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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttttagtcattatatgaatgatgtcttgttaactttgtttagatgattcaatgtgtttgcttgttggtttacattacaacgccactttatgtttgtacagGATAGAGATCGAAAACTAAGGATATTTGCTGGTGATGAGCACCCTTTCAATGACAGGCCTCTTGAACCTTATGTGATGCCGCCTCGGCAAGTACGAGAAA

Basic information

species Vitis vinifera
transcript Vv14s0171g00250.t01
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv14s0171g00250.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: LOC_Os05g15370.1 (Oryza sativa), 3'ss of exon 4
ttttagtcattatatgaatgatgtcttgttaactttg--tttagatgattcaatgtgtttgct-tgttggtttacattacaacgc-cactttatgtttgt-acagGATAGAGATCGAAAACTAAGGATATTTGCTGGTGATGAGCACCCTTTCAATGACAGGCCTCTTGAACCTTATGTGATGCCGCCTCGGCAAGTACGAGAAA
     | |   | ||  ||  | || |   |   | |  || | ||  || ||  |   |    || || |||   |||  | ||      | |  |  | |||||| || ||||| ||||| ||||||||| ||||  |||||||||| ||| ||||  | ||||||||||||| | ||||||| |  || ||||| || || |
-----ggcgaaagatccatattttcctacaattctcgtcttcaaattgttaaagcttcatataatgctgtttttgcttattaagcatgtactgttctgatcacagGACAGGGATCGTAAACTGAGGATATTTTCTGGAAATGAGCACCCATTCCATGATCGCCCTCTTGAACCTTTTATGATGCCACGACGCCAAGTGCGCGAGA

upper sequence: Vv14s0171g00250.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: LOC_Os05g15360.7 (Oryza sativa), 3'ss of exon 4
---ttttagtcattatatgaatgatgtcttgttaactttgtttagatgattcaatgtgtttgcttgttggtttacattacaacgccactttatgtttgtacagGATAGAGATCGAAAACTAAGGATATTTGCTGGTGATGAGCACCCTTTCAATGACAGGCCTCTTGAACCTTATGTGATGCCGCCTCGGCAAGTACGAGAAA
      |    ||| |   |    | || | ||    ||||| |  |   |  || |       |  | | |||  | |  | |     || || |   |||||| || ||||| ||| | ||||||||| ||||  |||||||||| ||| ||||  | ||||||||||||| ||||||||| || || ||||| |  || |
caaaaatgtatattttcctacaattctcatcttcgaattgttaaagtagcttcatataacgctgttattgcttat-taagcatgtactgttctgatc--acagGACAGGGATCGTAAATTGAGGATATTTTCTGGAAATGAGCACCCATTCCATGATCGCCCTCTTGAACCTTTTGTGATGCCACCACGCCAAGTGCAGGAGA

upper sequence: Vv14s0171g00250.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: LOC_Os01g67200.1 (Oryza sativa), 3'ss of exon 1
ttttagtcat-tatatgaatgatgtcttgttaactttgtttagatgattcaatgtgtttgcttgttggtttacattacaacgccactttatgtttgtacagGATAGAGATCGAAAACTAAGGATATTTGCTGGTGATGAGCACCCTTTCAATGACAGGCCTCTTGAACCTTATGTGATGCCGCCTCGGCAAGTACGAGAAA
  | |  ||| |||||      |   || |   |||    | | | |  |    | |     ||||| |    ||||      |||| | | |    |||||| || ||||| ||||| ||||||||| ||||  ||||||| || ||| ||||  | ||||||||||||| ||||||||| || || ||||| || || |
ggtaaaacatctatattttccttcaattctcgtcttcaaattgctaaagcttcatataatgctgttgttgcttattaagcatgcactgt-tctgatcacagGACAGGGATCGCAAACTGAGGATATTTTCTGGAAATGAGCATCCATTCCATGATCGCCCTCTTGAACCTTTTGTGATGCCACCACGCCAAGTGCGTGAGA

upper sequence: Vv14s0171g00250.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GRMZM2G044584_T02 (Zea mays), 3'ss of exon 5
tttta-gtcattatat-gaatgatgtcttgttaactttg--tttagatgattcaat--gtgtttgcttgttggtttacattacaacgccactttatgtttgtacagGATAGAGATCGAAAACTAAGGATATTTGCTGGTGATGAGCACCCTTTCAATGACAGGCCTCTTGAACCTTATGTGATGCCGCCTCGGCAAGTACGAGAAA
||| |   |||  ||| | || |||       ||   ||  ||| | || |    |     | |||||| || || ||||    |  |  || |  | |  | |||||||| ||||| || || ||||||||| ||||  | || || || ||| ||||| | ||||| ||||||| |||||||||||| ||||||||||| || |
tttcataacatcttattgtatcatggtcgaggaatcatgccttttgctggtcacgttaaaatgtgcttggtgtttgacat----atactgctct--ggtcctccagGATAGGGATCGCAAGCTGAGGATATTTTCTGGAAACGAACATCCATTCCATGACCGCCCTCTGGAACCTTTTGTGATGCCGCCACGGCAAGTACGCGAGA

upper sequence: Vv14s0171g00250.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GRMZM2G163473_T01 (Zea mays), 3'ss of exon 4
--------ttttagtcattatatgaatg-atgtcttgtta-actttgtttagatgattcaatgtgtttgcttgttggtttacattacaacgccactttatgtttgtacagGATAGAGATCGAAAACTAAGGATATTTGCTGGTGATGAGCACCCTTTCAATGACAGGCCTCTTGAACCTTATGTGATGCCGCCTCGGCAAGTACGAGAAA
           |     |||||| |||     | |||  | | |||||||       | |||||| |||    |||   || | | |          | || |  | |||||||| ||||| || ||  |||||||| ||||   |||||| || ||| ||||| | ||||||||| ||| ||||||||| || ||||||||||| || |
ttacgcgtggctgagatttatattaatttgcattttgcaatattttgtttgtcacgctaaatgtgcttgacctttgacatatactgc----------tctggtcttccagGATAGGGATCGCAAGCTGCGGATATTTTCTGGAATTGAGCATCCATTCCATGACCGCCCTCTTGAAGCTTTTGTGATGCCACCACGGCAAGTACGGGAGA

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|110381796|gb|EC935401.1|EC935401
EST:     TCATACGCAAAGCAGTCTTGCGCATGCTTCCAAGAAACAAATTGCGTGAT                         GATAGAGATCGAAAACTAAGGATATTTGCTGGTGATGAGCACCCTTTCAAT
genomic: TCATACGCAAAGCAGTCTTGCGCATGCTTCCAAGAAACAAATTGCGTGATgtaagtgatt ... gtttgtacagGATAGAGATCGAAAACTAAGGATATTTGCTGGTGATGAGCACCCTTTCAAT
EST: gi|110698261|gb|EE075596.1|EE075596
EST:     TCATACGCAAAGCAGTCTTGCGCATGCTTCCAAGAAACAAATTGCGTGAT                         GATAGAGATCGAAAACTAAGGATATTTGCTGGTGATGAGCACCCTTTCAAT
genomic: TCATACGCAAAGCAGTCTTGCGCATGCTTCCAAGAAACAAATTGCGTGATgtaagtgatt ... gtttgtacagGATAGAGATCGAAAACTAAGGATATTTGCTGGTGATGAGCACCCTTTCAAT
EST: gi|77585738|gb|DV221960.1|DV221960
EST:     TCATACGCAAAGCAGTCTTGCGCATGCTTCCAAGAAACAAATTGCGTGAT                         GATAGAGATCGAAAACTAAGGATATTTGCTGGTGATGAGCACCCTTTCAAT
genomic: TCATACGCAAAGCAGTCTTGCGCATGCTTCCAAGAAACAAATTGCGTGATgtaagtgatt ... gtttgtacagGATAGAGATCGAAAACTAAGGATATTTGCTGGTGATGAGCACCCTTTCAAT
EST: gi|71870914|gb|DT019969.1|DT019969
EST:     TCATACGCAAAGCAGTCTTGCGCATGCTTCCAAGAAACAAATTGCGTGAT                         GATAGAGATCGAAAACTAAGGATATTTGCTGGTGATGAGCACCCTTTCAAT
genomic: TCATACGCAAAGCAGTCTTGCGCATGCTTCCAAGAAACAAATTGCGTGATgtaagtgatt ... gtttgtacagGATAGAGATCGAAAACTAAGGATATTTGCTGGTGATGAGCACCCTTTCAAT
EST: gi|110382064|gb|EC938387.1|EC938387
EST:     TCATACGCAAAGCAGTCTTGCGCATGCTTCCAAGAAACAAATTGCGTGAT                         GATAGAGATCGAAAACTAAGGATATTTGCTGGTGATGAGCACCCTTTCAAT
genomic: TCATACGCAAAGCAGTCTTGCGCATGCTTCCAAGAAACAAATTGCGTGATgtaagtgatt ... gtttgtacagGATAGAGATCGAAAACTAAGGATATTTGCTGGTGATGAGCACCCTTTCAAT
EST: gi|26257383|gb|CA808446.1|CA808446
EST:     TCATACGCAAAGCAGTCTTGCGCATGCTTCCAAGAAACAAATTGCGTGAT                         GATAGAGATCGAAAACTAAGGATATTTGCTGGTGATGAGCACCCCTTTCAA
genomic: TCATACGCAAAGCAGTCTTGCGCATGCTTCCAAGAAACAAATTGCGTGATgtaagtgatt ... gtttgtacagGATAGAGATCGAAAACTAAGGATATTTGCTGGTGATGAGCACCC-TTTCAA
EST: gi|349826908|gb|FQ418999.1|FQ418999
EST:     TCATACGCAAAGCAGTCTTGCGCATGCTTCCAAGAAACAAATTGCGTGAT                         GATAGAGATCGAAAACTAAGGATATTTGCTGGTGATGAGCACCCTTTCAAT
genomic: TCATACGCAAAGCAGTCTTGCGCATGCTTCCAAGAAACAAATTGCGTGATgtaagtgatt ... gtttgtacagGATAGAGATCGAAAACTAAGGATATTTGCTGGTGATGAGCACCCTTTCAAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

attcaatgtgtttgcttgttggtttacattacaacgccactttatgtttgtacagGATAGAGATCGAAAACTAAGGATATTTGCTGGTGATGAGCACCCTTTCAATGACAGGCCTCTTGAACCTTATGTGATGCCGCCTCGGCAAGTACGAGAAA
                      tttacatta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttttagtcattatatgaatgatgtcttgttaactttgtttagatgattcaatgtgtttgcttgttggtttacattacaacgccactttatgtttgtacagGATAGAGATCGAAAACTAAGGATATTTGCTGGTGATGAGCACCCTTTCAATGACAGGCCTCTTGAACCTTATGTGATGCCGCCTCGGCAAGTACGAGAAA

- - - - - - - - - - -tgtcttg
- - - - - - - - - - - - - - - - - - - - - - - - caatgtg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gccactt