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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttgacactattaattgaagtcgttctctgttttggttccttattgtgccaaatagaactttgatgatattgtcttatcatgttacatcttctatgtccagCTTTGTGTGTGGAGCTCTGATGGATGGGAAAAGCAGAAGTCGAGATTCTTACAGGTTCCAGCTGGAAGGACATCAACAGGACAATCAGATACCCGTGTTC

Basic information

species Vitis vinifera
transcript Vv09s0002g08370.t01
intron # 22
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv09s0002g08370.t01 (Vitis vinifera), 3'ss of exon 22
lower sequence: GLYMA08G22910.2 (Glycine max), 3'ss of exon 23
--------------------------------------------------------------------ttgacactattaattgaagtcgttctct-gttttggttccttattgtgccaaata-----gaactttgatgatattg-----tcttatcatgttacatcttctatgtccagCTTTGTGTGTGGAGCTCTGATGGATGGGAAAAGCAGAAGTCGAGATTCTTACAGGTTCCAGCTGGAAGGACATCAACAGGACAATCAGATACCCGTGTTC
                                                                    || |  || |||| |  |||  || ||  || |||   ||||   ||    ||||     |  |  ||||||||| |     |  | | |||     | |  ||  | ||| ||||||| ||||   ||||||||||||||||||||||||| |||||||| ||| ||||  |||| || ||| || ||| ||| |||||||||||||| |
gtaatgatggcttagtacaatagatctggcatttctattattaaattgcactaaaataacttctagttttaaatcttttaact--agtttttatcaagtattgtcccctttcagtatagaatatggcagtgcagtgatgatatggggagttacttttatgccctgtttatta-atgcagATTTGTGTTTGGAATACTGATGGATGGGAAAAGCAGAAGTCTAGATTCTTGCAGCTTCCTCCTGGGAGAACACCACCAGCACAGTCAGATACCCGTGTAC

upper sequence: Vv09s0002g08370.t01 (Vitis vinifera), 3'ss of exon 22
lower sequence: GLYMA07G03180.1 (Glycine max), 3'ss of exon 21
--------------------------------------------------------------------ttgacactattaattgaagtcgttctctgttttggttccttattgtgccaaatagaactttgatgatattgtc--ttatcatgttacatcttctat--gtccagCTTTGTGTGTGGAGCTCTGATGGATGGGAAAAGCAGAAGTCGAGATTCTTACAGGTTCCAGCTGGAAGGACATCAACAGGACAATCAGATACCCGTGTTC
                                                                    ||||  || |||| ||   |  || ||   | | || |  |||          |   |  ||| ||||| |    |||   |  | |   || |||   | ||| ||||||| ||||   ||||||||||||||||||||||||| |||||||| ||| ||||  |||| || ||| || | | ||| |||||||||||||| |
gtaatgatggcttagtacaatacatctggcatttctatgattaaattgcactaaaataacttctagttttgaatcttttaactgttttt-ttatcaagtattgtgcagtatataatatggcaatgcagtgacgatatggatagttacttttgtgccctttttattaatgcagATTTGTGTCTGGAATACTGATGGATGGGAAAAGCAGAAGTCTAGATTCTTGCAGCTTCCTTCTGGGAGAACACCACCGGCACAGTCAGATACCCGTGTAC

upper sequence: Vv09s0002g08370.t01 (Vitis vinifera), 3'ss of exon 22
lower sequence: GLYMA13G44420.1 (Glycine max), 3'ss of exon 23
-----------------------------------------------------------------------------------ttgacactattaattgaagtcgttctctgttttggttccttattgtgccaaatagaactttgatgatattgtct-tatcatgttacatcttctatgtccagCTTTGTGTGTGGAGCTCTGATGGATGGGAAAAGCAGAAGTCGAGATTCTTACAGGTTCCAGCTGGAAGGACATCAACAGGACAATCAGATACCCGTGTTC
                                                                                   |    ||| || ||  |    |  | |  |||  |     | ||| || |   |   |       ||||  | | |||   ||||  | |    ||| ||| ||||||||||||   |||| |||||||||||||||||||| |||||||| ||  |||| ||||| |||||  || ||| |||  ||||||||||||| |
gtaataattgtccactggagatctttctccggaatcccttttctatgattaaattgcattaaaagacttagtttagtatcttataactacttttcatcaattatggccccc-tttgagcatgctgttg-gcaatgcattgccccttctatatcatatatatagagttatctgtctattgtgcagATTTGTGTGTGGAATACTGACGGATGGGAAAAGCAGAAGTCTAGATTCTTGCAACTTCCTGCTGGGAGGACTCCACCAGCACAGGCAGATACCCGTGTAC

upper sequence: Vv09s0002g08370.t01 (Vitis vinifera), 3'ss of exon 22
lower sequence: GLYMA15G00880.1 (Glycine max), 3'ss of exon 22
ttgacactattaattgaagtcgttctctgttttggttccttattgtgccaaatagaactttgatgatattgtctta-tcatg-ttacatct-tctat-gtccagCTTTGTGTGTGGAGCTCTGATGGATGGGAAAAGCAGAAGTCGAGATTCTTACAGGTTCCAGCTGGAAGGACATCAACAGGACAATCAGATACCCGTGTTC
 | || | |  |  |      ||| |  | ||  |||   |      ||| ||   |   | |  |  ||   | | | ||| |  | ||  ||||| || ||| ||||||||||||   |||| |||||||||||||| ||||| |||||||| ||  |||| ||||| |||||  || ||| |||| ||||||||||||| |
ctcaccccaggagctag----gttttggggttgagttaggtccaaacccacattctaagataaccacttttcatcaattatggtcccgtccgtctattgtgcagATTTGTGTGTGGAATACTGACGGATGGGAAAAGCAAAAGTCTAGATTCTTGCAACTTCCTGCTGGGAGGACTCCACCAGCACAAGCAGATACCCGTGTAC

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|349822443|gb|FQ412707.1|FQ412707
EST:     CCTTCTCTCATGTTCTTAATGTGCTAGTTTCGTCTGGAGCAGATGCTCAG                         CTTTGTGTGTGGAGCTCTGATGGATGGGAAAAGCAGAAGTCGAGATTCTTA
genomic: CCTTCTCTCATGTTCTTAATGTGCTAGTTTCGTCTGGAGCAGATGCTCAGgttttttaat ... ctatgtccagCTTTGTGTGTGGAGCTCTGATGGATGGGAAAAGCAGAAGTCGAGATTCTTA
EST: gi|351031457|gb|FQ446660.1|FQ446660
EST:     CCTTCTCTCATGTTCTTAATGTGCTAGTTTCGTCTGGAGCAGATGCTCAG                         CTTTGTGTGTGGAGCTCTGATGGATGGGAAAAGCAGAAGTCGAGATTCTTA
genomic: CCTTCTCTCATGTTCTTAATGTGCTAGTTTCGTCTGGAGCAGATGCTCAGgttttttaat ... ctatgtccagCTTTGTGTGTGGAGCTCTGATGGATGGGAAAAGCAGAAGTCGAGATTCTTA
EST: gi|161717398|gb|FC068869.1|FC068869
EST:     CCTTCTCTCATGTTCTTAATGTGCTAGTTTCGTCTGGAGCAGATGCTCAG                         CTTTGTGTGTGGAGCTCTGATGGATGGGAAAAGCAGAAGTCGAGATTCTTA
genomic: CCTTCTCTCATGTTCTTAATGTGCTAGTTTCGTCTGGAGCAGATGCTCAGgttttttaat ... ctatgtccagCTTTGTGTGTGGAGCTCTGATGGATGGGAAAAGCAGAAGTCGAGATTCTTA
EST: gi|349813140|gb|FQ411380.1|FQ411380
EST:     CCTTCTCTCATGTTCTTAATGTGCTAGTTTCGTCTGGAGCAGATGCTCAG                         CTTTGTGTGTGGAGCTCTGATGGATGGGAAAAGCAGAAGTCGAGATTCTTA
genomic: CCTTCTCTCATGTTCTTAATGTGCTAGTTTCGTCTGGAGCAGATGCTCAGgttttttaat ... ctatgtccagCTTTGTGTGTGGAGCTCTGATGGATGGGAAAAGCAGAAGTCGAGATTCTTA
EST: gi|349829095|gb|FQ419627.1|FQ419627
EST:     CCTTCTCTCATGTTCTTAATGTGCTAGTTTCGTCTGGAGCAGATGCTCAG                         CTTTGTGTGTGGAGCTCTGATGGATGGGAAAAGCAGAAGTCGAGATTCTTA
genomic: CCTTCTCTCATGTTCTTAATGTGCTAGTTTCGTCTGGAGCAGATGCTCAGgttttttaat ... ctatgtccagCTTTGTGTGTGGAGCTCTGATGGATGGGAAAAGCAGAAGTCGAGATTCTTA
EST: gi|349826376|gb|FQ417873.1|FQ417873
EST:     CCTTCTCTCATGTTCTTAATGTGCTAGTTTCGTCTGGAGCAGATGCTCAG                         CTTTGTGTGTGGAGCTCTGATGGATGGGAAAAGCAGAAGTCGAGATTCTTA
genomic: CCTTCTCTCATGTTCTTAATGTGCTAGTTTCGTCTGGAGCAGATGCTCAGgttttttaat ... ctatgtccagCTTTGTGTGTGGAGCTCTGATGGATGGGAAAAGCAGAAGTCGAGATTCTTA
EST: gi|71861049|gb|DT010104.1|DT010104
EST:     CCTTCTCTCATGTTCTTAATGTGCTAGTTTCGTCTGGAGCAGATGCTCAG                         CTTTGTGTGTGGAGCTCTGATGGATGGGAAAAGCAGAAGTCGAGATTCTTA
genomic: CCTTCTCTCATGTTCTTAATGTGCTAGTTTCGTCTGGAGCAGATGCTCAGgttttttaat ... ctatgtccagCTTTGTGTGTGGAGCTCTGATGGATGGGAAAAGCAGAAGTCGAGATTCTTA
EST: gi|71860540|gb|DT009595.1|DT009595
EST:     CCTTCTCTCATGTTCTTAATGTGCTAGTTTCGTCTGGAGCAGATGCTCAG                         CTTTGTGTGTGGAGCTCTGATGGATGGGAAAAGCAGAAGTCGAGATTCTTA
genomic: CCTTCTCTCATGTTCTTAATGTGCTAGTTTCGTCTGGAGCAGATGCTCAGgttttttaat ... ctatgtccagCTTTGTGTGTGGAGCTCTGATGGATGGGAAAAGCAGAAGTCGAGATTCTTA
EST: gi|351048584|gb|FQ448858.1|FQ448858
EST:     CCTCCTCTCATGTTCTTAATGTGCTAGTTTCGTCTGGAGCAGATGCTCAG                         CTTTGTGTGTGGAGCTCTGATGGATGGGAAAAGCAGAAGTCGAGATTCTTA
genomic: CCTTCTCTCATGTTCTTAATGTGCTAGTTTCGTCTGGAGCAGATGCTCAGgttttttaat ... ctatgtccagCTTTGTGTGTGGAGCTCTGATGGATGGGAAAAGCAGAAGTCGAGATTCTTA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgccaaatagaactttgatgatattgtcttatcatgttacatcttctatgtccagCTTTGTGTGTGGAGCTCTGATGGATGGGAAAAGCAGAAGTCGAGATTCTTACAGGTTCCAGCTGGAAGGACATCAACAGGACAATCAGATACCCGTGTTC
            ctttgat  putative branch site (score: 5)
                                       catcttct  putative PPT
                 atgatatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttgacactattaattgaagtcgttctctgttttggttccttattgtgccaaatagaactttgatgatattgtcttatcatgttacatcttctatgtccagCTTTGTGTGTGGAGCTCTGATGGATGGGAAAAGCAGAAGTCGAGATTCTTACAGGTTCCAGCTGGAAGGACATCAACAGGACAATCAGATACCCGTGTTC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
ttgacac
- - - - - -aattgaa
- - - - - - - - - - - - - - - - tggttcc
- - - - - - - - - - - - - - - - - - - - - - - - - aatagaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tcatgtt