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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttgcctgcaatctagatcctgttactttggttttcattattgtttaacatcatatgagaacctgaggaattttatttgggggtcaactctttggtggtttgaatttcagGAGAAAGAAGAAAAGCTGGATGGAGATGCAGCTCTGAACAAATTTTTCCGGGACATATATAAAGATGCAGACGAAGACACAAGAAGGGCCATGCAAAAAT

Basic information

species Vitis vinifera
transcript Vv16s0050g01510.t01
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv16s0050g01510.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: GLYMA10G37440.1 (Glycine max), 3'ss of exon 9
gtttgcctgcaatctagatcctgttactttggttttcattattgtttaacatcatatgagaacctgaggaattttatttgggggtcaactctttggtggtttgaatttcagGAGAAAGAAGAAAAGCTGGATGGAGATGCAGCTCTGAACAAATTTTTCCGGGACATATATAAAGATGCAGACGAAGACACAAGAAGGGCCATGCAAAAAT
                      |||  |  | | | |||     | ||| ||  | |       ||  |  |  ||        ||  || |        || | |||||||||||||||||||| || ||||| ||||| ||  |||||||||||||||| || |||||| |||||||||| || ||||||||||| || |||   ||||
----------------------gtttgtcagctctacat----atataaaatgtttttgttctttgtaggttggtacacttccttcccctatcctaacacttca-tttcagGAGAAAGAAGAAAAACTTGATGGTGATGCTGCGTTGAACAAATTTTTCCGTGATATATATCAAGATGCAGATGAGGACACAAGAAGAGCAATGAGCAAAT

upper sequence: Vv16s0050g01510.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: GLYMA16G29450.2 (Glycine max), 3'ss of exon 8
gtttgcctgcaatctagatcctgttactttggttttcattattgtttaacatcatatgagaacctgaggaattttat--ttgggggtca-actctttggtggtttgaatttcagGAGAAAGAAGAAAAGCTGGATGGAGATGCAGCTCTGAACAAATTTTTCCGGGACATATATAAAGATGCAGACGAAGACACAAGAAGGGCCATGCAAAAAT
                           ||||  |   ||  | ||  |   |  ||    |  ||  | ||||| |   |||    ||  |     |     | |  ||||||||||||||| |||||||| ||||| ||||| ||  |||||||||||||||| || |||||| |||||||||| || || ||||| ||||| ||| |||| |
--------------------------gtttgcctgctatcttcgtaaagtgtgtta----attctttgtaatttaacggttgcaactcttagctcctaacattcttcatttcagGAGAAAGACGAAAAGCTTGATGGCGATGCTGCGTTGAACAAATTTTTCCGTGAAATATATCAAGATGCAGATGAGGATACAAGGAGGGCAATGAAAAAGT

upper sequence: Vv16s0050g01510.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: GLYMA09G23980.1 (Glycine max), 3'ss of exon 8
gtttgcctgcaatctagatcctgttactttggttttcattattgtttaacatcata-tgagaacctgaggaattttatttgggggtcaactctttggtggtttgaatttcagGAGAAAGAAGAAAAGCTGGATGGAGATGCAGCTCTGAACAAATTTTTCCGGGACATATATAAAGATGCAGACGAAGACACAAGAAGGGCCATGCAAAAAT
                        ||  || | | || || |    |  | | ||  |  | |  | ||  |||  |  |   | ||    | ||  |  ||   ||||||||||||||| |||||||| ||||| ||||| ||  |||||||||||||||| || |||||| |||||||||| || || |||||||| || ||| |||| |
-----------------------gtatgtttgctgtctttgtaaagtctcttaattctttgtattttagtgattgcaactcttgctcctaacattcttcattc--atttcagGAGAAAGATGAAAAGCTTGATGGCGATGCTGCATTGAACAAATTTTTCCGCGAAATATATCAAGATGCAGATGAGGATACAAGAAGAGCAATGAAAAAGT

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|110731891|gb|EE106697.1|EE106697
EST:     AGACTAGAATGGTAGATTGGGATAAGCTGGAAGCACAAGTCAAGAAGGAG                         GAGAAAGAAGAAAAGCTGGATGGAGATGCAGCTCTGAACAAATTTTTCCGG
genomic: AGACTAGAATGGTAGATTGGGATAAGCTGGAAGCACAAGTCAAGAAGGAGgtttgcctgc ... tgaatttcagGAGAAAGAAGAAAAGCTGGATGGAGATGCAGCTCTGAACAAATTTTTCCGG
EST: gi|110421124|gb|EC987412.1|EC987412
EST:     AGACTAGAATGGTAGATTGGGATAAGCTGGAAGCACAAGTGAAGAAGGAG                         GAGAAAGAAGAAAAGCTGGATGGAGATGCAGCTCTGAACAAATTTTTCCGG
genomic: AGACTAGAATGGTAGATTGGGATAAGCTGGAAGCACAAGTCAAGAAGGAGgtttgcctgc ... tgaatttcagGAGAAAGAAGAAAAGCTGGATGGAGATGCAGCTCTGAACAAATTTTTCCGG
EST: gi|110421576|gb|EC987874.1|EC987874
EST:     AGACTAGAATGGTAGATTGGGATAAGCTGGAAGCACAAGTGAAGAAGGAG                         GAGAAAGAAGAAAAGCTGGATGGAGATGCAGCTCTGAACAAATTTTTCCGG
genomic: AGACTAGAATGGTAGATTGGGATAAGCTGGAAGCACAAGTCAAGAAGGAGgtttgcctgc ... tgaatttcagGAGAAAGAAGAAAAGCTGGATGGAGATGCAGCTCTGAACAAATTTTTCCGG
EST: gi|110364112|gb|EC927758.1|EC927758
EST:     AGACTAGAATGGTAGATTGGGATAAGCTGGAAGCACAAGTCAAGAAGGAG                         GAGAAAGAAGAAAAGCTGGATGGAGATGCAGCTCTGAACAAATTTTTCCGG
genomic: AGACTAGAATGGTAGATTGGGATAAGCTGGAAGCACAAGTCAAGAAGGAGgtttgcctgc ... tgaatttcagGAGAAAGAAGAAAAGCTGGATGGAGATGCAGCTCTGAACAAATTTTTCCGG
EST: gi|77581747|gb|DV219826.1|DV219826
EST:     AGACTAGAATGGTAGATTGGGATAAGCTGGAAGCACAAGTGAAGAAGGAG                         GAGAAAGAAGAAAAGCTGGATGGAGATGCAGCTCTGAACAAATTTTTCCGG
genomic: AGACTAGAATGGTAGATTGGGATAAGCTGGAAGCACAAGTCAAGAAGGAGgtttgcctgc ... tgaatttcagGAGAAAGAAGAAAAGCTGGATGGAGATGCAGCTCTGAACAAATTTTTCCGG
EST: gi|161716688|gb|FC067833.1|FC067833
EST:     AGACTAGAATGGTAGATTGGGATAAGCTGGAAGCACAAGTGAAGAAGGAG                         GAGAAAGAAGAAAAGCTGGATGGAGATGCAGCTCTGAACAAATTTTTCCGG
genomic: AGACTAGAATGGTAGATTGGGATAAGCTGGAAGCACAAGTCAAGAAGGAGgtttgcctgc ... tgaatttcagGAGAAAGAAGAAAAGCTGGATGGAGATGCAGCTCTGAACAAATTTTTCCGG
EST: gi|30329189|gb|CD012451.1|CD012451
EST:     AGACTAGAATGGTAGATTGGGATAAGCTGGAAGCACAAGTGAAGAAGGAG                         GAGAAAGAAGAAAAGCTGGATGGAGATGCAGCTCTGAACAAATTTTTCCGG
genomic: AGACTAGAATGGTAGATTGGGATAAGCTGGAAGCACAAGTCAAGAAGGAGgtttgcctgc ... tgaatttcagGAGAAAGAAGAAAAGCTGGATGGAGATGCAGCTCTGAACAAATTTTTCCGG
EST: gi|110383861|gb|EC948264.1|EC948264
EST:     AGACTAGAATGGTAGATTGGGATAAGCTGGAAGCACAAGTGAAGAAGGAG                         GAGAAAGAAGAAAAGCTGGATGGAGATGCAGCTCTGAACAAATTTTTCCGG
genomic: AGACTAGAATGGTAGATTGGGATAAGCTGGAAGCACAAGTCAAGAAGGAGgtttgcctgc ... tgaatttcagGAGAAAGAAGAAAAGCTGGATGGAGATGCAGCTCTGAACAAATTTTTCCGG
EST: gi|110384716|gb|EC949174.1|EC949174
EST:     AGACTAGAATGGTAGATTGGGATAAGCTGGAAGCACAAGTCAAGAAGGAG                         GAGAAAGAAGAAAAGCTGGATGGAGATGCAGCTCTGAACAAATTTTTCCGG
genomic: AGACTAGAATGGTAGATTGGGATAAGCTGGAAGCACAAGTCAAGAAGGAGgtttgcctgc ... tgaatttcagGAGAAAGAAGAAAAGCTGGATGGAGATGCAGCTCTGAACAAATTTTTCCGG
EST: gi|110426741|gb|EC993160.1|EC993160
EST:     AGACTAGAATGGTAGATTGGGATAAGCTGGAAGCACAAGTCAAGAAGGAG                         GAGAAAGAAGAAAAGCTGGATGGAGATGCAGCTCTGAACAAATTTTTCCGG
genomic: AGACTAGAATGGTAGATTGGGATAAGCTGGAAGCACAAGTCAAGAAGGAGgtttgcctgc ... tgaatttcagGAGAAAGAAGAAAAGCTGGATGGAGATGCAGCTCTGAACAAATTTTTCCGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgagaacctgaggaattttatttgggggtcaactctttggtggtttgaatttcagGAGAAAGAAGAAAAGCTGGATGGAGATGCAGCTCTGAACAAATTTTTCCGGGACATATATAAAGATGCAGACGAAGACACAAGAAGGGCCATGCAAAAAT
             aattttattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtttgcctgcaatctagatcctgttactttggttttcattattgtttaacatcatatgagaacctgaggaattttatttgggggtcaactctttggtggtttgaatttcagGAGAAAGAAGAAAAGCTGGATGGAGATGCAGCTCTGAACAAATTTTTCCGGGACATATATAAAGATGCAGACGAAGACACAAGAAGGGCCATGCAAAAAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG