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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TTTTAAGGAGTTCAATGCCAACAACATTCGTGACACCTTCAGAATTCTTCTTCAAATGGGCGCTGTTTTGATGTTCGGAGGGCAAGTTCCCGTAATCAAGgtcagatctctgttgttgtttgttgttgttgttggttttttttttttttttttgggatgatttgggattgtgcgtgtgaagttggttttgaattggggttgatggttgtttag

Basic information

species Vitis vinifera
transcript Vv18s0001g06250.t01
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv18s0001g06250.t01 (Vitis vinifera), 5'ss of exon 1
lower sequence: GLYMA14G35370.1 (Glycine max), 5'ss of exon 1
TTTTAAGGAGTTCAATGCCAACAACATTCGTGACACCTTCAGAATTCTTCTTCAAATGGGCGCTGTTTTGATGTTCGGAGGGCAAGTTCCCGTAATCAAGgtcagatctctgttgttgtttgttgttgttgttggttttttttttttttttttgggatgatttgggattgtgcgtgtgaagttggttttgaattggggttgatggttgtttag
 || ||||||||||||||||||||||| |||||||||||| | ||  | || || ||| |||  ||  |||||||||| || ||| | ||||| |||||||| |      || |      |       |      |||||| |    | || | | ||    |  ||       |   || |  |     | ||    |||||   |  | | 
CTTCAAGGAGTTCAATGCCAACAACATCCGTGACACCTTCCGCATCATCCTCCAGATGAGCGTCGTCATGATGTTCGGCGGCCAAATGCCCGTCATCAAGgtaaa-----tggtaacaaatagaaacat----atttttttatacaatcttctcgaatcgaataagaccac-tatcaaaactcagc---aagttccatttgattcctcgtgaa

upper sequence: Vv18s0001g06250.t01 (Vitis vinifera), 5'ss of exon 1
lower sequence: GLYMA02G37080.2 (Glycine max), 5'ss of exon 1
TTTTAAGGAGTTCAATGCCAACAACATTCGTGACACCTTCAGAATTCTTCTTCAAATGGGCGCTGTTTTGATGTTCGGAGGGCAAGTTCCCGTAATCAAGgtcagatct---ctgttgttgtttgttgttgttgttggttttttttttttttttttgggat---gatttgggattgtgcgtgtgaagttg-gttttgaattggggttgatggttgtttag----------------------------------------------------------
 || ||||||||||||||||||||||| |||||||||||| | ||  | || || ||| |||  ||  |||||||||| || ||| | || || |||||||| |   ||      ||      | || ||    |  |   |   |    |  ||    ||     | |    |||| | |  | | ||  |||||||||||   |  | ||   |  |                                                           
CTTCAAGGAGTTCAATGCCAACAACATCCGTGACACCTTCCGCATCATCCTCCAGATGAGCGTCGTCATGATGTTCGGCGGCCAAATGCCTGTCATCAAGgtaaatgctaacaaattcaaacatattcttcacataagaactggatggagtaattgaatattcaagtgtcaatttgttcatcagtattttcgttttgaattgacataaaaggggatgaaatttggttgtaaggtgtgaaatgagagtttttgttgttgttgtttgtttgtttgtttag
















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|34544767|gb|CF512999.1|CF512999
EST:     TTCAAATGGGCGCTGTTTTGATGTTCGGAGGGCAAGTGCCCGTAATCAAG                         GTCGGAAGAATGGCGGGTCAGTTTGCGAAGCCGAGGTCAGAATCGTTCGAG
genomic: TTCAAATGGGCGCTGTTTTGATGTTCGGAGGGCAAGTTCCCGTAATCAAGgtcagatctc ... ggttgtttagGTCGGAAGAATGGCGGGTCAGTTTGCGAAGCCGAGGTCAGAATCGTTCGAG
EST: gi|110699818|gb|EE077162.1|EE077162
EST:     TTC-AATGGGCGCTGTTTTGATGTTCGGAGGGCAAGTGCCCGTAATCAAG                         GTCGGAAGAATGGCGGGTCAGTTTGCGAAGCCGAGGTCTGAATCGTTCGAG
genomic: TTCAAATGGGCGCTGTTTTGATGTTCGGAGGGCAAGTTCCCGTAATCAAGgtcagatctc ... ggttgtttagGTCGGAAGAATGGCGGGTCAGTTTGCGAAGCCGAGGTCAGAATCGTTCGAG
EST: gi|110699229|gb|EE076046.1|EE076046
EST:     TTCAAATGGGCGCTGTTTTGATGTTCGGAGGGCAAGTGCCCGTAATCAAG                         GTCGGAAGAATGGCGGGTCAGTTTGCGAAGCCGAGGTCAGAATCGTTCGAG
genomic: TTCAAATGGGCGCTGTTTTGATGTTCGGAGGGCAAGTTCCCGTAATCAAGgtcagatctc ... ggttgtttagGTCGGAAGAATGGCGGGTCAGTTTGCGAAGCCGAGGTCAGAATCGTTCGAG
EST: gi|71863085|gb|DT012140.1|DT012140
EST:     TTCAAATGGGCGCTGTTTTGATGTTCGGAGGGCAAGTGCCCGTAATCAAG                         GTCGGAAGAATGGCGGGTCAGTTTGCGAAGCCGAGGTCAGAATCGTTCGAG
genomic: TTCAAATGGGCGCTGTTTTGATGTTCGGAGGGCAAGTTCCCGTAATCAAGgtcagatctc ... ggttgtttagGTCGGAAGAATGGCGGGTCAGTTTGCGAAGCCGAGGTCAGAATCGTTCGAG
EST: gi|110685780|gb|EE062798.1|EE062798
EST:     TTCAAATGGGCGCTGTTTTGATGTTCGGAGGGCAAGTTCCCGTAATCAAG                         GTCGGAAGAATGGCGGGTCAGTTTGCGAAGCCGAGGTCAGAATCGTTCGAG
genomic: TTCAAATGGGCGCTGTTTTGATGTTCGGAGGGCAAGTTCCCGTAATCAAGgtcagatctc ... ggttgtttagGTCGGAAGAATGGCGGGTCAGTTTGCGAAGCCGAGGTCAGAATCGTTCGAG
EST: gi|33406573|gb|CF212200.1|CF212200
EST:     TTCAAATGGGCGCTGTTTTGATGTTCGGAGGGCAAGTGCCCGTAATCAAG                         GTCGGAAGAATGGCGGGTCAGTTTGCGAAGCCGAGGTCAGAATCGTTCGAG
genomic: TTCAAATGGGCGCTGTTTTGATGTTCGGAGGGCAAGTTCCCGTAATCAAGgtcagatctc ... ggttgtttagGTCGGAAGAATGGCGGGTCAGTTTGCGAAGCCGAGGTCAGAATCGTTCGAG
EST: gi|110710673|gb|EE087013.1|EE087013
EST:     TTCAAATGGGCGCTGTTTTGATGTTCGGAGGGCAAGTGCCCGTAATCAAA                         GTCGGAAGAATGGCGGGTCAGTTTGCGAAGCCGNAG-TCAAAATCGTTCGA
genomic: TTCAAATGGGCGCTGTTTTGATGTTCGGAGGGCAAGTTCCCGTAATCAAGgtcagatctc ... ggttgtttagGTCGGAAGAATGGCGGGTCAGTTTGCGAAGCCG-AGGTCAGAATCGTTCGA
EST: gi|110724708|gb|EE100770.1|EE100770
EST:     TTCAAATGGGCGCTGTTTTGATGTTCGGAGGGCAAGTGCCCGTAATCAAG                         GTCGGAAAAATGGCGGGTCAGTTTGCGAAGCCGAGGTCAGAATCGTTCGAG
genomic: TTCAAATGGGCGCTGTTTTGATGTTCGGAGGGCAAGTTCCCGTAATCAAGgtcagatctc ... ggttgtttagGTCGGAAGAATGGCGGGTCAGTTTGCGAAGCCGAGGTCAGAATCGTTCGAG
EST: gi|161714856|gb|FC063007.1|FC063007
EST:     TCAAATGGGCGCTGTTTTGATGTTCGGAGGGGCA-GTTCCCGTA-TCAAG                         GTCGGAAGAATGGCGGGTCAGTTTGCGAA
genomic: TCAAATGGGCGCTGTTTTGATGTTCGGAGGG-CAAGTTCCCGTAATCAAGgtcagatctc ... ggttgtttagGTCGGAAGAATGGCGGGTCAGTTTGCGAA
EST: gi|34549685|gb|CF517917.1|CF517917
EST:     TTCAAATGGGCGCTGTTTTGATGTTCGGAGGGCAAGTGCCCGTAATCAAG                         GTCGGAAGAATGGCGGGTCAGTTTGCGAAGCCGAGGTCAGAATCGTTCGAG
genomic: TTCAAATGGGCGCTGTTTTGATGTTCGGAGGGCAAGTTCCCGTAATCAAGgtcagatctc ... ggttgtttagGTCGGAAGAATGGCGGGTCAGTTTGCGAAGCCGAGGTCAGAATCGTTCGAG
EST: gi|161713369|gb|FC062780.1|FC062780
EST:     TTCAAATGGGCGCTGTTTTGATGTTCGGAGGGCAAGTGCCCGTAATCAAG                         GTCGGAAGAATGGCGGGTCAGTTTGCGAAGCCGAGGTCAGAATCGTTCGAG
genomic: TTCAAATGGGCGCTGTTTTGATGTTCGGAGGGCAAGTTCCCGTAATCAAGgtcagatctc ... ggttgtttagGTCGGAAGAATGGCGGGTCAGTTTGCGAAGCCGAGGTCAGAATCGTTCGAG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TTTTAAGGAGTTCAATGCCAACAACATTCGTGACACCTTCAGAATTCTTCTTCAAATGGGCGCTGTTTTGATGTTCGGAGGGCAAGTTCCCGTAATCAAGgtcagatctctgttgttgtttgttgttgttgttggttttttttttttttttttgggatgatttgggattgtgcgtgtgaagttggttttgaattggggttgatggttgtttag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGTT