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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttagtgcatgtagcacctattttatttattctcttcgatttctttcgtttctactgttttgatgtgtcgattcaagtatgagtgaaaattaataatttatattgtttgatgtgtcaacatcatctctgcctttggcctgcagGATATATCGGTGAATTTGAGTATGTAGATGATCACAGATCAGGAAAAATTGTGGTTGAGCTGAATGGAAGGTTGAACAAGTGTGGTGTCATTAGTCCTCG

Basic information

species Vitis vinifera
transcript Vv08s0040g02460.t01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv08s0040g02460.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA15G10950.1 (Glycine max), 3'ss of exon 2
gttagtgcatgtagcacctattttatttattctcttcgatttctttcgtttctactgttttgatgtgtcgattcaagtatgagtgaaaattaataatttatattgtttgatgtgtcaacatcatctctgcctttggcctgcagGATATATCGGTGAATTTGAGTATGTAGATGATCACAGATCAGGAAAAATTGTGGTTGAGCTGAATGGAAGGTTGAACAAGTGTGGTGTCATTAGTCCTCG
                                               || | |  |  ||     | |   ||  | ||  ||   || ||  | | |    ||| || || |||     |   |  ||  | ||   |  ||| || || || || |||||||| || |||||||||||| | ||||||||||| |||||  ||||||| ||  ||||||| ||||| || |||||||| ||
-----------------------------------------------gtatttgtttgttaatcttcttttttttaataatagctcaatttggttactc---ttggttcatctgtt----tttgccttgattgtgttttctagGGTACATTGGAGAGTTTGAGTACGTTGATGATCACAGAGCTGGAAAAATTGTTGTTGAATTGAATGGTAGACTGAACAAATGTGGGGTTATTAGTCCGCG

upper sequence: Vv08s0040g02460.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA17G02200.1 (Glycine max), 3'ss of exon 2
gttagtgcatgtagcacctattttatttattctcttcgatttctttcgtttctactgttttgatgtgtcgattcaagtatgagtgaaaattaataatttatattgtttgatgtgtcaacatcatctctgcctttggcctgcagGATATATCGGTGAATTTGAGTATGTAGATGATCACAGATCAGGAAAAATTGTGGTTGAGCTGAATGGAAGGTTGAACAAGTGTGGTGTCATTAGTCCTCG
                                            |   | |||      |  | || | ||||  | |||   |    |||  || ||| | |  |   |  ||      |  |        ||    || |||||| ||||| || ||||||||||| ||||| |||||  | || ||||| ||||||||  |||| || ||  ||||||||||||| || |||||||| ||
-------------------------------------------gtatatctcttagtaatcaaagttttgattttattatttatttttatt--tagtttgtgtattgaaaaatgctgttgt-gttcggatgatttatgtgtagGATACATCGGAGAGTTTGAGTATGTTGATGACCACAGGGCTGGTAAAATCGTGGTTGAATTGAACGGTAGACTGAACAAGTGTGGGGTTATTAGTCCCCG

upper sequence: Vv08s0040g02460.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: AT2G39590.1 (Arabidopsis thaliana), 3'ss of exon 1
----------gttagtgcatgtagcacctattttatttattctcttcgatttctttcgtttctactg---ttttgatgtgtcgattcaagtatgagtgaaaattaataatttatattgtttgatgtgtca-acatca-tctctgcctttggcctgcagGATATATCGGTGAATTTGAGTATGTAGATGATCACAGATCAGGAAAAATTGTGGTTGAGCTGAATGGAAGGTTGAACAAGTGTGGTGTCATTAGTCCTCG
           ||| |  ||| |||  ||  ||  || |||    ||  ||| |||    | ||  |   || |   || |||| | ||  ||    |||  |    ||| |  | | |||||  ||  | |||  |   | | |||||||  |  ||| || || |  || ||||| ||||| |||||||||||||| || || |||||||||||||| ||||||||| | ||||| || ||||| |||||||||||
gtacaattgttttactcaatg-agcttcttcttgtttgatttctctcttttttttttaggtttaagggaattataccgtatcgaataaaacattctggaatctctcaaatgttcagt-tttgacttgaaacacacaaactttttcctttggtttatagGTTACATTGCAGAGTTTGAATATGTGGATGATCACAGATCCGGGAAGATTGTGGTTGAGCTTAATGGAAGGCTTAACAACTGCGGTGTTATTAGTCCTCG

upper sequence: Vv08s0040g02460.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: PP1S426_18V6.1 (Physcomitrella patens), 3'ss of exon 1
gttagtgcatgtagcacctattttatttattctcttcgatttctttcgtttctactgttttgatgtgtcgattcaagtatgagtgaaaattaataatttatattgtttgatgtgtcaacatcatctctgcctttggcctgcagGATATATCGGTGAATTTGAGTATGTAGATGATCACAGATCAGGAAAAATTGTGGTTGAGCTGAATGGAAGGTTGAACAAGTGTGGTGTCATTAGTCCTCG
                                   ||  | ||| ||   |||||     | |  | |  ||    |  |     ||  |  |  ||| |||  |  |  | |       ||   | || || |    | |||| ||||| || || ||||||  ||| ||||| ||| || | || || |||||||| ||||| |||||||| ||||||||||| |||||||| ||||||||
--------------------------------ctctctctctctctctcatctacgaaaataaactatttatcttcgcgt---ctaagttgcagcattgatagcggatcgttttc-----tctcttttggctct---tttcagGTTATATTGGAGAGTTTGAGCTTGTTGATGACCACCGAGCTGGCAAGATTGTGGTAGAGCTCAATGGAAGATTGAACAAGTGCGGTGTCATCAGTCCTCG

upper sequence: Vv08s0040g02460.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: PP1S45_88V6.2 (Physcomitrella patens), 3'ss of exon 1
gttagtgcatgtagcacctattttatttattctcttcgatttctttcgtttctactgttttgatgtgtcgattcaagtatgagtgaaaattaataatttatattgtttgatgtgtcaacatcatctctgcctttggcctgcagGATATATCGGTGAATTTGAGTATGTAGATGATCACAGATCAGGAAAAATTGTGGTTGAGCTGAATGGAAGGTTGAACAAGTGTGGTGTCATTAGTCCTCG
                              | | || |   |||| |  || |    ||| | | |   | |   ||  ||  | | ||    | |   |   | | |||    | |   |  || ||| ||||       |||||| || || |||||||||   |||||||| ||| || | ||||| || || || ||||| ||||| |||||||||||||| |||||||| ||||| ||
------------------------------tgtttttg---tcttccccttatggaatttggttatcctgtt---agcgtgctttacaac-gctgaagaaatctctctgactaattagtgttctc-ctgtctttt-----tagGATACATTGGAGAATTTGAGCTGGTAGATGACCACCGAGCTGGAAAGATCGTAGTGGAGCTTAATGGCAGGTTGAACAAGTGCGGTGTCATCAGTCCCCG

upper sequence: Vv08s0040g02460.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: PP1S61_209V6.1 (Physcomitrella patens), 3'ss of exon 1
gttagtgcatgtagcacctattttatttattctcttcgatttctttcgtttctactgttttgatgtgtcgattcaagtatgagtgaaaattaataatttatattgtttgatgtgtcaacatcatctctgcctttgg---cctgcagGATATATCGGTGAATTTGAGTATGTAGATGATCACAGATCAGGAAAAATTGTGGTTGAGCTGAATGGAAGGTTGAACAAGTGTGGTGTCATTAGTCCTCG
                                         |||||  ||||| |||| |    |||    | ||  | || || |  | || |   ||     |  | |   |  |  ||  | | | | | ||      | |||| || || || || || ||    || ||||| ||  || | || || |||||||| ||||| || || || ||||||||||||||||| || ||||||||
-----------------------------------------tctttt-tttcttctgtataagagtg---gtccatctctgtgttatcagtattgtattgcgaggaattacaaga-atgatgctgtttacttctgaattttttcagGGTACATTGGGGAGTTCGAACTGGTTGATGACCATCGAGCTGGCAAGATTGTGGTAGAGCTCAACGGTAGATTGAACAAGTGTGGTGTAATCAGTCCTCG

upper sequence: Vv08s0040g02460.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: PP1S115_101V6.1 (Physcomitrella patens), 3'ss of exon 1
gttagtgcatgtagcacctattttatttattctcttcgatttctttcgtttctactgttttgatgtgtcgattcaagtatgagtgaaaattaataatttatattgtttgatgtgtcaacatcatctctgcctttggcctgcagGATATATCGGTGAATTTGAGTATGTAGATGATCACAGATCAGGAAAAATTGTGGTTGAGCTGAATGGAAGGTTGAACAAGTGTGGTGTCATTAGTCCTCG
                                      ||       |    |      | |   ||| | |    |   ||| |    || || |  |  |     ||| ||      |  || |     ||     | |||| || || || || |||||   ||| ||||| |||||  |||| ||||||||||| |||||||| || |||||||||||||||||||| || ||||| ||
------------------------------------taatagtaagggaacatgtaacgtagtcatgttggt---ggatcgagcgtcctttcatgagcttga--acctgacgttcttttaaaatatacatattca--tttcagGCTACATTGGAGAGTTTGAACTTGTGGATGACCACAGGGCAGGGAAAATTGTGGTGGAGCTGAACGGCAGGTTGAACAAGTGTGGTGTGATCAGTCCCCG

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|110706292|gb|EE081689.1|EE081689
EST:     ACCTTCCTCAAAAGTTATTGTCAAGTTTCTTCTGGTTATGCAGAAGCACG                         GATATATCGGTGAATTTGAGTATGTAGATGATCACAGATCAGGAAAAATTG
genomic: ACCTTCCTCGAAAGTTATTGTCAAGTTTCTTCTGGTTATGCAGAAGCACGgttagtgcat ... tggcctgcagGATATATCGGTGAATTTGAGTATGTAGATGATCACAGATCAGGAAAAATTG
EST: gi|30297968|gb|CB974762.1|CB974762
EST:     ACCTTCCTCAAAAGTTATTGTCAAGTTTCTTCTGGTTATGCAGAAGCACG                         GATATATCGGTGAATTTGAGTATGTAGATGATCACAGATCAGGAAAAATTG
genomic: ACCTTCCTCGAAAGTTATTGTCAAGTTTCTTCTGGTTATGCAGAAGCACGgttagtgcat ... tggcctgcagGATATATCGGTGAATTTGAGTATGTAGATGATCACAGATCAGGAAAAATTG
EST: gi|26262523|gb|CA813586.1|CA813586
EST:     ACCTTCCTCAAAAGTTATTGTCAAGTTTCTTCTGGTTATGCAGAAGCACG                         GATATATCGGTGAATTTGAGTATGTAGATGATCACAGATCAGGAAAAATTG
genomic: ACCTTCCTCGAAAGTTATTGTCAAGTTTCTTCTGGTTATGCAGAAGCACGgttagtgcat ... tggcctgcagGATATATCGGTGAATTTGAGTATGTAGATGATCACAGATCAGGAAAAATTG
EST: gi|110695174|gb|EE072887.1|EE072887
EST:     ACCTTCCTCAAAAGTTATTGTCAAG-TTCTTCTGGTTATGCAGAAGCACG                         GATATATCGGTGAATTTGAGTATGTAGATGATCACAGATCAGGAAAAATTG
genomic: ACCTTCCTCGAAAGTTATTGTCAAGTTTCTTCTGGTTATGCAGAAGCACGgttagtgcat ... tggcctgcagGATATATCGGTGAATTTGAGTATGTAGATGATCACAGATCAGGAAAAATTG
EST: gi|110723278|gb|EE100404.1|EE100404
EST:     ACCTTCCTCAAAAGTTATTGTCAAGTTTCTTCTGGTTATGCAGAAGCACG                         GATATATCGGTGAATTTGAGTATGTAGATGATCACAGATCAGGAAAAATTG
genomic: ACCTTCCTCGAAAGTTATTGTCAAGTTTCTTCTGGTTATGCAGAAGCACGgttagtgcat ... tggcctgcagGATATATCGGTGAATTTGAGTATGTAGATGATCACAGATCAGGAAAAATTG
EST: gi|110421139|gb|EC987428.1|EC987428
EST:     ACCTTCCTCAAAAGTTATTGTCAAGTTTCTTCTGGTTATGCAGAAGCACG                         GATATATCGGTGAATTTGAGTATGTAGATGATCACAGATCAGGAAAAATTG
genomic: ACCTTCCTCGAAAGTTATTGTCAAGTTTCTTCTGGTTATGCAGAAGCACGgttagtgcat ... tggcctgcagGATATATCGGTGAATTTGAGTATGTAGATGATCACAGATCAGGAAAAATTG
EST: gi|110427515|gb|EC993958.1|EC993958
EST:     ACCTTCCTCAAAAGTTATTGTCAAGTTTCTTCTGGTTATGCAGAAGCACG                         GATATATCGGTGAATTTGAGTATGTAGATGATCACAGATCAGGAAAAATTG
genomic: ACCTTCCTCGAAAGTTATTGTCAAGTTTCTTCTGGTTATGCAGAAGCACGgttagtgcat ... tggcctgcagGATATATCGGTGAATTTGAGTATGTAGATGATCACAGATCAGGAAAAATTG
EST: gi|71866878|gb|DT015933.1|DT015933
EST:     ACCTTCCTCAAAAGTTATTGTCAAGTTTCTTCTGGTTATGCAGAAGCACG                         GATATATCGGTGAATTTGAGTATGTAGATGATCACAGATCAGGAAAAATTG
genomic: ACCTTCCTCGAAAGTTATTGTCAAGTTTCTTCTGGTTATGCAGAAGCACGgttagtgcat ... tggcctgcagGATATATCGGTGAATTTGAGTATGTAGATGATCACAGATCAGGAAAAATTG
EST: gi|28966564|gb|CB345597.1|CB345597
EST:     ACCTTCCTCAAAAGTTATTGTCGAGCTTCTTCTGGTTATGCAGAAGCACG                         GATATATCGGTGAATTTGAGTATGTAGATGATCACAGATCAGGAAAAATTG
genomic: ACCTTCCTCGAAAGTTATTGTCAAGTTTCTTCTGGTTATGCAGAAGCACGgttagtgcat ... tggcctgcagGATATATCGGTGAATTTGAGTATGTAGATGATCACAGATCAGGAAAAATTG
EST: gi|110696628|gb|EE072909.1|EE072909
EST:     ACCTTCCTCAAAAGTTATTGTCAAGTTTCTTCTGGTTATGCAGAAGCACG                         GATATATCGGTGAATTTGAGTATGTAGATGATCACAGATCAGGAAAAATTG
genomic: ACCTTCCTCGAAAGTTATTGTCAAGTTTCTTCTGGTTATGCAGAAGCACGgttagtgcat ... tggcctgcagGATATATCGGTGAATTTGAGTATGTAGATGATCACAGATCAGGAAAAATTG
EST: gi|110385929|gb|EC950489.1|EC950489
EST:     ACCTTCCTCAAAAGTTATTGTCAAGTTTCTTCTGGTTATGCAGAAGCACG                         GATATATCGGTGAATTTGAGTATGTAGATGATCACAGATCAGGAAAAATTG
genomic: ACCTTCCTCGAAAGTTATTGTCAAGTTTCTTCTGGTTATGCAGAAGCACGgttagtgcat ... tggcctgcagGATATATCGGTGAATTTGAGTATGTAGATGATCACAGATCAGGAAAAATTG
EST: gi|55778140|gb|AJ862926.1|AJ862926
EST:     ACCTTCCTCAAAAGTTATTGTCAAGTTTCTTCTGGTTATGCAGAAGCACG                         GATATATCGGTGAATTTGAGTATGTAGATGATCACAGATCAGGAAAAATTG
genomic: ACCTTCCTCGAAAGTTATTGTCAAGTTTCTTCTGGTTATGCAGAAGCACGgttagtgcat ... tggcctgcagGATATATCGGTGAATTTGAGTATGTAGATGATCACAGATCAGGAAAAATTG
EST: gi|110365476|gb|EC928529.1|EC928529
EST:     ACCTTCCTCAAAAGTTATTGTCAAGTTTCTTCTGGTTATGCAGAAGCACG                         GATATATCGGTGAATTTGAGTATGTAGATGATCACAGATCAGGAAAAATTG
genomic: ACCTTCCTCGAAAGTTATTGTCAAGTTTCTTCTGGTTATGCAGAAGCACGgttagtgcat ... tggcctgcagGATATATCGGTGAATTTGAGTATGTAGATGATCACAGATCAGGAAAAATTG
EST: gi|110731018|gb|EE108758.1|EE108758
EST:     ACCTTCCTCAAAAGTTATTGTCAAGTTTCTTCTGGTTATGCAGAAGCACG                         GATATATCGGTGAATTTGAGTATGTAGATGATCACAGATCAGGAAAAATTG
genomic: ACCTTCCTCGAAAGTTATTGTCAAGTTTCTTCTGGTTATGCAGAAGCACGgttagtgcat ... tggcctgcagGATATATCGGTGAATTTGAGTATGTAGATGATCACAGATCAGGAAAAATTG
EST: gi|110707241|gb|EE083471.1|EE083471
EST:     ACCTTCCTCAAAAGTTATTGTCAAGTTTCTTCTGGTTATGCAGAAGCACG                         GATATATCGGTGAATTTGAGTATGTAGATGATCACAGATCAGGAAAAATTG
genomic: ACCTTCCTCGAAAGTTATTGTCAAGTTTCTTCTGGTTATGCAGAAGCACGgttagtgcat ... tggcctgcagGATATATCGGTGAATTTGAGTATGTAGATGATCACAGATCAGGAAAAATTG
EST: gi|110387525|gb|EC952200.1|EC952200
EST:     ACCTTCCTCAAAAGTTATTGTCAAGTTTCTTCTGGTTATGCAGAAGCACG                         GATATATCGGTGAATTTGAGTATGTAGATGATCACAGATCAGGAAAAATTG
genomic: ACCTTCCTCGAAAGTTATTGTCAAGTTTCTTCTGGTTATGCAGAAGCACGgttagtgcat ... tggcctgcagGATATATCGGTGAATTTGAGTATGTAGATGATCACAGATCAGGAAAAATTG
EST: gi|110420349|gb|EC986621.1|EC986621
EST:     ACCTTCCTCAAAAGTTATTGTCAAGTTTCTTCTGGTTATGCAGAAGCACG                         GATATATCGGTGAATTTGAGTATGTAGATGATCACAGATCAGGAAAAATTG
genomic: ACCTTCCTCGAAAGTTATTGTCAAGTTTCTTCTGGTTATGCAGAAGCACGgttagtgcat ... tggcctgcagGATATATCGGTGAATTTGAGTATGTAGATGATCACAGATCAGGAAAAATTG
EST: gi|110405496|gb|EC971037.1|EC971037
EST:     ACCTTCCTCAAAAGTTATTGTCAAGTTTCTTCTGGTTATGCAGAAGCACG                         GATATATCGGTGAATTTGAGTATGTAGATGATCACAGATCAGGAAAAATTG
genomic: ACCTTCCTCGAAAGTTATTGTCAAGTTTCTTCTGGTTATGCAGAAGCACGgttagtgcat ... tggcctgcagGATATATCGGTGAATTTGAGTATGTAGATGATCACAGATCAGGAAAAATTG
EST: gi|30298030|gb|CB974824.1|CB974824
EST:     CCCTTCCTCAAAAGTTATTGTCAAGTTTCTTCTGGTTATGCAGAAGCACG                         GATATATCGGTGAATTTGAGTATGTAGATGATCCCAGATCAGGAAAAATTG
genomic: ACCTTCCTCGAAAGTTATTGTCAAGTTTCTTCTGGTTATGCAGAAGCACGgttagtgcat ... tggcctgcagGATATATCGGTGAATTTGAGTATGTAGATGATCACAGATCAGGAAAAATTG
EST: gi|110707255|gb|EE083506.1|EE083506
EST:     ACCTTCCTCAAAAGTTATTGTCAAGTTTCTTCTGGTTATGCAGAAGCACG                         GATATATCGGTGAATTTGAGTATGTAGATGATCACAGATCAGGAAAAATTG
genomic: ACCTTCCTCGAAAGTTATTGTCAAGTTTCTTCTGGTTATGCAGAAGCACGgttagtgcat ... tggcctgcagGATATATCGGTGAATTTGAGTATGTAGATGATCACAGATCAGGAAAAATTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

attaataatttatattgtttgatgtgtcaacatcatctctgcctttggcctgcagGATATATCGGTGAATTTGAGTATGTAGATGATCACAGATCAGGAAAAATTGTGGTTGAGCTGAATGGAAGGTTGAACAAGTGTGGTGTCATTAGTCCTCG
                                tcatctctgccttt  CT-rich tract
     taatttatattgtttg  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttagtgcatgtagcacctattttatttattctcttcgatttctttcgtttctactgttttgatgtgtcgattcaagtatgagtgaaaattaataatttatattgtttgatgtgtcaacatcatctctgcctttggcctgcagGATATATCGGTGAATTTGAGTATGTAGATGATCACAGATCAGGAAAAATTGTGGTTGAGCTGAATGGAAGGTTGAACAAGTGTGGTGTCATTAGTCCTCG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAAG