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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttgaatgtgtggggaggaaaactcaacttccagcccatctgctgaatgtgtttccttcagataatgcatcatgggttgtctttcatatgctctttttcagGTTGTTGTGGCTGATGCTGAGGCATACACTTATGATGATGAAGTGCTCAAGAAAGCAGAAGCTATGGGGAAGCCAGGGCTTGTGGAGATCTATGCCAAAG

Basic information

species Vitis vinifera
transcript Vv03s0180g00050.t01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv03s0180g00050.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: LOC_Os09g02284.1 (Oryza sativa), 3'ss of exon 2
-ttgaatgtgtggggag---gaaaactcaacttccagcccatctgctgaatgtgtttccttcagataatgcatcatgggttgtctttcatatgctctttttcagGTTGTTGTGGCTGATGCTGAGGCATACACTTATGATGATGAAGTGCTCAAGAAAGCAGAAGCTATGGGGAAGCCAGGGCTTGTGGAGATCTATGCCAAAG
  ||| | |    | |     | | |  ||  | |  |  || || || ||  |      |||  | ||   |||  |      |||  | ||  ||||  ||||| || || |  ||||| |||||||| || ||||||||||| ||  ||||||||||||| || ||||| ||||| ||  |  | |||||| ||||||| |
gctgattatagctgtactctaacagcataagattcttcatatttgttgtattggaacaaatca--tgat-tgtcacagagctaattttctgtga-ctttaccagGTGGTAGTTGAGGATGCAGAGGCATATACATATGATGATGAGGTCATCAAGAAAGCAGATGCCATGGGAAAGCCCGGATTGATAGAGATCAATGCCAAGG

upper sequence: Vv03s0180g00050.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA07G34610.1 (Glycine max), 3'ss of exon 2
-ttgaatgtgtggggaggaaaactcaacttc-cagcccatctgctgaatgtgtttccttcagataatgcatcatgggttgtctttcatatgctctttttcagGTTGTTGTGGCTGATGCTGAGGCATACACTTATGATGATGAAGTGCTCAAGAAAGCAGAAGCTATGGGGAAGCCAGGGCTTGTGGAGATCTATGCCAAAG
  || ||   ||   |  ||   | || ||  |  ||| ||      |||||||  ||| || ||||  |||||    ||| |||  | ||   ||| | ||||  | |||| |||||||||||||||||| ||||||||||| ||||| |||||||||||||||||||| ||||| |||||||| || |||  ||| |   
tatgtattgttgaacaaaaattttaaattttgctacccttcaaaatcatgtgttgtcttgaggtaatttatcatactatgttttt--tttggcttttattagGTGATGGTGGTTGATGCTGAGGCATACACATATGATGATGAGGTGCTTAAGAAAGCAGAAGCTATGGGCAAGCCTGGGCTTGTAGAAATCATTGCGAGGC

upper sequence: Vv03s0180g00050.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA20G02360.1 (Glycine max), 3'ss of exon 2
ttgaatgt-gtggggaggaaaactcaacttccagcccatctg---ctgaatgtgtttccttcagataatgcatcatgggttgtctttcatatgctctttttcagGTTGTTGTGGCTGATGCTGAGGCATACACTTATGATGATGAAGTGCTCAAGAAAGCAGAAGCTATGGGGAAGCCAGGGCTTGTGGAGATCTATGCCAAAG
|  | ||| |||   |  |  | | || || |  ||| ||     | ||  |||||  ||| || ||||  |||||     || |||    ||   ||| | ||||  | |||| |||||||||||||||||| |||||||| || ||||| |||||||||||||||||||| ||||| |||||||| || |||  ||| |   
tgtattgttgtgaacaaaagtattaaatttgctacccttcaaaatcagatggtgttgtctttaggtaatttatcatactaagtattt----tggcatttattagGTCATGGTGGTTGATGCTGAGGCATACACATATGATGACGAGGTGCTTAAGAAAGCAGAAGCTATGGGCAAGCCTGGGCTTGTAGAAATCATTGCGAGGC

upper sequence: Vv03s0180g00050.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: AT2G15430.1 (Arabidopsis thaliana), 3'ss of exon 2
ttgaatgtgtggggaggaaaac-tcaacttccagcccatctgctgaatgtgtttccttcagataatgcatcatgggt-tgtctttcatatgctctttttcagGTTGTTGTGGCTGATGCTGAGGCATACACTTATGATGATGAAGTGCTCAAGAAAGCAGAAGCTATGGGGAAGCCAGGGCTTGTGGAGATCTATGCCAAAG
   |  ||    | ||   | | |     |  ||     |   |   |     ||  |    | |  |||||    | |   ||| |||   |  || | ||||||| |||| |||| |||| ||||||||||| ||||| |||||| |||||||||| ||||| |||||||| || || ||  | ||||||  | | ||||
--aacagttacagtagtttatcgttggaatttagtatgccatttcttttgaagtctgttgcttgaatcatcacaactgtaatttttatactttgcttcttagGTTGTAGTGGTTGATCCTGAAGCATACACTTACGATGAAGAAGTGATCAAGAAAGCTGAAGCAATGGGGAAACCGGGACTCATTGAGATCAGTCCGAAAG

upper sequence: Vv03s0180g00050.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: AT2G15400.1 (Arabidopsis thaliana), 3'ss of exon 2
---ttgaatgtgtggggaggaaaactcaacttccagcccatctgctgaat-gtgtttccttcagataatgcatcatgggttgtctttcatatgctctttttcagGTTGTTGTGGCTGATGCTGAGGCATACACTTATGATGATGAAGTGCTCAAGAAAGCAGAAGCTATGGGGAAGCCAGGGCTTGTGGAGATCTATGCCAAAG
    ||||| | |    | |         | |  ||| ||| |  |     || | |  ||   || || ||  |  |  |   | | |||   |  || | ||||||| |||| |||| |||| ||||||||||| ||||| |||||| |||||||||| ||||| |||||||| || || ||  | |||||| || | ||| 
tgtatgaattt-tctttaagtgtttagtgcgtttagctcatttcttttgcagtctattgtttgaatcat-cacaactg--taattataatactttgcttcttagGTTGTGGTGGTTGATCCTGAAGCATACACTTACGATGAAGAAGTGATCAAGAAAGCTGAAGCAATGGGGAAACCGGGACTCATTGAGATCCATCCGAAAC

upper sequence: Vv03s0180g00050.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: PP1S79_74V6.1 (Physcomitrella patens), 3'ss of exon 3
---------------------------------ttgaatgtgtggggaggaa---aactcaacttccagcccatctgctgaatgtgtttcc---ttcagataatgcatcatgggttgtcttt-----catatgctcttttt-cagGTTGTTGTGGCTGATGCTGAGGCATACACTTATGATGATGAAGTGCTCAAGAAAGCAGAAGCTATGGGGAAGCCAGGGCTTGTGGAGATCTATGCCAAAG
                                 ||  |    |        |     ||| || | |||   || | ||||    ||   |      | ||   ||||  |   |    | |     | |||   | |  | ||||| || ||||  ||  |||| |||||||| ||||| || |||||||| |||||||||||||| ||||| ||||||||  | ||||| || ||   ||| |
gtagcatattcatttaactcatcttattgcagtttacaaccttaaatttcgattcgtctcgacgttcagagtattttctgagcaagtaatcgaccctatatgcggcattttaaatcacgtgttgctgcgtataaacatgctgcagGTGGTGGTGGTGGACCCTGAAGCATACACCTATGACGAAGAAGTGCTGAAGAAAGCAGAAGCCATGGGTAAGCCAGGTTTAGTGGAAATTTACAGCAAGG

upper sequence: Vv03s0180g00050.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: EFJ38153 (Selaginella moellendorffii), 3'ss of exon 3
ttgaatgtgtggggaggaaaactcaacttccagcccatctgctgaatgtgtttcct-tcagataatgcatcatgggttgtctttcatatgctctttttcagGTTGTTGTGGCTGATGCTGAGGCATACACTTATGATGATGAAGTGCTCAAGAAAGCAGAAGCTATGGGGAAGCCAGGGCTTGTGGAGATCTATGCCAAAG
                                     || ||     | | ||    |  |||||   |  |  | |        |     | ||    |||| |  |||   ||  | |||||||||||||||||||| |||||| |||||||||| ||||| ||||| ||||| || |||||||||||||||| ||| |
------------------------------------gtcagccagtcgagcttagagtttgataagaaactaaagctca------aagctttgttccatagGTGGAAGTGATCGACCCAGAGGCATACACTTATGATGACGAAGTGATCAAGAAAGCCGAAGCCATGGGAAAGCCTGGCCTTGTGGAGATCTATGGCAAGG

upper sequence: Vv03s0180g00050.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: EFJ15766 (Selaginella moellendorffii), 3'ss of exon 3
ttgaatgtgtggggaggaaaactcaacttccagcccatctgctgaatgtgtttcct-tcagataatgcatcatgggttgtctttcatatgctctttttcagGTTGTTGTGGCTGATGCTGAGGCATACACTTATGATGATGAAGTGCTCAAGAAAGCAGAAGCTATGGGGAAGCCAGGGCTTGTGGAGATCTATGCCAAAG
                                     || ||     | | ||    |  |||||   |  |  | |        |     | ||    |||| |  ||||  ||  | |||||||||||||||||||| |||||| |||||||||| ||||| ||||| ||||| || |||||||||||||||| ||| |
------------------------------------gtcagccagtcgagcttagagtttgataagaaactaaagctca------aagctttgttccatagGTGGAAGTGGTCGACCCAGAGGCATACACTTATGATGACGAAGTGATCAAGAAAGCGGAAGCCATGGGAAAGCCTGGCCTTGTGGAGATCTATGGCAAGG

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|110684915|gb|EE062742.1|EE062742
EST:     TTGAGAGCAGTCCCACAAAAGTTTTCGACATTGATGCTAGTTCCCAACAG                         GTTGTTGTGGCTGATGCTGAGGCATACACTTATGATGATGAAGTGCTCAAG
genomic: TTGAGAGCAGTCCCACAAAAGTTTTCGACATTGATGCTAGTTCCCAACAGgtttgcttct ... tctttttcagGTTGTTGTGGCTGATGCTGAGGCATACACTTATGATGATGAAGTGCTCAAG
EST: gi|110711905|gb|EE088914.1|EE088914
EST:     TTGAGAGCAGTCCCACAAA-GTTTTCGACATTGATGCTAGTTCCCAACAG                         GTTTGT-GTGGCTGATGCTGANGCATACACTTATGATGATGAAGTGCTC
genomic: TTGAGAGCAGTCCCACAAAAGTTTTCGACATTGATGCTAGTTCCCAACAGgtttgcttct ... tctttttcagGTT-GTTGTGGCTGATGCTGAGGCATACACTTATGATGATGAAGTGCTC
EST: gi|110705825|gb|EE083119.1|EE083119
EST:     TTGAGAGCAGTCCCACAAAAGTTTTCGACATTGATGCTAGTTCCCAACAG                         GTTGTTGTGGCTGATGCTGAGGCATACACTTATGATGATGAAGTGCTCAAG
genomic: TTGAGAGCAGTCCCACAAAAGTTTTCGACATTGATGCTAGTTCCCAACAGgtttgcttct ... tctttttcagGTTGTTGTGGCTGATGCTGAGGCATACACTTATGATGATGAAGTGCTCAAG
EST: gi|30128673|gb|CB914012.1|CB914012
EST:     TTGAGAGCAGTCCCACAAAAGTTTTCGACATTGATGCTAGTTCCCAACAG                         GTTGTTGTGGCTGATGCTGAGGCATACACTTATGATGATG
genomic: TTGAGAGCAGTCCCACAAAAGTTTTCGACATTGATGCTAGTTCCCAACAGgtttgcttct ... tctttttcagGTTGTTGTGGCTGATGCTGAGGCATACACTTATGATGATG
EST: gi|30305778|gb|CB982572.1|CB982572
EST:     TTGAGAGCAGTCCCACAAAAGTTTTCGACATTGATGCTAGTTCCCAACAG                         GTTGTTGTGGCTGATGCTGAGGCATACACTTATGATGATAAAGTGCTCAAG
genomic: TTGAGAGCAGTCCCACAAAAGTTTTCGACATTGATGCTAGTTCCCAACAGgtttgcttct ... tctttttcagGTTGTTGTGGCTGATGCTGAGGCATACACTTATGATGATGAAGTGCTCAAG
EST: gi|110691772|gb|EE070258.1|EE070258
EST:     TTGAGAGCAGTCCCACAAAAGTTTTCGACATTGATGCTAGTTCCCAACAG                         GTTGTTGTGGCTGATGCTGAGGCATACACTTATGATGATGAAGTGCTCAAG
genomic: TTGAGAGCAGTCCCACAAAAGTTTTCGACATTGATGCTAGTTCCCAACAGgtttgcttct ... tctttttcagGTTGTTGTGGCTGATGCTGAGGCATACACTTATGATGATGAAGTGCTCAAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atgtgtttccttcagataatgcatcatgggttgtctttcatatgctctttttcagGTTGTTGTGGCTGATGCTGAGGCATACACTTATGATGATGAAGTGCTCAAGAAAGCAGAAGCTATGGGGAAGCCAGGGCTTGTGGAGATCTATGCCAAAG
                                          tgctctttttc  CT-rich tract
                                   tttcatat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttgaatgtgtggggaggaaaactcaacttccagcccatctgctgaatgtgtttccttcagataatgcatcatgggttgtctttcatatgctctttttcagGTTGTTGTGGCTGATGCTGAGGCATACACTTATGATGATGAAGTGCTCAAGAAAGCAGAAGCTATGGGGAAGCCAGGGCTTGTGGAGATCTATGCCAAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATC
- - - gtgtggg
- - - - - - - -ggaaaac
- - - - - - - - - - - - - - -ccagccc
- - - - - - - - - - - - - - - - - - -tctgctg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aatgcat
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gggttgt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -catatgc