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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tcctactctcctacttgcttctgataatagaatgctaaagagatgttttccttgaagatgttttgtgaaacagttttatttgtttaattttctgttccagGTTGAAGTTTTCCAGCAACAGCTTGAACTTGCCAAAGAGTTGAAAAGACCAGTTTCTGTCCATTGCGTTCGTGCTTTTGGTGATCTTCTTCAGATAATGC

Basic information

species Vitis vinifera
transcript Vv15s0024g00050.t01
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv15s0024g00050.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: LOC_Os04g48820.2 (Oryza sativa), 3'ss of exon 4
tcctactctcctacttgcttctgataatagaatgctaaagagatgtttt-ccttgaagatgttttgtga----aacagttttatttg----tttaattttctgttccagGTTGAAGTTTTCCAGCAACAGCTTGAACTTGCCAAAGAGTTGAAAAGACCAGTTTCTGTCCATTGCGTTCGTGCTTTTGGTGATCTTCTTCAGATAATGC
            ||| |    | ||||   |   || |||   | ||    | |||  | | ||| ||     || |    |||  |    |  ||  |     | |||||||||||||||||||| || ||||||||||| || |||||||| |  || |||||||| ||||| || || || ||||||||||||||  ||||| |  
--------aatcactaggccat-ataacctatgcctcaagtccttttgcatcatgagcaagctttatgccaccaataagactatcagaagctaaaaaatatcactgcagGTTGAAGTTTTCCAGCAGCAACTTGAACTTGCTAAGGAGTTGAACAAGCCTGTTTCTGTTCATTGTGTGCGCGCCTTTGGTGATCTTCTGGAGATACTAA

upper sequence: Vv15s0024g00050.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GRMZM2G114131_T02 (Zea mays), 3'ss of exon 3
---------------------------------------------------------------------------------------tcctactctcctacttgct-----tctgataatag--aatgctaaagagatgttttccttgaagatgttttgtgaaacagtt--ttatttgtttaattttctgttccagGTTGAAGTTTTCCAGCAACAGCTTGAACTTGCCAAAGAGTTGAAAAGACCAGTTTCTGTCCATTGCGTTCGTGCTTTTGGTGATCTTCTTCAGATAATGC
                                                                                       |  | || |   |  |  |     |||| |  |||    |  ||   | ||||   | ||  |  | || | |  |   ||   | |       ||  |  | |  ||||||||||| ||||||| |||||| ||||| || || || ||| | ||||| |||||||| ||||| || || || ||||||||||||||  |  || || 
gttagtacttagcaatagcatgaaccctgtacttcatgttgcatgcttgtgtatcggttttgttagaaatttcagttgcatggtgaatattgctgtttcatctattaatggtctggttctagttgtttgtatctaaatgtacccttttgattttttatatccataggtccataacaacagcaaactcttatcacagGTTGAAGTGTTCCAGCGACAGCTCGAACTAGCTAAGGAATTGGAGAGACCTGTTTCTGTTCATTGTGTGCGGGCATTTGGTGATCTTCTGGAAGTATTGA

upper sequence: Vv15s0024g00050.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA16G26700.4 (Glycine max), 3'ss of exon 3
tcctactctcctacttgcttctgataatagaatgctaaagagatgttttccttgaagatgttttgtgaaacagt-----tttatttgtttaattttctgttccagGTTGAAGTTTTCCAGCAACAGCTTGAACTTGCCAAAGAGTTGAAAAGACCAGTTTCTGTCCATTGCGTTCGTGCTTTTGGTGATCTTCTTCAGATAATGC
    || |    ||         || |  ||  |   | ||    || | |   |  ||| |   |  |    |      | ||   ||      | ||| | || ||||||| ||   ||| |||||||||||||| |||||||| || | |||||  ||||| ||||| |||||||||||||||||||||||| || ||||| 
----acacattgaccaatcatatatcaaggacagaagatgaccatttatgcagaagaatgctacctagattgttggctgctaatacattaggacatttgtgc-agATTGAAGTATTGAGGCAGCAGCTTGAACTTGCAAAAGAGTTAAACAAACCAGCATCTGTTCATTGTGTTCGTGCTTTTGGTGATCTTCTTGAGCTAATGA

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|110378329|gb|EC943456.1|EC943456
EST:     TTGGTCTGGACAAGGGCTCACGTGGAAGGGAAATTGATTTTGTGAATCAG                         GTTGAAGTTTTCCAGCAACAGCTTGAACTTGCCAAAGAGTTGAAAAGACCA
genomic: TTGGTCTGGACAAGGGCTCACGTGGAAGGGAAATCAATTTTGTGAATCAGgtttcactaa ... tctgttccagGTTGAAGTTTTCCAGCAACAGCTTGAACTTGCCAAAGAGTTGAAAAGACCA
EST: gi|122691575|gb|EC980636.1|EC980636
EST:     TTGGTCTGGACAAGGGCTCACGTGGAAGGGAAATTGATTTTGTGAATCAG                         GTTGAAGTTTTCCAGCAACAGCTTGAACTTGCCAAAGAGTTGAAAAGACCA
genomic: TTGGTCTGGACAAGGGCTCACGTGGAAGGGAAATCAATTTTGTGAATCAGgtttcactaa ... tctgttccagGTTGAAGTTTTCCAGCAACAGCTTGAACTTGCCAAAGAGTTGAAAAGACCA
EST: gi|110376873|gb|EC941950.1|EC941950
EST:     TTGGTCTGGACAAGGGCTCACGTGGAAGGGAAATCAATTTTGTGAATCAG                         GTTGAAGTTTTCCAGCAACAGCTTGAACTTGCCAAAGAGTTGAAAAGACCA
genomic: TTGGTCTGGACAAGGGCTCACGTGGAAGGGAAATCAATTTTGTGAATCAGgtttcactaa ... tctgttccagGTTGAAGTTTTCCAGCAACAGCTTGAACTTGCCAAAGAGTTGAAAAGACCA
EST: gi|161713476|gb|FC063101.1|FC063101
EST:     TTGGTCTGGACAAGGGCTCACGTGGAAGGGAAATTGATTTTGTGAATCAG                         GTTGAAGTTTTCCAGCAACAGCTTGAACTTGCCAAAGAGTTGAAAAGACCA
genomic: TTGGTCTGGACAAGGGCTCACGTGGAAGGGAAATCAATTTTGTGAATCAGgtttcactaa ... tctgttccagGTTGAAGTTTTCCAGCAACAGCTTGAACTTGCCAAAGAGTTGAAAAGACCA
EST: gi|110394067|gb|EC958495.1|EC958495
EST:     TTGGTCTGGACAAGGGCTCACGTGGAAGGGAAATTGATTTTGTGAATCAG                         GTTGAAGTTTTCCAGCAACAGCTTGAACTTGCCAAAGAGTTGAAAAGACCA
genomic: TTGGTCTGGACAAGGGCTCACGTGGAAGGGAAATCAATTTTGTGAATCAGgtttcactaa ... tctgttccagGTTGAAGTTTTCCAGCAACAGCTTGAACTTGCCAAAGAGTTGAAAAGACCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttttccttgaagatgttttgtgaaacagttttatttgtttaattttctgttccagGTTGAAGTTTTCCAGCAACAGCTTGAACTTGCCAAAGAGTTGAAAAGACCAGTTTCTGTCCATTGCGTTCGTGCTTTTGGTGATCTTCTTCAGATAATGC
                                    gtttaat  putative branch site (score: 4)
                                          ttttctgttcc  CT-rich tract
                      aaacagttttatttgt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tcctactctcctacttgcttctgataatagaatgctaaagagatgttttccttgaagatgttttgtgaaacagttttatttgtttaattttctgttccagGTTGAAGTTTTCCAGCAACAGCTTGAACTTGCCAAAGAGTTGAAAAGACCAGTTTCTGTCCATTGCGTTCGTGCTTTTGGTGATCTTCTTCAGATAATGC

- - -ctctcct
- - - - - - - -tgcttct
- - - - - - - - - - - - -aatagaa
- - - - - - - - - - - - - - - - - - aaagaga
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gaaacag