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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttagcatggttttttcatcttatccagtctcactttctgtgctgattactgaataggcgacaaaaatataaaccataatcatatgcagcagctgacttcatacatactgtatgataagaagatcgtgtttgataatagttttacttccttagGTAATTGTTGCCGATAACTACTTCACCGGTTCTAAGGACAATCTCAAGAAATGGATTGGTCATCCAAGATTTGAGCTTATTCGTCATG

Basic information

species Vitis vinifera
transcript Vv06s0004g04390.t01
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv06s0004g04390.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GRMZM2G165357_T02 (Zea mays), 3'ss of exon 2
gttagcatggttttttcatcttatccagtctcactttctgtgctgattactgaataggcgacaaaaatataaaccataatcatatgcagcagctgactt-catacatactgtatgataagaagatcgtgtttgataatagttttacttccttagGTAATTGTTGCCGATAACTACTTCACCGGTTCTAAGGACAATCTCAAGAAATGGATTGGTCATCCAAGATTTGAGCTTATTCGTCATG
                                       | | |||  |   | |      | |   | ||  | || ||  ||||   |   || ||| || ||||  || ||| |     ||   ||||         |||||| | |  |||| |||||||| |||||||  ||||| ||||| || ||||| || ||||| |||||||| || |||||||||||||| || |||||||
------------------------------------gtggggttgagcaaccattgaatt-ctagggtctatgctatcatgctatgggtc--ttgtcttgcagacattttggatgtt-----gactttgttc--------ttttacgttc--agGTCATTGTTGCTGATAACTTTTTCACTGGTTCAAAAGACAACCTGAAGAAGTGGATTGGCCACCCAAGATTTGAGCTCATCCGTCATG

upper sequence: Vv06s0004g04390.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA12G06990.1 (Glycine max), 3'ss of exon 3
gttagcatggttttttcatcttatccagtctcactttctgtgctgattactgaataggcgacaaaaatataaaccataatcatatgcagcagctgacttcatacatactgtatgataagaagatcgtgtttgataatagttttacttccttagGTAATTGTTGCCGATAACTACTTCACCGGTTCTAAGGACAATCTCAAGAAATGGATTGGTCATCCAAGATTTGAGCTTATTCGTCATG
                                                           | ||      ||    ||  |  | |  || || |   ||  |     || |   |  |    ||  || ||   ||   |      |  | |||| |||||||| |||||||||||||| || || |||||||| ||||| ||||||||||||||||||||||| ||||||||||||||||
-----------------------------------------------------------gtcagctgattagtttattgtgtttttgagtagttttgttttt-----cttttcaacgattctattatgcttacaaaacataacttctaatcagGTCATTGTTGCTGATAACTACTTCACTGGATCAAAGGACAACCTCAAAAAATGGATTGGTCATCCAAGATTCGAGCTTATTCGTCATG

upper sequence: Vv06s0004g04390.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA13G40960.1 (Glycine max), 3'ss of exon 4
--------------------gttagcatggttttttcatcttatccagtctcactttctgtgctgattactgaataggcgacaaaaatataaaccataatcatatgcagcagctga----cttcatacatact---gtatga--taagaagatcgtgtttgataatagttttacttccttagGTAATTGTTGCCGATAACTACTTCACCGGTTCTAAGGACAATCTCAAGAAATGGATTGGTCATCCAAGATTTGAGCTTATTCGTCATG
                     | |  ||| | |  |  |  | | || ||    |||   | ||||||  |  | ||  | || || |    | |||  | |||||    |  | |    |  |||| | |     || |||  | | ||  |  ||    |  ||   | |  ||  | ||||||||||||| || ||||||||||| || || |||||||| ||||| |||||||| ||||||||||||||||||||||| |||||||
gtaagtgggttatctatttgctcataatgttgtacttctgatgttcactcatgattt---tactgatt-ttatacagatgccataacttgctatcatcct-atatgtgataaataagatacagcatatagaactaagtttgacttgataaagttctgccacaatatctctgtgtttaatcagGTAATTGTTGCTGACAACTACTTCACTGGATCCAAGGACAACCTCAAAAAATGGATAGGTCATCCAAGATTTGAGCTTATCCGTCATG

upper sequence: Vv06s0004g04390.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA11G15020.1 (Glycine max), 3'ss of exon 3
gttagcatggttttttcatcttatccagtctcactttctgtgctgattactgaataggcgacaaaaatataaaccataatcatatgcagcagctgacttcatacatactgtatgataagaagatcgtgtttgataatagttttacttccttagGTAATTGTTGCCGATAACTACTTCACCGGTTCTAAGGACAATCTCAAGAAATGGATTGGTCATCCAAGATTTGAGCTTATTCGTCATG
                                                           |  |   |  ||    ||  |  | |  || || |   ||  |     || |     ||    ||  || ||   ||   |      |  | |||| |||||||| || ||||||||||| || || |||||||| ||||| |||||||||||||||||||||||||||||||| |||||||
-----------------------------------------------------------gttagctaattagtttattgtgtttttgagtagttttgttttt-----cttttcagcaattctattatgcttacaaaacataacttctaatcagGTCATTGTTGCTGACAACTACTTCACTGGATCAAAGGACAACCTCAAAAAATGGATTGGTCATCCAAGATTTGAGCTTATCCGTCATG

upper sequence: Vv06s0004g04390.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA15G04500.2 (Glycine max), 3'ss of exon 4
--------------------gttagcatggttttttcatcttatccagtctcactttctgtgctgattactgaataggcgacaaaaatataaaccataatcatatgcagcagctga----cttcatacatact---gtatgataagaagatcgtgtt-tgataatagttttacttccttagGTAATTGTTGCCGATAACTACTTCACCGGTTCTAAGGACAATCTCAAGAAATGGATTGGTCATCCAAGATTTGAGCTTATTCGTCATG
                     | |  ||| | | ||  |  | | || ||    |||   | |||| |  |  | ||  | || || |    | |||  | |||||    |  | |    |  |||| | |     || ||||  ||  |  ||  |   | || |  |||  ||  | |||| |||||||| || ||||||||||| || || ||||| || ||||| || ||||||||||||||||||||||||||||| |||||||
gtaagagggttatctatttgctcataatgttatatttctgatgttcactcatgattt---tactgact-ttatacagatggcataacttgctatcatcct-atatgtgataaataagatacagcatatagaactaagtttgatttgataaaagttctgccacaaaatctttgtttaatcagGTCATTGTTGCTGACAACTACTTCACTGGATCCAAGGATAACCTCAAAAAGTGGATTGGTCATCCAAGATTTGAGCTTATCCGTCATG

upper sequence: Vv06s0004g04390.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA11G15010.1 (Glycine max), 3'ss of exon 3
gttagcatggttttttcatcttatccagtctcactttctgtgctgattactgaataggcgacaaaaatataaaccataatcatatgcagcagctgacttcatacatactgtatgataagaagatcgtgtttgataatagttttacttccttagGTAATTGTTGCCGATAACTACTTCACCGGTTCTAAGGACAATCTCAAGAAATGGATTGGTCATCCAAGATTTGAGCTTATTCGTCATG
                                            | |  ||   | |    |     | |      |  | | ||  |  || | | |  | |  |||  ||| |       |   | | ||||| ||   |    |  | |||| |||||||| || ||||||||||| || ||||| ||||| || || | ||||||||| ||||||||||||||||| ||||||||||
--------------------------------------------gttagcttggttgatatctttt-tgttcttagttttgaaatttattagtt-attcaacaagtacgatataactttggaacaatatgtgatagtatgctggtctaatcagGTCATTGTTGCTGACAACTACTTCACTGGATCTAAAGACAACCTTAAAAGATGGATTGGCCATCCAAGATTTGAGCTAATTCGTCATG

upper sequence: Vv06s0004g04390.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA12G06980.2 (Glycine max), 3'ss of exon 2
gttagcatggttttttcatcttatccagtctcactttctgtgctgattactgaataggcgacaaaaatataaacc--ataatcatatgcagcagctgacttcatacatactgtatgataagaagatcgtgtttgataatagttttacttccttagGTAATTGTTGCCGATAACTACTTCACCGGTTCTAAGGACAATCTCAAGAAATGGATTGGTCATCCAAGATTTGAGCTTATTCGTCATG
                                                      | |  || |    | |   |    |  | | ||     || | | |  | |  |||  ||  | |     |   | | ||||| ||   ||   |  | |||| |||||||| || |||| |||||| || ||||| ||||| || || ||||||||||| ||||||||||| ||||| ||||||||||
------------------------------------------------------tggttgatatctttctgttcttagtttttaaattttttagtt-attcaacaagtacaataaaacattggaacaatatgtgatagtacgcttgtctaatcagGTCATTGTTGCTGACAACTTCTTCACTGGATCTAAAGACAACCTTAAAAAATGGATTGGCCATCCAAGATTCGAGCTAATTCGTCATG

upper sequence: Vv06s0004g04390.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA12G06980.3 (Glycine max), 3'ss of exon 3
gttagcatggttttttcatcttatccagtctcactttctgtgctgattactgaataggcgacaaaaatataaaccataatcatatgcagcagctgacttcatacatactgtatgataagaagatcgtgtttgataatagttttacttccttagGTAATTGTTGCCGATAACTACTTCACCGGTTCTAAGGACAATCTCAAGAAATGGATTGGTCATCCAAGATTTGAGCTTATTCGTCATG
                                            | |  ||   | |    |     | |      |  | | ||     || | | |  | |  |||  ||  | |     |   | | ||||| ||   ||   |  | |||| |||||||| || |||| |||||| || ||||| ||||| || || ||||||||||| ||||||||||| ||||| ||||||||||
--------------------------------------------gttggcttggttgatatctttc-tgttcttagtttttaaattttttagtt-attcaacaagtacaataaaacattggaacaatatgtgatagtacgcttgtctaatcagGTCATTGTTGCTGACAACTTCTTCACTGGATCTAAAGACAACCTTAAAAAATGGATTGGCCATCCAAGATTCGAGCTAATTCGTCATG

upper sequence: Vv06s0004g04390.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: AT3G46440.1 (Arabidopsis thaliana), 3'ss of exon 3
gttagcatggttttttcatcttatccagtctcactttctgtgctgattactgaataggcgacaaaaatataaaccataatcatatgcagcagctgacttcatacatactgtatgataagaagatcgtgtttgataatagttttacttccttagGTAATTGTTGCCGATAACTACTTCACCGGTTCTAAGGACAATCTCAAGAAATGGATTGGTCATCCAAGATTTGAGCTTATTCGTCATG
                                                                  ||  |||     |||  || ||  ||  |  || || |      | |||| |     |  |||||    ||| ||||  || |  |||| |||||||| |||||||| ||||| ||||| |||||||| || ||||| ||||||||||||||||||||||||||||| ||||| |
------------------------------------------------------------gtttgcattgaaattcctatccgatacaatagtag--tttatgcgcg--atttgattaagtactgatgttt----atatttttttttacc-agGTGATTGTTGCTGATAACTATTTCACTGGTTCAAAGGACAACCTTAAGAAGTGGATTGGTCATCCAAGATTTGAGCTTATCCGTCACG

upper sequence: Vv06s0004g04390.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: AT5G59290.2 (Arabidopsis thaliana), 3'ss of exon 2
gttagcatggttttttcatcttatccagtctcactttctgtgctgattactgaataggcgacaaaaatataaaccataatcatatgcagcagctgacttcatacatactgtatgataagaagatcgtgtttgataata--gttttacttccttagGTAATTGTTGCCGATAACTACTTCACCGGTTCTAAGGACAATCTCAAGAAATGGATTGGTCATCCAAGATTTGAGCTTATTCGTCATG
                                                                               |  ||| ||  |  |||| |  |    |  || |||| | |      | |||||   |   |||||| ||| | ||||  ||||||| |||||||| ||||| || || || || || |||||||| ||||| ||||| || || ||||| ||||||||||| |
-----------------------------------------------------------------------------gtttgtatacaa-aattgacatgcttttcaa-gtttgatcata------tttttgaaggtttcgtttta-ttcttcagGTGGTTGTTGCTGATAACTATTTCACTGGCTCAAAAGAAAACCTCAAGAAGTGGATCGGTCACCCCAGGTTTGAACTTATTCGTCACG

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|33409748|gb|CF215375.1|CF215375
EST:     TCATTGGTTCACATTTGGTGGACAAGCTGATGGAAAATGAAAAGAATGAG                         GTAATTGTTGCCGATAACTACTTCACCGGTTCTAAGGACAATCTCAAGAAA
genomic: TCATTGGTTCACATTTGGTGGACAAGCTGATGGAAAATGAAAAGAATGAGgttagcatgg ... acttccttagGTAATTGTTGCCGATAACTACTTCACCGGTTCTAAGGACAATCTCAAGAAA
EST: gi|33408202|gb|CF213829.1|CF213829
EST:     TCATTGGTTCACATTTGGTGGACAAGCTGATGGAAAATGAAAAGAATGAG                         GTAATTGTTGCCGATAACTACTTCACCGGTTCTAAGGACAATCTCAAGAAA
genomic: TCATTGGTTCACATTTGGTGGACAAGCTGATGGAAAATGAAAAGAATGAGgttagcatgg ... acttccttagGTAATTGTTGCCGATAACTACTTCACCGGTTCTAAGGACAATCTCAAGAAA
EST: gi|71879035|gb|DT028090.1|DT028090
EST:     TCATTGGTTCACATTTGGTGGACAAGCTGATGGAAAATGAAAAGAATGAG                         GTAATTGTTGCCGATAACTACTTCACCGGTTCTAAGGACAATCTCAAGAAA
genomic: TCATTGGTTCACATTTGGTGGACAAGCTGATGGAAAATGAAAAGAATGAGgttagcatgg ... acttccttagGTAATTGTTGCCGATAACTACTTCACCGGTTCTAAGGACAATCTCAAGAAA
EST: gi|71879209|gb|DT028264.1|DT028264
EST:     TCATTGGTTCACATTTGGTGGACAAGCTGATGGAAAATGAAAAGAATGAG                         GTAATTGTTGCCGATAACTACTTCACCGGTTCTAAGGACAATCTCAAGAAA
genomic: TCATTGGTTCACATTTGGTGGACAAGCTGATGGAAAATGAAAAGAATGAGgttagcatgg ... acttccttagGTAATTGTTGCCGATAACTACTTCACCGGTTCTAAGGACAATCTCAAGAAA
EST: gi|33407209|gb|CF212836.1|CF212836
EST:     TCATTGGTTCACATTTGGTGGACAAGCTGATGGAAAATGAAAAGAACGAG                         GTAATTGTTGCCGATAACTACTTCACCGGTTCTAAGGACAATCTCAAGAAA
genomic: TCATTGGTTCACATTTGGTGGACAAGCTGATGGAAAATGAAAAGAATGAGgttagcatgg ... acttccttagGTAATTGTTGCCGATAACTACTTCACCGGTTCTAAGGACAATCTCAAGAAA
EST: gi|37190531|gb|CF609880.1|CF609880
EST:     TCATTGGTTCACATTTGGTGGACAAGCTGATGGAAAATGAAAAGAATGAG                         GTAATTGTTGCCGATAACTACTTCACCGGTTCTAAGGACAATCTCAAGAAA
genomic: TCATTGGTTCACATTTGGTGGACAAGCTGATGGAAAATGAAAAGAATGAGgttagcatgg ... acttccttagGTAATTGTTGCCGATAACTACTTCACCGGTTCTAAGGACAATCTCAAGAAA
EST: gi|71881039|gb|DT030094.1|DT030094
EST:     TCATTGGTTCACATTTGGTGGACAAGCTGATGGAAAATGAAAAGAATGAG                         GTAATTGTTGCCGATAACTACTTCACCGGTTCTAAGGACAATCTCAAGAAA
genomic: TCATTGGTTCACATTTGGTGGACAAGCTGATGGAAAATGAAAAGAATGAGgttagcatgg ... acttccttagGTAATTGTTGCCGATAACTACTTCACCGGTTCTAAGGACAATCTCAAGAAA
EST: gi|30297461|gb|CB974255.1|CB974255
EST:     TCATTGGTTCACATTTGGTGGACGAGCTGATGGAAAATGAAAAGAATGAG                         GTAATTGTTGCCGATAACTACTTCACCGGTTCTAAGGACAATCTCAAGAAA
genomic: TCATTGGTTCACATTTGGTGGACAAGCTGATGGAAAATGAAAAGAATGAGgttagcatgg ... acttccttagGTAATTGTTGCCGATAACTACTTCACCGGTTCTAAGGACAATCTCAAGAAA
EST: gi|33407983|gb|CF213610.1|CF213610
EST:     TCATTGGTTCACATTTGGTGGACAAGCTGATGGAAAATGAAAAGAATGAG                         GTAATTGTTGCCGATAACTACTTCACCGGTTCTAAGGACAATCTCAAGAAA
genomic: TCATTGGTTCACATTTGGTGGACAAGCTGATGGAAAATGAAAAGAATGAGgttagcatgg ... acttccttagGTAATTGTTGCCGATAACTACTTCACCGGTTCTAAGGACAATCTCAAGAAA
EST: gi|33406260|gb|CF211887.1|CF211887
EST:     TCATTGGTTCACATTTGGTGGACAAGCTGATGGAAAATGAAAAGAATGAG                         GTAATTGTTGCCGATAACTACTTCACCGGTTCTAAGGACAATCTCAAGAAA
genomic: TCATTGGTTCACATTTGGTGGACAAGCTGATGGAAAATGAAAAGAATGAGgttagcatgg ... acttccttagGTAATTGTTGCCGATAACTACTTCACCGGTTCTAAGGACAATCTCAAGAAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcatacatactgtatgataagaagatcgtgtttgataatagttttacttccttagGTAATTGTTGCCGATAACTACTTCACCGGTTCTAAGGACAATCTCAAGAAATGGATTGGTCATCCAAGATTTGAGCTTATTCGTCATG
                             gtttgat  putative branch site (score: 5)
                                         ttttacttcctt  putative PPT
                              tttgataatagtttta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttagcatggttttttcatcttatccagtctcactttctgtgctgattactgaataggcgacaaaaatataaaccataatcatatgcagcagctgacttcatacatactgtatgataagaagatcgtgtttgataatagttttacttccttagGTAATTGTTGCCGATAACTACTTCACCGGTTCTAAGGACAATCTCAAGAAATGGATTGGTCATCCAAGATTTGAGCTTATTCGTCATG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGCTT