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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGAAGAAAAGCTGGATGGAGATGCAGCTCTGAACAAATTTTTCCGGGACATATATAAAGATGCAGACGAAGACACAAGAAGGGCCATGCAAAAATCTTTTgtaagacttcaataccggagttacataaaatatcattctaattgagtatgggattataaaagggaaattagcaaattaacggaaggtgacattgtttttcttggggctattttttaacag

Basic information

species Vitis vinifera
transcript Vv16s0050g01510.t01
intron # 9
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv16s0050g01510.t01 (Vitis vinifera), 5'ss of exon 9
lower sequence: GLYMA16G29450.2 (Glycine max), 5'ss of exon 9
AGAAGAAAAGCTGGATGGAGATGCAGCTCTGAACAAATTTTTCCGGGACATATATAAAGATGCAGACGAAGACACAAGAAGGGCCATGCAAAAATCTTTTgtaag------acttcaataccgga------gttacataaaatatca--ttctaattgagtatgggattataaaagggaaattagcaaattaacg--gaaggtgacattg---tttttcttggggctattttttaacag----------------------------------------
||| |||||||| ||||| ||||| ||  |||||||||||||||| || |||||| |||||||||| || || ||||| ||||| ||| |||| |||||||||||      ||||  || |   |      || | |  | ||  ||  || |||||   ||| |    ||           | |  |||| |    ||   || ||      ||| ||||      ||  |  ||                                           
AGACGAAAAGCTTGATGGCGATGCTGCGTTGAACAAATTTTTCCGTGAAATATATCAAGATGCAGATGAGGATACAAGGAGGGCAATGAAAAAGTCTTTTgtaagttttgcacttgtatccttaattccttgtcataatatatgccaatttttaattccttattgtggcatcttctcatttcttgttaatttatattgagaatgccagcaaattttatcttcacagcatactgcaatgtacattgcacctgatctcttttctattattttcttgtatag

upper sequence: Vv16s0050g01510.t01 (Vitis vinifera), 5'ss of exon 9
lower sequence: GLYMA10G37440.1 (Glycine max), 5'ss of exon 10
AGAAGAAAAGCTGGATGGAGATGCAGCTCTGAACAAATTTTTCCGGGACATATATAAAGATGCAGACGAAGACACAAGAAGGGCCATGCAAAAATCTTTTgtaagac------ttcaataccggagttacataaaatatcattctaa--ttgagtatgggattataaaagggaaattagcaaattaacggaaggtgacattgtttttcttggggctattttttaacag
||||||||| || ||||| ||||| ||  |||||||||||||||| || |||||| |||||||||| || ||||||||||| || |||   ||||| ||||| ||        ||   || |   | ||  ||   ||  || | ||  ||  ||     |||||   |    |||    | |||    ||   |    |  ||     ||  ||  | || |  |||
AGAAGAAAAACTTGATGGTGATGCTGCGTTGAACAAATTTTTCCGTGATATATATCAAGATGCAGATGAGGACACAAGAAGAGCAATGAGCAAATCATTTgtgagtttttttgttttctatctatgatagttattctacaatgccaaattttggttccttattattggacatcaatactaatattttttgactatatagtgattgcatctgatgc-gtgttcttgcag

upper sequence: Vv16s0050g01510.t01 (Vitis vinifera), 5'ss of exon 9
lower sequence: GLYMA09G23980.1 (Glycine max), 5'ss of exon 9
AGAAGAAAAGCTGGATGGAGATGCAGCTCTGAACAAATTTTTCCGGGACATATATAAAGATGCAGACGAAGACACAAGAAGGGCCATGCAAAAATCTTTTgtaagacttcaataccggagttacataaaatatcattctaattgagtatgggattataaaagggaaattagcaaatta-acggaaggtgacattg---tttttcttggggctattttttaacag---------------------------------------
||| |||||||| ||||| ||||| ||  |||||||||||||||| || |||||| |||||||||| || || |||||||| || ||| |||| || |||||||| | |    |    |  | || ||  | | ||||      | | ||| ||  |  ||   |  ||   || ||| |  ||   || ||      ||| ||||      ||  |  ||                                          
AGATGAAAAGCTTGATGGCGATGCTGCATTGAACAAATTTTTCCGCGAAATATATCAAGATGCAGATGAGGATACAAGAAGAGCAATGAAAAAGTCATTTgtaagtcctggtcataatatattca-aatttttaattcctccctattgtggcatcttctaat--atcttgttaatttatattgagaatgccagcaaattttgtcttcactgcatactgcaatgtatacattgcacctgatctcttttctattttcttgtatag

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:     TATACAAAGATGCAGATGAAGACACAAGAAGGGCCATGCAAAAATCTTTT                         GTGGAGTCAAATGGGACAGTGCTGTCGACAAACTGGAAGGAAGTTGGATCG
genomic: TATATAAAGATGCAGACGAAGACACAAGAAGGGCCATGCAAAAATCTTTTgtaagacttc ... tttttaacagGTGGAGTCAAATGGGACAGTGCTGTCGACAAACTGGAAGGAAGTTGGATCG
EST: gi|110421124|gb|EC987412.1|EC987412
EST:     TATACAAAGATGCAGACGAAGACACAAGAAGGGCCATGCAAAAATCTTTT                         GTGGAGTCAAATGGGACAGTGCTGTCGACAAACTGGAAGGAAGTTGGATCG
genomic: TATATAAAGATGCAGACGAAGACACAAGAAGGGCCATGCAAAAATCTTTTgtaagacttc ... tttttaacagGTGGAGTCAAATGGGACAGTGCTGTCGACAAACTGGAAGGAAGTTGGATCG
EST: gi|110421576|gb|EC987874.1|EC987874
EST:     TATACAAAGATGCAGACGAAGACACAAGAAGGGCCATGCAAAAATCTTTT                         GTGGAGTCAAATGGGACAGTGCTGTCGACAAACTGGAAGGAAGTTGGATCG
genomic: TATATAAAGATGCAGACGAAGACACAAGAAGGGCCATGCAAAAATCTTTTgtaagacttc ... tttttaacagGTGGAGTCAAATGGGACAGTGCTGTCGACAAACTGGAAGGAAGTTGGATCG
EST: gi|110364112|gb|EC927758.1|EC927758
EST:     TATATAAAGATGCAGACGAAGACACAAGAAGGGCCATGCAAAAATCTTTT                         GTGGAGTCAAATGGGACAGTGCTGTCGACAAACTGGAAGGAAGTTGGATCG
genomic: TATATAAAGATGCAGACGAAGACACAAGAAGGGCCATGCAAAAATCTTTTgtaagacttc ... tttttaacagGTGGAGTCAAATGGGACAGTGCTGTCGACAAACTGGAAGGAAGTTGGATCG
EST: gi|110382038|gb|EC938317.1|EC938317
EST:     CGAAGACACAAGAAGGGCCATGCAAAAATCTTTT                         GTGGAGTCAAATGGGACAGTGCTGTCGACAAACTGGAAGGAAGTTGGATCG
genomic: CGAAGACACAAGAAGGGCCATGCAAAAATCTTTTgtaagacttc ... tttttaacagGTGGAGTCAAATGGGACAGTGCTGTCGACAAACTGGAAGGAAGTTGGATCG
EST: gi|77581747|gb|DV219826.1|DV219826
EST:     TATACAAAGATGCAGACGAAGACACAAGAAGGGCCATGCAAAAATCTTTT                         GTGGAGTCAAATGGG
genomic: TATATAAAGATGCAGACGAAGACACAAGAAGGGCCATGCAAAAATCTTTTgtaagacttc ... tttttaacagGTGGAGTCAAATGGG
EST: gi|110415639|gb|EC981564.1|EC981564
EST:     TATACAAAGATGCAGATGAAGACACAAGAAGGGCCATGCAAAAATCTTTT                         GTGGAGTCAAATGGGACAGTGCTGTCGACAAACTGGAAGGAAGTTGGATCG
genomic: TATATAAAGATGCAGACGAAGACACAAGAAGGGCCATGCAAAAATCTTTTgtaagacttc ... tttttaacagGTGGAGTCAAATGGGACAGTGCTGTCGACAAACTGGAAGGAAGTTGGATCG
EST: gi|161716688|gb|FC067833.1|FC067833
EST:     TATACAAAGATGCAGACGAAGACACAAGAAGGGCCATGCAAAAATCTTTT                         GTGGAGTCAAATGGGACAGTGCTGTCAACAAACTGGAAGGAAGTTGGATCG
genomic: TATATAAAGATGCAGACGAAGACACAAGAAGGGCCATGCAAAAATCTTTTgtaagacttc ... tttttaacagGTGGAGTCAAATGGGACAGTGCTGTCGACAAACTGGAAGGAAGTTGGATCG
EST: gi|30329189|gb|CD012451.1|CD012451
EST:     TATACAAAGATGCAGACGAAGACACAAGAAGGGCCATGCAAAAATCTTTT                         GTGGAGTCAAATGGGACAGTGCTGTCGACAAACTGGAAGGAAGTTGGATCG
genomic: TATATAAAGATGCAGACGAAGACACAAGAAGGGCCATGCAAAAATCTTTTgtaagacttc ... tttttaacagGTGGAGTCAAATGGGACAGTGCTGTCGACAAACTGGAAGGAAGTTGGATCG
EST: gi|51050756|gb|CO818711.1|CO818711
EST:     TATATAAAGATGCAGACGAAGACACAAGAAGGGCCATGCAAAAATCTTTT                         GTGGAGTCAAATGGGACAGTGCTGTCGACAAACTGGAAGGAAGTTGGATCG
genomic: TATATAAAGATGCAGACGAAGACACAAGAAGGGCCATGCAAAAATCTTTTgtaagacttc ... tttttaacagGTGGAGTCAAATGGGACAGTGCTGTCGACAAACTGGAAGGAAGTTGGATCG
EST: gi|110383861|gb|EC948264.1|EC948264
EST:     TATACAAAGATGCAGACGAAGACACAAGAAGGGCCATGCAAAAATCTTTT                         GTGGAGTCAAATGGGACAGTGCTGTCAACAAACTGGAAGGAAGTTGGATCG
genomic: TATATAAAGATGCAGACGAAGACACAAGAAGGGCCATGCAAAAATCTTTTgtaagacttc ... tttttaacagGTGGAGTCAAATGGGACAGTGCTGTCGACAAACTGGAAGGAAGTTGGATCG
EST: gi|110384716|gb|EC949174.1|EC949174
EST:     TATATAAAGATGCAGACGAAGACACAAGAAGGGCCATGCAAAAATCTTTT                         GTGGAGTCAAATGGGACAGTGCTGTCGACAAACTGGAAGGAAGTTGGATCG
genomic: TATATAAAGATGCAGACGAAGACACAAGAAGGGCCATGCAAAAATCTTTTgtaagacttc ... tttttaacagGTGGAGTCAAATGGGACAGTGCTGTCGACAAACTGGAAGGAAGTTGGATCG
EST: gi|110426741|gb|EC993160.1|EC993160
EST:     TATACAAAGATGCAGATGAAGACACAAGAAGGGCCATGCAAAAATCTTTT                         GTGGAGTCAAATGGGACAGTGCTGTCGACAAACTGGAAGGAAGTTGGATCG
genomic: TATATAAAGATGCAGACGAAGACACAAGAAGGGCCATGCAAAAATCTTTTgtaagacttc ... tttttaacagGTGGAGTCAAATGGGACAGTGCTGTCGACAAACTGGAAGGAAGTTGGATCG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AGAAGAAAAGCTGGATGGAGATGCAGCTCTGAACAAATTTTTCCGGGACATATATAAAGATGCAGACGAAGACACAAGAAGGGCCATGCAAAAATCTTTTgtaagacttcaataccggagttacataaaatatcattctaattgagtatgggattataaaagggaaattagcaaattaacggaaggtgacattgtttttcttggggctattttttaacag

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