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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacatttgagattttattggctgctccagtttggatatttgtgtaaaaagaatctcaaatgctattcaatccaatcttttgttcattactttgtagGTACCTGTGTACATAGCTGAAATATCACCTCAGAACTTGAGAGGAGGCTTGGGTTCAGTGAACCAG

Basic information

species Vitis vinifera
transcript Vv18s0001g12560.t01
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv18s0001g12560.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA14G08070.1 (Glycine max), 3'ss of exon 5
gtacatttgagattttattggctgctccagtttggatatttgtgtaaaaagaatctcaaatgctattcaatccaatcttttgttcattactttgtagGTACCTGTGTACATAGCTGAAATATCACCTCAGAACTTGAGAGGAGGCTTGGGTTCAGTGAACCAG
|||  ||| | || || |||  |   | ||| |||   || ||         || |   |  |  ||  ||  | | |||        | ||   |||| ||||||||||||||||| ||||||||||  |||||||| || || |||| |||||| ||||||
gtaattttaaaatgtttttgcttttgctagtgtgggatttagtt--------atgtgtgacacagtt--attgagtgtttaaacttcaaattcacagGTGCCTGTGTACATAGCTGAGATATCACCTCCAAACTTGAGGGGGGGTTTGGTTTCAGTTAACCAG

upper sequence: Vv18s0001g12560.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA17G36950.1 (Glycine max), 3'ss of exon 5
-gtacatttgagattttattggctgctccagtttggatatttgtgtaaaaagaatctcaaatgctattcaatccaatcttttgttcattactttgtagGTACCTGTGTACATAGCTGAAATATCACCTCAGAACTTGAGAGGAGGCTTGGGTTCAGTGAACCAG
 |||  ||| | || || |||  |   | | | |||   ||  |  |   |   | |   |  | |||  ||  | | |||        | ||   |||| ||||||||||||||||| ||||||||||  |||||| | || || |||| |||||| ||||| 
ggtaattttaaaatgtttttgcttttgctaatgtgggc-ttaattcagtta---tgtgtgacacaatt--attgagtgtttaaacttcaaattcacaGGTGCCTGTGTACATAGCTGAGATATCACCTCCAAACTTGCGGGGGGGTTTGGTTTCAGTTAACCA-
















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|110687404|gb|EE064795.1|EE064795
EST:     ACATGGGAAGGTTGTTGGAAGGATTTGGTGTGGGAATAATCTCTTACACG                         GTACCTGTGTATATAGCTGAAATATCACCTCAGAACTTGAGAGGAGGCTTG
genomic: ACATGGGAAGGTTGTTGGAAGGATTTGGTGTGGGAATAATCTCTTACACGgtacatttga ... tactttgtagGTACCTGTGTACATAGCTGAAATATCACCTCAGAACTTGAGAGGAGGCTTG
EST: gi|110701968|gb|EE080148.1|EE080148
EST:     ACATGGGAAGGTTGTTGGAAGGATTTGGTGTGGGAATAATCTCTTACACG                         GTACCTGTGTATATAGCTGAAATATCACCTCAGAACTTGAGAGGAGGCTTG
genomic: ACATGGGAAGGTTGTTGGAAGGATTTGGTGTGGGAATAATCTCTTACACGgtacatttga ... tactttgtagGTACCTGTGTACATAGCTGAAATATCACCTCAGAACTTGAGAGGAGGCTTG
EST: gi|110699858|gb|EE077237.1|EE077237
EST:     ACATGGGAAGGTTGTTGGAAGGATTTGGTGTGGGAATAATCTCTTACACG                         GTACCTGTGTACATAGCTGAAATATCACCTCAGAACTTGAGAGGAGGCTTG
genomic: ACATGGGAAGGTTGTTGGAAGGATTTGGTGTGGGAATAATCTCTTACACGgtacatttga ... tactttgtagGTACCTGTGTACATAGCTGAAATATCACCTCAGAACTTGAGAGGAGGCTTG
EST: gi|110732428|gb|EE107716.1|EE107716
EST:     ACATGGGAAGGTTGTTGGAAGGATTTGGTGTGGGAATAATCTCTTACACG                         GTACCTGTGTACATAGCTGAAATATCACCTCAAAACTTGAGAGGAGGCTTG
genomic: ACATGGGAAGGTTGTTGGAAGGATTTGGTGTGGGAATAATCTCTTACACGgtacatttga ... tactttgtagGTACCTGTGTACATAGCTGAAATATCACCTCAGAACTTGAGAGGAGGCTTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgtaaaaagaatctcaaatgctattcaatccaatcttttgttcattactttgtagGTACCTGTGTACATAGCTGAAATATCACCTCAGAACTTGAGAGGAGGCTTGGGTTCAGTGAACCAG
                                            ttacttt  CT-rich tract
                     tattcaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtacatttgagattttattggctgctccagtttggatatttgtgtaaaaagaatctcaaatgctattcaatccaatcttttgttcattactttgtagGTACCTGTGTACATAGCTGAAATATCACCTCAGAACTTGAGAGGAGGCTTGGGTTCAGTGAACCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAG