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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatttttgatattgccttgtgtgatttaagatgatcttgtgagtactacactgtttattgcatcatccttgtgcttgtatcccttggattgtattgcaatcactgcccaattaaatgggcctgatttcctactttctttgaagGGAGAGGAACTGAGAAAGCTGATTGGAGCTCCTGCTTACATTGAATGTAGTTCAAAAACACAGCAG

Basic information

species Vitis vinifera
transcript Vv03s0038g02380.t01
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv03s0038g02380.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GLYMA11G11510.1 (Glycine max), 3'ss of exon 5
-------gtatttttga-tattgcctt---gtgtgatttaagatgatcttgtgagtactacactgtttattgcatcatccttgtgcttgtatcccttggattgtattgcaatcac------tgcccaattaaatgggc-------ctgatttcctactttctttgaagGGAGAGGAACTGAGAAAGCTGATTGGAGCTCCTGCTTACATTGAATGTAGTTCAAAAACACAGCAG
        |||||   | || | ||||    | |    | |  || | |||||     |      || | ||  |   | ||  || | | |   |||| |   | |     ||       ||     ||  || ||        || ||||  |   || | ||||||| ||||||||||||||||| || || |||||   ||||||||||||||||||||||||||| |||
gtgcttgctatttgcaactacttcctttgaatatacaattaattgcttttgtgtcgtttttttatttcactgttttgacttttagcctttgtttgttgg-tcacactatgggcatgcatgatgttacttttgataggttagtgatctaatttaatgtattttgtgaagGGTGAGGAACTGAGAAAGCTTATCGGTGCTCCAATTTACATTGAATGTAGTTCAAAAACACAACAG

upper sequence: Vv03s0038g02380.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GLYMA12G03660.1 (Glycine max), 3'ss of exon 5
--------------------------gtatttttgatattgccttgtgtgatttaagatgatcttgtgagtactacactgtttattgcatcatccttgtgcttgt-atcccttggattgtattgcaatcactgcc--caattaaatgggcctgatttcctactttctttgaagGGAGAGGAACTGAGAAAGCTGATTGGAGCTCCTGCTTACATTGAATGTAGTTCAAAAACACAGCAG
                           ||| | |   |||   |  | || |||   || || || |   || | |||||||| ||   | | || | |  ||||    |   | || |   ||   | |||      |  | | |||  ||||||| ||   || | ||||||| ||||| ||||||||||| || || ||||| | |||||||||||||||||||||||| || |||
gtgcttgctatttgccactacttcctttatatatacaattaattaat-tgcttttgcattattttttttttatttcactgttttttcttttagccctttttttgttggtcacagtatgggcatgagcttacttttgataggttagtgg-tctgatttactgtattttgtgaagGGTGAGGAGCTGAGAAAGCTTATCGGTGCTCCAGTTTACATTGAATGTAGTTCAAAAACGCAACAG
















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|27581311|gb|CB004006.1|CB004006
EST:     AGCAGTTCTTCATAGATCACCCTGGTGCAGTGCCCATTACCACAGCTCAG                         GGAGAGGAACTGAGAAAGCTGATTGGAGCTCCTGCTTACATTGAATGTAGT
genomic: AGCAGTTCTTCATAGATCACCCTGGTGCAGTGCCCATTACCACAGCTCAGgtatttttga ... ttctttgaagGGAGAGGAACTGAGAAAGCTGATTGGAGCTCCTGCTTACATTGAATGTAGT
EST: gi|77585106|gb|DV221640.1|DV221640
EST:     AGCAGTTCTTCATAGATCACCCTGGTGCAGTGCCCATTACCACAGCTCAG                         GGAGAGGAACTGAGAAAGCTGATTGGAGCTCCTGCTTACATTGAATGTAGT
genomic: AGCAGTTCTTCATAGATCACCCTGGTGCAGTGCCCATTACCACAGCTCAGgtatttttga ... ttctttgaagGGAGAGGAACTGAGAAAGCTGATTGGAGCTCCTGCTTACATTGAATGTAGT
EST: gi|161720989|gb|FC070698.1|FC070698
EST:     AGCAGTTCTTCATAGATCACCCTGGTGCAGTGCCCATTACCACAGCTCAG                         GGAGAGGAACTGAGAAAGCTGATTGGAGCTCCTGCTTACATTGAATGTAGT
genomic: AGCAGTTCTTCATAGATCACCCTGGTGCAGTGCCCATTACCACAGCTCAGgtatttttga ... ttctttgaagGGAGAGGAACTGAGAAAGCTGATTGGAGCTCCTGCTTACATTGAATGTAGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgtattgcaatcactgcccaattaaatgggcctgatttcctactttctttgaagGGAGAGGAACTGAGAAAGCTGATTGGAGCTCCTGCTTACATTGAATGTAGTTCAAAAACACAGCAG
                              gcctgat  putative branch site (score: 4)
                                    tttcctactttcttt  CT-rich tract
                    aattaaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatttttgatattgccttgtgtgatttaagatgatcttgtgagtactacactgtttattgcatcatccttgtgcttgtatcccttggattgtattgcaatcactgcccaattaaatgggcctgatttcctactttctttgaagGGAGAGGAACTGAGAAAGCTGATTGGAGCTCCTGCTTACATTGAATGTAGTTCAAAAACACAGCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT