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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaatggatctctgtttagttaaattgatattagaattctttctgtgaggtgaattatgtggtcaagcagtagattttggtgttactcaatctaaagatttttcttttgttggtgtgctagtggaaattcatttgtttcatgtttaacagGAGAAAGGCAGGCAAACATTAACATTGCAGATGGGAATAAAAGCTCCGTGATATTAGAATCTGAAGCTGCAAAGATGGACCAGGTTAACAGAGCTCAAG

Basic information

species Vitis vinifera
transcript Vv09s0002g01630.t01
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv09s0002g01630.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA04G40420.1 (Glycine max), 3'ss of exon 5
----------------------gtaatggat-ctctgtttagttaaattgatattagaattct--ttctgtgaggtgaattatgtggtcaagcagtagattttggtg-ttactcaatctaaagatttttcttttgttggtgtgctagtggaaattcatttgtttcatgtttaacagGAGAAAGGCAGGCAAACATTAACATTGCAGATGGGAATAAAAGCTCCGTGATATTAGAATCTGAAGCTGCAAAGATGGACCAGGTTAACAGAGCTCAAG
| | || || ||| | | || || | | | | || | | | || | | | || ||| | | | || ||| | | || | ||| |||| | | || || | || ||| |||| |||||||||||| ||||| |||| |||||||| ||||| || || || || ||||| |||| ||| |||||||| | |||||| || ||||||||||||||||
gtaatcaatttgatattccaatccatcgtatgttcaatttttcttatttttcatcatgaatatagttttagtacccacgtcatttaaccgaaaag--gatcctattactcacccaacttctacatgtagcttctgtt--tttactggtattggt-cacctgtg--gtgttaaacagGAGAAAGACAGGCTCACATAAACATTGCTGATGGAAAGAAGAGTTCAGTGATCTTAGCATCAGAAGCTGCGAGGATGGATCAAGTTAACAGAGCTCAAG

upper sequence: Vv09s0002g01630.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA06G14340.1 (Glycine max), 3'ss of exon 5
---------------------------------gtaatggatctctgtttagttaaattgatatta--gaattctttctgtgaggtgaattatgtggtcaagcagtagattttggtgttactcaatctaaagatttttcttttgttggtgtgctagtggaaattcatttgtttcatgtttaacagGAGAAAGGCAGGCAAACATTAACATTGCAGATGGGAATAAAAGCTCCGTGATATTAGAATCTGAAGCTGCAAAGATGGACCAGGTTAACAGAGCTCAAG
||| |||| ||| | || || | |||| ||| | | || | | || | | | | || ||| | | | | ||| | | || | || || || || ||| |||| |||||||||||| ||||| |||| |||||||| ||||| || || || || || || |||| ||| ||||| |||| |||||| || ||||||||||||||||
gttatcaatttgatattcccatccttcatatgctcaatttatcttattttgcactatttttcatcattaaattatttttagtacccatgacattcaaccgaaaagcatcctattcc-tcacccaacttctacctgtagcttctat--gtttactggtactgat-cacctgtg--gtgttaaacagGAGAAAGACAGGCTCACATAAACATTGCTGATGGAAAGAAGAGTTCAGTTATCTTAGCATCAGAAGCCGCAAGGATGGATCAAGTTAACAGAGCTCAAG

upper sequence: Vv09s0002g01630.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: AT4G27585.1 (Arabidopsis thaliana), 3'ss of exon 5
-------------------------------------gtaatggatctctgtttagttaaattgatattagaattctttctgtgaggtgaattatgtggtcaagcagtagattttggtgttactcaatctaaagatttttcttttg-ttggtgtgctagtggaaattcatttgtttcatgtttaacagGAGAAAGGCAGGCAAACATTAACATTGCAGATGGGAATAAAAGCTCCGTGATATTAGAATCTGAAGCTGCAAAGATGGACCAGGTTAACAGAGCTCAAG
| | || | || || | | ||| | |||||| | | | ||| || | | | || ||| || || || | || | || || | || | | ||| ||| | | ||| |||||||||||||| | | || |||||||| ||||| || ||||| || || || || | ||||||||| ||||||||||||||||| || |||| ||||
gtaaccttgactgacttgtctttgagaactcatcttcgagactgagcagtgcttgctacggctcataatgttattcttggc-taaaat---ctatctgttattccttttgagtttcgttttttgcatttggaaaagaagaggcctgcttagcatgtttctaatcattgctttact--aaatttgacagGAGAAAGGCAATCCCATATCAACATTGCTGATGGTAAGAAAAGTTCTGTAATCTTGGCATCTGAAGCAGCAAAGATGGACCAGGTGAATCGAGCACAAG

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|30324273|gb|CD007535.1|CD007535
EST:     GCAAGCAGAAGCAGAACGTAAAAAGAGAGCTCAAATTCTTGAATCAGAGG                         GAGAAAGGCAGTCAAACATTAACATTGCAGATGGGAATAAAAGCTCTGTGA
genomic: GCAAGCAGAAGCAGAACGTAAAAAGAGAGCTCAAATTCTTGAATCAGAGGgtaatggatc ... tgtttaacagGAGAAAGGCAGGCAAACATTAACATTGCAGATGGGAATAAAAGCTCCGTGA
EST: gi|110377134|gb|EC942193.1|EC942193
EST:     GCAAGCAGAAGCAGAACGTAAAAAGAGAGCTCAAATTCTTGAATCAGAGG                         GAGAAAGGCAGGCAAACATTAACATTGCAGATGGGAATAAAAGCTCTGTGA
genomic: GCAAGCAGAAGCAGAACGTAAAAAGAGAGCTCAAATTCTTGAATCAGAGGgtaatggatc ... tgtttaacagGAGAAAGGCAGGCAAACATTAACATTGCAGATGGGAATAAAAGCTCCGTGA
EST: gi|110393459|gb|EC958711.1|EC958711
EST:     GCAAGCAGAAGCAGAACGTAAAAAGAGAGCTCAAATTCTTGAATCAGAGG                         GAGAAAGGCAGGCAAACATTAACATTGCAGATGGGAATAAAAGCTCTGTGA
genomic: GCAAGCAGAAGCAGAACGTAAAAAGAGAGCTCAAATTCTTGAATCAGAGGgtaatggatc ... tgtttaacagGAGAAAGGCAGGCAAACATTAACATTGCAGATGGGAATAAAAGCTCCGTGA
EST: gi|110385372|gb|EC949890.1|EC949890
EST:     GCAAGCAGAAGCAGAACGTAAAAAGAGAGCTCAAATTCTTGAATCAGAGG                         GAGAAAGGCAGGCAAACATTAACATTGCAGATGGGAATAAAAGCTCTGTGA
genomic: GCAAGCAGAAGCAGAACGTAAAAAGAGAGCTCAAATTCTTGAATCAGAGGgtaatggatc ... tgtttaacagGAGAAAGGCAGGCAAACATTAACATTGCAGATGGGAATAAAAGCTCCGTGA
EST: gi|30325554|gb|CD008816.1|CD008816
EST:     GCAAGCAGAAGCAGAACGTAAAAAGAGAGCTCAAATTCTTGAATCAGAGG                         GAGAAAGGCAGTCAAACATTAACATTGCAGATGGGAATAAAAGCTCTGTGA
genomic: GCAAGCAGAAGCAGAACGTAAAAAGAGAGCTCAAATTCTTGAATCAGAGGgtaatggatc ... tgtttaacagGAGAAAGGCAGGCAAACATTAACATTGCAGATGGGAATAAAAGCTCCGTGA
EST: gi|30327281|gb|CD010543.1|CD010543
EST:     GCAAGCAGAAGCAGAACGTAAAAAGAGAGCTCAAATTCTTGAATCAGAGG                         GAGAAAGGCAGTCAAACATTAACATTGCAGATGGGAATAAAAGCTCTGTGA
genomic: GCAAGCAGAAGCAGAACGTAAAAAGAGAGCTCAAATTCTTGAATCAGAGGgtaatggatc ... tgtttaacagGAGAAAGGCAGGCAAACATTAACATTGCAGATGGGAATAAAAGCTCCGTGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agatttttcttttgttggtgtgctagtggaaattcatttgtttcatgtttaacagGAGAAAGGCAGGCAAACATTAACATTGCAGATGGGAATAAAAGCTCCGTGATATTAGAATCTGAAGCTGCAAAGATGGACCAGGTTAACAGAGCTCAAG
                             aaattcatttgttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaatggatctctgtttagttaaattgatattagaattctttctgtgaggtgaattatgtggtcaagcagtagattttggtgttactcaatctaaagatttttcttttgttggtgtgctagtggaaattcatttgtttcatgtttaacagGAGAAAGGCAGGCAAACATTAACATTGCAGATGGGAATAAAAGCTCCGTGATATTAGAATCTGAAGCTGCAAAGATGGACCAGGTTAACAGAGCTCAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
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- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG
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- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTCA