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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...agtgtcacttcagttctgggcatagccctggtatctatttaattggacttagcacaaaccctgtgacaacaatttctcataaccaattcttttgtggcagGATACGTGATGATATTGAAAAGGAAGATGCTTTCCGAGGCCTATGTGCCATG

Basic information

species Vitis vinifera
transcript Vv03s0038g02830.t01
intron # 25
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv03s0038g02830.t01 (Vitis vinifera), 3'ss of exon 25
lower sequence: PP1S276_77V6.1 (Physcomitrella patens), 3'ss of exon 25
agtgtcacttcagttctgggcatagccctggtatctatttaattggacttagcacaaaccctgtgacaacaatttctcataaccaattcttttgtgg----cagGATACGTGATGATATTGAAAAGGAAGATGCTTTCCGAGGCCTATGTGCCATG
 || ||  ||  |||    |   |  |      || | ||  ||  ||            || |   | || |||   |  || | || || | |      ||||||||| |||||| |||| || ||||||||||| |||||||| ||||| |||
-gtatctattttgttacttgttcaatctct---tcaacttggttttaccgtttgatcgttctttcgtatcagttttaaactactattttttcttttcttctcagGATACGAGATGATTTTGAGAAAGAAGATGCTTTTCGAGGCCTGTGTGCTATG

upper sequence: Vv03s0038g02830.t01 (Vitis vinifera), 3'ss of exon 25
lower sequence: PP1S41_175V6.1 (Physcomitrella patens), 3'ss of exon 24
agtgtcacttcagttctgggcatagcc-ctggtatctatttaattggacttagca---caaaccctgtgacaacaatttctcataaccaattcttttgtggcagGATACGTGATGATATTGAAAAGGAAGATGCTTTCCGAGGCCTATGTGCCATG
   ||   |   ||| ||      |    | |  | | | | ||   | | |  |   ||  |||| | ||      | | |  ||  |  ||||   || ||||||||| |||||| |||| ||||||||||| ||||| ||| | |||||||||
---gtttttgaggttgtgtttgaggttgtttgcgtttgtatgatgataatgaagaagtcagtcccttttactcatgatgcactgaaatatatcttgcttg-cagGATACGAGATGATTTTGAGAAGGAAGATGCATTCCGGGGCTTGTGTGCCATG

upper sequence: Vv03s0038g02830.t01 (Vitis vinifera), 3'ss of exon 25
lower sequence: PP1S14_82V6.1 (Physcomitrella patens), 3'ss of exon 25
agtgtcacttcagttctgggcatagccctggtatctatttaattggacttagcacaaaccctgtgacaacaatttctcataaccaattcttttgtg---gcagGATACGTGATGATATTGAAAAGGAAGATGCTTTCCGAGGCCTATGTGCCATG
  |   | ||     || |    | | ||  ||| |   ||  |  | || |         |   | ||  |||||  | |  || || |||| |     ||||||||| |||||| |||| |||||||||||||| |||||  | ||||| |||
tataataattagaaacttgctcaacctcttatattttggtatct--aatttgtttgttttttaatataa-gatttcaaacactcactttttttctcttcacagGATACGAGATGATTTTGAGAAGGAAGATGCTTTTCGAGGATTGTGTGCTATG

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|71885305|gb|DT034360.1|DT034360
EST:     TCACTGCATATGGAGCATTTTATGCAATCATGGTGTACTGCTTTATCCAT                         GATACGTGATGATATTGAAAAGGAAGATGCTTTCCGAGGCCTATGTGCCAT
genomic: TCACTGCATATGGAGCATTTTATGCAATCATGGTGTACTGCTTTATCCATgtacgtattt ... tttgtggcagGATACGTGATGATATTGAAAAGGAAGATGCTTTCCGAGGCCTATGTGCCAT
EST: gi|71882863|gb|DT031918.1|DT031918
EST:     TCACTGCATATGGAGCATTTTATGCAATCATGGTGTACTGCTTTATCCAT                         GATACGTGATGATATTGAAAAGGAAGATGCTTTCCGAGGCCTATGTGCCAT
genomic: TCACTGCATATGGAGCATTTTATGCAATCATGGTGTACTGCTTTATCCATgtacgtattt ... tttgtggcagGATACGTGATGATATTGAAAAGGAAGATGCTTTCCGAGGCCTATGTGCCAT
EST: gi|71887036|gb|DT036091.1|DT036091
EST:     TCACTGCATATGGAGCATTTTATGCAATCATGGTGTACTGCTTTATCCAT                         GATACGTGATGATATTGAAAAGGAAGATGCTTTCCGAGGCCTATGTGCCAT
genomic: TCACTGCATATGGAGCATTTTATGCAATCATGGTGTACTGCTTTATCCATgtacgtattt ... tttgtggcagGATACGTGATGATATTGAAAAGGAAGATGCTTTCCGAGGCCTATGTGCCAT
EST: gi|71885604|gb|DT034659.1|DT034659
EST:     TCACTGCATATGGAGCATTTTATGCAATCATGGTGTACTGCTTTATCCAT                         GATACGTGATGATATTGAAAAGGAAGATGCTTTCCGAGGCCTATGTGCCAT
genomic: TCACTGCATATGGAGCATTTTATGCAATCATGGTGTACTGCTTTATCCATgtacgtattt ... tttgtggcagGATACGTGATGATATTGAAAAGGAAGATGCTTTCCGAGGCCTATGTGCCAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gacttagcacaaaccctgtgacaacaatttctcataaccaattcttttgtggcagGATACGTGATGATATTGAAAAGGAAGATGCTTTCCGAGGCCTATGTGCCATG
                               tcataac  putative branch site (score: 2)
                                         ttcttttgt  putative PPT
                                       aattctttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
agtgtcacttcagttctgggcatagccctggtatctatttaattggacttagcacaaaccctgtgacaacaatttctcataaccaattcttttgtggcagGATACGTGATGATATTGAAAAGGAAGATGCTTTCCGAGGCCTATGTGCCATG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGATG
- - -cacttca
- - - - - - gttctgg
- - - - - - - - - - - - -ccctggt
- - - - - - - - - - - - - - - - - - - - - - - - - - -acaaacc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -acaacaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aaccaat