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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...atggtttgacaaaatatacttccacaaaagttatgaaggagtctgagggtaagaagtttggcatcatgtatcatcctgattgcttatattctttgtgcagTCAACTTCCAACCGAACTTTGGACCAGCAATGCACTGTTACACGTCCAGGGCTTGCTCCTATTGCTTCGGCTCTTGCTGTAGAGCTTTTAGTAGGAATCC

Basic information

species Vitis vinifera
transcript Vv10s0003g01150.t01
intron # 13
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv10s0003g01150.t01 (Vitis vinifera), 3'ss of exon 13
lower sequence: GLYMA12G01250.1 (Glycine max), 3'ss of exon 11
atggtttgacaaaatatacttccacaaaagttatgaaggagtctgagggtaa---gaagtttggcatcatgtatcatcctgattgcttatattctttgtgcagTCAACTTCCAACCGAACTTTGGACCAGCAATGCACTGTTACACGTCCAGGGCTTGCTCCTATTGCTTCGGCTCTTGCTGTAGAGCTTTTAGTAGGAATCC
                         ||      ||  | | | || | || |   ||| |   | | |||   | || |   |||  | | | || | |||||||||| |||||||| ||||||||||||||||| ||||| || || |||||||| |||||||||||||| || ||||| || || ||||||||||| ||  
-----------------------gtaatttccgtgctgcattgtgtgcgttatttgaactaatgtaacataactgattcatgttggctttctgctctctgcagTCAACATCCAACCGCACTTTGGACCAGCAATGTACTGTGACCCGACCAGGGCTAGCTCCTATTGCTTCAGCCCTTGCAGTTGAACTTTTAGTAGGGATTT

upper sequence: Vv10s0003g01150.t01 (Vitis vinifera), 3'ss of exon 13
lower sequence: AT5G45900.1 (Arabidopsis thaliana), 3'ss of exon 8
atggtttgacaaaatatacttccacaaaagttatgaaggagtctgagggtaagaagtttggcatcatgtatcatcctgattgcttatattctttgtgcagTCAACTTCCAACCGAACTTTGGACCAGCAATGCACTGTTACACGTCCAGGGCTTGCTCCTATTGCTTCGGCTCTTGCTGTAGAGCTTTTAGTAGGAATCC
 |  ||        | | | |    ||  ||| ||        ||        |  |  | | | ||   || | |  | | ||| | || | | |||||||||   |  | |||||| | ||||| ||||||||||||||||| || || || |||||||||||    ||||| || || || || ||||| ||| |||
gtaattccctggtttcttcattttgaattgttttgtttcg---tgttacctccagttcagtcctgattcgtcgtacccact-cttttcttgtatttgcagTCAATGACTGATCGAACTCTAGACCAACAATGCACTGTTACACGCCCGGGTCTAGCTCCTATTGCAGGAGCTCTCGCCGTTGAACTCTTAGTCGGAGTCC
















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|352773017|gb|FQ470632.1|FQ470632
EST:     GCAGAGATTGGGTTGTTACTTCTGCAATGATGTGGTTGCCCCAGTTGAT                         TCAACTTCCAACCGAACTTTGGACCAGCAATGCACTGTTACACGTCCAGGG
genomic: GCAGAGATTGGGTTGTTACTTCTGCAATGATGTGGTTGCCCCAGTTGATgtaattgtct ... ctttgtgcagTCAACTTCCAACCGAACTTTGGACCAGCAATGCACTGTTACACGTCCAGGG
EST: gi|352764553|gb|FQ472910.1|FQ472910
EST:     GGGTTGTTACTTCTGCAATGATGTGGTTGCCCCAGTTGAT                         TCAACTTCCAACCGAACTTTGGACCAGCAATGCACTGTTACACGTCCAGGG
genomic: GGGTTGTTACTTCTGCAATGATGTGGTTGCCCCAGTTGATgtaattgtct ... ctttgtgcagTCAACTTCCAACCGAACTTTGGACCAGCAATGCACTGTTACACGTCCAGGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agggtaagaagtttggcatcatgtatcatcctgattgcttatattctttgtgcagTCAACTTCCAACCGAACTTTGGACCAGCAATGCACTGTTACACGTCCAGGGCTTGCTCCTATTGCTTCGGCTCTTGCTGTAGAGCTTTTAGTAGGAATCC
                            tcctgat  putative branch site (score: 3)
                                         tattcttt  putative PPT
                                      ttatattcttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
atggtttgacaaaatatacttccacaaaagttatgaaggagtctgagggtaagaagtttggcatcatgtatcatcctgattgcttatattctttgtgcagTCAACTTCCAACCGAACTTTGGACCAGCAATGCACTGTTACACGTCCAGGGCTTGCTCCTATTGCTTCGGCTCTTGCTGTAGAGCTTTTAGTAGGAATCC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGCTT
- - - -gacaaaa
- - - - - - - - - - -ccacaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tcatgta