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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gaatacatggttctttcatcatatgatctgacattggtgttaatggaaaaaaaagataactttggcaatgtatttgacatattttctttttgacacccagGTGATATACATGGTCAATATTCGGATCTTTTAAGGCTTTTCGACTATGGTGGATTCCCTCCTCAAGCCAATTACTTATTTTTGGGGGATTACGTAGATCG

Basic information

species Vitis vinifera
transcript Vv14s0036g00370.t01
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv14s0036g00370.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GLYMA10G30970.1 (Glycine max), 3'ss of exon 1
----gaatacatggttctttcatcatatgatctgacattggtgttaatggaaaaaaaagataactttggcaatgtatttgacatattttctttttga-cacccagGTGATATACATGGTCAATATTCGGATCTTTTAAGGCTTTTCGACTATGGTGGATTCCCTCCTCAAGCCAATTACTTATTTTTGGGGGATTACGTAGATCG
      ||  |  ||| |   ||  |   |  |   | || | ||| |||   | | ||| || | ||  | | | | | | || |  | || |||| | | |||||||| |||||||||||||||| ||||||||||||||||| || ||||||||| | |||||  | ||||| |||||||||||||||||||| ||||||||
aacaatatcaacagttttgcaat--tgctacatagtactg-tatta-tggtttacagagaaaaatgtgtgattatttctta-atgtccttttgttgatctctcagGTGATGTACATGGTCAATATTCTGATCTTTTAAGGCTTTTTGAGTATGGTGGACTACCTCCCGAGGCCAACTACTTATTTTTGGGGGATTATGTAGATCG

upper sequence: Vv14s0036g00370.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GLYMA20G36510.1 (Glycine max), 3'ss of exon 1
---gaatacatggttctttcatcatatgatctgacattg-gtgttaatggaaaaaaaagataactttggcaatgtatttgacatattttctttttgacacccagGTGATATACATGGTCAATATTCGGATCTTTTAAGGCTTTTCGACTATGGTGGATTCCCTCCTCAAGCCAATTACTTATTTTTGGGGGATTACGTAGATCG
    | | | | ||  |   ||  |   |  |   | ||  | ||  |  | | | || | || | ||   || | ||  |  |  ||| | ||   | | |||||||| |||||||||||||||| ||||||||||||||||| || ||||| ||| | |||||| | ||||| |||||||||||||||||||| || |||||
ttgtagtccttagtattgcaat--tgctacatagtactgtattttggtttacagagaaaa-aattgtgatgatttcttaaaagtccttt-tgttgatctctcagGTGATGTACATGGTCAATATTCTGATCTTTTAAGGCTTTTTGAGTATGGCGGACTACCTCCTGAGGCCAACTACTTATTTTTGGGGGATTATGTGGATCG

upper sequence: Vv14s0036g00370.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GLYMA03G41200.1 (Glycine max), 3'ss of exon 1
gaatacatggttctttcatcatatgatctgacattggtgttaatggaaaaaaaa--gataactttggcaatgtatttgacatattttctttttgacacc-cagGTGATATACATGGTCAATATTCGGATCTTTTAAGGCTTTTCGACTATGGTGGATTCCCTCCTCAAGCCAATTACTTATTTTTGGGGGATTACGTAGATCG
   ||        ||  | ||||| ||     |||| |||  |    ||||| |  |     ||| | | | | | |  |||||  |  | ||||     |||||||| ||||||| |||||||| ||||||||||||||||| || || |||||||| |||||| ||||||| || || |||||||||||||| || |||||
---tattacacatttgtaccatataatactctattgttgtacacaagaaaaatattgtgtgttttaggagtttctgtttcatatccttatattgatgtttcagGTGATGTACATGGGCAATATTCTGATCTTTTAAGGCTTTTTGAGTACGGTGGATTACCTCCTGAAGCCAACTATTTGTTTTTGGGGGATTATGTTGATCG

upper sequence: Vv14s0036g00370.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GLYMA19G43800.1 (Glycine max), 3'ss of exon 1
gaatacatggttctttcatcatatgatctgacattggtgttaatggaaaaaaaagataactttggcaatgtatttgacatattttctttttgacacc-cagGTGATATACATGGTCAATATTCGGATCTTTTAAGGCTTTTCGACTATGGTGGATTCCCTCCTCAAGCCAATTACTTATTTTTGGGGGATTACGTAGATCG
  |||        ||  | ||||| ||     |||| |||  |    ||||| |      ||| |   | | |||  |||||  |  | ||||     |||||||| ||||||| |||||||| ||||||||||||||||| || || |||||||| |||||  ||||||| ||||| |||||||||||||| || |||||
-catattacacatttgtaccatataatactctattgttgtacacaagaaaaatattgtgttttaggggtttgtttttcatatccttgtattgatgtttcagGTGATGTACATGGGCAATATTCTGATCTTTTAAGGCTTTTTGAGTACGGTGGATTACCTCCAGAAGCCAACTACTTGTTTTTGGGGGATTATGTGGATCG

upper sequence: Vv14s0036g00370.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: PP1S97_286V6.1 (Physcomitrella patens), 3'ss of exon 2
---gaatacatggttctttcatc-atatgatctgacattggtgttaatggaaaaaaaagataactttggcaatgtatttgacatattttctttttgacacccagGTGATATACATGGTCAATATTCGGATCTTTTAAGGCTTTTCGACTATGGTGGATTCCCTCCTCAAGCCAATTACTTATTTTTGGGGGATTACGTAGATCG
   |  |  |||   ||| | || |  | || |    | | |  |  ||    | ||   |  |    | | ||  ||  ||    |||  |  ||   |  ||||||||| |||||||||||||| || || || ||| | ||||| |||||||| ||||| ||| | || |||||| ||||||| |||||||| || ||  |
tgagctttgatgagacttgcctctaagtaatatcctgtagataat--tgtttcacaatcttctccaaagtagtggcttaaacgcgcttttgtgatggtgc--agGTGATATCCATGGTCAATATTCTGACCTCTTGAGGTTGTTCGAATATGGTGGCTTCCCACCTGAGGCTAATTACCTATTTTTAGGGGATTATGTTGACAG

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|27582773|gb|CB005468.1|CB005468
EST:     CTTAAAACAGCCCAATTTGTTGGAGCTATGTGCACCCATCAAGATTTGCG                         GTGATATACATGGTCAATATTCGGATCTTTTAAGGCTTTTCGACTATGGTG
genomic: CTTAAAACAGCCCAATTTGTTGGAGCTATGTGCACCCATCAAGATTTGCGgtacttttgt ... tgacacccagGTGATATACATGGTCAATATTCGGATCTTTTAAGGCTTTTCGACTATGGTG
EST: gi|351051974|gb|FQ450665.1|FQ450665
EST:     ACAGCCCAATTTGTTGGAGCTATGTGCACCCATCAAGATTTGCG                         GTGATATACATGGTCAATATTCGGATCTTTTAAGGCTTTTCGACTATGGTG
genomic: ACAGCCCAATTTGTTGGAGCTATGTGCACCCATCAAGATTTGCGgtacttttgt ... tgacacccagGTGATATACATGGTCAATATTCGGATCTTTTAAGGCTTTTCGACTATGGTG
EST: gi|352798401|gb|FQ480426.1|FQ480426
EST:     ACAGCCCAATTTGTTGGAGCTATGTGCACCCATCAAGATTTGCG                         GTGATATACATGGTCAATATTCGGATCTTTTAAGGCTTTTCGACTATGGTG
genomic: ACAGCCCAATTTGTTGGAGCTATGTGCACCCATCAAGATTTGCGgtacttttgt ... tgacacccagGTGATATACATGGTCAATATTCGGATCTTTTAAGGCTTTTCGACTATGGTG
EST: gi|161712552|gb|FC061857.1|FC061857
EST:     CTTAAAACAGCCCAATTTGTTGGAGCTATGTGCACCCATCAAGATTTGCG                         GTGATATACATGGTCAATATTCGGATCTTTTAAGGCTTTTCGACTATGGTG
genomic: CTTAAAACAGCCCAATTTGTTGGAGCTATGTGCACCCATCAAGATTTGCGgtacttttgt ... tgacacccagGTGATATACATGGTCAATATTCGGATCTTTTAAGGCTTTTCGACTATGGTG
EST: gi|161720275|gb|FC070536.1|FC070536
EST:     CTTAAAACAGCCCAATTTGTTGGAGCTATGTGCACCCATCAAGATTTGCG                         GTGATATACATGGTCAATATTCGGATCTTTTAAGGCTTTTCGACTATGGTG
genomic: CTTAAAACAGCCCAATTTGTTGGAGCTATGTGCACCCATCAAGATTTGCGgtacttttgt ... tgacacccagGTGATATACATGGTCAATATTCGGATCTTTTAAGGCTTTTCGACTATGGTG
EST: gi|110426835|gb|EC993260.1|EC993260
EST:     CTTAAAACAGCCCAATTTGTTGGAGCTATGTGCACCCATCAAGATTTGCG                         GTGATATACATGGTCAATATTCGGATCTTTTAAGGCTTTTCGACTATGGTG
genomic: CTTAAAACAGCCCAATTTGTTGGAGCTATGTGCACCCATCAAGATTTGCGgtacttttgt ... tgacacccagGTGATATACATGGTCAATATTCGGATCTTTTAAGGCTTTTCGACTATGGTG
EST: gi|161721520|gb|FC070080.1|FC070080
EST:     CTTAAAACAGCCCAATTTGTTGGAGCTATGTGCACCCATCAAGATTTGCG                         GTGATATACATGGTCAATATTCGGATCTTTTAAGGCTTTTCGACTATGGTG
genomic: CTTAAAACAGCCCAATTTGTTGGAGCTATGTGCACCCATCAAGATTTGCGgtacttttgt ... tgacacccagGTGATATACATGGTCAATATTCGGATCTTTTAAGGCTTTTCGACTATGGTG
EST: gi|351053762|gb|FQ441528.1|FQ441528
EST:     ACAGCCCAATTTGTTGGAGCTATGTGCACCCATCAAGATTTGCG                         GTGGTATACATGGTCAATATTCGGATCTTTTAAGGCTTTTCGACTATGGTG
genomic: ACAGCCCAATTTGTTGGAGCTATGTGCACCCATCAAGATTTGCGgtacttttgt ... tgacacccagGTGATATACATGGTCAATATTCGGATCTTTTAAGGCTTTTCGACTATGGTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gaaaaaaaagataactttggcaatgtatttgacatattttctttttgacacccagGTGATATACATGGTCAATATTCGGATCTTTTAAGGCTTTTCGACTATGGTGGATTCCCTCCTCAAGCCAATTACTTATTTTTGGGGGATTACGTAGATCG
                                          ttttgac  putative branch site (score: 3)
                                catattttcttttt  CT-rich tract
                         tatttgacatattttc  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gaatacatggttctttcatcatatgatctgacattggtgttaatggaaaaaaaagataactttggcaatgtatttgacatattttctttttgacacccagGTGATATACATGGTCAATATTCGGATCTTTTAAGGCTTTTCGACTATGGTGGATTCCCTCCTCAAGCCAATTACTTATTTTTGGGGGATTACGTAGATCG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTCCTC
- -tacatgg
- - - - - - - - - - - - - -ctgacat
- - - - - - - - - - - - - - - - - tggtgtt
- - - - - - - - - - - - - - - - - - - - - - - aaaaaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -caatgta