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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tttgtaaacctctttctctgtggtggtttctatttttagccttcctctttgcaagctactttcctgactgattttattatttaattttgtttggaagcagGCTAGTTGCAAAGACAACACAGCTGGAGGGTGAAAAAAAGCAGAAAGAGACTGAAGTCCAGAAACTTATGGAAGAAAATGTGAGGTTGAGTGCTCTTCTT

Basic information

species Vitis vinifera
transcript Vv04s0023g03250.t01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv04s0023g03250.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA02G05520.1 (Glycine max), 3'ss of exon 2
tttgtaaacctctttctctgtgg--tggtttctatttttagccttcctctttgcaagctactttcctgactgattttattatttaattttgtttg---gaagcagGCTAGTTGCAAAGACAACACAGCTGGAGGGTGAAAAAAAGCAGAAAGAGACTGAAGTCCAGAAACTTATGGAAGAAAATGTGAGGTTGAGTGCTCTTCTT
   | |      |     || ||  |  ||| || ||| |    || | |  | | | |  |||  |  || |||| |   |  |  | | ||||     ||||||||||||| |||||| || ||  |||||||||| |||| |||||||||| ||||||| ||||||||||||||||| |||||||||||||||||||| |||
--cgcattttcttgctaatggggtttaatttttaatttcaattctcatgta-gtaggtttttttttt--cttatttaaaactagagatgtatttgtcttgagcagGCTAGTTGGAAAGACTACCCAATTGGAGGGTGAGAAAATGCAGAAAGAGGCTGAAGTTCAGAAACTTATGGAAGAGAATGTGAGGTTGAGTGCTCTGCTT

upper sequence: Vv04s0023g03250.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA16G23960.1 (Glycine max), 3'ss of exon 2
tttgtaaacctctttctctgtggtggtttctatttttagccttcctctttgca-agctactttcctgactgattttatta---tttaattttgtttgg---aagcagGCTAGTTGCAAAGACAACACAGCTGGAGGGTGAAAAAAAGCAGAAAGAGACTGAAGTCCAGAAACTTATGGAAGAAAATGTGAGGTTGAGTGCTCTTCTT
     | |  |  ||  || ||| |  ||  || ||||   ||  |  |     || |  |||  | | |  |||| | |   |  |  |   ||||     |||||| |||||| |||||| || ||  |||| ||||| |||| |||||||||| ||||||| ||||||||||||||||| |||||||||||||||||||| |||
-----acattttcttgcctatgggg--tttaatatttaattttaattctcatgcagttggtttatttatttcttttttaaaactaaagatgcatttgtcttgagcagGTTAGTTGGAAAGACTACCCAATTGGAAGGTGAGAAAATGCAGAAAGAGGCTGAAGTACAGAAACTTATGGAAGAGAATGTGAGGTTGAGTGCTCTGCTT

upper sequence: Vv04s0023g03250.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA11G08100.1 (Glycine max), 3'ss of exon 2
-tttgta-aacctctttctctgtggtggtttctatttttagccttcctctttgcaagctactttcctgactgattttattatttaattttgtttggaagcagGCTAGTTGCAAAGACAACACAGCTGGAGGGTGAAAAAAAGCAGAAAGAGACTGAAGTCCAGAAACTTATGGAAGAAAATGTGAGGTTGAGTGCTCTTCTT
  ||| |     |     |   |     ||   || || |   ||| | | | |   ||  | || | |||  | | |||   |||| ||  || | |||||||||||||||||||| || ||  | |||||||| |||| |||||||||| ||||||| ||||||||||||||||| ||||| ||||||||||| || |||
ggttgcatggtgtgaacattcatttcaattctcatgttcaatgttcatttctacct-ctgatatcgt-acttgtctaattgactaatgttcctttggagcagGCTAGTTGCAAAGACTACTCAATTAGAGGGTGAGAAAATGCAGAAAGAGGCTGAAGTTCAGAAACTTATGGAAGAGAATGTTAGGTTGAGTGCACTGCTT

upper sequence: Vv04s0023g03250.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA01G37180.1 (Glycine max), 3'ss of exon 2
----------tttgtaaacctctttctctgtggtggtttctatttttagccttcctctttgcaagctactttcctgactgattttattatttaattttgtttggaagcagGCTAGTTGCAAAGACAACACAGCTGGAGGGTGAAAAAAAGCAGAAAGAGACTGAAGTCCAGAAACTTATGGAAGAAAATGTGAGGTTGAGTGCTCTTCTT
            ||| ||| |  || ||        ||   || |  |   ||| | | | |      |  | |  |||  | |||||   | || ||  || | |||||||||||||||||||| || ||  | |||||||| |||| |||||||||| ||||||| ||||||||||||||||| ||||| ||||||| ||| || |||
gtggtagcatggtgtgaacattcttttc------aattctcatgtacaatgttcatttctac----ctcgatacgtacttgtcttattgactgatgttcctttggagcagGCTAGTTGCAAAGACTACTCAATTAGAGGGTGAGAAAATGCAGAAAGAGGCTGAAGTTCAGAAACTTATGGAAGAGAATGTCAGGTTGAATGCACTGCTT

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|83276165|gb|DV940173.1|DV940173
EST:     CTGCTGTCATCAGAGAAGCAATTTCAAACTATTGAGAGGCTTTTTGAACG                         GCTAGTTGCAAAGACAACACAGCTGGAGGGTGNNNNNNNGCAGAAAGAGAC
genomic: CTGCTGTCATCAGAGAAGCAATTTCAAACTATTGAGAGGCTTTTTGAACGgtcagtataa ... ttggaagcagGCTAGTTGCAAAGACAACACAGCTGGAGGGTGAAAAAAAGCAGAAAGAGAC
EST: gi|45368193|gb|CK906552.1|CK906552
EST:     CTGCTGTCATCAGAGAAGCAATTTCAAACTATTGAGAGGCTTTTTGAACG                         GCTAGTTGCAAAGACAACACAGCTGGAGGGTGNNNNNNNGCAGAAAGAGAC
genomic: CTGCTGTCATCAGAGAAGCAATTTCAAACTATTGAGAGGCTTTTTGAACGgtcagtataa ... ttggaagcagGCTAGTTGCAAAGACAACACAGCTGGAGGGTGAAAAAAAGCAGAAAGAGAC
EST: gi|27581755|gb|CB004450.1|CB004450
EST:     CTGCTGTCATCAGAGAAGCAATTTCAAACTATTGAGAGGCTTTTTGAACG                         GCTAGTTGCAAAGACAACACAGCT
genomic: CTGCTGTCATCAGAGAAGCAATTTCAAACTATTGAGAGGCTTTTTGAACGgtcagtataa ... ttggaagcagGCTAGTTGCAAAGACAACACAGCT
EST: gi|110360984|gb|EC924432.1|EC924432
EST:     CTGCTGTCATCAGAGAAGCAATTTCAAACTATTGAGAGGCTTTTTGAACG                         GCTAGTTGCAAAGACAACACAGCTGGAGGGTGNNNNNNNGCAGAAAGAGAC
genomic: CTGCTGTCATCAGAGAAGCAATTTCAAACTATTGAGAGGCTTTTTGAACGgtcagtataa ... ttggaagcagGCTAGTTGCAAAGACAACACAGCTGGAGGGTGAAAAAAAGCAGAAAGAGAC
EST: gi|30305538|gb|CB982332.1|CB982332
EST:     CTGCTGTCATCAGAGAAGCAATTTCAAACTATTGAGAGGCTTTTTGAACG                         GCTAGTTGCAAAGACAACACAGCTGGAGGGTGNNNNNNNGCAGAAAGAGAC
genomic: CTGCTGTCATCAGAGAAGCAATTTCAAACTATTGAGAGGCTTTTTGAACGgtcagtataa ... ttggaagcagGCTAGTTGCAAAGACAACACAGCTGGAGGGTGAAAAAAAGCAGAAAGAGAC
EST: gi|83274638|gb|DV938734.1|DV938734
EST:     CTGCTGTCATCAGAGAAGCAATTTCAAACTATTGAGAGGCTTTTTGAACG                         GCTAGTTGCAAAGACAACACAGCTGGAGGGTGNNNNNNNGCAGAAAGAGAC
genomic: CTGCTGTCATCAGAGAAGCAATTTCAAACTATTGAGAGGCTTTTTGAACGgtcagtataa ... ttggaagcagGCTAGTTGCAAAGACAACACAGCTGGAGGGTGAAAAAAAGCAGAAAGAGAC
EST: gi|34549319|gb|CF517551.1|CF517551
EST:     CTGCTGTCATCAGAGAAGCAATTTCAAACTATTGAGAGGCTTTTTGAACG                         GCTAGTTGCAAAGACAACACAGCTGGAGGGTGNNNNNNNGCAGAAAGAGAC
genomic: CTGCTGTCATCAGAGAAGCAATTTCAAACTATTGAGAGGCTTTTTGAACGgtcagtataa ... ttggaagcagGCTAGTTGCAAAGACAACACAGCTGGAGGGTGAAAAAAAGCAGAAAGAGAC
EST: gi|27583875|gb|CB006570.1|CB006570
EST:     CTGCTGTCATCAGAGAAGCAATTTCAAACTATTGAGAGGCTTTTTGAACG                         GCTAGTTGCAAAGACAACACAGCTGGAGGGTGNNNNNNNGCAGAAAGAGAC
genomic: CTGCTGTCATCAGAGAAGCAATTTCAAACTATTGAGAGGCTTTTTGAACGgtcagtataa ... ttggaagcagGCTAGTTGCAAAGACAACACAGCTGGAGGGTGAAAAAAAGCAGAAAGAGAC
EST: gi|33402359|gb|CF207986.1|CF207986
EST:     CTGCTGTCATCAGAGAAGCAATTTCAAACTATTGAGAGGCTTTTTGAACG                         GCTAGTTGCAAAGACAACACAGCTGGAGGGTGNNNNNNNGCAGAAAGAGAC
genomic: CTGCTGTCATCAGAGAAGCAATTTCAAACTATTGAGAGGCTTTTTGAACGgtcagtataa ... ttggaagcagGCTAGTTGCAAAGACAACACAGCTGGAGGGTGAAAAAAAGCAGAAAGAGAC
EST: gi|33402278|gb|CF207905.1|CF207905
EST:     CTGCTGTCATCAGAGAAGCAATTTCAAACTATTGAGAGGCTTTTTGAACG                         GCTAGTTGCAAAGACAACACAGCTGGAGGGTGNNNNNNNGCAGAAAGAGAC
genomic: CTGCTGTCATCAGAGAAGCAATTTCAAACTATTGAGAGGCTTTTTGAACGgtcagtataa ... ttggaagcagGCTAGTTGCAAAGACAACACAGCTGGAGGGTGAAAAAAAGCAGAAAGAGAC
EST: gi|46911014|gb|CN546389.1|CN546389
EST:     CTGCTGTCATCAGAGAAGCAACTTCAAACTATTGAGAGGCTTTTTGAACG                         GCTAGTTGCAAAGACAACACAGCTGGAGGGTGNNNNNNNGCAGAAAGAGAC
genomic: CTGCTGTCATCAGAGAAGCAATTTCAAACTATTGAGAGGCTTTTTGAACGgtcagtataa ... ttggaagcagGCTAGTTGCAAAGACAACACAGCTGGAGGGTGAAAAAAAGCAGAAAGAGAC
EST: gi|161712683|gb|FC062255.1|FC062255
EST:     CTGCTGTCATCAGAGAAGCAATTTCAAACTATTGAGAGGCTTTTTGAACG                         C
genomic: CTGCTGTCATCAGAGAAGCAATTTCAAACTATTGAGAGGCTTTTTGAACGgtcagtataa ... ttggaagcag-
EST: gi|161712683|gb|FC062255.1|FC062255
EST:     CTGCTGTCATCAGAGAAGCAATTTCAAACTATTGAGAGGCTTTTTGAACG                         C
genomic: CTGCTGTCATCAGAGAAGCAATTTCAAACTATTGAGAGGCTTTTTGAACGgtcagtataa ... ttggaagcag-
EST: gi|161712683|gb|FC062255.1|FC062255
EST:     CTGCTGTCATCAGAGAAGCAATTTCAAACTATTGAGAGGCTTTTTGAACG                         C
genomic: CTGCTGTCATCAGAGAAGCAATTTCAAACTATTGAGAGGCTTTTTGAACGgtcagtataa ... ttggaagcag-
EST: gi|45770840|gb|CN006692.1|CN006692
EST:     CTGCTGTCATCAGAGAAGCAATTTCAAACTATTGAGAGGCTTTTTGAACG                         GCTAGTTGCAAAGACAACACAGCTGGAGGGTGNNNNNNNGCAGAAAGAGAC
genomic: CTGCTGTCATCAGAGAAGCAATTTCAAACTATTGAGAGGCTTTTTGAACGgtcagtataa ... ttggaagcagGCTAGTTGCAAAGACAACACAGCTGGAGGGTGAAAAAAAGCAGAAAGAGAC
EST: gi|32245217|gb|CD711036.1|CD711036
EST:     CTGCTGTCATCAGAGAAGCAATTTCAAACTATTGAGAGGCTTTTTGAACG                         GCTAGTTGCAAAGACAACACAGCTGGAGGGTGNNNNNNNGCAGAAAGAGAC
genomic: CTGCTGTCATCAGAGAAGCAATTTCAAACTATTGAGAGGCTTTTTGAACGgtcagtataa ... ttggaagcagGCTAGTTGCAAAGACAACACAGCTGGAGGGTGAAAAAAAGCAGAAAGAGAC
EST: gi|27581566|gb|CB004261.1|CB004261
EST:     CTGCTGTCATCAGAGAAGCAATTTCAAACTATTGAGAGGCTTTTTGAACG                         GCTAGTTGCAAAGACAACACAGCTGGAGGGTG
genomic: CTGCTGTCATCAGAGAAGCAATTTCAAACTATTGAGAGGCTTTTTGAACGgtcagtataa ... ttggaagcagGCTAGTTGCAAAGACAACACAGCTGGAGGGTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tctttgcaagctactttcctgactgattttattatttaattttgtttggaagcagGCTAGTTGCAAAGACAACACAGCTGGAGGGTGAAAAAAAGCAGAAAGAGACTGAAGTCCAGAAACTTATGGAAGAAAATGTGAGGTTGAGTGCTCTTCTT
                                       ttttgttt  CT-rich tract
                   tgactgattttattat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tttgtaaacctctttctctgtggtggtttctatttttagccttcctctttgcaagctactttcctgactgattttattatttaattttgtttggaagcagGCTAGTTGCAAAGACAACACAGCTGGAGGGTGAAAAAAAGCAGAAAGAGACTGAAGTCCAGAAACTTATGGAAGAAAATGTGAGGTTGAGTGCTCTTCTT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA
- - - - - - - - - -gtggtgg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ttcctga