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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ggttgtttatatgtattcttcctatatcttcagctgtctaatactttatagtgttttgatgtgaagtaaatctaattttatgtatttcttcatctttcagTGTCATTAAGATCGTGCTTCAGTTTTGTAAAGAAAATTCCTTGCACCAAACGTTTCAGACATTACAAAGTGAGTGTCAGGTATCTTTGAATACGGTCGAC

Basic information

species Vitis vinifera
transcript Vv17s0000g08930.t01
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv17s0000g08930.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GLYMA08G13560.2 (Glycine max), 3'ss of exon 1
-----------------------------------------------------------ggttgtttatatgtattcttcctatatcttcagctgtctaat----actt-tatagtg-ttttgatgtgaagtaaatctaat------tttatgtatt----tcttcatctttcagTGTCATTAAGATCGTGCTTCAGTTTTGTAAAGAAAATTCCTTGCACCAAACGTTTCAGACATTACAAAGTGAGTGTCAGGTATCTTTGAATACGGTCGAC
                                                                 | | |||| |   |  | ||| ||    ||||||||    |||  | || || || |   |   |||| ||||  |      ||| || |||    | | |   |  ||||||||| ||||| |||||||||||||| ||||||||||| ||||| || || |||||||   | || |  || || ||||| ||| |||| || || |||
gtaagtagtttcatttggcaactcttgaaaatcgggaaaatttaattttcttcgtttactaaatctcacatgtttcaattttgtatttttca-tgtctaattggaactcgtttaatggttctttcgcacagtagatcttttcccctctttttgaattaaagtttgcccttcgcagTGTCATCAAGATTGTGCTTCAGTTTTGCAAAGAAAATTCGTTGCATCAGACTTTTCAGATGCTGCAGAACGAATGCCAGGTTTCTCTGAACACCGTTGAC

upper sequence: Vv17s0000g08930.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GLYMA05G30430.2 (Glycine max), 3'ss of exon 1
----------------------------------------------------------------------------------ggttgtttatatgtattcttcctatatcttcagctgtctaatactttatagtgttttgatgtgaagtaaatctaattttatgtatttcttcatcttt---cagTGTCATTAAGATCGTGCTTCAGTTTTGTAAAGAAAATTCCTTGCACCAAACGTTTCAGACATTACAAAGTGAGTGTCAGGTATCTTTGAATACGGTCGAC
                                                                                   |  || ||  || |       ||    |||    |   ||||  |  |  |  |||  |   |  ||  | | |||||   | | | ||   |  |   ||||||||| || || |||||||||||||| ||||| ||||| ||||| || || |||||||   | || |  || || ||||| ||| |||| || || |||
gtaagtagtttcatttgccaactcttgaaaatcgggaaatttaattttcttcgtttactgaatcacatgtttcaattttgtttgacgtctaattgaagctcgtttaatggttctttcgcacaatagatcttttttctttttta-aatttatgtgtcattttcaatttctgtttgccccttcgcagTGTCATCAAAATTGTGCTTCAGTTTTGCAAAGAGAATTCGTTGCATCAGACTTTTCAGATGCTGCAGAACGAATGCCAGGTTTCTCTGAACACTGTTGAC

upper sequence: Vv17s0000g08930.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: AT1G73720.1 (Arabidopsis thaliana), 3'ss of exon 1
ggttgtttatatgtattcttcctatatcttcagctgtctaatactttatagtgttttgatgtgaag-taaatc-----taattttatgtatttcttcatctttcagTGTCATTAAGATCGTGCTTCAGTTTTGTAAAGAAAATTCCTTGCACCAAACGTTTCAGACATTACAAAGTGAGTGTCAGGTATCTTTGAATACGGTCGAC
      || | | || |  |  |  ||    | |  | | || || |||      ||  |||  |  |  |||     ||  | | | |  |  |  || | ||||||| || |||||  |||||||||| || ||||||||||||||| | || || || |||||||||||||| ||||||||||| || |||||||| || |||
-----attttgt-tagtaatattggatggagaacgttttgatgctatatgtcagctttgtgtagatcttcatccctaatagctctctattgtgttgaatgtctcagTGTAATAAAGATTATGCTTCAGTTCTGCAAAGAAAATTCCTTGAATCAGACATTCCAGACATTACAAAGCGAGTGTCAGGTTTCCTTGAATACAGTAGAC

upper sequence: Vv17s0000g08930.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: PP1S136_176V6.1 (Physcomitrella patens), 3'ss of exon 1
ggttgtttatatgtattcttcctatatcttcagctgtctaatactttatagtgttttgatgtgaagtaaat-ctaattttatgtatttcttca--tctttcagTGTCATTAAGATCGTGCTTCAGTTTTGTAAAGAAAATTCCTTGCACCAAACGTTTCAGACATTACAAAGTGAGTGTCAGGTATCTTTGAATACGGTCGAC
  |    | | | || | ||   |   ||     ||   |   ||||  |  | ||| || |||  | | |  | |    | |  ||| ||    |  | |||||||||||| || ||||| ||||| ||||| || || |||||||| || || ||||||||| | |||| |||||||||||| ||  | || || || |||
--tcaggtcttt-tagttttggaagtgctcagattgatgagagcttttaacagatttcatttgacctcagtgttcaccgaaggcttttgttggagttgtgcagTGTCATTAAAATAGTGCTGCAGTTCTGTAAGGAGAACTCCTTGCAGCAGACTTTTCAGACACTGCAAAATGAGTGTCAGGTTTCCCTCAACACTGTGGAC

upper sequence: Vv17s0000g08930.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: PP1S31_68V6.1 (Physcomitrella patens), 3'ss of exon 1
----ggttgtttatatgtattcttcctatatcttcagctgtctaatactttatagtgttttgatgtgaagtaaatctaattttatgtatttcttc---atctttcagTGTCATTAAGATCGTGCTTCAGTTTTGTAAAGAAAATTCCTTGCACCAAACGTTTCAGACATTACAAAGTGAGTGTCAGGTATCTTTGAATACGGTCGAC
    |   | | | |   |   ||  |  || || ||    |||  | |   | |  || |  |     ||   | |  | | | |   ||  |    |   | ||||||||||||||| ||||| ||||| |||||||| || || ||||| || || || |||||| |||||| |||||||||||| ||| | || || || |||
cgtagtacgatgaaacagagcatttttgaat-ttgag----ctagaattcggtggatttctcctccactgtg--tgtggtctaaagacctttgtggggactgtgcagTGTCATTAAGATAGTGCTGCAGTTCTGTAAAGAGAACTCATTGCAGCAGACTTTCCAGACACTACAAAATGAGTGTCAGGTTTCTCTCAACACTGTGGAC

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|71857684|gb|DT006739.1|DT006739
EST:     CTACAACTGTTTGCGACAATGTCATCGATCTTAGAAATCGAAGCTCGAGA                         TGTCATTAAGATCGTGCTTCAGTTTTGTAAAGAAAATTCCTTGCACCAAAC
genomic: CTACAACTGTTTGCGACAATGTCATCGACCTTAGAAATCGAAGCTCGAGAgtaagttttc ... catctttcagTGTCATTAAGATCGTGCTTCAGTTTTGTAAAGAAAATTCCTTGCACCAAAC
EST: gi|71863353|gb|DT012408.1|DT012408
EST:     CTACAACTGTTTGCGACAATGTCATCGACCTTAGAAATCGAAGCTCGAGA                         TGTCATTAAGATCGTGCTTCAGTTTTGTAAAGAAAATTCCTTGCACCAAAC
genomic: CTACAACTGTTTGCGACAATGTCATCGACCTTAGAAATCGAAGCTCGAGAgtaagttttc ... catctttcagTGTCATTAAGATCGTGCTTCAGTTTTGTAAAGAAAATTCCTTGCACCAAAC
EST: gi|71859941|gb|DT008996.1|DT008996
EST:     CTACAACTGTTTGCGACAATGTCATCGACCTTAGAAATCGAAGCTCGAGA                         TGTCATTAAGATCGTGCTTCAGTTTTGTAAAGAAAATTCCTTGCACCAAAC
genomic: CTACAACTGTTTGCGACAATGTCATCGACCTTAGAAATCGAAGCTCGAGAgtaagttttc ... catctttcagTGTCATTAAGATCGTGCTTCAGTTTTGTAAAGAAAATTCCTTGCACCAAAC
EST: gi|33403436|gb|CF209063.1|CF209063
EST:     CTACAACTGTTTGCGACAATGTCATCGACCTTAGAAATCGAAGCTCGAGA                         TGTCATTAAGATCGTGCTTCAGTTTTGTAAAGAAAATTCCTTGCACCAAAC
genomic: CTACAACTGTTTGCGACAATGTCATCGACCTTAGAAATCGAAGCTCGAGAgtaagttttc ... catctttcagTGTCATTAAGATCGTGCTTCAGTTTTGTAAAGAAAATTCCTTGCACCAAAC
EST: gi|71863915|gb|DT012970.1|DT012970
EST:     CTACAACTGTTTGCGACAATGTCATCGACCTTAGAAATCGAAGCTCGAGA                         TGTCATTAAGATCGTGCTTCAGTTTTGTAAAGAAAATTCCTTGCACCAAAC
genomic: CTACAACTGTTTGCGACAATGTCATCGACCTTAGAAATCGAAGCTCGAGAgtaagttttc ... catctttcagTGTCATTAAGATCGTGCTTCAGTTTTGTAAAGAAAATTCCTTGCACCAAAC
EST: gi|71861729|gb|DT010784.1|DT010784
EST:     CTACAACTGTTTGCGACAATGTCATCGACCTTAGAAATCGAAGCTCGAGA                         TGTCATTAAGATCGTGCTTCAGTTTTGTAAAGAAAATTCCTTGCACCAAAC
genomic: CTACAACTGTTTGCGACAATGTCATCGACCTTAGAAATCGAAGCTCGAGAgtaagttttc ... catctttcagTGTCATTAAGATCGTGCTTCAGTTTTGTAAAGAAAATTCCTTGCACCAAAC
EST: gi|71862537|gb|DT011592.1|DT011592
EST:     CTACAACTGTTTGCGACAATGTCATCGACCTTAGAAATCGAAGCTCGAGA                         TGTCATTAAGATCGTGCTTCAGTTTTGTAAAGAAAATTCCTTGCACCAAAC
genomic: CTACAACTGTTTGCGACAATGTCATCGACCTTAGAAATCGAAGCTCGAGAgtaagttttc ... catctttcagTGTCATTAAGATCGTGCTTCAGTTTTGTAAAGAAAATTCCTTGCACCAAAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttatagtgttttgatgtgaagtaaatctaattttatgtatttcttcatctttcagTGTCATTAAGATCGTGCTTCAGTTTTGTAAAGAAAATTCCTTGCACCAAACGTTTCAGACATTACAAAGTGAGTGTCAGGTATCTTTGAATACGGTCGAC
                        atctaat  putative branch site (score: 3)
                                     tatttcttcatctttc  putative PPT
                  aagtaaatctaatttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ggttgtttatatgtattcttcctatatcttcagctgtctaatactttatagtgttttgatgtgaagtaaatctaattttatgtatttcttcatctttcagTGTCATTAAGATCGTGCTTCAGTTTTGTAAAGAAAATTCCTTGCACCAAACGTTTCAGACATTACAAAGTGAGTGTCAGGTATCTTTGAATACGGTCGAC

- - - - - - - -ttcttcc
- - - - - - - - - - - - - - ttcagct
- - - - - - - - - - - - - - - - - - - - - - - - - - - - tgatgtg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aagtaaa