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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagcttcacaaaaacccatcatccaaacattgtatttaaatccaaacatgattgaaacaagctaattgactttgtttctgtgatgaaaaacagGGGAAGTATCACGGGTCGTTCGACTTCATATTCGTGGACGCAGACAAGGACAATTATCTGAACTACCACAAGAGATTGATCGATTTGGTGAAGGTGGGGG

Basic information

species Vitis vinifera
transcript Vv03s0063g00140.t01
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv03s0063g00140.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GRMZM2G127948_T04 (Zea mays), 3'ss of exon 6
gtaagct-tcacaaaaacccatcatccaaacat-----tgtatttaaatccaaacatgattgaaacaagctaattgactt-tgtttctgtgatgaaaaacagGGGAAGTATCACGGGTCGTTCGACTTCATATTCGTGGACGCAGACAAGGACAATTATCTGAACTACCACAAGAGATTGATCGATTTGGTGAAGGTGGGGG------------------------------------------------
||| |   |  | |   | |   |||    | |       ||| |  ||| |       |||| |  |  |    |||   ||| | | ||        |||| |||| | |||||||||||||||||| | ||||||||||| ||||||||||| || || ||||||||| || |  || |  |  |||||||| |||| |                                                
gtacgaaatggccaggccgccagatctgtgcttcttcgcctatatcgatcgagtagaagttgacatgacatctcggacccgtgtctgtctgcatctgcgcaggagaagaaccacgggtcgttcgacttcgtcttcgtggacgccgacaagGACAACTACCTCAACTACCACGAGCGGCTGCTGAAGCTGGTGAAGCTGGGCGGCCTCATCGGCTACGACAACACGCTGTGGAACGGCTCCGTCGTGCTCC

upper sequence: Vv03s0063g00140.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GRMZM2G127948_T02 (Zea mays), 3'ss of exon 5
gtaagct-tcacaaaaacccatcatccaaacattgt-----atttaaatccaaacatgattgaaacaagctaattgactt-tgtttctgtgatgaaaaacagGGGAAGTATCACGGGTCGTTCGACTTCATATTCGTGGACGCAGACAAGGACAATTATCTGAACTACCACAAGAGATTGATCGATTTGGTGAAGGTGGGGG
||| |   |  | |   | |   |||    | |  |     || |  ||| |       |||| |  |  |    |||   ||| | | ||        |||| |||| | |||||||||||||||||| | ||||||||||| ||||||||||| || || ||||||||| || |  || |  |  |||||||| |||| |
gtacgaaatggccaggccgccagatctgtgcttcttcgcctatatcgatcgagtagaagttgacatgacatctcggacccgtgtctgtctgcatctgcgcagGAGAAGAACCACGGGTCGTTCGACTTCGTCTTCGTGGACGCCGACAAGGACAACTACCTCAACTACCACGAGCGGCTGCTGAAGCTGGTGAAGCTGGGCG

upper sequence: Vv03s0063g00140.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA02G11530.1 (Glycine max), 3'ss of exon 4
---gtaagcttcacaaaaacccatcatccaa-acattgtatttaaatccaaacatgattgaaacaagctaattgact--ttgtttc-tgtgatgaaaaacagGGGAAGTATCACGGGTCGTTCGACTTCATATTCGTGGACGCAGACAAGGACAATTATCTGAACTACCACAAGAGATTGATCGATTTGGTGAAGGTGGGGG
     ||  | ||       ||||||  ||| | |   || | || |   |  |   |  ||| | | ||||||  |     || | |||| |||||  |||| |||| | || |||   |  |||||||| || |||||||||||||||||||| || || |||||||||||||| ||||| ||  | || || || ||||
taaaaaaaatgcaagtttttccatcactcaataaaaaataatcaatttagagga--gtaaaaagagggtaattgggtagcgattgcgtgtggtgaaatgcagGAGAAGAACCATGGGAGCTATGACTTCATCTTTGTGGACGCAGACAAGGACAACTACCTCAACTACCACAAGAGGTTGATAGAGCTTGTCAAAGTTGGGG

upper sequence: Vv03s0063g00140.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: PP1S16_28V6.1 (Physcomitrella patens), 3'ss of exon 4
---gtaagcttcacaaaa-acccatcatccaaacattgtatttaaatccaaacatgattgaaacaagctaattgactttgtttctgtgatgaaa--aacagGGGAAGTATCACGGGTCGTTCGACTTCATATTCGTGGACGCAGACAAGGACAATTATCTGAACTACCACAAGAGATTGATCGATTTGGTGAAGGTGGGGG
   | |||  | | ||      ||   |    | |    |   |  |    || ||  |     | || || | |     || |     || ||    ||||  ||| ||||||  || ||||||||||| ||||| ||||| ||||| ||||| |||||||||||||||||||   | ||  | ||||||| |||||| |
caaggaagtgtaagaagctgtacagggtgtggaaagaaaaac-agttattgacctgtctatgtgaggccaactcatcagattgcaaacttggaattggcagGACAAGAATCACGATTCTTTCGACTTCATCTTCGTAGACGCGGACAAAGACAACTATCTGAACTACCACAAGAAGCTCATGAAGTTGGTGAGGGTGGGAG

upper sequence: Vv03s0063g00140.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: EFJ22516 (Selaginella moellendorffii), 3'ss of exon 4
gtaagcttcacaaaaacccatcatccaaacattgtatttaaatccaaacatgattgaaacaagctaattgactttgtttctgtgatgaaaaacagGGGAAGTATCACGGGTCGTTCGACTTCATATTCGTGGACGCAGACAAGGACAATTATCTGAACTACCACAAGAGATTGATCGATTTGGTGAAGGTGGGGG
||||||||      ||  || | |      ||  ||  |  | ||||  |  ||        ||| |   |||||  |              |||| |  | |||| ||  | ||||||||||| || ||||| || ||||||||||||||  |||||||||||||||| ||||||  |||||| || || || |
gtaagctttc----aatacaacttttctttatcttaccttgaaccaacgacaat--------gctgac--actttcctc------------gcagGAGGCGAATCATGGCGCATTCGACTTCATCTTTGTGGATGCTGACAAGGACAATTACTTGAACTACCACAAGAGGTTGATCTCTTTGGTTAAAGTCGGAG

upper sequence: Vv03s0063g00140.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: EFJ11728 (Selaginella moellendorffii), 3'ss of exon 4
gtaagcttcacaaaaacccatcatccaaacattgtatttaaatccaaacatgattgaaacaagctaattgactttgtttctgtgatgaaaaacagGGGAAGTATCACGGGTCGTTCGACTTCATATTCGTGGACGCAGACAAGGACAATTATCTGAACTACCACAAGAGATTGATCGATTTGGTGAAGGTGGGGG
||||||||      ||  || | |      ||  ||  |  | ||||  |  ||        ||| |   |||||  |              |||| |  | |||| ||  ||||||||||||| || ||||| || ||||||||||||||  |||||||||||||||| ||||||  |||||| || || || |
gtaagctttc----aatacaacttttctttatcttaccttgaaccaacgacaat--------gctgac--actttcctc------------gcagGAGGCGAATCATGGCGCGTTCGACTTCATCTTTGTGGATGCTGACAAGGACAATTACTTGAACTACCACAAGAGGTTGATCTCTTTGGTTAAAGTCGGAG

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|33409666|gb|CF215293.1|CF215293
EST:     ACTTCAAAGAAGGCCCTGCTTTGCCTGTTCTTGATCAGATGATCGAAGAT                         GGGAAGTATCACGGGTCGTTCGACTTCATATTCGTGGACGCAGACAAGGAC
genomic: ACTTCAAAGAAGGCCCTGCTTTGCCTGTTCTTGATCAGATGATCGAAGATgtaagcttca ... tgaaaaacagGGGAAGTATCACGGGTCGTTCGACTTCATATTCGTGGACGCAGACAAGGAC
EST: gi|110392855|gb|EC957377.1|EC957377
EST:     ACTTCAAAGAAGGCCCTGCTTTGCCTGTTCTTGATCAGATGATCGAAGAT                         GGGAAGTATCACGGGTCGTTCGACTTCATATTCGTGGACGCAGACAAGGAC
genomic: ACTTCAAAGAAGGCCCTGCTTTGCCTGTTCTTGATCAGATGATCGAAGATgtaagcttca ... tgaaaaacagGGGAAGTATCACGGGTCGTTCGACTTCATATTCGTGGACGCAGACAAGGAC
EST: gi|110392663|gb|EC956866.1|EC956866
EST:     ACTTCAAAGAAGGCCCTGCTTTGCCTGTTCTTGATCAGATGATCGAAGAT                         GGCAAGTATCACGGGTCGTTCGACTTCATATTCGTGGACGCAGACAAGGAC
genomic: ACTTCAAAGAAGGCCCTGCTTTGCCTGTTCTTGATCAGATGATCGAAGATgtaagcttca ... tgaaaaacagGGGAAGTATCACGGGTCGTTCGACTTCATATTCGTGGACGCAGACAAGGAC
EST: gi|77586769|gb|DV222527.1|DV222527
EST:     ACTTCAAAGAAGGCCCTGCTTTGCCTGTTCTTGATCAGATGATCGAAGAT                         GGCAAGTATCACGGGTCGTTCGACTTCATATTCGTGGACGCAGACTAGGAC
genomic: ACTTCAAAGAAGGCCCTGCTTTGCCTGTTCTTGATCAGATGATCGAAGATgtaagcttca ... tgaaaaacagGGGAAGTATCACGGGTCGTTCGACTTCATATTCGTGGACGCAGACAAGGAC
EST: gi|33407984|gb|CF213611.1|CF213611
EST:     ACTTCAAAGAAGGCCCTGCTTTGCCTGTTCTTGATCAGATGATCGAAGAT                         GGCAAGTATCACGGGTCGTTCGACTTCATATTCGTGGACGCAGACAAGGAC
genomic: ACTTCAAAGAAGGCCCTGCTTTGCCTGTTCTTGATCAGATGATCGAAGATgtaagcttca ... tgaaaaacagGGGAAGTATCACGGGTCGTTCGACTTCATATTCGTGGACGCAGACAAGGAC
EST: gi|110418329|gb|EC984475.1|EC984475
EST:     ACTTCAAAGAAGGCCCTGCTTTGCCTGTTCTTGATCAGATGATCGAAGAT                         GGGAAGTATCACGGGTCGTTCGACTTTATATTCGTGGACGCAGACAAGGAC
genomic: ACTTCAAAGAAGGCCCTGCTTTGCCTGTTCTTGATCAGATGATCGAAGATgtaagcttca ... tgaaaaacagGGGAAGTATCACGGGTCGTTCGACTTCATATTCGTGGACGCAGACAAGGAC
EST: gi|34548696|gb|CF516928.1|CF516928
EST:     ACTTCAAAGAAGGCCCTGCTTTGCCTGTTCTTGATCAGATGATCGAAGAT                         GGCAAGTATCACGGGTCGTTCGACTTCATATTCGTGGACGCAGACAAGGAC
genomic: ACTTCAAAGAAGGCCCTGCTTTGCCTGTTCTTGATCAGATGATCGAAGATgtaagcttca ... tgaaaaacagGGGAAGTATCACGGGTCGTTCGACTTCATATTCGTGGACGCAGACAAGGAC
EST: gi|110378003|gb|EC943111.1|EC943111
EST:     ACTTCAAAGAAGGCCCTGCTTTGCCTGTTCTTGATCAGATGATCGAAGAT                         GGCAAGTATCACGGGTCGTTCGACTTCATATTCGTGGACGCAGACAAGGAC
genomic: ACTTCAAAGAAGGCCCTGCTTTGCCTGTTCTTGATCAGATGATCGAAGATgtaagcttca ... tgaaaaacagGGGAAGTATCACGGGTCGTTCGACTTCATATTCGTGGACGCAGACAAGGAC
EST: gi|34550193|gb|CF518411.1|CF518411
EST:     ACTTCAAAGAAGGCCCTGCTTTGCCTGTTCTTGATCAGATGATCGAAGAT                         GGCAAGTATCACGGGTCATTCGACTTCATATTCGTGGACGCAGACAAGGAC
genomic: ACTTCAAAGAAGGCCCTGCTTTGCCTGTTCTTGATCAGATGATCGAAGATgtaagcttca ... tgaaaaacagGGGAAGTATCACGGGTCGTTCGACTTCATATTCGTGGACGCAGACAAGGAC
EST: gi|110372307|gb|EC936462.1|EC936462
EST:     ACTTCAAAGAAGGCCCTGCTTTGCCTGTTCTTGATCAGATGATCGAAGAT                         GGCAAGTATCACGGGTCGTTCGACTTCATATTCGTGGACGCAGACAAGGAC
genomic: ACTTCAAAGAAGGCCCTGCTTTGCCTGTTCTTGATCAGATGATCGAAGATgtaagcttca ... tgaaaaacagGGGAAGTATCACGGGTCGTTCGACTTCATATTCGTGGACGCAGACAAGGAC
EST: gi|110378272|gb|EC943395.1|EC943395
EST:     ACTTCAAAGAAGGCCCTGCTTTGCCTGTTCTTGATCAGATGATCGAAGAT                         GGGAAGTATCACGGGTCGTTCGACTTCATATTCGTGGACGCAGACAAGGAC
genomic: ACTTCAAAGAAGGCCCTGCTTTGCCTGTTCTTGATCAGATGATCGAAGATgtaagcttca ... tgaaaaacagGGGAAGTATCACGGGTCGTTCGACTTCATATTCGTGGACGCAGACAAGGAC
EST: gi|110365089|gb|EC928834.1|EC928834
EST:     ACTTCAAAGAAGGCCCTGCTTTGCCTGTTCTTGATCAGATGATCGAAGAT                         GGGAAGTATCACGGGTCGTTCGACTTCATATTCGTGGACGCAGACAAGGAC
genomic: ACTTCAAAGAAGGCCCTGCTTTGCCTGTTCTTGATCAGATGATCGAAGATgtaagcttca ... tgaaaaacagGGGAAGTATCACGGGTCGTTCGACTTCATATTCGTGGACGCAGACAAGGAC
EST: gi|352794669|gb|FQ475167.1|FQ475167
EST:     ACTTCAAAGAAGGCCCTGCTTTGCCTGTTCTTGATCAGATGATCGAAGAT                         GGCAAGTATCACGGGTCGTTCGACTTCATATTCGTGGACGCAGACNAGGAC
genomic: ACTTCAAAGAAGGCCCTGCTTTGCCTGTTCTTGATCAGATGATCGAAGATgtaagcttca ... tgaaaaacagGGGAAGTATCACGGGTCGTTCGACTTCATATTCGTGGACGCAGACAAGGAC
EST: gi|34548780|gb|CF517012.1|CF517012
EST:     ACTTCAAAGAAGGCCCTGCTTTGCCTGTTCTTGATCAGATGATCGAAGAT                         GGCAAGTATCACGGGTCGTTCGACTTCATATTCGTGGACGCAGACAAGGAC
genomic: ACTTCAAAGAAGGCCCTGCTTTGCCTGTTCTTGATCAGATGATCGAAGATgtaagcttca ... tgaaaaacagGGGAAGTATCACGGGTCGTTCGACTTCATATTCGTGGACGCAGACAAGGAC
EST: gi|33407910|gb|CF213537.1|CF213537
EST:     ACTTCAAAGAAGGCCCTGCTTTGCCTGTTCTTGATCAGATGATCGAAGAT                         GGGAAGTATCACGGGTCGTTCGACTTCATATTCGTGGACGCAGACAAGGAC
genomic: ACTTCAAAGAAGGCCCTGCTTTGCCTGTTCTTGATCAGATGATCGAAGATgtaagcttca ... tgaaaaacagGGGAAGTATCACGGGTCGTTCGACTTCATATTCGTGGACGCAGACAAGGAC
EST: gi|33409385|gb|CF215012.1|CF215012
EST:     ACTTCAAAGAAGGCCCTGCTTTGCCTGTTCTTGATCAGATGATCGAAGAT                         GGGAAGTATCACGGGTCGTTCGACTTCATATTCGTGGACGCAGACAAGGAC
genomic: ACTTCAAAGAAGGCCCTGCTTTGCCTGTTCTTGATCAGATGATCGAAGATgtaagcttca ... tgaaaaacagGGGAAGTATCACGGGTCGTTCGACTTCATATTCGTGGACGCAGACAAGGAC
EST: gi|33409469|gb|CF215096.1|CF215096
EST:     ACTTCAAAGAAGGCCCTGCTTTGCCTGTTCTTGATCAGATGATCGAAGAT                         GGGAAGTATCACGGGTCGTTCGACTTCATATTCGTGGACGCAGACAAGGAC
genomic: ACTTCAAAGAAGGCCCTGCTTTGCCTGTTCTTGATCAGATGATCGAAGATgtaagcttca ... tgaaaaacagGGGAAGTATCACGGGTCGTTCGACTTCATATTCGTGGACGCAGACAAGGAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aatccaaacatgattgaaacaagctaattgactttgtttctgtgatgaaaaacagGGGAAGTATCACGGGTCGTTCGACTTCATATTCGTGGACGCAGACAAGGACAATTATCTGAACTACCACAAGAGATTGATCGATTTGGTGAAGGTGGGGG
                         aattgac  putative branch site (score: 3)
                                            atgaaaaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagcttcacaaaaacccatcatccaaacattgtatttaaatccaaacatgattgaaacaagctaattgactttgtttctgtgatgaaaaacagGGGAAGTATCACGGGTCGTTCGACTTCATATTCGTGGACGCAGACAAGGACAATTATCTGAACTACCACAAGAGATTGATCGATTTGGTGAAGGTGGGGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA