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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tatacttacatgtgttgggtatataaatttacagatggtggaaatagatatcgctgattgttcatgctgtttctaactttgattcttttgtgttctccagGTAGTACTAGGAGGTGGTCAAGATGCATCACATGTCACAACAACTGATCATCGTGCTGGAAAGTTTGAGGCAAAATTCTATGATAAG

Basic information

species Vitis vinifera
transcript Vv01s0011g06630.t01
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv01s0011g06630.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA01G03610.2 (Glycine max), 3'ss of exon 5
--tatacttacatgtgttgggtatataaattta----cagatggtggaaatagatat-cgctgattgttcatgctgtttctaactttgattcttttgtgttctccagGTAGTACTAGGAGGTGGTCAAGATGCATCACATGTCACAACAACTGATCATCGTGCTGGAAAGTTTGAGGCAAAATTCTATGATAAG----
   ||  ||    ||      |  | |  |||      | ||  |  |  | |  ||  | |  ||||  ||| | ||   || |  |  || | |||||     |||| ||||| ||||||||||| |||||||||  ||| || || ||||||||||||||||| || ||||| || ||||||||||| |||    
ttcatcattgatagtaccctatgaacatctttgaccttatattttttatttggtcatatgttccttgt--atgattttctgaattccgtgtcctgtgtgt-----agGTGGTACTTGGAGGTGGTCAGGATGCATCAGCTGTTACTACTACTGATCATCGTGCTGGCAAATTTGAAGCCAAATTCTATGACAAGGTAA

upper sequence: Vv01s0011g06630.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA01G03610.1 (Glycine max), 3'ss of exon 5
--tatacttacatgtgttgggtatataaattta----cagatggtggaaatagatat-cgctgattgttcatgctgtttctaactttgattcttttgtgttctccagGTAGTACTAGGAGGTGGTCAAGATGCATCACATGTCACAACAACTGATCATCGTGCTGGAAAGTTTGAGGCAAAATTCTATGATAAG
   ||  ||    ||      |  | |  |||      | ||  |  |  | |  ||  | |  ||||  ||| | ||   || |  |  || | |||||     |||| ||||| ||||||||||| |||||||||  ||| || || ||||||||||||||||| || ||||| || ||||||||||| |||
ttcatcattgatagtaccctatgaacatctttgaccttatattttttatttggtcatatgttccttgt--atgattttctgaattccgtgtcctgtgtgt-----agGTGGTACTTGGAGGTGGTCAGGATGCATCAGCTGTTACTACTACTGATCATCGTGCTGGCAAATTTGAAGCCAAATTCTATGACAAG

upper sequence: Vv01s0011g06630.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA12G00510.1 (Glycine max), 3'ss of exon 2
----------tatacttacatgtgttgggtatataaatttacagatggtggaaatagatatcgctgattgttcatgctgtttctaactttgattcttttgtgttctccagGTAGTACTAGGAGGTGGTCAAGATGCATCACATGTCACAACAACTGATCATCGTGCTGGAAAGTTTGAGGCAAAATTCTATGATAAG
          |   ||   || || |   | | |   |  |    |  |     | ||||| | |  ||||  ||| | ||   || | |    | | ||||     ||||| ||  | ||||||||||| ||||| |||  ||| ||||| ||||||||||||||||| || ||||| || ||||||| ||| |||
ataaaataaatgccctcctatatgcttt-tgtttccttccatgttttatttgggt-gatat-gttacttgt--atggttttctgaattctatgccctgtgtg-----cagGTGGTTATTGGAGGTGGTCAGGATGCGTCAGCTGTTACAACTACTGATCATCGTGCTGGCAAATTTGAAGCCAAATTCTTTGACAAG

upper sequence: Vv01s0011g06630.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA09G36870.1 (Glycine max), 3'ss of exon 2
---tatacttacatgtgttgggtatataaatttacagatggtggaaatagatatcgctgattgttcatgctgtttctaactttgattcttttgtgttctccagGTAGTACTAGGAGGTGGTCAAGATGCATCACATGTCACAACAACTGATCATCGTGCTGGAAAGTTTGAGGCAAAATTCTATGATAAG
    ||| ||     | ||   |||||   ||               |  || | | ||||  | |    ||| |     | ||| |  | |   || |  |||| ||  | ||||||||||| ||||| |||  ||| ||||| ||||||||||||||||| || || || || ||||||| ||| |||
caaaatatttcatcatcttc--tatatgctttagtttccttccatgttttatttgggtgat-atgcgacttgtgtgattttctgaattctataccttgtgtagGTGGTTATTGGAGGTGGTCAGGATGCCTCAGCTGTTACAACTACTGATCATCGTGCTGGCAAATTCGAAGCCAAATTCTTTGACAAG

upper sequence: Vv01s0011g06630.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: AT2G46280.1 (Arabidopsis thaliana), 3'ss of exon 5
-tatacttacatgtgttgggtatataaatttacagatggtggaaatagatatcgctgattgttcatgctgtttctaactttgattcttttgtgttctccagGTAGTACTAGGAGGTGGTCAAGATGCATCACATGTCACAACAACTGATCATCGTGCTGGAAAGTTTGAGGCAAAATTCTATGATAAG
 ||| |    |||  |   | |  | ||||| |  ||    |||  ||  |    ||||       | | | | |     || ||||  | | |  |  |||| ||||| |||||||||||||||||||||  ||| || || |||||||||||||||||||||||||| || || || || || |||
gtatgcactaatgcttcatgaaattcaattt-cgaatcccagaatcagcaaggcatgat-------gttatctttgtgaatgtttctgctctctcttttagGTTGTACTTGGAGGTGGTCAAGATGCATCAGCTGTGACTACCACTGATCATCGTGCTGGAAAGTTTGAAGCTAAGTTTTACGACAAG

upper sequence: Vv01s0011g06630.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: AT2G46290.1 (Arabidopsis thaliana), 3'ss of exon 6
tatacttacatgtgttgggtatataaatttacagatggtggaaatagatatcgctgattgttcatgctgtttctaactttgattcttttgtgttctccagGTAGTACTAGGAGGTGGTCAAGATGCATCACATGTCACAACAACTGATCATCGTGCTGGAAAGTTTGAGGCAAAATTCTATGATAAG
  ||   ||   || |   | |  ||||| | |   |||    | |   | |     ||| |  |    ||   ||  ||  | || | |  |  |  |||| || || |||||||||||||||||||||  ||| || || ||||||||||||||||| |||||||| || || || || || | |
-gtatgcactaatgct---tcttgaaattcaaattcggttcccaaaagcaacaagtcttgatgttatctttgtgaatgtttctgctctcgc-tcttttagGTTGTGCTTGGAGGTGGTCAAGATGCATCAGCTGTGACTACCACTGATCATCGTGCTGGGAAGTTTGAAGCTAAGTTTTACGACACG

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|351053113|gb|FQ455570.1|FQ455570
EST:     TAACAGAACGCCCGGTCAATGCAGTTACAATGTCTCCACTTCTTGATCAT                         GTAGTACTAGGAGGTGGTCAAGATGCATCACAT
genomic: TAACAGAACGCCCGGTCAATGCAGTTACAATGTCTCCACTTCTTGATCATgtatgtattg ... tgttctccagGTAGTACTAGGAGGTGGTCAAGATGCATCACAT
EST: gi|351045922|gb|FQ441305.1|FQ441305
EST:     TAACAGAACGCCCGGTCAATGCAGTTACAATGTCTCCACTTCTTGATCAT                         GTAGTACTAGGAGGTGGTCAAGATGCATCACATGTCACAACAACTGATCAT
genomic: TAACAGAACGCCCGGTCAATGCAGTTACAATGTCTCCACTTCTTGATCATgtatgtattg ... tgttctccagGTAGTACTAGGAGGTGGTCAAGATGCATCACATGTCACAACAACTGATCAT
EST: gi|351049149|gb|FQ449871.1|FQ449871
EST:     TAACAGAACGCCCGGTCAATGCAGTTACAATGTCTCCACTTCTTGATCAT                         GTAGTACTAGGAG
genomic: TAACAGAACGCCCGGTCAATGCAGTTACAATGTCTCCACTTCTTGATCATgtatgtattg ... tgttctccagGTAGTACTAGGAG
EST: gi|29783544|gb|CB349778.2|CB349778
EST:     TAACAGAACGCCCGGTCAATGCAGTTACAATGTCTCCACTTCTTGATCAT                         GTAGTACTAGGAGGTGGTCAAGATGCATCACATGTCACAACAACTGATCAT
genomic: TAACAGAACGCCCGGTCAATGCAGTTACAATGTCTCCACTTCTTGATCATgtatgtattg ... tgttctccagGTAGTACTAGGAGGTGGTCAAGATGCATCACATGTCACAACAACTGATCAT
EST: gi|351035651|gb|FQ463496.1|FQ463496
EST:     TAACAGAACGCCCGGTCAATGCAGTTACAATGTCTCCCCTTCTTGATCAT                         GTAGTACTAGGA
genomic: TAACAGAACGCCCGGTCAATGCAGTTACAATGTCTCCACTTCTTGATCATgtatgtattg ... tgttctccagGTAGTACTAGGA
EST: gi|349811971|gb|FQ410768.1|FQ410768
EST:     TACAGAACGCCCCGGTCA-TGCAGTTACAATGTCTCCACTTCTTGATCAT                         GTAGTACTAGGAAGTGGTCAAGAATGC-TCACATGTCACAACAAC
genomic: AACAGAACGCCC-GGTCAATGCAGTTACAATGTCTCCACTTCTTGATCATgtatgtattg ... tgttctccagGTAGTACTAGGAGGTGGTCAAGA-TGCATCACATGTCACAACAAC
EST: gi|351036544|gb|FQ457257.1|FQ457257
EST:     TAACAGAACGCCCGGTCAATGCAGTTACAACGTCTCCACTTCTTGATCAT                         GTAGTACTAGGAGGTGGTCAAGATGCATCACATGTCACAACAACTGATCAT
genomic: TAACAGAACGCCCGGTCAATGCAGTTACAATGTCTCCACTTCTTGATCATgtatgtattg ... tgttctccagGTAGTACTAGGAGGTGGTCAAGATGCATCACATGTCACAACAACTGATCAT
EST: gi|110697326|gb|EE074214.1|EE074214
EST:     TAACAGAACGCCCGGTCAATGCAGTTACAATGTCTCCACTTCTTGATCAT                         GTAGTACTAGGAGGTGGTCAAGATGCATCACATGTCACAACAACTGATCAT
genomic: TAACAGAACGCCCGGTCAATGCAGTTACAATGTCTCCACTTCTTGATCATgtatgtattg ... tgttctccagGTAGTACTAGGAGGTGGTCAAGATGCATCACATGTCACAACAACTGATCAT
EST: gi|110380898|gb|EC946200.1|EC946200
EST:     TAACAGAACGCCCGGTCAATGCAGTTACAATGTCTCCACTTCTTGATCAT                         GTAGTACTAGGAGGTGGTCAAGATGCATCACATGTCACAACAACTGATCAT
genomic: TAACAGAACGCCCGGTCAATGCAGTTACAATGTCTCCACTTCTTGATCATgtatgtattg ... tgttctccagGTAGTACTAGGAGGTGGTCAAGATGCATCACATGTCACAACAACTGATCAT
EST: gi|351055042|gb|FQ440381.1|FQ440381
EST:     TNACAGAACGCCCGGTCAATGCAGTTACCATGTCTCCACTTCTTGATCAT                         GTAGTACTAGGAGGTGGTCAAGATGCATCACATGTCACAACAACTGATCAT
genomic: TAACAGAACGCCCGGTCAATGCAGTTACAATGTCTCCACTTCTTGATCATgtatgtattg ... tgttctccagGTAGTACTAGGAGGTGGTCAAGATGCATCACATGTCACAACAACTGATCAT
EST: gi|351012497|gb|FQ430061.1|FQ430061
EST:     TAACAGAACGCCCGGTCAATGCAGTTACAATGTCTCCACTTCTTGATCAT                         GTAGTACTAGGAGGTGGTCAAGATGCATCACATGTCACAACAACTGATCAT
genomic: TAACAGAACGCCCGGTCAATGCAGTTACAATGTCTCCACTTCTTGATCATgtatgtattg ... tgttctccagGTAGTACTAGGAGGTGGTCAAGATGCATCACATGTCACAACAACTGATCAT
EST: gi|110411322|gb|EC977030.1|EC977030
EST:     TAACAGAACGCCCGGTCAATGCAGTTACAATGTCTCCACTTCTTGATCAT                         GTAGTACTAGGAGGTGGTCAAGATGCATCACATGTCACAACAACTGATCAT
genomic: TAACAGAACGCCCGGTCAATGCAGTTACAATGTCTCCACTTCTTGATCATgtatgtattg ... tgttctccagGTAGTACTAGGAGGTGGTCAAGATGCATCACATGTCACAACAACTGATCAT
EST: gi|110369193|gb|EC933345.1|EC933345
EST:     TAACAGAACGCCCGGTCAATGCAGTTACAATGTCTCCACTTCTTGATCAT                         GTAGTACTAGGAGGTGGTCAAGATGCATCACATGTCACAACAACTGATCAT
genomic: TAACAGAACGCCCGGTCAATGCAGTTACAATGTCTCCACTTCTTGATCATgtatgtattg ... tgttctccagGTAGTACTAGGAGGTGGTCAAGATGCATCACATGTCACAACAACTGATCAT
EST: gi|349810075|gb|FQ401521.1|FQ401521
EST:     TAACAGAACGCCCGGTCAATGCAGTTACAATGTCTCCACTTCTTGATCAT                         GTAGTACTAGGAGGTGGTCAAGATGCATCACATGTCACAACAACTGATCAT
genomic: TAACAGAACGCCCGGTCAATGCAGTTACAATGTCTCCACTTCTTGATCATgtatgtattg ... tgttctccagGTAGTACTAGGAGGTGGTCAAGATGCATCACATGTCACAACAACTGATCAT
EST: gi|351012844|gb|FQ430407.1|FQ430407
EST:     TAACAGAACGCCCGGTCAATGCAATTACAATGTCTCCACTTCTTGATCAT                         GTAGTACTAGGAGGTGGTCAAGATGC
genomic: TAACAGAACGCCCGGTCAATGCAGTTACAATGTCTCCACTTCTTGATCATgtatgtattg ... tgttctccagGTAGTACTAGGAGGTGGTCAAGATGC
EST: gi|351053994|gb|FQ441760.1|FQ441760
EST:     TAACAGAACGCCCGGTCAATGCAGTTACCATGTCTCCACTTCTTGATCAT                         GTAGTACTAGGAGGTGGTCAAGATGCATCACATGTCACAACAACTGATCAT
genomic: TAACAGAACGCCCGGTCAATGCAGTTACAATGTCTCCACTTCTTGATCATgtatgtattg ... tgttctccagGTAGTACTAGGAGGTGGTCAAGATGCATCACATGTCACAACAACTGATCAT
EST: gi|351055014|gb|FQ440353.1|FQ440353
EST:     TAACAGAACGCCCGGTCAATGCAGTTACAATGTCTCCACTTCTTGATCAT                         GTAGTACTAGGAGGTGGTCAAGATGCATCACATGTCACAACAACTGATCAT
genomic: TAACAGAACGCCCGGTCAATGCAGTTACAATGTCTCCACTTCTTGATCATgtatgtattg ... tgttctccagGTAGTACTAGGAGGTGGTCAAGATGCATCACATGTCACAACAACTGATCAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agatatcgctgattgttcatgctgtttctaactttgattcttttgtgttctccagGTAGTACTAGGAGGTGGTCAAGATGCATCACATGTCACAACAACTGATCATCGTGCTGGAAAGTTTGAGGCAAAATTCTATGATAAG
                                     ttcttttgtgttctcc  CT-rich tract
                                    attctttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tatacttacatgtgttgggtatataaatttacagatggtggaaatagatatcgctgattgttcatgctgtttctaactttgattcttttgtgttctccagGTAGTACTAGGAGGTGGTCAAGATGCATCACATGTCACAACAACTGATCATCGTGCTGGAAAGTTTGAGGCAAAATTCTATGATAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA
- - - - catgtgt
- - - - - - - - - - - - - - - -cagatgg
- - - - - - - - - - - - - - - - - - - -ggaaata
- - - - - - - - - - - - - - - - - - - - - - - - - - -ctgattg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tcatgct