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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tggtttgagctctaattgattcatgttaaattgctcatttggagattcatttagtattggatagcagaggactgatgtctaatcatggaaatacttgcagACATGTGGGCAGTTGGTGCAATACTAGCTGAGCTTTTCACTTTGTGCCCAATTTTCCCTGGTGAAAG

Basic information

species Vitis vinifera
transcript Vv07s0151g00350.t01
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv07s0151g00350.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: LOC_Os03g63020.1 (Oryza sativa), 3'ss of exon 8
------------------------------------------------tggtttgagctctaattgattcatgttaaattgctcatttggagattcatttagtattggatagcagaggactgatgtctaatc-atggaaatacttgcagACATGTGGGCAGTTGGTGCAATACTAGCTGAGCTTTTCACTTTGTGCCCAATTTTCCCTGGTGAAAG
                                                |  |   ||||| |  |||   || | |  |||  ||| |  | | ||   | | ||   |   | ||    | ||  || ||  |||   |      |||| |||||||| |||||||||||  | ||||||||||||||  |||  ||| |||||||||||| |||
gtgatgcctattatcccagcccctgcattttactacttccatttttattaatgccagctcaacatgaa--atttgagtttgtgcatataaa-actcgcattgcatgaaactactgaattat-ataactgatagatgtgcacttcctcagATATGTGGGCTGTTGGTGCAATTTTGGCTGAGCTTTTCACACTGTCTCCACTTTTCCCTGGTGGAAG

upper sequence: Vv07s0151g00350.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: GRMZM2G045241_T07 (Zea mays), 3'ss of exon 4
tggtttgagctctaattgattcatgttaaattgctcatttggagattcatttagtattggatagcagaggac-tgatgtctaatcatggaaatacttg-cagACATGTGGGCAGTTGGTGCAATACTAGCTGAGCTTTTCACTTTGTGCCCAATTTTCCCTGGTGAAAG
  |    | |  | |    ||| | |    |        |     |||  || ||      ||||    ||  | |    ||||    |   |  ||  ||||||||||||| |||||||| ||  | ||||||||||| ||  ||| |||| |||| |||||||||||
--gggcaaacaatgaagtgttcttttctcttaaaatgcataacttttctctttgtggcttttagcttgtgatatcaccattaatagctgtgctctttttcagACATGTGGGCGGTTGGTGCTATTTTGGCTGAGCTTTTTACACTGTCCCCACTTTTTCCTGGTGAAAG

upper sequence: Vv07s0151g00350.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: GLYMA16G10820.2 (Glycine max), 3'ss of exon 9
tggtttgagctctaattg-----attcatgttaaattgctcatttggagattcatttagtattggatagcagaggactgatgtctaatcatggaaatacttgcagACATGTGGGCAGTTGGTGCAATACTAGCTGAGCTTTTCACTTTGTGCCCAATTTTCCCTGGTGAAAG
||   |||    |  |||     ||| |||  | |  ||  ||   || |||    | |  ||       ||  |    ||  | ||| ||  || || ||||||||||||||||||||||||| ||| ||||||||||||| ||||||  ||| || || |||||||||||
tgtgatgaaacttgtttgccattatttatgccataacgcagat---gatattatgcttgctttcttcttaaggtggtgaataacaaat-ata-aattatttgcagACATGTGGGCAGTTGGTGCCATATTAGCTGAGCTTTTTACTTTGACCCCTATATTTCCTGGTGAAAG

upper sequence: Vv07s0151g00350.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: GLYMA03G21610.2 (Glycine max), 3'ss of exon 8
----tggtttgagctctaattgattcatgttaaattgctcatttggagattcatttagtattggatagcagaggactgatgtctaatcatggaaatacttgcagACATGTGGGCAGTTGGTGCAATACTAGCTGAGCTTTTCACTTTGTGCCCAATTTTCCCTGGTGAAAG
    ||      | |     | ||| ||| |  |   ||||  ||    |    ||  | |    |    | ||    ||  | |||   | || || ||||||||||||||||||||||||| ||| ||||||||||||| ||||||  ||| || || |||||||||||
atggtgaaacttgtttgcccttatttatggtgta--actcagatgatattatgcttgctttcttcttaaggtggtgaaataacaaata--gaaattatttgcagACATGTGGGCAGTTGGTGCTATATTAGCTGAGCTTTTTACTTTGACCCCCATATTTCCTGGTGAAAG

upper sequence: Vv07s0151g00350.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: AT4G13020.1 (Arabidopsis thaliana), 3'ss of exon 8
-------------------------------------------------------------------------------------tggtttg-agctctaattgattcatgttaaattgctcatttggagattcatttagt--attggatagcagaggactgatgtctaatcatggaaatacttgcagACATGTGGGCAGTTGGTGCAATACTAGCTGAGCTTTTCACTTTGTGCCCAATTTTCCCTGGTGAAAG
                                                                                     |  || |  ||| | | |  || | |  |  ||     | ||     |||| || |  || |  | ||| |    |   | ||||   |  ||| |  ||||||||||||||||||||| || |||||||||||||||| | ||||    ||  | || |||||||||||
gtatgtttgcgaaatccttttgtgcctcatcacatttcattagtatcatgtgatcatgtcaaaagtctagctaaaccatggctaatacttcgtggctttgaatagtttaagacattttttctttctgttttgtcatctattggatcgctttgcaaatctttatagactaacatttaaaagaactgcagACATGTGGGCAGTTGGAGCGATACTAGCTGAGCTTTACGCTTTAACTCCGTTATTTCCTGGTGAAAG

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|351053929|gb|FQ441695.1|FQ441695
EST:     CCGAGCACCAGAAGTCCTGTTCCAGTCTTCATCATACACCCCTGCAATTG                         ACATGTGGGCAGTTGGTGCAATACTAGCTGAGCTTTTCACTTTGTGCCCAA
genomic: CCGAGCACCAGAAGTCCTGTTCCAGTCTTCATCATACACCCCTGCAATTGgtatgaacta ... atacttgcagACATGTGGGCAGTTGGTGCAATACTAGCTGAGCTTTTCACTTTGTGCCCAA
EST: gi|352794086|gb|FQ479328.1|FQ479328
EST:     CCGAGCACCAGAAGTCCTGTTCCAGTCTTCATCATACACCCCTGCAATTG                         ACATGTGGGCAGTTGGTGCAATACTAGCTGAGCTTTTCACTTTGTGCCCAA
genomic: CCGAGCACCAGAAGTCCTGTTCCAGTCTTCATCATACACCCCTGCAATTGgtatgaacta ... atacttgcagACATGTGGGCAGTTGGTGCAATACTAGCTGAGCTTTTCACTTTGTGCCCAA
EST: gi|351036041|gb|FQ463886.1|FQ463886
EST:     CCGAGCACCAGAAGTCCTGTTCCAGTCTTCATCATACACCCCTGCAATTG                         ACATGTGGGCAGTTGGTGCAATACTAGCTGAGCTTTTCACTTTGTGCCCAA
genomic: CCGAGCACCAGAAGTCCTGTTCCAGTCTTCATCATACACCCCTGCAATTGgtatgaacta ... atacttgcagACATGTGGGCAGTTGGTGCAATACTAGCTGAGCTTTTCACTTTGTGCCCAA
EST: gi|352794210|gb|FQ479452.1|FQ479452
EST:     CCGAGCACCAGAAGTCCTGTTCCAGTCTTCATCATACACCCCTGCAATTG                         ACATGTGGGCAGTTGGTGCAATACTAGCTGAGCTTTTCACTTTGTGCCCAA
genomic: CCGAGCACCAGAAGTCCTGTTCCAGTCTTCATCATACACCCCTGCAATTGgtatgaacta ... atacttgcagACATGTGGGCAGTTGGTGCAATACTAGCTGAGCTTTTCACTTTGTGCCCAA
EST: gi|351046353|gb|FQ452969.1|FQ452969
EST:     CCGAGCACCAGAAGTCCTGTTCCAGTCTTCATCATACACCCCTGCAATTG                         ACATGTGGGCAGTTGGTGCAATACTAGCTGAGCTTTTCACTTTGTGCCCAA
genomic: CCGAGCACCAGAAGTCCTGTTCCAGTCTTCATCATACACCCCTGCAATTGgtatgaacta ... atacttgcagACATGTGGGCAGTTGGTGCAATACTAGCTGAGCTTTTCACTTTGTGCCCAA
EST: gi|352794331|gb|FQ481562.1|FQ481562
EST:     CCGAGCACCAGAAGTCCTGTTCCAGTCTTCATCATACACCCCTGCAATTG                         ACATGTGGGCAGTTGGTGCAATACTAGCTGAGCTTTTCACTTTGTGCCCAA
genomic: CCGAGCACCAGAAGTCCTGTTCCAGTCTTCATCATACACCCCTGCAATTGgtatgaacta ... atacttgcagACATGTGGGCAGTTGGTGCAATACTAGCTGAGCTTTTCACTTTGTGCCCAA
EST: gi|352794414|gb|FQ481645.1|FQ481645
EST:     CCGAGCACCAGAAGTCCTGTTCCAGTCTTCATCATACACCCCTGCAATTG                         ACATGTGGGCAGTTGGTGCAATACTAGCTGAGCTTTTCACTTTGTGCCCAA
genomic: CCGAGCACCAGAAGTCCTGTTCCAGTCTTCATCATACACCCCTGCAATTGgtatgaacta ... atacttgcagACATGTGGGCAGTTGGTGCAATACTAGCTGAGCTTTTCACTTTGTGCCCAA
EST: gi|110729354|gb|EE105534.1|EE105534
EST:     CCGAGCACCAGAAGTCCTGTTCCAGTCTTCATCATACACCCCTGCAATTG                         ACATGTGGGCAGTTGGTGCAATACTAGCTGAGCTTTTCACTTTGTGCCCAA
genomic: CCGAGCACCAGAAGTCCTGTTCCAGTCTTCATCATACACCCCTGCAATTGgtatgaacta ... atacttgcagACATGTGGGCAGTTGGTGCAATACTAGCTGAGCTTTTCACTTTGTGCCCAA
EST: gi|351047787|gb|FQ459007.1|FQ459007
EST:     CCGAGCACCAGAAGTCCTGTTCCAGTCTTCATCATACACCCCTGCAATTG                         ACATGTGGGCAGTTGGTGCAATACTAGCTGAGCTTTTCACTTTGTGCCCAA
genomic: CCGAGCACCAGAAGTCCTGTTCCAGTCTTCATCATACACCCCTGCAATTGgtatgaacta ... atacttgcagACATGTGGGCAGTTGGTGCAATACTAGCTGAGCTTTTCACTTTGTGCCCAA
EST: gi|349807444|gb|FQ401401.1|FQ401401
EST:     CCGAGCACCAGAAGTCCTGTTCCAGTCTTCATCATACACCCCTGCAATTG                         ACATGTGGGCAGTTGGTGCAATACTAGCTGAGCTTTTCACTTTGTGCCCAA
genomic: CCGAGCACCAGAAGTCCTGTTCCAGTCTTCATCATACACCCCTGCAATTGgtatgaacta ... atacttgcagACATGTGGGCAGTTGGTGCAATACTAGCTGAGCTTTTCACTTTGTGCCCAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttcatttagtattggatagcagaggactgatgtctaatcatggaaatacttgcagACATGTGGGCAGTTGGTGCAATACTAGCTGAGCTTTTCACTTTGTGCCCAATTTTCCCTGGTGAAAG
                               gtctaat  putative branch site (score: 3)
     ttagtatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tggtttgagctctaattgattcatgttaaattgctcatttggagattcatttagtattggatagcagaggactgatgtctaatcatggaaatacttgcagACATGTGGGCAGTTGGTGCAATACTAGCTGAGCTTTTCACTTTGTGCCCAATTTTCCCTGGTGAAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGCTT
tggtttg
- - - - - - - - - - tcatgtt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - -tggatag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgatgtc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -catggaa