTTCAGgtaaattaaa ... gtttttccagGCACACTGCTTTCTTCCTTGTGGCTGGAGATGAGTTGAAGAATCGTAACCA
EST: gi|110426742|gb|EC993161.1|EC993161
EST:     GTCACAGAAATTGATGCAGATTCAAAAACCAAAATGATGAATTTTTTCAG                         GCACACTGCTTTCTTCCTTGTGGCTGGAGATGAGTTGAAGAATCGTAACCA
genomic: GTCACAGAAATTGATGCAGATTCAAAAACCAAAATGATGAATTTTTTCAGgtaaattaaa ... gtttttccagGCACACTGCTTTCTTCCTTGTGGCTGGAGATGAGTTGAAGAATCGTAACCA
EST: gi|30304131|gb|CB980925.1|CB980925
EST:     GTCGCAGAAATTGATGCAGATTCAAAAACCAAAATGATGAATTTTTTCAG                         GCACACTGCTTTCTTCCTGGTGGCTGGAGATGAGTTGAAGAATCGTAACCA
genomic: GTCACAGAAATTGATGCAGATTCAAAAACCAAAATGATGAATTTTTTCAGgtaaattaaa ... gtttttccagGCACACTGCTTTCTTCCTTGTGGCTGGAGATGAGTTGAAGAATCGTAACCA
EST: gi|33410442|gb|CF216069.1|CF216069
EST:     GTCACAGAAATTGATGCAGATTCAAAAACCAAAATGATGAATTTTTTCAG                         GCACACTGCTTTCTTCCTTGTGGCTGGAGATGAGTTGAAGAATCGTAGCCA
genomic: GTCACAGAAATTGATGCAGATTCAAAAACCAAAATGATGAATTTTTTCAGgtaaattaaa ... gtttttccagGCACACTGCTTTCTTCCTTGTGGCTGGAGATGAGTTGAAGAATCGTAACCA
EST: gi|32457324|gb|CD798498.1|CD798498
EST:     GTCACAGAAATTGATGCAGATTCAAAAACCAAAATGATGAATTTTTTCAG                         GCACACTGCTTTCTTCCTTGTGGCTGGAGATGAGTTGAAGAATCGTAACCA
genomic: GTCACAGAAATTGATGCAGATTCAAAAACCAAAATGATGAATTTTTTCAGgtaaattaaa ... gtttttccagGCACACTGCTTTCTTCCTTGTGGCTGGAGATGAGTTGAAGAATCGTAACCA
EST: gi|26261673|gb|CA812736.1|CA812736
EST:     GTCACAGAAATTGATGCAGATTCAAAAACCAAAATGATGAATTTTTTCAG                         GCACACTGCTT-CTTCCTTGTGGCTGGAGATGAGTTGAAGAATCGTAGCCA
genomic: GTCACAGAAATTGATGCAGATTCAAAAACCAAAATGATGAATTTTTTCAGgtaaattaaa ... gtttttccagGCACACTGCTTTCTTCCTTGTGGCTGGAGATGAGTTGAAGAATCGTAACCA
EST: gi|110378909|gb|EC944067.1|EC944067
EST:     GTCACAGAAATTGATGCAGATTCAAAAACCAAAATGATGAATTTTTTCAG                         GCACACTGCTTTCTTCCTTGTGGCTGGAGATGAGTTGAAGAATCGTAACCA
genomic: GTCACAGAAATTGATGCAGATTCAAAAACCAAAATGATGAATTTTTTCAGgtaaattaaa ... gtttttccagGCACACTGCTTTCTTCCTTGTGGCTGGAGATGAGTTGAAGAATCGTAACCA
EST: gi|27583881|gb|CB006576.1|CB006576
EST:     GTCACAGAAATTGATGCAGATTCAAAAACCAAAATGATGAATTTTTTCAG                         GCACACTGCTTTCTTCCTTGTGGCTGGAGATGAGTTGAAGAATCGTAGCCA
genomic: GTCACAGAAATTGATGCAGATTCAAAAACCAAAATGATGAATTTTTTCAGgtaaattaaa ... gtttttccagGCACACTGCTTTCTTCCTTGTGGCTGGAGATGAGTTGAAGAATCGTAACCA
EST: gi|33407799|gb|CF213426.1|CF213426
EST:     GTCACAGAAATTGATGCAGATTCAAAAACCAAAATGATGAATTTTTTCAG                         GCACACTGCTTTCTTCCTTGTGGCTGGAGATGAGTTGAAGAATCGTAGCCA
genomic: GTCACAGAAATTGATGCAGATTCAAAAACCAAAATGATGAATTTTTTCAGgtaaattaaa ... gtttttccagGCACACTGCTTTCTTCCTTGTGGCTGGAGATGAGTTGAAGAATCGTAACCA
EST: gi|46918728|gb|CN548057.1|CN548057
EST:     GTCACAGAAATTGATGCAGATTCAAAAACCAAAATGATGAATTTTTTCAG                         GCACACTGCTTTCTTCCTTGTGGCTGGAGATGAGTTGAAGAATCGTAACCA
genomic: GTCACAGAAATTGATGCAGATTCAAAAACCAAAATGATGAATTTTTTCAGgtaaattaaa ... gtttttccagGCACACTGCTTTCTTCCTTGTGGCTGGAGATGAGTTGAAGAATCGTAACCA
EST: gi|110411856|gb|EC977582.1|EC977582
EST:     GTCACAGAAATTGATGCAGATTCAAAAACCAAAATGATGAATTTTTTCAG                         GCACACTGCTTTTTTCCTTGTGGCTGGAGATGAGTTGAAGAATCGTAACCA
genomic: GTCACAGAAATTGATGCAGATTCAAAAACCAAAATGATGAATTTTTTCAGgtaaattaaa ... gtttttccagGCACACTGCTTTCTTCCTTGTGGCTGGAGATGAGTTGAAGAATCGTAACCA
EST: gi|46919557|gb|CN548886.1|CN548886
EST:     GTCACAGAAATTGATGCAGATTCAAAAACCAAAATGATGAATTTTTTCAG                         GCACACTGCTTTCTTCCTTGTGGCTGGAGATGAGTTGAAGAATCGTAACCA
genomic: GTCACAGAAATTGATGCAGATTCAAAAACCAAAATGATGAATTTTTTCAGgtaaattaaa ... gtttttccagGCACACTGCTTTCTTCCTTGTGGCTGGAGATGAGTTGAAGAATCGTAACCA
EST: gi|26257789|gb|CA808852.1|CA808852
EST:     GTCACAGAAATTGATGCAGATTCAAAAACCAAAATGATGAATTTTTTCAG                         GCACACTGCTTTCTTCCTTGTGGCTGGAGATGAGTTGAAGAATCGTAACCA
genomic: GTCACAGAAATTGATGCAGATTCAAAAACCAAAATGATGAATTTTTTCAGgtaaattaaa ... gtttttccagGCACACTGCTTTCTTCCTTGTGGCTGGAGATGAGTTGAAGAATCGTAACCA
EST: gi|46919746|gb|CN549075.1|CN549075
EST:     GTCACAGAAATTGATGCAGATTCAAAAACCAAAATGATGAATTTTTTCAG                         GCACACTGCTTTCTTCCTTGTGGCTGGAGATGAGTTGAAGAATCGTAGCCA
genomic: GTCACAGAAATTGATGCAGATTCAAAAACCAAAATGATGAATTTTTTCAGgtaaattaaa ... gtttttccagGCACACTGCTTTCTTCCTTGTGGCTGGAGATGAGTTGAAGAATCGTAACCA
EST: gi|30305341|gb|CB982135.1|CB982135
EST:     GTCACAGAAATTGATGCAGATTCAAAAACCAAAATGATGAATTTTTTCAG                         GCACACTGCTTTCTTCCTTGTGGCTGGAGATGAGTTGAAGAATCGTAACCA
genomic: GTCACAGAAATTGATGCAGATTCAAAAACCAAAATGATGAATTTTTTCAGgtaaattaaa ... gtttttccagGCACACTGCTTTCTTCCTTGTGGCTGGAGATGAGTTGAAGAATCGTAACCA
EST: gi|110717237|gb|EE092920.1|EE092920
EST:     GTCACAGAAATTGATGCAGATTCAAAAACCAAAATGATGAATTTTTTCAG                         GCACACTGCTTTCTTCCTTGTGGCTGGAGATGAGTTGAAGAATCGTAACCA
genomic: GTCACAGAAATTGATGCAGATTCAAAAACCAAAATGATGAATTTTTTCAGgtaaattaaa ... gtttttccagGCACACTGCTTTCTTCCTTGTGGCTGGAGATGAGTTGAAGAATCGTAACCA
EST: gi|110407274|gb|EC972871.1|EC972871
EST:     GTCACAGAAATTGATGCAGATTCAAAAACCAAAATGATGAATTTTTTCAG                         GCACACTGCTTTCTTCCTTGTGGCTGGAGATGAGTTGAAGAATCGTAACCA
genomic: GTCACAGAAATTGATGCAGATTCAAAAACCAAAATGATGAATTTTTTCAGgtaaattaaa ... gtttttccagGCACACTGCTTTCTTCCTTGTGGCTGGAGATGAGTTGAAGAATCGTAACCA
EST: gi|110427333|gb|EC993768.1|EC993768
EST:     GTCACAGAAATTGATGCAGATTCAAAAACCAAAATGATGAATTTTTTCAG                         GCACACTGCTTTCTTCCTTGTGGCTGGAGATGAGTTGAAGAATCGTAACCA
genomic: GTCACAGAAATTGATGCAGATTCAAAAACCAAAATGATGAATTTTTTCAGgtaaattaaa ... gtttttccagGCACACTGCTTTCTTCCTTGTGGCTGGAGATGAGTTGAAGAATCGTAACCA
EST: gi|110385358|gb|EC949875.1|EC949875
EST:     GTCACAGAAATTGATGCAGATTCAAAAACCAAAATGATGAATTTTTTCAG                         GCACACTGCTTTCTTCCTTGTGGCTGGAGATGAGTTGAAGAATCGTAACCA
genomic: GTCACAGAAATTGATGCAGATTCAAAAACCAAAATGATGAATTTTTTCAGgtaaattaaa ... gtttttccagGCACACTGCTTTCTTCCTTGTGGCTGGAGATGAGTTGAAGAATCGTAACCA
EST: gi|30305413|gb|CB982207.1|CB982207
EST:     GTCACAGAAATTGATGCAGATTCAAAAACCAAAATGATGAATTTTTTCAG                         GCACACTGCTTTCTTCCTTGTGGCTGGAGATGAGTTGAAGAATCGTAACCA
genomic: GTCACAGAAATTGATGCAGATTCAAAAACCAAAATGATGAATTTTTTCAGgtaaattaaa ... gtttttccagGCACACTGCTTTCTTCCTTGTGGCTGGAGATGAGTTGAAGAATCGTAACCA
EST: gi|30304203|gb|CB980997.1|CB980997
EST:     GTCGCAGAAATTGATGCAGATTCAAAAACCAAAATGATGAATTTTTTCAG                         GCACACTGCTTTCTTCCTGGTGGCTGGAGATGAGTTGAAGAATCGTAACCA
genomic: GTCACAGAAATTGATGCAGATTCAAAAACCAAAATGATGAATTTTTTCAGgtaaattaaa ... gtttttccagGCACACTGCTTTCTTCCTTGTGGCTGGAGATGAGTTGAAGAATCGTAACCA
EST: gi|351033864|gb|FQ447902.1|FQ447902
EST:     GTCACAGAAATTGATGCAGATTCAAAAACCAAAATGATGAATTTTTTCAG                         GCACACTGCTTTCTTCCTTGTGGCTGGAGATGAGTTGAAGAATCGTAGCCA
genomic: GTCACAGAAATTGATGCAGATTCAAAAACCAAAATGATGAATTTTTTCAGgtaaattaaa ... gtttttccagGCACACTGCTTTCTTCCTTGTGGCTGGAGATGAGTTGAAGAATCGTAACCA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ACCAAGCTGCGGAGAGGTGGTTGCATCACATGCAACAAGCACTGGATAGTGTCACAGAAATTGATGCAGATTCAAAAACCAAAATGATGAATTTTTTCAGgtaaattaaactcccccccccccctaattagcctctcattggttgctttctcaattgatacctaaacagcatctttcatttcaaaattagaacacattgcatatctggttttgtttttccag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGAT