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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgcaccacctgttattctctttattttttcttcagtcttgattataattttgggttgggtgcccagaaaattaattcctttttttttggttgtatttcagTGTGATCTGCTGGATATGCCTGCAGTAGGACAATTGGAGAAAGACGCTAAATATGCATTGGTCTATCAGCTTCTGAAGATTTTTCTCACTCAGAGGCTTG

Basic information

species Vitis vinifera
transcript Vv14s0068g00220.t01
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv14s0068g00220.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA10G28080.2 (Glycine max), 3'ss of exon 4
---tgcaccacctgttattctctttattttttcttcagtcttgattataattttgggttgggtgcccagaaaattaattcctttttttttggttgtatttcagTGTGATCTGCTGGATATGCCTGCAGTAGGACAATTGGAGAAAGACGCTAAATATGCATTGGTCTATCAGCTTCTGAAGATTTTTCTCACTCAGAGGCTTG
   |     |  | | | ||   |  ||||   | || | |||  ||  ||| | |  |  || |    | | ||  |   | | ||  | ||||| ||| |||||||| |||| ||  ||||||| || | |||| ||||||| || || ||||||||  || | ||||||||||| ||||||||||| || |||||||| |
tactcttatatatctaaatccaatatttttaattccatttttggctaagattgttg--taagttcttgaagagttt-tcaatatgttgattgttgtgttttagTGTGATTTGCTAGACTTGCCTGCTGTTGCACAACTGGAGAAGGATGCCAAATATGCTCTGTTATATCAGCTTCTTAAGATTTTTCTTACCCAGAGGCTGG

upper sequence: Vv14s0068g00220.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA13G06410.1 (Glycine max), 3'ss of exon 5
--tgcaccacctgttattctctttattttttcttcagtcttgattataattttgggttgggtgcccagaaaattaattcctttttttttggttgtatttcagTGTGATCTGCTGGATATGCCTGCAGTAGGACAATTGGAGAAAGACGCTAAATATGCATTGGTCTATCAGCTTCTGAAGATTTTTCTCACTCAGAGGCTTG
  | |  ||     ||    |  |||||||  | |  | ||     ||  || |  ||  ||  |  ||| |  | |  ||   |   | ||  | ||  |||||||| |||| ||  ||||||| || || ||| ||||||| || || ||||||||  || | ||||||||||| ||||||||||| || |||||||| |
tattcttcaatatctaagtgcactatttttaatgctatttttggcctagatt-gctttaagt-tctggaagagcattcactaagtggattgtcatgttgtagTGTGATTTGCTTGACTTGCCTGCTGTTGGGCAACTGGAGAAGGATGCCAAATATGCTCTGTTATATCAGCTTCTTAAGATTTTTCTTACCCAGAGGCTAG

upper sequence: Vv14s0068g00220.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA20G22090.1 (Glycine max), 3'ss of exon 5
---tgcaccacctgttattctctttattttttcttcagtcttgattataattttgggttgggtgcccagaaaattaattcctttttttttggttgtatttcagTGTGATCTGCTGGATATGCCTGCAGTAGGACAATTGGAGAAAGACGCTAAATATGCATTGGTCTATCAGCTTCTGAAGATTTTTCTCACTCAGAGGCTTG
   |     |  | | | ||   |  ||||    |||   |||   |  ||| | |  |  || |   ||| |  | |  ||   ||  | ||||| ||  |||||||| | || ||  ||||||| ||   |||| ||||||| || || ||||||||  || | ||||||||||| ||||||||||| || |||||||| |
aactcttgtatatctaagtccaatacttttaatgtcatgtttggccaagattgtag--taagttctt-gaagagcattcactaagttgattgttgtgttgtagTGTGATTTACTAGACTTGCCTGCTGTTACACAACTGGAGAAGGATGCCAAATATGCTCTGTTATATCAGCTTCTTAAGATTTTTCTTACCCAGAGGCTGG

upper sequence: Vv14s0068g00220.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: AT3G02200.1 (Arabidopsis thaliana), 3'ss of exon 5
tgcaccacc-tgttattctctttattttttcttcagtcttgattataattttgggttgggtgcccagaaaattaattcctttttttttggttgtatttcagTGTGATCTGCTGGATATGCCTGCAGTAGGACAATTGGAGAAAGACGCTAAATATGCATTGGTCTATCAGCTTCTGAAGATTTTTCTCACTCAGAGGCTTG
 | | ||   ||| | |    ||  | ||||||  ||| |||   |  | ||   |    ||    |||  | ||         | ||     | || ||||||||| |  ||||  |||| || |||| ||||||||| || || ||||||||||||   || || || ||||||||||||||||| ||||||||| |  
-gtatcataatgtgaattggatttgtctttctt--gtcctgacactgctcttttat-atttgattggaatttcaacgatggcaatcttaa--atcttgcagTGTGATTTATTGGACTTGCCAGCCGTAGCACAATTGGAAAAGGATGCTAAATATGCACCTGTTTACCAACTTCTGAAGATTTTTCTTACTCAGAGGTTAA

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|30326179|gb|CD009441.1|CD009441
EST:     AAGCTGTCCGCACTATTATGGAATTTGTGAGGGCACCAGACATGTTTCAG                         TGTGATCTGCTGGATATGCCTGCAGTAGGACAATTGGAGAAAGACGCTAAA
genomic: AAGCTGTCCGCACTATTATGGAATTTGTGAGGGCACCAGACATGTTTCAGgtatttgagc ... tgtatttcagTGTGATCTGCTGGATATGCCTGCAGTAGGACAATTGGAGAAAGACGCTAAA
EST: gi|77586427|gb|DV222339.1|DV222339
EST:     AAGCTGTCCGCACTATTATGGAATTTGTGAGGGCACCAGACATGTTTCAG                         TGTGATCTGCTGGATATGCCTGCAGTAGGACAATTGGAGAAAGAC
genomic: AAGCTGTCCGCACTATTATGGAATTTGTGAGGGCACCAGACATGTTTCAGgtatttgagc ... tgtatttcagTGTGATCTGCTGGATATGCCTGCAGTAGGACAATTGGAGAAAGAC
EST: gi|37187675|gb|CF607028.1|CF607028
EST:     AAGCTGTCCGCACTATTATGGAATTTGTGAGGGCACCAGACATGTTTCAG                         TGTGATCTGCTGGATATGCCTGCAGTAGGACAATTGGAGAAAGACGCTAAA
genomic: AAGCTGTCCGCACTATTATGGAATTTGTGAGGGCACCAGACATGTTTCAGgtatttgagc ... tgtatttcagTGTGATCTGCTGGATATGCCTGCAGTAGGACAATTGGAGAAAGACGCTAAA
EST: gi|87586086|gb|DY474543.1|DY474543
EST:     AAGCTGTCCGCACTATTATGGAATTTGTGAGGGCACCAGACATGTTTCAG                         TGTGATCTGCTGGATATGCCTGCAGTAGGACAATTGGAGAAAGACACTAAA
genomic: AAGCTGTCCGCACTATTATGGAATTTGTGAGGGCACCAGACATGTTTCAGgtatttgagc ... tgtatttcagTGTGATCTGCTGGATATGCCTGCAGTAGGACAATTGGAGAAAGACGCTAAA
EST: gi|110421499|gb|EC987796.1|EC987796
EST:     AAGCTGTCCGCACTATTATGGAATTTGTGAGGGCACCAGACATGTTTCAG                         TGTGATCTGCTGGATATGCCTGCAGTAGGACAATTGGAGAAAGACGCTAAA
genomic: AAGCTGTCCGCACTATTATGGAATTTGTGAGGGCACCAGACATGTTTCAGgtatttgagc ... tgtatttcagTGTGATCTGCTGGATATGCCTGCAGTAGGACAATTGGAGAAAGACGCTAAA
EST: gi|30127269|gb|CB912608.1|CB912608
EST:     AAGCTGTCCGCACTATTATGGAATTTGTGAGGGCACCAGACATGTTTCAG                         TGTGATCTGCTGGATATGCCTGCAGTAGGACAATTGGAGAAAGACGCTAAA
genomic: AAGCTGTCCGCACTATTATGGAATTTGTGAGGGCACCAGACATGTTTCAGgtatttgagc ... tgtatttcagTGTGATCTGCTGGATATGCCTGCAGTAGGACAATTGGAGAAAGACGCTAAA
EST: gi|110390588|gb|EC955507.1|EC955507
EST:     AAGCTGTCCGCACTATTATGGAATTTGTGAGGGCACCAGACATGTTTCAG                         TGTGATCTGCTGGATATGCCTGCAGTAGGACAATTGGAGAAAGACACTAAA
genomic: AAGCTGTCCGCACTATTATGGAATTTGTGAGGGCACCAGACATGTTTCAGgtatttgagc ... tgtatttcagTGTGATCTGCTGGATATGCCTGCAGTAGGACAATTGGAGAAAGACGCTAAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aattttgggttgggtgcccagaaaattaattcctttttttttggttgtatttcagTGTGATCTGCTGGATATGCCTGCAGTAGGACAATTGGAGAAAGACGCTAAATATGCATTGGTCTATCAGCTTCTGAAGATTTTTCTCACTCAGAGGCTTG
                       aattaat  putative branch site (score: 3)
                             ttcctttttttttggt  CT-rich tract
                   agaaaattaattcctt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgcaccacctgttattctctttattttttcttcagtcttgattataattttgggttgggtgcccagaaaattaattcctttttttttggttgtatttcagTGTGATCTGCTGGATATGCCTGCAGTAGGACAATTGGAGAAAGACGCTAAATATGCATTGGTCTATCAGCTTCTGAAGATTTTTCTCACTCAGAGGCTTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- caccacc
- - - - - - - - - - - - - - - - - - - - - - - - - - ggttggg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -cagaaaa