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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...atttacatgttgtttttgattcttgaaatttattcaaactaaagctggtctttatttattcgtttttttccttctttttgattgtgtttcataattgcagAACTTGAAAAGCACATTCCCGACCTCCATGTTCTCATATCTACCCCCTTCCACCCTGCCTATGTAACGGCAGAGAGGATCAAGAAGGCCAAAAATCTACA

Basic information

species Vitis vinifera
transcript Vv14s0066g01320.t01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv14s0066g01320.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: LOC_Os06g29220.1 (Oryza sativa), 3'ss of exon 2
atttacatgttgtttttgattcttgaaatttattcaaactaaagct---ggtctttattt---att-cgtttttttccttctttttgattgtgtttcataattgcagAACTTGAAAAGCACATTCCCGACCTCCATGTTCTCATATCTACCCCCTTCCACCCTGCCTATGTAACGGCAGAGAGGATCAAGAAGGCCAAAAATCTACA
      | ||   |   |  || | ||||||  ||  ||||||  |   |||||| | |    ||| ||       |   |  ||   ||||   ||| | |  |||| || || ||||||||    ||   ||| || || ||  | ||||| |||||||| |||||  | || ||||||||||||||||||||||| || ||  |
-----gaggtatctgaaggatcataaaattt-ctctgactaaatatataggtcttaagtctgaattgcgcacacaactgacgcttctgttgtacatca-attcccagAGCTGGAGAAGCACATCGAGGATGCCCACGTCCTGATCACCACCCCATTCCACCCAGCCTACATCACCGCAGAGAGGATCAAGAAGGCCAAGAACCTGGA

upper sequence: Vv14s0066g01320.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA19G01210.4 (Glycine max), 3'ss of exon 2
atttacatgttgtttttgattcttgaaatttattcaaactaaagctggtc-tttatttattcgtttttttccttctttttgattgtgtttcata----attgcagAACTTGAAAAGCACATTCCCGACCTCCATGTTCTCATATCTACCCCCTTCCACCCTGCCTATGTAACGGCAGAGAGGATCAAGAAGGCCAAAAATCTACA
           ||  |  |  ||  ||  | ||  ||   |||  || |  |   || |    |||  || |||    |  || |  ||| ||       |||||||||||| || |||||||| ||    |||||  |||||||||| || |||||||| |||||||| || ||||| || || ||||| ||||||||| |  |
-----atcagagtaatcaacactataatatcatggaatgcaaatgtgtttgtcccttcaagattttaattgcttgaactcaatggaatttgatgttctgctgcagAACTTGAGAAACACATTCCAGATGCACATGTCATCATATCTACTCCATTCCACCCCGCCTATGTCACCGCAGAAAGAATTAAGAAAGCCAAAAATTTGGA
















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|349812372|gb|FQ406393.1|FQ406393
EST:     ACAAGGGCACCAGTACATTGTTACTGATGACAAAGAAGGGCCAGATTGTG                         AACTTGAAAAGCACATTCCCGACCTCCATGTTCTCATATCTACCCCCTTCC
genomic: ACAAGGGCACCAGTACATTGTTACTGATGACAAAGAAGGGCCAGATTGTGgttagtacgt ... ataattgcagAACTTGAAAAGCACATTCCCGACCTCCATGTTCTCATATCTACCCCCTTCC
EST: gi|161706829|gb|FC057618.1|FC057618
EST:     ACAAGGGCACCAGTACATAGTTACTGATGACAAAGAAGGACCAGATTGTG                         AACTTGAAAAGCACATTCCCGACCTCCATGTTCTCATATCTACCCCCTTCC
genomic: ACAAGGGCACCAGTACATTGTTACTGATGACAAAGAAGGGCCAGATTGTGgttagtacgt ... ataattgcagAACTTGAAAAGCACATTCCCGACCTCCATGTTCTCATATCTACCCCCTTCC
EST: gi|352785918|gb|FQ475921.1|FQ475921
EST:     ACAAGGGCACCAGTACATTGTTACTGATGACAAAGAAGGGCCAGATTGTG                         AACTTGAAAAGCACATTCCCGACCTCCATGTTCTCATATCTACCCCCTTCC
genomic: ACAAGGGCACCAGTACATTGTTACTGATGACAAAGAAGGGCCAGATTGTGgttagtacgt ... ataattgcagAACTTGAAAAGCACATTCCCGACCTCCATGTTCTCATATCTACCCCCTTCC
EST: gi|110426720|gb|EC993138.1|EC993138
EST:     ACAAGGGCACCAGTACATTGTTACTGATGACAAAGAAGGGCCAGATTGTG                         AACTTGAAAAGCACATTCCTGACCTCCATGTTCTCATATCTACCCCCTTCC
genomic: ACAAGGGCACCAGTACATTGTTACTGATGACAAAGAAGGGCCAGATTGTGgttagtacgt ... ataattgcagAACTTGAAAAGCACATTCCCGACCTCCATGTTCTCATATCTACCCCCTTCC
EST: gi|352764500|gb|FQ472857.1|FQ472857
EST:     ACAAGGGCACCAGTACATTGTTACTGATGACAAAGAAGGGCCAGATTGTG                         AACTTGAAAAGCACATTCCCGACCTCCATGTTCTCATATCTACCCCCTTCC
genomic: ACAAGGGCACCAGTACATTGTTACTGATGACAAAGAAGGGCCAGATTGTGgttagtacgt ... ataattgcagAACTTGAAAAGCACATTCCCGACCTCCATGTTCTCATATCTACCCCCTTCC
EST: gi|71875782|gb|DT024837.1|DT024837
EST:     ACAAGGGCACCAGTACATTGTTACTGATGACAAAGAAGGGCCAGATTGTG                         AACTTGAAAAGCACATTCCCGACCTCCATGTTCTCATATCTACCCCCTTCC
genomic: ACAAGGGCACCAGTACATTGTTACTGATGACAAAGAAGGGCCAGATTGTGgttagtacgt ... ataattgcagAACTTGAAAAGCACATTCCCGACCTCCATGTTCTCATATCTACCCCCTTCC
EST: gi|110403313|gb|EC964815.1|EC964815
EST:     ACAAGGGCACCAGTACATTGTTACTGATGACAAAGAAGGGCCAGATTGTG                         AACTTGAAAAGCACATTCCCGACCTCCATGTTCTCATATCTACCCCCTTCC
genomic: ACAAGGGCACCAGTACATTGTTACTGATGACAAAGAAGGGCCAGATTGTGgttagtacgt ... ataattgcagAACTTGAAAAGCACATTCCCGACCTCCATGTTCTCATATCTACCCCCTTCC
EST: gi|29781912|gb|CB346743.2|CB346743
EST:     ACAAGGGCACCAGTACATTGTTACTGATGACAAAGAAGGGCCAGATTGTG                         AACTTGAAAAGCACATTCCCGACCTCCATGTTCTCATATCTACCCCCTTCC
genomic: ACAAGGGCACCAGTACATTGTTACTGATGACAAAGAAGGGCCAGATTGTGgttagtacgt ... ataattgcagAACTTGAAAAGCACATTCCCGACCTCCATGTTCTCATATCTACCCCCTTCC
EST: gi|161716875|gb|FC068803.1|FC068803
EST:     ACAAGGGCACCAGTACATTGTTACTGATGACAAAGAAGGGCCAGATTGTG                         AACTTGAAAAGCACATTCCCGACCTCCATGTTCTCATATCTACCCCCTTCC
genomic: ACAAGGGCACCAGTACATTGTTACTGATGACAAAGAAGGGCCAGATTGTGgttagtacgt ... ataattgcagAACTTGAAAAGCACATTCCCGACCTCCATGTTCTCATATCTACCCCCTTCC
EST: gi|349814228|gb|FQ414847.1|FQ414847
EST:     ACAAGGGCACCAGTACATTGTTACTGATGACAAAGAAGGGCCAGATTGTG                         AACTTGAAAAGCACATTCCCGACCTCCATGTTCTCATATCTACCCCCTTCC
genomic: ACAAGGGCACCAGTACATTGTTACTGATGACAAAGAAGGGCCAGATTGTGgttagtacgt ... ataattgcagAACTTGAAAAGCACATTCCCGACCTCCATGTTCTCATATCTACCCCCTTCC
EST: gi|110374898|gb|EC939839.1|EC939839
EST:     ACAAGGGCACCAGTACATAGTTACTGATGACAAAGAAGGACCAGATTGTG                         AACTTGAAAAGCACATTCCCGACCTCCATGTTCTCATATCTACCCCCTTCC
genomic: ACAAGGGCACCAGTACATTGTTACTGATGACAAAGAAGGGCCAGATTGTGgttagtacgt ... ataattgcagAACTTGAAAAGCACATTCCCGACCTCCATGTTCTCATATCTACCCCCTTCC
EST: gi|352781404|gb|FQ468248.1|FQ468248
EST:     ACAAGGGCACCAGTACATTGTTACTGATGACAAAGAAGGGCCAGATTGTG                         AACTTGAAAAGCACATTCCCGACCTCCATGTTCTCATATCTACCCCCTTCC
genomic: ACAAGGGCACCAGTACATTGTTACTGATGACAAAGAAGGGCCAGATTGTGgttagtacgt ... ataattgcagAACTTGAAAAGCACATTCCCGACCTCCATGTTCTCATATCTACCCCCTTCC
EST: gi|30300514|gb|CB977308.1|CB977308
EST:     ACAAGGGCTCCAGTACATAGTTACTGATGACAAAGAAGGACCAGATTGTG                         AACTTGAAAAGCACATTCCCGACCTCCATGTTCTCATATCTACCCCCTTCC
genomic: ACAAGGGCACCAGTACATTGTTACTGATGACAAAGAAGGGCCAGATTGTGgttagtacgt ... ataattgcagAACTTGAAAAGCACATTCCCGACCTCCATGTTCTCATATCTACCCCCTTCC
EST: gi|161714888|gb|FC063039.1|FC063039
EST:     ACAAGGGCACCAGTACATTGTTACTGATGACAAAGAAGGGCCAGATTGTG                         AACTTGAAAAGCACATTCCCGACCTCCATGTTCTCATATCTACCCCCTTCC
genomic: ACAAGGGCACCAGTACATTGTTACTGATGACAAAGAAGGGCCAGATTGTGgttagtacgt ... ataattgcagAACTTGAAAAGCACATTCCCGACCTCCATGTTCTCATATCTACCCCCTTCC
EST: gi|349814411|gb|FQ398851.1|FQ398851
EST:     ACAAGGGCACCAGTACATTGTTACTGATGACAAAGAAGGGCCAGATTGTG                         AACTTGAAAAGCACATTCCCGACCTCCATGTTCTCATATCTACCCCCTTCC
genomic: ACAAGGGCACCAGTACATTGTTACTGATGACAAAGAAGGGCCAGATTGTGgttagtacgt ... ataattgcagAACTTGAAAAGCACATTCCCGACCTCCATGTTCTCATATCTACCCCCTTCC
EST: gi|349808355|gb|FQ405523.1|FQ405523
EST:     ACAAGGGCACCAGTACATTGTTACTGATGACAAAGAAGGGCCAGATTGTG                         AACTTGAAAAGCACATTCCCGACCTCCATGTTCTCATATCTACCCCCTTCC
genomic: ACAAGGGCACCAGTACATTGTTACTGATGACAAAGAAGGGCCAGATTGTGgttagtacgt ... ataattgcagAACTTGAAAAGCACATTCCCGACCTCCATGTTCTCATATCTACCCCCTTCC
EST: gi|161712335|gb|FC061660.1|FC061660
EST:     ACAAGGGCACCAGTACATTGTTACTGATGACAAAGAAGGGCCAGATTGTG                         AACTTGAAAAGCACATTCCCGACCTCCATGTTCTCATATCTACCCCCTTCC
genomic: ACAAGGGCACCAGTACATTGTTACTGATGACAAAGAAGGGCCAGATTGTGgttagtacgt ... ataattgcagAACTTGAAAAGCACATTCCCGACCTCCATGTTCTCATATCTACCCCCTTCC
EST: gi|352781529|gb|FQ468373.1|FQ468373
EST:     ACAAGGGCACCAGTACATTGTTACTGATGACAAAGAAGGGCCAGATTGTG                         AACTTGAAAAGCACATTCCCGACCTCCATGTTCTCATATCTACCCCCTTCC
genomic: ACAAGGGCACCAGTACATTGTTACTGATGACAAAGAAGGGCCAGATTGTGgttagtacgt ... ataattgcagAACTTGAAAAGCACATTCCCGACCTCCATGTTCTCATATCTACCCCCTTCC
EST: gi|349826487|gb|FQ418578.1|FQ418578
EST:     ACAAGGGCACCAGTACATTGTTACTGATGACAAAGAAGGGCCAGATTGTG                         AACTTGAAAAGCACATTCCCGACCTCCATGTTCTCATATCTACCCCCTTCC
genomic: ACAAGGGCACCAGTACATTGTTACTGATGACAAAGAAGGGCCAGATTGTGgttagtacgt ... ataattgcagAACTTGAAAAGCACATTCCCGACCTCCATGTTCTCATATCTACCCCCTTCC
EST: gi|110409955|gb|EC975630.1|EC975630
EST:     ACAAGGGCACCAGTACATTGTTACTGATGACAAAGAAGGGCCAGATTGTG                         AACTTGAAAAGCACATTCCCGACCTCCATGTTCTCATATCTACCCCCTTCC
genomic: ACAAGGGCACCAGTACATTGTTACTGATGACAAAGAAGGGCCAGATTGTGgttagtacgt ... ataattgcagAACTTGAAAAGCACATTCCCGACCTCCATGTTCTCATATCTACCCCCTTCC
EST: gi|110374890|gb|EC939831.1|EC939831
EST:     ACAAGGGCACCAGTACATAGTTACTGATGACAAAGAAGGACCAGATTGTG                         AACTTGAAAAGCACATTCCCGACCTCCATGTTCTCATATCTACCCCCTTCC
genomic: ACAAGGGCACCAGTACATTGTTACTGATGACAAAGAAGGGCCAGATTGTGgttagtacgt ... ataattgcagAACTTGAAAAGCACATTCCCGACCTCCATGTTCTCATATCTACCCCCTTCC
EST: gi|110685149|gb|EE063240.1|EE063240
EST:     ACAAGGGCACCAGTACATTGTTACTGATGACAAAGAAGGGCCAGATTGTG                         AACTTGAAAAGCACATTCCCGACCTCCATGTTCTCATATCTACCCCCTTCC
genomic: ACAAGGGCACCAGTACATTGTTACTGATGACAAAGAAGGGCCAGATTGTGgttagtacgt ... ataattgcagAACTTGAAAAGCACATTCCCGACCTCCATGTTCTCATATCTACCCCCTTCC
EST: gi|71866313|gb|DT015368.1|DT015368
EST:     ACAAGGGCACCAGTACATAGTTACTGATGACAAAGAAGGACCAGATTGTG                         AACTTGAAAAGCACATTCCCGACCTCCATGTTCTCATATCTACCCCCTTCC
genomic: ACAAGGGCACCAGTACATTGTTACTGATGACAAAGAAGGGCCAGATTGTGgttagtacgt ... ataattgcagAACTTGAAAAGCACATTCCCGACCTCCATGTTCTCATATCTACCCCCTTCC
EST: gi|34548582|gb|CF516814.1|CF516814
EST:     ACAAGGGCACCAGTACATAGTTACTGATGACAAAGAAGGACCAGATTGTG                         AACTTGAAAAGCACATTCCCGACCTCCATGTTCTCATATCTACCCCCTTCC
genomic: ACAAGGGCACCAGTACATTGTTACTGATGACAAAGAAGGGCCAGATTGTGgttagtacgt ... ataattgcagAACTTGAAAAGCACATTCCCGACCTCCATGTTCTCATATCTACCCCCTTCC
EST: gi|34543645|gb|CF511877.1|CF511877
EST:     TACATTGTTACTGATGACAAAGAAGGGCCAGATTGTG                         AACTTGAAAAGCACATTCCCGACCTCCATGTTCTCATATCTACCCCCTTCC
genomic: TACATTGTTACTGATGACAAAGAAGGGCCAGATTGTGgttagtacgt ... ataattgcagAACTTGAAAAGCACATTCCCGACCTCCATGTTCTCATATCTACCCCCTTCC
EST: gi|110732811|gb|EE108422.1|EE108422
EST:     GACAAAGAAGGACCAGATTGTG                         AACTTGAAAAGCACATTCCCGACCTCCATGTTCTCATATCTACCCCCTTCC
genomic: GACAAAGAAGGGCCAGATTGTGgttagtacgt ... ataattgcagAACTTGAAAAGCACATTCCCGACCTCCATGTTCTCATATCTACCCCCTTCC
EST: gi|161719093|gb|FC065413.1|FC065413
EST:     ACAAGGGCACCAGTACATTGTTACTGATGACAAAGAAGGGCCAGATTGTG                         AACTTGAAAAGCACATTCCCGACCTCCATGTTCTCATATCTACCCCCTTCC
genomic: ACAAGGGCACCAGTACATTGTTACTGATGACAAAGAAGGGCCAGATTGTGgttagtacgt ... ataattgcagAACTTGAAAAGCACATTCCCGACCTCCATGTTCTCATATCTACCCCCTTCC
EST: gi|349826629|gb|FQ418720.1|FQ418720
EST:     ACAAGGGCACCAGTACATTGTTACTGATGACAAAGAAGGGCCAGATTGTG                         AACTTGAAAAGCACATTCCCGACCTCCATGTTCTCATATCTACCCCCTTCC
genomic: ACAAGGGCACCAGTACATTGTTACTGATGACAAAGAAGGGCCAGATTGTGgttagtacgt ... ataattgcagAACTTGAAAAGCACATTCCCGACCTCCATGTTCTCATATCTACCCCCTTCC
EST: gi|352768908|gb|FQ468099.1|FQ468099
EST:     ACAAGGGCACCAGTACATTGTTACTGATGACAAAGAAGGGCCAGATTGTG                         AACTTGAAAAGCACATTCCCGACCTCCATGTTCTCATATCTACCCCCTTCC
genomic: ACAAGGGCACCAGTACATTGTTACTGATGACAAAGAAGGGCCAGATTGTGgttagtacgt ... ataattgcagAACTTGAAAAGCACATTCCCGACCTCCATGTTCTCATATCTACCCCCTTCC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tggtctttatttattcgtttttttccttctttttgattgtgtttcataattgcagAACTTGAAAAGCACATTCCCGACCTCCATGTTCTCATATCTACCCCCTTCCACCCTGCCTATGTAACGGCAGAGAGGATCAAGAAGGCCAAAAATCTACA
                              ttttgat  putative branch site (score: 4)
     tttatttattcgtttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
atttacatgttgtttttgattcttgaaatttattcaaactaaagctggtctttatttattcgtttttttccttctttttgattgtgtttcataattgcagAACTTGAAAAGCACATTCCCGACCTCCATGTTCTCATATCTACCCCCTTCCACCCTGCCTATGTAACGGCAGAGAGGATCAAGAAGGCCAAAAATCTACA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - acatgtt
- - - - - - - - - - - - - - - - - -aaactaa