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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgctttcttttgtttaaataaaattaatttagaattagtgtgtgtaccttcattctggatgttaaatcaaggaattaatatctaagtgtcattgtctcagAACTGAACTCTGCCGATTCAGTGGTGCCAAGATATACCCTGGGAAAGGAATCAGATTTGTTCGTTCAGATTCTCAG

Basic information

species Vitis vinifera
transcript Vv08s0007g04210.t01
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv08s0007g04210.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GLYMA10G07680.1 (Glycine max), 3'ss of exon 1
----tgctttcttttgtttaaataaaattaat-ttagaattagtgtgtgtaccttcattctggatgttaaatcaaggaattaatatctaagtgtcattgtctcagAACTGAACTCTGCCGATTCAGTGGTGCCAAGATATACCCTGGGAAAGGAATCAGATTTGTTCGTTCAGATTCTCAG
       ||   |||| | |||  |||| | | |    |  | | ||| |      ||   | ||  | | |      |||||||| | | | |   ||| ||||||| ||||| ||||||||||| ||||||||||| ||||| |||||||| |||||||||||||||   |||||||||
tgaaaaattagatttgct-aaaccaaatcagtgtcttcagcattatgtttgataaaat---gaataatcatttttcttattaatatttga-tattcctgtatcagAACCGAACTATGCCGATTCAGCGGTGCCAAGATCTACCCAGGGAAAGGCATCAGATTTGTTCGTGGTGATTCTCAG

upper sequence: Vv08s0007g04210.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GLYMA03G34700.1 (Glycine max), 3'ss of exon 1
tgctttcttttgtttaaataa--aattaatttagaatta-gtgtgtgtaccttcattctggatgttaaatcaaggaat--taatatctaagtgtcattgtctcagAACTGAACTCTGCCGATTCAGTGGTGCCAAGATATACCCTGGGAAAGGAATCAGATTTGTTCGTTCAGATTCTCAG
       | ||| | ||  ||  | |   || || |||| || ||   |  |  ||  |   | ||     ||| |||  |||||| | | | |   ||| ||||||||||||| ||||||||||||||||||||||| ||||| || || || |||||||||||||||   |||||||||
----aattattgctaaaccaatcagtgtcttgagcattatgtttgatcaaatgaataatcatttttcttagaagtaatattaatatttga-tattcctgtatcagAACTGAACTATGCCGATTCAGTGGTGCCAAGATCTACCCCGGAAAGGGCATCAGATTTGTTCGTGGTGATTCTCAG

upper sequence: Vv08s0007g04210.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GLYMA19G37370.2 (Glycine max), 3'ss of exon 1
tgctttcttttgtttaaataaaattaatttaga--attagtgtgtgt-accttcattctggatgttaaatcaag-gaattaatatctaagtgtcattgtctcagAACTGAACTCTGCCGATTCAGTGGTGCCAAGATATACCCTGGGAAAGGAATCAGATTTGTTCGTTCAGATTCTCAG
   |   | ||| | ||| ||  |   | | ||  |||| | | | | |  |  ||  |   | ||     ||| | |||||||| | | | |   | | ||||||||||||| ||||||||||||||||||||||| ||||| || || || |||||||||||||||   |||||||||
---taattattgctaaaacaatctgtgtcttgagcattattttttatcaaatgaataatcatttttcttgtaagtgtattaatatttga-tattcctttatcagAACTGAACTATGCCGATTCAGTGGTGCCAAGATCTACCCAGGAAAGGGCATCAGATTTGTTCGTGGTGATTCTCAG

upper sequence: Vv08s0007g04210.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GLYMA13G21520.1 (Glycine max), 3'ss of exon 1
--tgctttcttttgtttaaataaaattaatttagaattagtgtgtgtaccttcattctggatgttaaatcaaggaattaatatctaagtgtcattgtctcagAACTGAACTCTGCCGATTCAGTGGTGCCAAGATATACCCTGGGAAAGGAATCAGATTTGTTCGTTCAGATTCTCAG
    |    || ||| |   |   ||||  || || | | ||      | ||  |  |   ||  | || |    |||||||| |  |  |   ||| ||||||| || || ||||||||||| ||||||||||| ||||| |||||||| |||||||||||||||   |||||||||
taaaccaatttgtgtcttc-tggcattatgtttgattaaatgaacaatcatttttcttatgtgccacataagtatattaatatttg-gcattgctgtatcagAACCGAGCTGTGCCGATTCAGCGGTGCCAAGATCTACCCAGGGAAAGGCATCAGATTTGTTCGTGGTGATTCTCAG

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|33408532|gb|CF214159.1|CF214159
EST:     TTCTAGGGTTTCCGAGGCGCAGCAGCAGCAACAGCAGCCATGGTTCTCAA                         AACTGAACTCTGCCGATTCAGTGGTGCCAAGATATACCCTGGGAAAGGAAT
genomic: TTCTAGGGTTTCCGAGGCGCAGCAGCAGCAACAGCAGCCATGGTTCTCAAgtatctttct ... attgtctcagAACTGAACTCTGCCGATTCAGTGGTGCCAAGATATACCCTGGGAAAGGAAT
EST: gi|110404057|gb|EC970014.1|EC970014
EST:     TTCTAGGGTTTCCGAGGCGCAGCAGCAGCAACAGCAGCCATGGTTCTCAA                         AACTGAACTCTGCCGATTCAGTGGTGCCAAGATATACCCTGGGAAAGGAAT
genomic: TTCTAGGGTTTCCGAGGCGCAGCAGCAGCAACAGCAGCCATGGTTCTCAAgtatctttct ... attgtctcagAACTGAACTCTGCCGATTCAGTGGTGCCAAGATATACCCTGGGAAAGGAAT
EST: gi|26262650|gb|CA813713.1|CA813713
EST:     AGGCGCAGCAGCAGCAACAGCAGCCATGGTTCTCAA                         AACTGAACTCTGCCGATTCAGTGGTGCCAAGATATACCCTGGGAAAGGAAT
genomic: AGGCGCAGCAGCAGCAACAGCAGCCATGGTTCTCAAgtatctttct ... attgtctcagAACTGAACTCTGCCGATTCAGTGGTGCCAAGATATACCCTGGGAAAGGAAT
EST: gi|26261571|gb|CA812634.1|CA812634
EST:     TTCTAGGGTTTCCGAGGCGCAGCAGCAGCAACAGCAGCCATGGTTCTCAA                         AACTGAACTCTGCCGATTCAGTGGTGCCAAGATATACCCTGGGAAAGGAAT
genomic: TTCTAGGGTTTCCGAGGCGCAGCAGCAGCAACAGCAGCCATGGTTCTCAAgtatctttct ... attgtctcagAACTGAACTCTGCCGATTCAGTGGTGCCAAGATATACCCTGGGAAAGGAAT
EST: gi|110398469|gb|EC964851.1|EC964851
EST:     TTCTAGGGTTTCCGAGGCGCAGCAGCAGCAACAGCAGCCATGGTTCTCAA                         AACTGAACTCTGCCGATTCAGTGGTGCCAAGATATACCCTGGGAAAGGAAT
genomic: TTCTAGGGTTTCCGAGGCGCAGCAGCAGCAACAGCAGCCATGGTTCTCAAgtatctttct ... attgtctcagAACTGAACTCTGCCGATTCAGTGGTGCCAAGATATACCCTGGGAAAGGAAT
EST: gi|26261679|gb|CA812742.1|CA812742
EST:     TTCTAGGGTTT-CGAGGCGCAGCAGCAGCAACAGCAGCCATGGTTCTCAA                         AACTGAACTCTGCCGATTCAGTGGTGCCAAGATATACCCTGGGAAAGGAAT
genomic: TTCTAGGGTTTCCGAGGCGCAGCAGCAGCAACAGCAGCCATGGTTCTCAAgtatctttct ... attgtctcagAACTGAACTCTGCCGATTCAGTGGTGCCAAGATATACCCTGGGAAAGGAAT
EST: gi|294966178|gb|GW839401.1|GW839401
EST:     TCCTAGGGTTTCCGAGGCGCAGCAGCAGCAACAGCAGCCATGGTTCTCAA                         AACTGAACTCTGCCGATTCAGTGGTGCCAAGATATACCCTGGGAAAGGAAT
genomic: TTCTAGGGTTTCCGAGGCGCAGCAGCAGCAACAGCAGCCATGGTTCTCAAgtatctttct ... attgtctcagAACTGAACTCTGCCGATTCAGTGGTGCCAAGATATACCCTGGGAAAGGAAT
EST: gi|71867860|gb|DT016915.1|DT016915
EST:     TTCTAGGGTTTCCGAGGCGCAGCAGCAGCAACAGCAGCCATGGTTCTCAA                         AACTGACCTCTGCCGATTCAGTGGTGCCAAGATATACCCTGGGAAAGGAAT
genomic: TTCTAGGGTTTCCGAGGCGCAGCAGCAGCAACAGCAGCCATGGTTCTCAAgtatctttct ... attgtctcagAACTGAACTCTGCCGATTCAGTGGTGCCAAGATATACCCTGGGAAAGGAAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

accttcattctggatgttaaatcaaggaattaatatctaagtgtcattgtctcagAACTGAACTCTGCCGATTCAGTGGTGCCAAGATATACCCTGGGAAAGGAATCAGATTTGTTCGTTCAGATTCTCAG
                           aattaat  putative branch site (score: 3)
                                              ttgtctc  putative PPT
                           aattaatatctaagt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgctttcttttgtttaaataaaattaatttagaattagtgtgtgtaccttcattctggatgttaaatcaaggaattaatatctaagtgtcattgtctcagAACTGAACTCTGCCGATTCAGTGGTGCCAAGATATACCCTGGGAAAGGAATCAGATTTGTTCGTTCAGATTCTCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA
tgctttc
- - - - - - - -aaataaa
- - - - - - - - - - - - - - - - - - -gtgtgtg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aaatcaa