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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgcgcgctagaatcttgggttttttgtgtctttgtttgcagattatgggaactctcaaccagagctttgtgataatgcagGTGTCTAACTGGTTCATAAATGCTCGGGTTCGTCTCTGGAAGCCAATGGTGGAAGAAATGTACATGGAGGAAGTCAAGGACCACGAAGAGAATGGATCAG

Basic information

species Vitis vinifera
transcript Vv08s0105g00230.t01
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv08s0105g00230.t01 (Vitis vinifera), 3'ss of exon 11
lower sequence: GLYMA19G38690.1 (Glycine max), 3'ss of exon 7
----gtgcgcgctagaatcttgggttttttgtgtctttgtttg-cagattatgggaactctcaaccagagctttgtgataatgcagGTGTCTAACTGGTTCATAAATGCTCGGGTTCGTCTCTGGAAGCCAATGGTGGAAGAAATGTACATGGAGGAAGTCAAGGACCACGAAGAGAATGGATCAG
     |   |    |||     |||  ||      ||  ||||    ||  |     |||| ||  |  | || ||| |    ||||| || || ||||| ||||||||||| ||||| || ||||||||||||||||| |||||||||||||||||  | ||||| || ||| |||||||||| |
gtaactagactgatgaagtaatggtacttgactctttcatttgatgaatggttcttcctcttaat-aatgtttggtg-tgtgacagGTTTCAAATTGGTTTATAAATGCTCGAGTTCGGCTTTGGAAGCCAATGGTGGAGGAAATGTACATGGAGGAGATGAAGGATCATGAACAGAATGGATCTG

upper sequence: Vv08s0105g00230.t01 (Vitis vinifera), 3'ss of exon 11
lower sequence: GLYMA02G35450.1 (Glycine max), 3'ss of exon 5
--------------gtgcgcgctagaatcttg-----ggttttttgtgtctttgtttgcagattatgggaactctcaacca--gagctttgtgataatgcagGTGTCTAACTGGTTCATAAATGCTCGGGTTCGTCTCTGGAAGCCAATGGTGGAAGAAATGTACATGGAGGAAGTCAAGGACCACGAAGAGAATGGATCAG
               |    |  |||||  |        || ||||  |   || ||  |    ||||    |   ||| |   |  || || ||    ||||| || || ||||||||||||||||| ||||| || ||||||||||||||||| ||||||||| |||||||  | || || || |||   ||||| || |
tacactcttaattcattattgtcagaattctattaaaacttgtttgcattcctggttataa--catggatcatgcaaacaatgaatattggtaatggaacagGTTTCAAATTGGTTCATAAATGCTCGAGTTCGGCTTTGGAAGCCAATGGTGGAGGAAATGTACTTGGAGGAGATGAAAGATCATGAACTAAATGGTTCTG

upper sequence: Vv08s0105g00230.t01 (Vitis vinifera), 3'ss of exon 11
lower sequence: GLYMA03G36070.1 (Glycine max), 3'ss of exon 5
gtgcgcgctagaatcttgggttttttgtgtctttgtttgcagattatgggaactctcaaccagagctttgtgataatgcagGTGTCTAACTGGTTCATAAATGCTCGGGTTCGTCTCTGGAAGCCAATGGTGGAAGAAATGTACATGGAGGAAGTCAAGGACCACGAAGAGAATGGATCAG
  |    ||| | |  |||  |||   | | |   || |   ||  |     |||| ||  |    |||||  |  | ||||| || || ||||| ||||||||||| ||||| || ||||||||||||||||| |||||||||| ||||||  | ||||| || ||| ||||| | || |
--gta-actaaactaatggtatttgactctttcatttggtgaatggttcttcctcttaataatg--tttgttgtgttacagGTTTCAAATTGGTTTATAAATGCTCGAGTTCGGCTTTGGAAGCCAATGGTGGAGGAAATGTACACGGAGGAGATGAAGGATCATGAACAGAATCGGTCTG

upper sequence: Vv08s0105g00230.t01 (Vitis vinifera), 3'ss of exon 11
lower sequence: GLYMA10G10040.1 (Glycine max), 3'ss of exon 5
---gtgcgcgctagaatcttg----ggttttttgtgtctttgtttgca-----gattatgggaactctca-------accagagctttgtgataatgcagGTGTCTAACTGGTTCATAAATGCTCGGGTTCGTCTCTGGAAGCCAATGGTGGAAGAAATGTACATGGAGGAAGTCAAGGACCACGAAGAGAATGGATCAG
    | | | ||  | | |||       ||| |  |   |||||||||     | |||||  |    |||       | |  |  || || ||    ||||| || || |||||||| |||||| | ||||| || ||||||||||||||||| ||||||||| |||||||  | || || || |||   ||||| || |
gtaatacactcttcattattgtcaaaaatttattagaacttgtttgcaatcctggttatgatattggtcatgctaacaacgaatattggtaatggaacagGTTTCAAATTGGTTCATTAATGCTAGAGTTCGGCTTTGGAAGCCAATGGTGGAGGAAATGTACTTGGAGGAGATGAAAGAGCATGAACTAAATGGTTCTG

upper sequence: Vv08s0105g00230.t01 (Vitis vinifera), 3'ss of exon 11
lower sequence: AT2G35940.2 (Arabidopsis thaliana), 3'ss of exon 4
gtgcgcgctagaatcttgggttttttgtgtctttgtttgcagattatgggaac--tctcaaccagag-----ctttgtgataatgcagGTGTCTAACTGGTTCATAAATGCTCGGGTTCGTCTCTGGAAGCCAATGGTGGAAGAAATGTACATGGAGGAAGTCAAGGACCACGAAGAGAATGGATCAG
|| ||    | |||   |  | |||  ||| ||  |  |    ||| |  | |  | | ||  | |       | | | || ||  ||||||| |||||||| ||||| ||  | |||||  | ||||| ||||||||||| || ||||||||||||||| | ||||| || | | ||||      | 
gtacgtttcaaaat---gattctttcttgtgttattaggttacttaagaaagcgtttttaagtaaatttattttctttaattatttagGTGTCGAACTGGTTTATAAACGCGAGAGTTCGGTTATGGAAACCAATGGTGGAGGAGATGTACATGGAGGAAATGAAGGAGCAGGCAAAGAACATGGGAT

upper sequence: Vv08s0105g00230.t01 (Vitis vinifera), 3'ss of exon 11
lower sequence: PP1S258_6V6.1 (Physcomitrella patens), 3'ss of exon 4
--------------gtgcgcgctagaatcttgggttttttg-------tgtctttgtttgcagattatgggaactctcaaccagagctttgtgataatgcagGTGTCTAACTGGTTCATAAATGCTCGGGTTCGTCTCTGGAAGCCAATGGTGGAAGAAATGTACATGGAGGAAGTCAAGGACCACGAAGAGAATGGATCAG
              |     | || |        ||| |         |    ||  ||||||||     ||       ||  ||  | ||||| ||| ||||| |||||||||||||| || || || |||||  | |||||||||||||| || ||||||||| ||||||||   || ||  ||   ||  ||   ||  
ccagtatccagaacgcttttgttaaacatccacttttgtcagaggggatagaattacttgcagatggcttgacagagttacgtgacttctgtga-aat-cagGTCTCTAACTGGTTCATCAACGCACGAGTTCGATTATGGAAGCCAATGGTAGAGGAAATGTACGTGGAGGAACAGAAAGAGTACTCCGAAGATCATTCTA

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|161714978|gb|FC063948.1|FC063948
EST:     ATTCAGACAAGCACATGCTCGCCAAACAAACAGGGCTCACCCGGAGTCAG                         GTGTCTAACTGGTTCATAAATGCTCGGGTTCGTCTCTGGAAGCCA-TGGTG
genomic: ATTCAGACAAGCACATGCTCGCCAAACAAACAGGGCTCACCCGGAGTCAGgtgcgcgcta ... gataatgcagGTGTCTAACTGGTTCATAAATGCTCGGGTTCGTCTCTGGAAGCCAATGGTG
EST: gi|38516686|gb|CF983861.1|CF983861
EST:     TCAGACAAGCACATGCTCGCCAAACAAACAGGGNCTCACCCGGNAGTCAG                         GTGTCTAACTGGTTCATAAATGCTCGGGTTCGTCTCTGGAAGCCAATGGT
genomic: TCAGACAAGCACATGCTCGCCAAACAAACAGGG-CTCACCCGG-AGTCAGgtgcgcgcta ... gataatgcagGTGTCTAACTGGTTCATAAATGCTCGGGTTCGTCTCTGGAAGCCAATGGT
EST: gi|161716829|gb|FC068101.1|FC068101
EST:     ATTCAGACAAGCACATGCTCGCCAAACAAACAGGGCTCACCCGGAGTCAG                         GTGTCTAACTGGTTCATAAATGCTCGGGTTCGTCTCTGGAAGCCAATGGTG
genomic: ATTCAGACAAGCACATGCTCGCCAAACAAACAGGGCTCACCCGGAGTCAGgtgcgcgcta ... gataatgcagGTGTCTAACTGGTTCATAAATGCTCGGGTTCGTCTCTGGAAGCCAATGGTG
EST: gi|29786121|gb|CB343619.2|CB343619
EST:     ATTCAGACAAGCACATGCTCGCCAAACAAACAGGGCTCACCCGGAGTCAG                         GTGTCTAACTGGTTCATAAATGCTCGGGTTCGTCTCTGGAAGCCAATGGTG
genomic: ATTCAGACAAGCACATGCTCGCCAAACAAACAGGGCTCACCCGGAGTCAGgtgcgcgcta ... gataatgcagGTGTCTAACTGGTTCATAAATGCTCGGGTTCGTCTCTGGAAGCCAATGGTG
EST: gi|110728156|gb|EE103480.1|EE103480
EST:     ATTCAGACAAGCACATGCTCGCCAAACAAACAGGGCTCACCCGGAGTCAG                         GTGTCTAACTGGTTCATAAATGCTCGGGTTCGTCTCTGGAAGCCAATGGTG
genomic: ATTCAGACAAGCACATGCTCGCCAAACAAACAGGGCTCACCCGGAGTCAGgtgcgcgcta ... gataatgcagGTGTCTAACTGGTTCATAAATGCTCGGGTTCGTCTCTGGAAGCCAATGGTG
EST: gi|110712074|gb|EE089283.1|EE089283
EST:     ATTCAGACAAGCACATGCTCGCCAAACAAACAGGGCTCACCCGGAGTCAG                         GTGTCTAACTGGTTCATAAATGCTCGGGTTCGTCTCTGGGAGCCAATGGTG
genomic: ATTCAGACAAGCACATGCTCGCCAAACAAACAGGGCTCACCCGGAGTCAGgtgcgcgcta ... gataatgcagGTGTCTAACTGGTTCATAAATGCTCGGGTTCGTCTCTGGAAGCCAATGGTG
EST: gi|351056024|gb|FQ453485.1|FQ453485
EST:     ATTCAGACAAGCACATGCTCGCCAAACAAACAGGTCTCACCCGGAGTCAG                         GTGTCTAACTGGTTCATAAATGCTCGGGTTCGTCTCTGGAAGCCAATGGTG
genomic: ATTCAGACAAGCACATGCTCGCCAAACAAACAGGGCTCACCCGGAGTCAGgtgcgcgcta ... gataatgcagGTGTCTAACTGGTTCATAAATGCTCGGGTTCGTCTCTGGAAGCCAATGGTG
EST: gi|161720884|gb|FC069618.1|FC069618
EST:     ATTCAGACAAGCACATGCTCGCCAAACAAACAGGGCTCACCCGGAGTCAG                         GTGTCTAACTGGTTCATAAATGCTCGGGTTCGTCTCTGGAAGCCAATGGTG
genomic: ATTCAGACAAGCACATGCTCGCCAAACAAACAGGGCTCACCCGGAGTCAGgtgcgcgcta ... gataatgcagGTGTCTAACTGGTTCATAAATGCTCGGGTTCGTCTCTGGAAGCCAATGGTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtgtctttgtttgcagattatgggaactctcaaccagagctttgtgataatgcagGTGTCTAACTGGTTCATAAATGCTCGGGTTCGTCTCTGGAAGCCAATGGTGGAAGAAATGTACATGGAGGAAGTCAAGGACCACGAAGAGAATGGATCAG
     tttgttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgcgcgctagaatcttgggttttttgtgtctttgtttgcagattatgggaactctcaaccagagctttgtgataatgcagGTGTCTAACTGGTTCATAAATGCTCGGGTTCGTCTCTGGAAGCCAATGGTGGAAGAAATGTACATGGAGGAAGTCAAGGACCACGAAGAGAATGGATCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA