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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...atagaagaatggatgtaagggagaaaaacttgataaactcgataaataaatcatttatttataagctttttccattattaatggatcttttttatcccagGGGTTTGGGAATGTGGGTTCTTGGGCTGCCCAACTCATCAGTGAACACGGTGGAAAGATTGTTGCTGTAAGTGACATCACTGGAGCCATTAAGAATAGCA

Basic information

species Vitis vinifera
transcript Vv08s0007g07400.t01
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv08s0007g07400.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: GLYMA02G07940.1 (Glycine max), 3'ss of exon 6
atagaagaa-tggatgtaagggagaaaaacttgataaactcgataaataaatcatttatttataagctttttccattattaatggatcttttttatcc-cagGGGTTTGGGAATGTGGGTTCTTGGGCTGCCCAACTCATCAGTGAACACGGTGGAAAGATTGTTGCTGTAAGTGACATCACTGGAGCCATTAAGAATAGCA
|| || | | | || | ||| | | | | ||| | || | || |||| | | | |||| | ||| || | | | || ||||| ||||| |||||||| |||||||||||| || | |||||||| | |||||||| |||||||||| |||||||| ||||| ||||| ||||||||||
gtaaaaattctccaagaaaagaagatcatcagttcatgcctaatattttgatgaatttgagataaacgcatgcaattaatcatg--tcgtgtgtgtcttcagGGTTTTGGAAATGTGGGGTCTTGGGCTGCCAAATTGATCAGTGAGAAAGGTGGAAAAGTTGTTGCTGTGAGTGACATAACTGGGGCCATCAAGAATAGCA

upper sequence: Vv08s0007g07400.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: GLYMA16G26940.1 (Glycine max), 3'ss of exon 5
-atagaagaatggatgtaagggagaaaaacttgataaactcgataaataaatcatttatttataagctttttccattattaatggatcttttttatcccagGGGTTTGGGAATGTGGGTTCTTGGGCTGCCCAACTCATCAGTGAACACGGTGGAAAGATTGTTGCTGTAAGTGACATCACTGGAGCCATTAAGAATAGCA
|| || |||| | || | | | || ||| | || | || | || | | | || | | || | | | | ||||| ||||| |||||||| ||||||||||||||| | |||||||| | |||||||| ||||||| || |||||||| ||||| ||||| ||||||| ||
aatgtaaaaatgctccaagaaaagttcatcaatgcatacctaatattttgatgaatttgagacaaaatcctgcaatcaatcctgt-tgtgtgtctcttcagGGATTTGGAAATGTGGGGTCTTGGGCTGCCCAATTGATCAGTGAGAAAGGTGGAAAAGTTGTTGCAGTGAGTGACATAACTGGGGCCATAAAGAATACCA

upper sequence: Vv08s0007g07400.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: GLYMA19G28770.1 (Glycine max), 3'ss of exon 5
atagaagaatggatgtaa---gggagaaaaacttgataaactcgataaataaatcatttatttataagctttttccattattaatggatcttttttatcccagGGGTTTGGGAATGTGGGTTCTTGGGCTGCCCAACTCATCAGTGAACACGGTGGAAAGATTGTTGCTGTAAGTGACATCACTGGAGCCATTAAGAATAGCA
||| | |||| | | || || || | | | || || | || |||| || | | || || | |||| | |||||| ||||| ||||| || || |||||||||||| | || ||||| | |||||||| |||| ||||| |||||||| ||||||||||| ||||| ||||
atatatagatggtaaagaactgctcaaagaagttcttggatttagtattatgatgaatttgacataaactcatgctatatcatattgtgtttttct---ccagGGTTTTGGAAATGTAGGGTCATGGGCTGCCCAATTAATTAGTGAGAAAGGTGGAAAAGTTGTAGCTGTGAGTGACATAACTGGAGCCATAAAGAACAGCA

upper sequence: Vv08s0007g07400.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: GLYMA11G16320.1 (Glycine max), 3'ss of exon 7
----atagaagaatggatgtaagggagaaaaacttgataaactcgataaataaatcatttatttataagctttttccattattaatggatcttttttatcccagGGGTTTGGGAATGTGGGTTCTTGGGCTGCCCAACTCATCAGTGAACACGGTGGAAAGATTGTTGCTGTAAGTGACATCACTGGAGCCATTAAGAATAGCA
||||| | | | | || || | | | | || || | || |||| || | | || || | |||| | |||||| ||||| ||||| || || |||||||||||| | || ||||| | |||||||| |||||| ||| |||||||| ||||||||||| ||||| ||||
gtacatagatgg-taaagaactgctcaaagaagtgcttggatttagtattatgatgaatttgacataaactcatgctatatcatattgtgtttttct---ccagGGTTTTGGAAATGTAGGGTCATGGGCTGCCCAATTAATTAGTGATAAAGGTGGAAAAGTTGTTGTTGTCAGTGACATAACTGGAGCCATAAAGAACAGCA

upper sequence: Vv08s0007g07400.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: GLYMA16G04560.2 (Glycine max), 3'ss of exon 6
atagaagaatggatgtaagggagaaaaacttgataaactcgataaataaatcatttatttataagctttttccatta-ttaatggatc-ttttttatcccagGGGTTTGGGAATGTGGGTTCTTGGGCTGCCCAACTCATCAGTGAACACGGTGGAAAGATTGTTGCTGTAAGTGACATCACTGGAGCCATTAAGAATAGCA
|| | | || || | ||| | || | || | | ||| |||| | | ||| ||| | | || || | | || ||||| ||||| ||||| || || |||||||||||| | || ||| | | |||||||| |||||||||| |||||||| ||||||||||| ||||| ||||
--agcattagctatatagatggtaaagaactgctgaaagaagttcttgaatttagtattatgatgaatttgacataaactcatatattgtgtatttcttcagGGTTTTGGAAATGTAGGGTCATGGGCTGCCCAATTAATTAGTAATAAAGGTGGAAAAGTTGTTGCTGTGAGTGACATAACTGGAGCCATAAAGAACAGCA

upper sequence: Vv08s0007g07400.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: AT5G18170.1 (Arabidopsis thaliana), 3'ss of exon 5
atagaagaatggatgtaagggagaaaaacttgataaactcgataaataaatcatttatttataagctttttccattattaatggatcttttttatcccagGGGTTTGGGAATGTGGGTTCTTGGGCTGCCCAACTCATCAGTGAACACGGTGGAAAGATTGTTGCTGTAAGTGACATCACTGGAGCCATTAAGAATAGCA
| | || | | | | | | || ||||| ||| | | || | |||| ||||| ||||||||||||||||| || | || || |||||| | ||||| ||||||||||| || |||||||| || ||||| || ||||| |
----------------------gtgacctttcttttattgcggtttcctgcgagccaa--agaaacttttcttattctggtttacatattggttcattagGGATTTGGTAATGTGGGTTCTTGGGCGGCAAAGCTGATAAGTGAAAAGGGTGGGAAGATTGTTGCCGTGAGTGACATTACCGGAGCAATCAAGAACAAGG

upper sequence: Vv08s0007g07400.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: PP1S62_236V6.1 (Physcomitrella patens), 3'ss of exon 6
atagaagaatggatgta-agggagaaaaacttgataaactcgataaataaatcatttatttataagc-tttttccattattaatggatcttttttatcccagGGGTTTGGGAATGTGGGTTCTTGGGCTGCCCAACTCATCAGTGAACACGGTGGAAAGATTGTTGCTGTAAGTGACATCACTGGAGCCATTAAGAATAGCA
| | || | | | || | | | | || | | || | | | || | ||||| ||| ||| | | | ||| ||||| ||||||||||||||||||||||| | |||| ||| ||| | |||||||| ||| ||||| ||||| | ||||||||||| ||||| | |
gttcgcaattgcaccttcatggctttgatgctcgccagtatggtatcttattcgtctgtctaagtgaattttttcatgatt--ttctattgtgatatgacagGGCTTTGGGAATGTGGGTTCTTGGGCATCGAAACTTATCCACGAAAAGGGTGGAAAAATTAAGGCTGTTAGTGATGTTACTGGAGCCATCAAGAACAACT

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|33404746|gb|CF210373.1|CF210373
EST:     TTCTTCATGAACATGGGAAGAGCATTGCCGGACAACGGTTTGTCATACAG                         GGGTTTGGGAATGTGGGTTCTTGGGCTGCCCAACTCATCAGTGAACACGGT
genomic: TTCTTCATGAACATGGGAAGAGCATTGCCGGACAACGGTTTGTCATACAGgtgacctttt ... tttatcccagGGGTTTGGGAATGTGGGTTCTTGGGCTGCCCAACTCATCAGTGAACACGGT






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ataaatcatttatttataagctttttccattattaatggatcttttttatcccagGGGTTTGGGAATGTGGGTTCTTGGGCTGCCCAACTCATCAGTGAACACGGTGGAAAGATTGTTGCTGTAAGTGACATCACTGGAGCCATTAAGAATAGCA
                              tattaat  putative branch site (score: 2)
 tcttttttatccc  putative PPT
 atttatttataagctt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
atagaagaatggatgtaagggagaaaaacttgataaactcgataaataaatcatttatttataagctttttccattattaatggatcttttttatcccagGGGTTTGGGAATGTGGGTTCTTGGGCTGCCCAACTCATCAGTGAACACGGTGGAAAGATTGTTGCTGTAAGTGACATCACTGGAGCCATTAAGAATAGCA

- agaagaa
- - - - -tggatgt
- - - - - - - - - - -agaaaaa
- - - - - - - - - - - - - - - -gataaac
- - - - - - - - - - - - - - - - - - - - - -aaataaa