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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aatttttgacaaatatgatcgaaactctgtaaatcgtctctctagttcagcaaattttcagaaactgaatttggatatttttggaattgggtttctgcagGAATGGCTCTGTACGGTGAAAAGGAGTGGTACTTCTTCTCTCCAAGGGACCGCAAATATCCCAACGGTTCAAGGCCTAACCGGGCGGCCGGATCCGGCTA

Basic information

species Vitis vinifera
transcript Vv07s0031g02610.t01
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv07s0031g02610.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: LOC_Os05g34830.1 (Oryza sativa), 3'ss of exon 1
aatttttgacaaatatgatcgaaactctgtaaatcgtctctctagttca-gcaaattttcagaaactgaatttggatatttttggaattgggtttctgcagGAATGGCTCTGTACGGTGAAAAGGAGTGGTACTTCTTCTCTCCAAGGGACCGCAAATATCCCAACGGTTCAAGGCCTAACCGGGCGGCCGGATCCGGCTA
                        ||||   |     |||     | || ||||| ||  ||  ||||    | |||  |        ||  |   |||||||||||| |||||||| || |||||||||||||||||||| ||  |||||||||| || || ||||| ||  |||| ||||| || ||||| ||||| ||
------------------gtacgtctcttccatctccctcctccatccatgcaaacttatagctactgttcatcgatcgtcca-----tgactccatgcagGAATGGCGCTGTACGGCGAGAAGGAGTGGTACTTCTTCTCCCCTCGGGACCGCAAGTACCCGAACGGGTCGCGGCCGAACCGCGCCGCCGGGTCCGGGTA

upper sequence: Vv07s0031g02610.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: LOC_Os05g34830.2 (Oryza sativa), 3'ss of exon 1
----aatttttgacaaatat-gatcgaaactctgtaaatcgtctctctagttca-gcaaattttcagaaactgaatttggatatttttggaattgggtttctgcagGAATGGCTCTGTACGGTGAAAAGGAGTGGTACTTCTTCTCTCCAAGGGACCGCAAATATCCCAACGGTTCAAGGCCTAACCGGGCGGCCGGATCCGGCTA
     ||   || ||  |    |      ||||   |     |||     | || ||||| ||  ||  ||||    | |||  |        ||  |   |||||||||||| |||||||| || |||||||||||||||||||| ||  |||||||||| || || ||||| ||  |||| ||||| || ||||| ||||| ||
gttcgatccatggcatctcccaagtacgtctcttccatctccctcctccatccatgcaaacttatagctactgttcatcgatcgtcca-----tgactccatgcagGAATGGCGCTGTACGGCGAGAAGGAGTGGTACTTCTTCTCCCCTCGGGACCGCAAGTACCCGAACGGGTCGCGGCCGAACCGCGCCGCCGGGTCCGGGTA

upper sequence: Vv07s0031g02610.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: LOC_Os01g66120.1 (Oryza sativa), 3'ss of exon 1
aatttttgacaaatatgatcgaa-actctgtaaatcgtctctctagttca-gcaaattttcagaaactga---atttggatatttttggaattgggtttctgcagGAATGGCTCTGTACGGTGAAAAGGAGTGGTACTTCTTCTCTCCAAGGGACCGCAAATATCCCAACGGTTCAAGGCCTAACCGGGCGGCCGGATCCGGCTA
    |  || ||   |  ||    |  ||   |||| || |     |  | ||     |  |   | |||   |||||| |   ||||   ||||  || || ||| ||||| |||||||| || |||||||||||||||||||| ||  | |||||||| || || ||||| ||  |||| ||||| || ||||| || || ||
---gtacgataatcctcctcctccatcctcccaatcatcaccaccatcaacgccgtcgtgaattgattgattgatttggtttgatttg---ttggtgttgtgtagGGATGGCGCTGTACGGAGAGAAGGAGTGGTACTTCTTCTCCCCGCGAGACCGCAAGTACCCGAACGGGTCGCGGCCGAACCGCGCCGCCGGGTCGGGGTA

upper sequence: Vv07s0031g02610.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GRMZM2G014653_T03 (Zea mays), 3'ss of exon 1
-------------------aatttttgacaaatatgatcgaaactctgtaaatcgtctctctagttcagcaaattttcagaaactgaatttggatatttttggaattgggtttctgcagGAATGGCTCTGTACGGTGAAAAGGAGTGGTACTTCTTCTCTCCAAGGGACCGCAAATATCCCAACGGTTCAAGGCCTAACCGGGCGGCCGGATCCGGCTA
                      || |  ||       | | | |   || || |   |  ||       |         |  |   |||      |||  |  || |   | | |||||| ||||| |||||||| || |||||||||||||||||||| ||  |||||||||| || || ||||| || ||||| ||||| || |||||  | || ||
gtacgtcccgtcgtcctcggtcttcttgcagcagcagtagcagcc--gtgaaccaatttcctgtgcggccgtgacgatggcgagctaatcgatcgattgct--aactctctgtgtgcagGGATGGCGCTGTACGGCGAGAAGGAGTGGTACTTCTTCTCCCCGCGGGACCGCAAGTACCCGAACGGGTCCAGGCCCAACCGCGCCGCCGGGGCTGGGTA

upper sequence: Vv07s0031g02610.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GRMZM2G180328_T01 (Zea mays), 3'ss of exon 1
-----aatttttgacaaatatgatcgaaactctgtaaatcgtctctctagttcagcaaattttcagaaactgaatttggatatttttggaattgg-gtttctgcagGAATGGCTCTGTACGGTGAAAAGGAGTGGTACTTCTTCTCTCCAAGGGACCGCAAATATCCCAACGGTTCAAGGCCTAACCGGGCGGCCGGATCCGGCTA
       |  |   |             | ||  |    |   | |||      ||    |  | |   |||| |   ||| |   |   | ||  || | |||||| ||||| |||||||| || |||||||||||||||||||| ||  |||||||||| || || ||||| ||  |||| ||||| || |||||  |||| ||
gtacgtgtcgtccgccgccgctccacgcagtcgttgttccaggtttcttagctcgccctgtacctgctgctgactcctgatctcggtactactgctgtctgtgcagGGATGGCGCTGTACGGCGAGAAGGAGTGGTACTTCTTCTCCCCGCGGGACCGCAAGTACCCGAACGGGTCGCGGCCGAACCGCGCCGCCGGCGCCGGGTA

upper sequence: Vv07s0031g02610.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GRMZM2G123667_T05 (Zea mays), 3'ss of exon 1
-aatttttgacaaat--atgatcgaaact--ctgtaaatcgtctct-ctagttcagcaaattttcagaaactgaatttggatatt--tttggaattgggtttctgcagGAATGGCTCTGTACGGTGAAAAGGAGTGGTACTTCTTCTCTCCAAGGGACCGCAAATATCCCAACGGTTCAAGGCCTAACCGGGCGGCCGGATCCGGCTA
  |  |   ||||    || ||||  |     ||| | |  ||    |||| |  |  |     | |   ||||  |       |    |||   | |||   |||||  | |||  |    || || |||||||||||||||||||| ||  | |||||||| || || || || || ||||||||||||||||||||  | || ||
gtacgtcgaacaatcggatcatcgtcagcgagtgttagttatccgagctagctaggtgacgaccccgcg-ctgacctcatcagctggcatggtgatcggtggttgcagAGAAGGCGTTCGGTGGGGAGAAGGAGTGGTACTTCTTCTCGCCGCGCGACCGCAAGTACCCGAATGGCTCCAGGCCTAACCGGGCGGCCGGGACAGGGTA

upper sequence: Vv07s0031g02610.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GLYMA05G32850.1 (Glycine max), 3'ss of exon 1
-------------------------aatttttg-acaaatatgatcgaaactctgtaaatcgtctctctagttcagcaaattttcagaaactgaatttggatatttttggaattgggtttctg----cagGAATGGCTCTGTACGGTGAAAAGGAGTGGTACTTCTTCTCTCCAAGGGACCGCAAATATCCCAACGGTTCAAGGCCTAACCGGGCGGCCGGATCCGGCTA
                         | | | || |    | ||          | | | | |  |||  | |  |  | |||||      ||  |  |  |  |  |   | ||  |||| |     |||  |||||||| |||||||| || ||||||||||| ||||||||  | ||||| ||||| || |||||||| || || |||||||| ||||||  ||| ||
gtacctttttttcttttctcactctagtctctgtattcttttgccttttttaatttcattagggtcttaattctactacattttttttctctccaccttaaagtcctattatttatgtttttatgtacagAGATGGCTCTTTACGGTGAGAAAGAGTGGTACTTTTTCTCTCCTCGAGACCGAAAATACCCAAACGGTTCGAGACCGAACCGGGCTGCCGGAAGCGGGTA

upper sequence: Vv07s0031g02610.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GLYMA04G38560.1 (Glycine max), 3'ss of exon 1
aatttttgacaaatatgatcgaaactctgtaaatcgtctctctagttcagcaaattttcagaaactgaatttggatatttttggaattgggtttctgcagGAATGGCTCTGTACGGTGAAAAGGAGTGGTACTTCTTCTCTCCAAGGGACCGCAAATATCCCAACGGTTCAAGGCCTAACCGGGCGGCCGGATCCGGCTA
    || |   | | |  |      |  ||     ||    | | |||      | |     |  | ||||  |||   ||  || |||| |   ||||| ||| | | | ||||| || || || ||||||||||| |||||  ||||||| ||||| || ||||||||| |||| ||||| || ||||||  ||||||
---gttcgtttagtttcttatgggtttcgttttgtgtgaaaccaattccaattgtatcgtttagttcaatt--gattgattatgagttgg-tcaatgcagAAATTGGTTTTTACGGCGAGAAAGAATGGTACTTCTTTTCTCCTCGGGACCGGAAATACCCGAACGGTTCACGGCCGAACCGCGCCGCCGGAAGCGGCTA

upper sequence: Vv07s0031g02610.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: AT5G08790.1 (Arabidopsis thaliana), 3'ss of exon 1
aatttttgacaaatatgatcgaaactctgtaaatcgtctctc-tagttcagcaaattttcagaaactgaatttggatatttttggaattgggtttctg-cagGAATGGCTCTGTACGGTGAAAAGGAGTGGTACTTCTTCTCTCCAAGGGACCGCAAATATCCCAACGGTTCAAGGCCTAACCGGGCGGCCGGATCCGGCTA
            | |     |    |||   |||  | | ||             | |||   ||  |   |||  ||||       |||   ||||  |||  ||| |||||||||| || || ||||||||||||||||| || || || || ||||| || ||||||||  | ||||||||||| || ||| |||| ||
----------gtacacctatgggcttcttctaattatttttcgcgaaatcatgtgtcttcgagaatcg---ttgtttattgagatgtttgttcttctttcagAGATGTCTCTGTACGGAGAGAAAGAGTGGTACTTCTTCTCACCTAGAGATCGGAAATACCCAAACGGTTCGCGTCCTAACCGGGCAGCAGGAACCGGTTA

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|161711194|gb|FC058664.1|FC058664
EST:     GATTATTGCCGAGGTTGATCTCTACAAGTACGATCCATGGCAGCTTCCAG                         GAATGGCTCTGTACGGTGAAAAGGAGTGGTACTTCTTCTCTCCAAGGGACC
genomic: GATTATTGCCGAGGTTGATCTCTACAAGTACGATCCATGGCAGCTTCCAGgtattttttt ... gtttctgcagGAATGGCTCTGTACGGTGAAAAGGAGTGGTACTTCTTCTCTCCAAGGGACC
EST: gi|161713294|gb|FC064024.1|FC064024
EST:     GATTATTGCCGAGGTTGATCTCTACAAGTACGATCCATGGCAGCTTCCAG                         GAATGGCTCTGTACGGTGAAAAGGAGTGGTACTTCTTCTCTCCAAGGGACC
genomic: GATTATTGCCGAGGTTGATCTCTACAAGTACGATCCATGGCAGCTTCCAGgtattttttt ... gtttctgcagGAATGGCTCTGTACGGTGAAAAGGAGTGGTACTTCTTCTCTCCAAGGGACC
EST: gi|161708409|gb|FC057859.1|FC057859
EST:     GATTATTGCCGAGGTTGATCTCTACAAGTACGATCCATGGCAGCTTCCAG                         GAATGGCTCTGTACGGTGAAAAGGAGTGGTACTTCTTCTCTCCAAGGGACC
genomic: GATTATTGCCGAGGTTGATCTCTACAAGTACGATCCATGGCAGCTTCCAGgtattttttt ... gtttctgcagGAATGGCTCTGTACGGTGAAAAGGAGTGGTACTTCTTCTCTCCAAGGGACC
EST: gi|161708027|gb|FC056076.1|FC056076
EST:     GATTATTGCCGAGGTTGATCTCTACAAGTACGATCCATGGCAGCTTCCAG                         GAATGGCTCTGTACGGTGAAAAGGAGTGGTACTTCTTCTCTCCAAGGGACC
genomic: GATTATTGCCGAGGTTGATCTCTACAAGTACGATCCATGGCAGCTTCCAGgtattttttt ... gtttctgcagGAATGGCTCTGTACGGTGAAAAGGAGTGGTACTTCTTCTCTCCAAGGGACC
EST: gi|37185841|gb|CF605194.1|CF605194
EST:     GATTATTGCCGAGGTTGATCTCTACAAGTACGATCCATGGCAGCTTCCAG                         GAATGGCTCTGTACGGTGAAAAGGAGTGGTACTTCTTCTCTCCAAGGGACC
genomic: GATTATTGCCGAGGTTGATCTCTACAAGTACGATCCATGGCAGCTTCCAGgtattttttt ... gtttctgcagGAATGGCTCTGTACGGTGAAAAGGAGTGGTACTTCTTCTCTCCAAGGGACC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttcagcaaattttcagaaactgaatttggatatttttggaattgggtttctgcagGAATGGCTCTGTACGGTGAAAAGGAGTGGTACTTCTTCTCTCCAAGGGACCGCAAATATCCCAACGGTTCAAGGCCTAACCGGGCGGCCGGATCCGGCTA
                                              tttctgc  CT-rich tract
                      aatttggatattttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aatttttgacaaatatgatcgaaactctgtaaatcgtctctctagttcagcaaattttcagaaactgaatttggatatttttggaattgggtttctgcagGAATGGCTCTGTACGGTGAAAAGGAGTGGTACTTCTTCTCTCCAAGGGACCGCAAATATCCCAACGGTTCAAGGCCTAACCGGGCGGCCGGATCCGGCTA

- - - - acaaata
- - - - - - - - - - - - ctctgta
- - - - - - - - - - - - - - - - - - tctctct
- - - - - - - - - - - - - - - - - - - - - - - tcagcaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - cagaaac