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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaattctttttcgaaatccttgcttgtcttctcccatgatacggttttttttacttgtttttgccttattattttcagGAAAGTAACATCAAATGGGCTTCACGGTGGGATACATACCTCCTTATGAACGATGATCAGATCCACTGGTTCTCCATCATAAACTCTCTGATGATTGTCC

Basic information

species Vitis vinifera
transcript Vv09s0002g02140.t01
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv09s0002g02140.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: LOC_Os06g37160.1 (Oryza sativa), 3'ss of exon 6
--gtaattctttttcgaaatccttgcttgtcttctcccatgatacggttttttttacttgtttttgccttattattttcagGAAAGTAACATCAAATGGGCTTCACGGTGGGATACATACCTCCTTATGAACGATGATCAGATCCACTGGTTCTCCATCATAAACTCTCTGATGATTGTCC
    |  |   ||  |||  |  |  |  |   || |  || | |  |   ||| | || |||       | | ||  ||||  ||| | |||| |||||| || || ||||||   || || |||   |  |||   |||||||| |||||||| ||||| ||||| |||||||||||||
gtagagcttccttctgaagactcttttgatgaactact-tgttcccctcgatttgatttatttgaattgaactgttg-cagGCTAGTGAGATCATATGGGCATCTCGTTGGGATGTCTATCTTCTTTCAAGTGATAGCCAGATCCATTGGTTCTCAATCATTAACTCACTGATGATTGTCC

upper sequence: Vv09s0002g02140.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GLYMA08G20640.1 (Glycine max), 3'ss of exon 6
gtaattctttttcgaaatccttgct----------tgtcttctcccatgatacggttttttttacttgtttttgccttattattttcagGAAAGTAACATCAAATGGGCTTCACGGTGGGATACATACCTCCTTATGAACGATGATCAGATCCACTGGTTCTCCATCATAAACTCTCTGATGATTGTCC
||| | ||  ||  ||||| | |||          | ||  |||   || || | |   || |      |||     || | ||||||||||||| | ||||||||||| ||||||||||| ||||| ||  | ||||| ||||||||||||||||||||||||||||| ||||||||||||||||| |
gtattgctgatt-aaaatcttggctaccaataaactttcacctcatttgttatgatacgttatggcaagtttgttggtact-ttttcagGAAAGTGATATCAAATGGGCATCACGGTGGGACACATATCTTTTAATGAATGATGATCAGATCCACTGGTTCTCCATCATTAACTCTCTGATGATTGTTC

upper sequence: Vv09s0002g02140.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GLYMA07G01240.1 (Glycine max), 3'ss of exon 6
---------gtaattctttttcgaaatccttgcttgtcttctc--ccatgatacggttttttttacttgtttttgccttattattttcagGAAAGTAACATCAAATGGGCTTCACGGTGGGATACATACCTCCTTATGAACGATGATCAGATCCACTGGTTCTCCATCATAAACTCTCTGATGATTGTCC
          | |   | ||    | || |   || ||  |||   ||| ||| | |   ||   |     ||||      | ||||||||||||| | ||||||||||| ||||||||||| ||||| ||  | ||||| ||||||||||||||||||||||||||||| |||||| |||||||||| |
gtattgctgattaaaatcttggctactcataaattttcacctcattcattatatgatacgttaagccaaagtttgttggtattttttcagGAAAGTGATATCAAATGGGCATCACGGTGGGACACATATCTTTTAATGAATGATGATCAGATCCACTGGTTCTCCATCATTAACTCTTTGATGATTGTTC

upper sequence: Vv09s0002g02140.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: AT3G13772.1 (Arabidopsis thaliana), 3'ss of exon 6
gtaattctttttcgaaatccttgcttgtcttctcccatgatacggttttttttacttgtttttgccttattattttcagGAAAGTAACATCAAATGGGCTTCACGGTGGGATACATACCTCCTTATGAACGATGATCAGATCCACTGGTTCTCCATCATAAACTCTCTGATGATTGTCC
    | | |     | |      ||| | ||     |   |  || ||  |  || | ||   |  ||      | ||||| ||| | |||||||||||||| |||||||| || ||||| || |||||||||||||| ||||||||||| ||||||||||| || || ||||||||||
---gtacatgacttacacttagccttcttttgctttactttttgggttgctaaacattttccggaatttgatgatccagGAGAGTGAAATCAAATGGGCTTCTCGGTGGGACACGTACCTTCTCATGAACGATGATCAAATCCACTGGTTTTCCATCATAAATTCACTTATGATTGTCC

upper sequence: Vv09s0002g02140.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: AT1G55130.1 (Arabidopsis thaliana), 3'ss of exon 6
gtaattctttttcgaaatccttgcttgtcttctcccatgatacggttttttttacttgtttttgcct-tattattttcagGAAAGTAACATCAAATGGGCTTCACGGTGGGATACATACCTCCTTATGAACGATGATCAGATCCACTGGTTCTCCATCATAAACTCTCTGATGATTGTCC
|||| |  |||     |  || |   |   |||    | || ||    | |  || | || |    | |   || | ||||| |||   |||||||||||||| || ||||| |||||| | ||||||||||||||||| ||||||||||| || ||||||||||| || ||||||||||
gtaactaattt-----actctgga--gaactctttatttatgcg---ctgtaaacatattatgaagtatgaaatatgcagGAGAGTGTTATCAAATGGGCTTCGCGCTGGGACACATACTTGCTTATGAACGATGATCAAATCCACTGGTTTTCAATCATAAACTCGCTTATGATTGTCC

upper sequence: Vv09s0002g02140.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: EDP05803 (Chlamydomonas reinhardtii), 3'ss of exon 5
----------gtaattctttttcgaaatccttgcttg-tcttctcccatgatacggttt---tttttacttgtttttgccttattatt-------ttcagGAAAGTAACATCAAATGGGCTTCACGGTGGGATACATACCTCCTTATGAACGATGATCAGATCCACTGGTTCTCCATCATAAACTCTCTGATGATTGTCC
          | ||  | |  | |   |     || | |||   | |  |     |      |  |    |||  |||| ||  |  |       | ||||  ||  | |||   ||||| || || ||||| || ||||| || ||||  || || ||||| ||||||||||||||||| |||||  ||||||||||||
gcggtgaccggaaacccatgctgggtctgagcactgggtctgagcgcgaggccttgaccgcatcctgggctgtccttgctttgctggtggcgacgtgcagGCTAGCGAGATCCGCTGGGCCTCGCGCTGGGACACCTACCTGCTGATGATGGACGACCAGATTCACTGGTTCTCCATCATTAACTCGGTGATGATTGTCC

upper sequence: Vv09s0002g02140.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: PP1S140_64V6.1 (Physcomitrella patens), 3'ss of exon 6
---------------------------gtaattctttttcgaaatc---cttgcttgtcttctcccatgatacggttttttttacttgtttttgccttattatttt---cagGAAAGTAACATCAAATGGGCTTCACGGTGGGATACATACCTCCTTATGAACGATGATCAGATCCACTGGTTCTCCATCATAAACTCTCTGATGATTGTCC
                           |    || | |  ||  |     |   || || | ||   || |   |  | | ||   |     |   ||||    ||   ||| | ||| |  ||||||||||||| || ||||||||||| || || ||||  ||||  ||||| ||||||||||||||||| ||||| || |||||||| |
gtgagaaattcgtctcataaccgttctgctcatcatgtgtgaggttgaattaatttttcatgtcttgtgctttcgaatctattttctaacaatattttatgtgcttacgcagTACAGTCATGTCAAATGGGCTTCTCGCTGGGATACATATCTACTCATGACAGATGCGCAGATTCACTGGTTCTCCATCATCAACTCCCTCATGATTGTGC

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|110691298|gb|EE069240.1|EE069240
EST:     AAGTTGATGCAGATAAGGATATTGTATTTACATATGATGTTTCCTTCGAG                         GAAAGTAACATCAAATGGGCTTCACGGTGGGATACATACCTCCTTATGAAC
genomic: AAGTTGATGCAGATAAGGATATTGTATTTACATATGATGTTTCCTTCGAGgtaattcttt ... ttattttcagGAAAGTAACATCAAATGGGCTTCACGGTGGGATACATACCTCCTTATGAAC
EST: gi|110719001|gb|EE096474.1|EE096474
EST:     AAGTTGATGCAGATAAGGATATTGTATTTACATATGATGTTTCCTTCGAG                         GAAAGTAACATCAAATGGGCTTCACGGTGGGATACATACCTCCTTATGAAC
genomic: AAGTTGATGCAGATAAGGATATTGTATTTACATATGATGTTTCCTTCGAGgtaattcttt ... ttattttcagGAAAGTAACATCAAATGGGCTTCACGGTGGGATACATACCTCCTTATGAAC
EST: gi|34546863|gb|CF515095.1|CF515095
EST:     AAGTTGATGCAGATAAGGATATTGTATTTACATATGATGTTTCCTTCGAG                         GAAAGTAACATCAAATGGGCTTCACGGTGGGATACATACCTCCTTATGAAC
genomic: AAGTTGATGCAGATAAGGATATTGTATTTACATATGATGTTTCCTTCGAGgtaattcttt ... ttattttcagGAAAGTAACATCAAATGGGCTTCACGGTGGGATACATACCTCCTTATGAAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgtcttctcccatgatacggttttttttacttgtttttgccttattattttcagGAAAGTAACATCAAATGGGCTTCACGGTGGGATACATACCTCCTTATGAACGATGATCAGATCCACTGGTTCTCCATCATAAACTCTCTGATGATTGTCC
                                             ttattttc  CT-rich tract
                     ttttttttacttgttt  TA-rich tract