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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tggtgctgagtctgcagttgctcctttccatcttgtttgtgattttagtatccatcccttattaatgtgttttctacaatattttcttatttgcatgcagGTTTTGGGCACCCCAACAAGAGAGGAAATTAAGTGCATGAATCCCAATTACACAGAATTTAAATTCCCACAAATTAAAGCCCACCCATGGCACAAG

Basic information

species Vitis vinifera
transcript Vv07s0005g02100.t01
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv07s0005g02100.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: LOC_Os05g04340.2 (Oryza sativa), 3'ss of exon 9
tggtgctgagtctgcagttgctcctttccatcttgtttgtgattttagtatccatcccttattaatgtgttttctacaatattttcttatttgcatgcagGTTTTGGGCACCCCAACAAGAGAGGAAATTAAGTGCATGAATCCCAATTACACAGAATTTAAATTCCCACAAATTAAAGCCCACCCATGGCACAAG
                     |   ||  |||||| ||      |    |||  |||||| ||  ||| ||  || | |  |       | | |   |||||| |||| ||||| ||| ||||||| |||||||||||||| || |||||||| || |||||||| || ||||| ||||| |||||||||||||||
--------------------gtaaattatatcttgcttcca---tcgaaatcactccctttttgttgt-ttacctcctacttaactgactattctctcagGTTCTGGGTACCCCTACACGAGAGGAGATTAAGTGCATGAACCCAAATTACACCGAGTTTAAATTTCCGCAAATCAAAGCTCACCCATGGCACAAG

upper sequence: Vv07s0005g02100.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: LOC_Os01g19150.4 (Oryza sativa), 3'ss of exon 8
tggtgctgagtctgcagttgctcctttccatcttgtttgtgattttagtatccatcccttattaatgtgttttctacaatattttcttatttgcatgcagGTTTTGGGCACCCCAACAAGAGAGGAAATTAAGTGCATGAATCCCAATTACACAGAATTTAAATTCCCACAAATTAAAGCCCACCCATGGCACAAG
    |     ||||   | | |   |   || || ||      | |||| |||  |  || ||   |  |  |  |  | | || ||    | ||| |||||  |||| || |||||||| || ||||| ||    |||||||| || ||||| || ||||| ||||| ||||| ||||| |||||||||||||||
----gtaacatctgatttagtttagtggaatattattcta---tgtagtttcccccttttcttttagc-tcatgcaggagacttactgtacttcattcagGTACTGGGTACTCCAACAAGGGAAGAAATCAAACATATGAATCCGAACTACACTGAGTTTAAGTTCCCCCAAATCAAAGCTCACCCATGGCACAAG

upper sequence: Vv07s0005g02100.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: GRMZM2G155836_T01 (Zea mays), 3'ss of exon 9
tggtgctgagtctgcagttgctcctttccatcttgtttgtgattttagtatccatcccttattaatgtgttttctacaatattttcttatttgcatgcagGTTTTGGGCACCCCAACAAGAGAGGAAATTAAGTGCATGAATCCCAATTACACAGAATTTAAATTCCCACAAATTAAAGCCCACCCATGGCACAAG
                   |     | | |||||  |   ||||  |    |     | |||   ||  ||  || |||| |  ||| ||   |   |||||| ||||||| || ||| | || |||||||||||||||||||| ||||| || || ||||||||||| ||||| ||||| ||||||||||| |||
-------------------gtaaactactatctttgtcccgattaaa----ctcctgcatatcgttgctttacctccaatttaatctcatcctctctcagGTTCTGGGCACACCCACACGTGAAGAAATTAAGTGCATGAATCCAAATTATACCGAGTTTAAATTCCCGCAAATCAAAGCTCACCCATGGCATAAG

upper sequence: Vv07s0005g02100.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: GRMZM2G075992_T01 (Zea mays), 3'ss of exon 5
tggtgctgagtctgcagttgctcctttccatcttgtttgtgattttagtatccatcccttattaatgtgttttctacaatattttcttatttgcatgcagGTTTTGGGCACCCCAACAAGAGAGGAAATTAAGTGCATGAATCCCAATTACACAGAATTTAAATTCCCACAAATTAAAGCCCACCCATGGCACAAG----
               |||  || ||||| ||      | |   ||   ||   |  | ||   | |    |          | || || |||     |||||| | || || |||||| | || ||||||||| |||||||||| || ||||| |||||||| || || ||||| ||||| ||||||||||||||     
----------gtaatagtgacttctttcaattgaagatttagctt-gctagttacacatttccagttgactcatggaggcttatttttcttt-----cagGTTCTAGGTACTCCAACACGGGATGAAATTAAGCGCATGAATCCAAACTACACCGAATTTAAGTTTCCGCAAATCAAAGCTCACCCATGGCACAAAGTAA

upper sequence: Vv07s0005g02100.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: GLYMA10G01280.1 (Glycine max), 3'ss of exon 9
tggtgctgagtctgcagttgctcctttccatcttgtttgt-gattttagtatccatcccttattaatgtgtt-----ttctacaatattttcttatttgcatgcagGTTTTGGGCACCCCAACAAGAGAGGAAATTAAGTGCATGAATCCCAATTACACAGAATTTAAATTCCCACAAATTAAAGCCCACCCATGGCACAAG
      || |  |||| || ||| |  | | ||||||||| ||| ||  ||    | || |  | || | ||     ||||  |    | | | |||  ||| |||||||| || ||||||||||| || ||||| |||||||||||||| ||||| || || |  ||||| |||||||||||||| |||||||||||||||
------tgtgattgcattttctcttaactagcttgtttgtagatattcataatagttcccttgttatcttttcatacttctgaagaggtctgtgattcacattcagGTTTTAGGTACCCCAACAAGGGAAGAAATCAAGTGCATGAATCCTAATTATACCGAGTCCAAATTTCCACAAATTAAAGCTCACCCATGGCACAAG

upper sequence: Vv07s0005g02100.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: GLYMA02G01220.1 (Glycine max), 3'ss of exon 9
-----tggtgctgagtctgcagttgctcctttccatcttgtttgtgattttagtatccatcccttattaatgtgttttctacaatattttcttatttgcatgcagGTTTTGGGCACCCCAACAAGAGAGGAAATTAAGTGCATGAATCCCAATTACACAGAATTTAAATTCCCACAAATTAAAGCCCACCCATGGCACAAG
     |  |  |    |    |||     ||||| | |||  |     || |||  || |    | ||   ||  ||   |  | ||||    |||  |||||||||||| || ||||| ||||| || ||||| ||||| |||||||| |||||||| || || ||||| |||||||||||||| || |||||||| |||
atccataataatagtccccttgttttatttttcccttttgcctca---ttcagtg-ccgtgttatctttgagtacttgtaaagagatttggg-attcacatgcagGTTTTAGGAACCCCGACAAGGGAAGAAATCAAGTGTATGAATCCTAATTACACCGAGTTCAAATTTCCACAAATTAAAGCTCATCCATGGCATAAG

upper sequence: Vv07s0005g02100.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: PP1S306_62V6.1 (Physcomitrella patens), 3'ss of exon 7
-------------------------tggtgctgagtctgcagttgctccttt--ccatcttgtttgtgattttagtatccatcccttatta-atgtgttttctacaatattttcttatttgcatg---cagGTTTTGGGCACCCCAACAAGAGAGGAAATTAAGTGCATGAATCCCAATTACACAGAATTTAAATTCCCACAAATTAAAGCCCACCCATGGCACAAG
                         | |||  ||     |   | ||   ||  |  | | ||||||   | | |||||     | | ||  |||||  |    |  |         ||| | ||   ||||||||||| || || ||  | ||||| || |||||||||||||| || |||||||| || || || |||||||| || || ||||| |||||||| 
gtgggacacacgtggtacacgttgtttgtgtggaagggtcgccttctgggttggcggtttggtttgtagctgtggtatcttgttcgtgttggatgtgagtatggcgttgaccagacgtttccgtgtggcagGTTTTGGGGACACCGACTCGTGAGGAGATCAAGTGCATGAATCCGAACTACACAGAGTTCAAGTTTCCACAAATCAAGGCGCACCCGTGGCACAAA

upper sequence: Vv07s0005g02100.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: EFJ07216 (Selaginella moellendorffii), 3'ss of exon 9
tggtgctgagtctgcagttgctcctttccatcttgtttgtgattttagtatccatcccttattaatgtgttttctacaatattttcttatttgcatgcagGTTTTGGGCACCCCAACAAGAGAGGAAATTAAGTGCATGAATCCCAATTACACAGAATTTAAATTCCCACAAATTAAAGCCCACCCATGGCACAAG
                   |  |   | |||  |   | |  ||||  | |   |   ||   | |   | ||   ||| | || ||| |      |||||| || || || || ||  | |||||||| || ||||||||||| || ||||| || ||||| ||||| || |||||||| || || |||||||||
-------------------gtacgcatgcattcttgctcttttttttctgtt--ttttttgcgagtcgctcttgctcaagacttgctttt------gcagGTCTTAGGTACTCCTACTCGCGAGGAAATCAAATGCATGAATCCAAACTACACGGAGTTTAAGTTCCCTCAGATTAAAGCGCATCCCTGGCACAAG

upper sequence: Vv07s0005g02100.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: EFJ07923 (Selaginella moellendorffii), 3'ss of exon 9
tggtgctgagtctgcagttgctcctttccatcttgtttgtgattttagtatccatcccttattaatgtgttttctacaatattttcttatttgcatgcagGTTTTGGGCACCCCAACAAGAGAGGAAATTAAGTGCATGAATCCCAATTACACAGAATTTAAATTCCCACAAATTAAAGCCCACCCATGGCACAAG
                                  |  ||   | ||  | ||  |    | ||   | ||         |     |||  ||   ||||||| || || || || ||  | |||||||| || ||||||||||| || ||||| || ||||| ||||| || |||||||| || || |||||||||
------------------------------gtacgcatgcattcttgctctcttttttctttttgcgagtcgctcttgctcaagacttgctt--ttgcagGTCTTAGGTACTCCTACTCGGGAGGAAATCAAATGCATGAATCCAAACTACACGGAGTTTAAGTTCCCTCAGATTAAAGCGCATCCCTGGCACAAG

upper sequence: Vv07s0005g02100.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: EFJ04915 (Selaginella moellendorffii), 3'ss of exon 8
tggtgctgagtctgcagttgctcctttccatcttgtttgtgattttagtatccatcccttattaatgtgttttctacaatattttcttatttgcatgcagGTTTTGGGCACCCCAACAAGAGAGGAAATTAAGTGCATGAATCCCAATTACACAGAATTTAAATTCCCACAAATTAAAGCCCACCCATGGCACAAG
                                      ||    |   | |   | ||||||   ||  |   |    |||   |   | |||   ||||||| | || ||||| ||  | ||||| || ||||| ||||||||||| ||||| ||||| || ||||| ||||| || |||||||| |||||||||
--------------------------------------gttggctcgttgtttttgccttat-ggtggctgggcgctcataaagttggacttgg--gcagGTTCTTGGAACCCCTACTCGCGAGGAGATCAAGTGTATGAATCCCAACTACACGGAATTCAAGTTCCCTCAAATCAAGGCCCACCCTTGGCACAAG

upper sequence: Vv07s0005g02100.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: EFJ10962 (Selaginella moellendorffii), 3'ss of exon 8
tggtgctgagtctgcagttgctcctttccatcttgtttgtgattttagtatccatcccttattaatgtgttttctacaatattttcttatttgcatgcagGTTTTGGGCACCCCAACAAGAGAGGAAATTAAGTGCATGAATCCCAATTACACAGAATTTAAATTCCCACAAATTAAAGCCCACCCATGGCACAAG
                                      ||    |   | |   | ||||||   ||  |   |    |||   |   | ||||  ||||||| | || ||||| ||  | ||||| || ||||| ||||||||||| ||||| ||||| || ||||| ||||| || ||||| || |||||||||
--------------------------------------gttggctcgttgtttttgccttat-ggtggctgggcgctcataaagttggacttgc--gcagGTTCTTGGAACCCCTACTCGCGAGGAGATCAAGTGTATGAATCCCAACTACACGGAATTCAAGTTCCCTCAAATCAAGGCCCATCCTTGGCACAAG

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|33405137|gb|CF210764.1|CF210764
EST:     CTCTCTTTCCCGGGGAGAGTGGAGTGGATCAGCTTGTGGAAATCATTAAG                         GTTTTGGGCACCCCAACAAGGGAGGAAATTAAGTGCATGAATCCCAATTAC
genomic: CTCTCTTTCCCGGGGAGAGTGGAGTGGATCAGCTTGTGGAAATCATTAAGgtgatcatac ... ttgcatgcagGTTTTGGGCACCCCAACAAGAGAGGAAATTAAGTGCATGAATCCCAATTAC
EST: gi|26262991|gb|CA814054.1|CA814054
EST:     CTCTCTTTCCCGGGGAGAGTGGAGTGGATCAGCTTGTGGAAATCATTAAG                         GTTTTGGGCACCCCAACAAGAGAGGAAATTAAGTGCATGAATCCCAATTAC
genomic: CTCTCTTTCCCGGGGAGAGTGGAGTGGATCAGCTTGTGGAAATCATTAAGgtgatcatac ... ttgcatgcagGTTTTGGGCACCCCAACAAGAGAGGAAATTAAGTGCATGAATCCCAATTAC
EST: gi|161712353|gb|FC061927.1|FC061927
EST:     CTCTCTTTCCCGGGGAGAGTGGAGTGGATCAGCTTGTGGAAATCATTAAG                         GTTTTGGGCACCCCAACAAGAGAGGAAATTAAGTGCATGAATCCCAATTAC
genomic: CTCTCTTTCCCGGGGAGAGTGGAGTGGATCAGCTTGTGGAAATCATTAAGgtgatcatac ... ttgcatgcagGTTTTGGGCACCCCAACAAGAGAGGAAATTAAGTGCATGAATCCCAATTAC
EST: gi|110360806|gb|EC924193.1|EC924193
EST:     CTCTCTTTCCCGGGGAGAGTGGAGTGGATCAGCTTGTGGAAATCATTAAG                         GTTTTGGGCACCCCAACAAGAGAGGAAATTAAGTGCATGAATCCCAATTAC
genomic: CTCTCTTTCCCGGGGAGAGTGGAGTGGATCAGCTTGTGGAAATCATTAAGgtgatcatac ... ttgcatgcagGTTTTGGGCACCCCAACAAGAGAGGAAATTAAGTGCATGAATCCCAATTAC
EST: gi|110710881|gb|EE087442.1|EE087442
EST:     CTCTCTTTCCCGGGGAGAGTGGAGTGGATCAGCTTGTGGAAATCATTAAG                         GTTTTGGGCACCCCAACA-GAGAGGAAATTAAGTGCATGAATCCCAATTAC
genomic: CTCTCTTTCCCGGGGAGAGTGGAGTGGATCAGCTTGTGGAAATCATTAAGgtgatcatac ... ttgcatgcagGTTTTGGGCACCCCAACAAGAGAGGAAATTAAGTGCATGAATCCCAATTAC
EST: gi|33405222|gb|CF210849.1|CF210849
EST:     CTCTCTTTCCCGGGGAGAGTGGAGTGGATCAGCTTGTGGAAATCATTAAG                         GTTTTGGGCACCCCAACAAGGGAGGAAATTAAGTGCATGAATCCCAATTAC
genomic: CTCTCTTTCCCGGGGAGAGTGGAGTGGATCAGCTTGTGGAAATCATTAAGgtgatcatac ... ttgcatgcagGTTTTGGGCACCCCAACAAGAGAGGAAATTAAGTGCATGAATCCCAATTAC
EST: gi|110383074|gb|EC947423.1|EC947423
EST:     CTCTCTTTCCCGGGGAGAGTGGAGTGGATCAGCTTGTGGAAATCATTAAG                         GTTTTGGGCACCCCAACAAGGGAGGAAATTAAGTGCATGAATCCCAATTAC
genomic: CTCTCTTTCCCGGGGAGAGTGGAGTGGATCAGCTTGTGGAAATCATTAAGgtgatcatac ... ttgcatgcagGTTTTGGGCACCCCAACAAGAGAGGAAATTAAGTGCATGAATCCCAATTAC
EST: gi|110378688|gb|EC943832.1|EC943832
EST:     CTCTCTTTCCCGGGGAGAGTGGAGTGGATCAGCTTGTGGAAATCATTAAG                         GTTTTGGGCACCCCAACAAGGGAGGAAATTAAGTGCATGAATCCCAATTAC
genomic: CTCTCTTTCCCGGGGAGAGTGGAGTGGATCAGCTTGTGGAAATCATTAAGgtgatcatac ... ttgcatgcagGTTTTGGGCACCCCAACAAGAGAGGAAATTAAGTGCATGAATCCCAATTAC
EST: gi|110700287|gb|EE078155.1|EE078155
EST:     CTCTCTTTCCCGGGGAGAGTGGAGTGGATCAGCTTGTGGAAATCATTAAG                         GTTTTGGGCACCCCAACAAGAGAGGAAATTAAGTGCATGAATCCCAATTAC
genomic: CTCTCTTTCCCGGGGAGAGTGGAGTGGATCAGCTTGTGGAAATCATTAAGgtgatcatac ... ttgcatgcagGTTTTGGGCACCCCAACAAGAGAGGAAATTAAGTGCATGAATCCCAATTAC
EST: gi|30252766|gb|CB970317.1|CB970317
EST:     CTCTCTTTCCCGGGGAGAGTGGAGTGGATCAGCTTGTGGAAATCATTAAG                         GTTTTGGGCACCCCAACAAGGGAGGAAATTAAGTGCATGAATCCCAATTAC
genomic: CTCTCTTTCCCGGGGAGAGTGGAGTGGATCAGCTTGTGGAAATCATTAAGgtgatcatac ... ttgcatgcagGTTTTGGGCACCCCAACAAGAGAGGAAATTAAGTGCATGAATCCCAATTAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tagtatccatcccttattaatgtgttttctacaatattttcttatttgcatgcagGTTTTGGGCACCCCAACAAGAGAGGAAATTAAGTGCATGAATCCCAATTACACAGAATTTAAATTCCCACAAATTAAAGCCCACCCATGGCACAAG
              tattaat  putative branch site (score: 2)
                                    ttttcttattt  putative PPT
             ttattaatgtgttttc  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tggtgctgagtctgcagttgctcctttccatcttgtttgtgattttagtatccatcccttattaatgtgttttctacaatattttcttatttgcatgcagGTTTTGGGCACCCCAACAAGAGAGGAAATTAAGTGCATGAATCCCAATTACACAGAATTTAAATTCCCACAAATTAAAGCCCACCCATGGCACAAG

tggtgct
- - - - - tctgcag
- - - - - - - - - - - cctttcc