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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttcgtaggactccatagtaatactaataattcagtcagacaagttttctacagagaaagttcttgattgcagccatatgatagaattgatgttttttcagATTTGACAAGATTATAGCTAAGGAGATTCCTTCAACCATTGTGTATGAGGATGAAAAAGTTCTAGCATTTCGGGATGTCAACCCACAAGCTCCAGTTCAT

Basic information

species Vitis vinifera
transcript Vv01s0011g01610.t01
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv01s0011g01610.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA15G17330.1 (Glycine max), 3'ss of exon 3
--ttcgtaggactccatagtaatactaataattcagtcagacaagttttctacagagaaagttcttgattgcagccatatgatagaat-tgatgttttttcagATTTGACAAGATTATAGCTAAGGAGATTCCTTCAACCATTGTGTATGAGGATGAAAAAGTTCTAGCATTTCGGGATGTCAACCCACAAGCTCCAGTTCAT
  | | |          |  || ||| |||||   |    |  | |||  |   |      ||||| |||   |  || |  ||   | || | |  |||||||||||| ||||| |||  |||||| || ||||| | |||||| |||||||||||||| ||||| |||||||| ||  | || ||||| ||||| ||||||
catacatgcatagatgcatgaagacttataat--ggcttaatcattttattgt-gtttcttttctttatttgtgtaattttgtaacttctgttttcatttcagATTTGATAAGATCATAAATAAGGAAATCCCTTCGAGCATTGTATATGAGGATGAAAAGGTTCTTGCATTTCGTGACATTAATCCACAGGCTCCGGTTCAT

upper sequence: Vv01s0011g01610.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: AT1G31160.1 (Arabidopsis thaliana), 3'ss of exon 3
------------------------------------------------------------------ttcgtaggactccatagtaatactaataattca--gtcagacaagttttctacagagaaagttcttgattg-cagccatatg-atagaattgatgttttttcagATTTGACAAGATTATAGCTAAGGAGATTCCTTCAACCATTGTGTATGAGGATGAAAAAGTTCTAGCATTTCGGGATGTCAACCCACAAGCTCCAGTTCAT
                                                                   || |   | |   |        ||||  |||    |       | | |     | | |||||  || | | |   | | || ||     |  |||  ||| |||||||||||||||||||| || |||||||| |||   ||||| ||||| |||||||| ||| | |||||  | ||  | ||||| || ||||| ||||||
gtatggtttctcttaattttgatttcaaagcaatccatgtttgtgtttttgctacaaatgatcctaatctttcaaatatgtgacctagttaattcttcgttattgatttggatgtgattcgtggaagtttatgctagacgctcttgtgtatgtgtatcttgtggttttagATTTGACAAGATTATAGCAAAAGAGATTCCCTCAGATATTGTCTATGAAGATGAAAACGTTTTGGCATTCAGAGACATTAACCCTCAGGCTCCTGTTCAT
















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|34362915|gb|CF404500.1|CF404500
EST:     CAGT-GAGCTCCAACCAT                         ATTTGACAAGATTATAGCTAAGGAGATTCCTTCAACCATTGTGTATGAGGA
genomic: CAGTGGAGCTCCAACCATgtatctacct ... gttttttcagATTTGACAAGATTATAGCTAAGGAGATTCCTTCAACCATTGTGTATGAGGA
EST: gi|110389333|gb|EC954162.1|EC954162
EST:     GCTACTGCCAAAGCTGCTGCAGCCAATGCCGACAGTGGAGCTCCAACCAT                         ATTTGACAAGATTATAGCTAAGGAGATTCCTTCAACCATTGTGTATGAGGA
genomic: GCTACTGCCAAAGCTGCTGCAGCCAATGCCGACAGTGGAGCTCCAACCATgtatctacct ... gttttttcagATTTGACAAGATTATAGCTAAGGAGATTCCTTCAACCATTGTGTATGAGGA
EST: gi|349818483|gb|FQ403118.1|FQ403118
EST:     GCTACTGCCAAAGCTGCTGCAGCCAATGCCGACAGTGGAGCTCCAACCAT                         ATTTGACAAGATTATAGCTAAGGAGATTCCTTCAACCATTGTGTATGAGGA
genomic: GCTACTGCCAAAGCTGCTGCAGCCAATGCCGACAGTGGAGCTCCAACCATgtatctacct ... gttttttcagATTTGACAAGATTATAGCTAAGGAGATTCCTTCAACCATTGTGTATGAGGA
EST: gi|110384323|gb|EC948751.1|EC948751
EST:     GCTACTGCCAAAGCTGCTGCAGCCAATGCCGACAGTGGAGCTCCAACCAT                         ATTTGACAAGATTATAGCTAAGGAGATTCCTTCAACCATTGTGTATGAGGA
genomic: GCTACTGCCAAAGCTGCTGCAGCCAATGCCGACAGTGGAGCTCCAACCATgtatctacct ... gttttttcagATTTGACAAGATTATAGCTAAGGAGATTCCTTCAACCATTGTGTATGAGGA
EST: gi|71867299|gb|DT016354.1|DT016354
EST:     GCTACTGCCAAAGCTGCTGCAGCCAATGCCGACAGTGGAGCTCCAACCAT                         ATTTGACAAGATTATAGCTAAGGAGATTCCTTCAACCATTGTGTATGAGGA
genomic: GCTACTGCCAAAGCTGCTGCAGCCAATGCCGACAGTGGAGCTCCAACCATgtatctacct ... gttttttcagATTTGACAAGATTATAGCTAAGGAGATTCCTTCAACCATTGTGTATGAGGA
EST: gi|71867022|gb|DT016077.1|DT016077
EST:     GCTACTGCCAAAGCTGCTGCAGCCAATGCCGACAGTGGAGCTCCAACCAT                         ATTTGACAAGATTATAGCTAAGGAGATTCCTTCAACCATTGTGTATGAGGA
genomic: GCTACTGCCAAAGCTGCTGCAGCCAATGCCGACAGTGGAGCTCCAACCATgtatctacct ... gttttttcagATTTGACAAGATTATAGCTAAGGAGATTCCTTCAACCATTGTGTATGAGGA
EST: gi|110379724|gb|EC944942.1|EC944942
EST:     CAAAGCTGCTGCAGCCAATGCCGACAGTGGAGCTCCAACCAT                         ATTTGACAAGATTATAGCTAAGGAGATTCCTTCAACCATTGTGTATGAGGA
genomic: CAAAGCTGCTGCAGCCAATGCCGACAGTGGAGCTCCAACCATgtatctacct ... gttttttcagATTTGACAAGATTATAGCTAAGGAGATTCCTTCAACCATTGTGTATGAGGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttctacagagaaagttcttgattgcagccatatgatagaattgatgttttttcagATTTGACAAGATTATAGCTAAGGAGATTCCTTCAACCATTGTGTATGAGGATGAAAAAGTTCTAGCATTTCGGGATGTCAACCCACAAGCTCCAGTTCAT
                                      aattgat  putative branch site (score: 4)
                                            tgttttttc  CT-rich tract
                                      aattgatgtttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttcgtaggactccatagtaatactaataattcagtcagacaagttttctacagagaaagttcttgattgcagccatatgatagaattgatgttttttcagATTTGACAAGATTATAGCTAAGGAGATTCCTTCAACCATTGTGTATGAGGATGAAAAAGTTCTAGCATTTCGGGATGTCAACCCACAAGCTCCAGTTCAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAAGCT
- - - -gactcca
- - - - - - - - - - - - - - - - - -cagacaa
- - - - - - - - - - - - - - - - - - - - - - - - - -agagaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gcagcca