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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagtcttctccatggtcttagttgctgacaactgtgagtatgtagttcggtactgattttggtactgctacattgtcttgcagGGAAGAAATGCAGACTCCTTGTCCCAGTACTTTGGAGAAGATCCAGCTCGGTGTCCATTTGAGCAAG

Basic information

species Vitis vinifera
transcript Vv02s0033g01360.t01
intron # 16
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv02s0033g01360.t01 (Vitis vinifera), 3'ss of exon 16
lower sequence: GLYMA09G34830.1 (Glycine max), 3'ss of exon 16
-----------------------------------------------------------------------------------------------------------gtgagtcttctccatggtcttagttgctgacaactgtgagtatgtagttcggtactgattttggtactgctacattgtcttgcagGGAAGAAATGCAGACTCCTTGTCCCAGTACTTTGGAGAAGATCCAGCTCGGTGTCCATTTGAGCAAG
                                                                                                              |||| |     ||| ||  |||| | || |        |  || ||   |  || |||||||  || | | || | || |||||||||| ||||||||| |||||||||||||||||||| ||||||||| | || || ||||| ||||
gtgagtcctgttaaagttatatttcatctcttcctcctttttccttggtgttgctattgacttgtattttgcctgctcagaggagaatttgatgcaccgtcccagataatagtcattagtttggactatgttgataaccaagtctgccaactacttattttttggttttggtcttgattctttcttttccagGGAAGAAGTGCAGACTCTTTGTCCCAGTACTTTGGAGAGGATCCAGCTAGATGCCCTTTTGAACAAG

upper sequence: Vv02s0033g01360.t01 (Vitis vinifera), 3'ss of exon 16
lower sequence: GLYMA04G14770.1 (Glycine max), 3'ss of exon 16
-----------------------------------------------------------------------------------------------------------gtgagtcttctccatggtcttagttgctgacaactgtgagtatgtagttcggtactgattttggtactgctacattgtcttgcagGGAAGAAATGCAGACTCCTTGTCCCAGTACTTTGGAGAAGATCCAGCTCGGTGTCCATTTGAGCAAG
                                                                                                              ||||       ||| ||  |||| | || |        |  ||  |   |  || |||||||  || | | || | || |||||||||| ||||||||| ||||||||||||||||| || ||||||||| | || || ||||| ||||
gtgagtcctgttaaagttatatttcctctcttcctcctttttccttggtgttgctcttgacttgtagattgcctgctcagaggagaatttgatgcaccatcccagataatagtcactagtttggactatgttgataactaagtctgccaactacgtattttttggttttggtcttgattctttcttttccagGGAAGAAGTGCAGACTCTTTGTCCCAGTACTTTGGGGAGGATCCAGCTAGATGCCCTTTTGAACAAG

upper sequence: Vv02s0033g01360.t01 (Vitis vinifera), 3'ss of exon 16
lower sequence: AT1G31810.1 (Arabidopsis thaliana), 3'ss of exon 16
gtgagtcttctccatggtctta---gttgct--gacaactgt--gagtatgtagttcgg-tactgattttggtactgctac--attgt--cttgcagGGAAGAAATGCAGACTCCTTGTCCCAGTACTTTGGAGAAGATCCAGCTCGGTGTCCATTTGAGCAAG
||||||  | |  |    || |   ||| ||   |||  | |  |   | | |||||     |   ||    | ||   |   ||||    |  ||||||||||||||||| || || || || ||||| || || ||||||||||| ||||| ||||||||||
gtgagttatatttaacagctcatcagttacttaaacactttttgggacaagcagttcaaactcatgttccaatcctaaaattaattgcaattcacagGGAAGAAATGCAGATTCTTTATCTCACTACTTCGGTGAGGATCCAGCTCGATGTCCTTTTGAGCAAG

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|22010858|gb|BQ795892.1|BQ795892
EST:     ACACTGCTGAAGCTGAAGTAAGGTCGCTTATCTCCTTGTATTCTGAAGTG                         GGAAGAAATGCAGACTCCTTGTCCCAGTACTTTGGAGAAGATCCAGCTCGG
genomic: ACACTGCTGAAGCTGAAGTAAGGTCGCTTATCTCCTTGTATTCTGAAGTGgtgagtcttc ... tgtcttgcagGGAAGAAATGCAGACTCCTTGTCCCAGTACTTTGGAGAAGATCCAGCTCGG






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

caactgtgagtatgtagttcggtactgattttggtactgctacattgtcttgcagGGAAGAAATGCAGACTCCTTGTCCCAGTACTTTGGAGAAGATCCAGCTCGGTGTCCATTTGAGCAAG
                      tactgat  putative branch site (score: 2)
                                            ttgtctt  putative PPT
                         tgatttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagtcttctccatggtcttagttgctgacaactgtgagtatgtagttcggtactgattttggtactgctacattgtcttgcagGGAAGAAATGCAGACTCCTTGTCCCAGTACTTTGGAGAAGATCCAGCTCGGTGTCCATTTGAGCAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG