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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTTGCATCTATTCAATATCGAGCCTTAGCAGAAAAGGCATCTGATGCTTTCTATAAGCTCAGCAACACCAGAGCACAGATCCAAGCCTACGTCTTTGATGgtatggacctgaatcttaagcttgtagcaaaattttcaaaaccttaatcatgttttttttttacttgatctgttctctatagacaattgagcatccatcc...

Basic information

species Vitis vinifera
transcript Vv01s0026g01640.t01
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv01s0026g01640.t01 (Vitis vinifera), 5'ss of exon 4
lower sequence: GLYMA01G04950.1 (Glycine max), 5'ss of exon 2
GTTGCATCTATTCAATATCGAGCCTTAGCAGAAAAGGCATCTGATGCTTTCTATAAGCTCAGCAACACCAGAGCACAGATCCAAGCCTACGTCTTTGATGgtatggacctgaatcttaagcttgtagcaaaattttcaaaaccttaatcatgttttttttttacttgatctgttctctatagacaattgagcatccatcc
||||| ||||| || |||||||| || |||||||||||||| ||||||| ||| || |||||||| |||||||||||||| ||| |||| |||||||||||||        ||| |   ||||||      | ||   ||||     | ||||   | ||  | ||||    || | ||       ||     ||     
GTTGCCTCTATCCAGTATCGAGCATTGGCAGAAAAGGCATCAGATGCTTACTACAAACTCAGCAATACCAGAGCACAGATACAATCCTATGTCTTTGATGgtag-----ctaatttagtgcttgtgaatctactta-gaaactaggtttatgtgcgtcttcaagttgaaac-ttatttactcctgtttctatttcag---

upper sequence: Vv01s0026g01640.t01 (Vitis vinifera), 5'ss of exon 4
lower sequence: GLYMA02G02550.1 (Glycine max), 5'ss of exon 3
GTTGCATCTATTCAATATCGAGCCTTAGCAGAAAAGGCATCTGATGCTTTCTATAAGCTCAGCAACACCAGAGCACAGATCCAAGCCTACGTCTTTGATGgtatggacctgaatcttaagcttgta--gcaaa---attttcaaaaccttaatcatgttttttttttacttg-atctgttctctatagacaattgagcatccatcc-------------
||||| || || ||||||||||| || |||||||||||||| ||||||| ||| || |||| ||| |||| ||||||||| ||| |||| ||||||||||||    |  | ||| |  |||||||   |  ||   | ||  || |    ||| | |||  |||| |   || ||||  |||  |     ||   |   | |  |              
GTTGCCTCAATCCAATATCGAGCATTGGCAGAAAAGGCATCAGATGCTTACTACAAACTCACCAATACCAAAGCACAGATACAATCCTATGTCTTTGATGgttaatatttcaat-tagagcttgtgttgtgaatctacttagaagaaggaaattaggttaattttatgtgtgcatcttatcttcaggttgaaactaatttactcctattgttattttag

upper sequence: Vv01s0026g01640.t01 (Vitis vinifera), 5'ss of exon 4
lower sequence: GLYMA02G02500.1 (Glycine max), 5'ss of exon 3
GTTGCATCTATTCAATATCGAGCCTTAGCAGAAAAGGCATCTGATGCTTTCTATAAGCTCAGCAACACCAGAGCACAGATCCAAGCCTACGTCTTTGATGgtatggacctgaatcttaagcttgta--gcaaa---attttcaaaaccttaatcatgttttttttttacttg-atctgttctctatagacaattgagcat--ccatcc---
||||| || || ||||||||||| || |||||||||||||| ||||||| ||| || |||| ||| |||| ||||||||| ||| |||| ||||||||||||    |  | ||| |  |||||||   |   |   | ||  || |  ||||| | |||  |||| |   || ||||      |  |    ||| |   |  | ||     
GTTGCCTCAATCCAATATCGAGCATTGGCAGAAAAGGCATCAGATGCTTACTACAAACTCACCAATACCAAAGCACAGATACAATCCTATGTCTTTGATGgtgaatattttaat-tagagcttgtgttgtggatctacttaaaagaaattaattaggttaattttatgtgtgcatcttcaggttgaaacttattcacgtttgctatttcag

upper sequence: Vv01s0026g01640.t01 (Vitis vinifera), 5'ss of exon 4
lower sequence: GLYMA02G02540.2 (Glycine max), 5'ss of exon 2
GTTGCATCTATTCAATATCGAGCCTTAGCAGAAAAGGCATCTGATGCTTTCTATAAGCTCAGCAACACCAGAGCACAGATCCAAGCCTACGTCTTTGATGgtatggacctgaatcttaagcttgtagc---aaaattttcaaaaccttaatcatgttttttttttacttgatctgttctctatagacaattgagcatccatcc---
||||| ||||| ||||||||||| || ||||||||||||   ||||||| ||| || |||||||| |||||| ||||||| ||  |||| ||||||||||||    |  | |         ||||        ||| | |   |   |||| | |||| | | |   |      |||     |     | |  |     ||     
GTTGCTTCTATCCAATATCGAGCATTGGCAGAAAAGGCAGTGGATGCTTACTACAAACTCAGCAATACCAGATCACAGATTCAGTCCTATGTCTTTGATGgtggctattttagatcctgtgttgtgatttgcgaatctgcttcaaagtaattaggtttatgtgtgcatcttcacgttaaaacttatttactctgttgttatttcag

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|161721397|gb|FC070773.1|FC070773
EST:     CTATAAGCTCAGCAACACCAGAGCACAGATCCAAGCCTATGTCTTTGATG                         TAATTAGAGCTAGTGTTCCAAAGTTAGACCTGGATTCAACCTTTGAACAGA
genomic: CTATAAGCTCAGCAACACCAGAGCACAGATCCAAGCCTACGTCTTTGATGgtatggacct ... attgctttagTAATTAGAGCTAGTGTTCCAAAGTTAGACCTGGATTCAACCTTTGAACAGA
EST: gi|26262182|gb|CA813245.1|CA813245
EST:     CTATAAGCTCAGCAACACCAGAGCACAGATCCAAGCCTACGTCTTTGATG                         TAATTAGAGCTAGTGTTCCGAAGTTAGACCTGGATTCAACCTTTGAACAGA
genomic: CTATAAGCTCAGCAACACCAGAGCACAGATCCAAGCCTACGTCTTTGATGgtatggacct ... attgctttagTAATTAGAGCTAGTGTTCCAAAGTTAGACCTGGATTCAACCTTTGAACAGA
EST: gi|110724693|gb|EE100742.1|EE100742
EST:     CTATAAGCTCAGCAACACCAGAGCACAGATCCAAGCCTACGTCTTTGATG                         TAATTAGAGCTAGTGTTCCAAAGTTAGACCTGGATTCAACCTTTGAACAGA
genomic: CTATAAGCTCAGCAACACCAGAGCACAGATCCAAGCCTACGTCTTTGATGgtatggacct ... attgctttagTAATTAGAGCTAGTGTTCCAAAGTTAGACCTGGATTCAACCTTTGAACAGA
EST: gi|110697820|gb|EE075232.1|EE075232
EST:     CTATAAGCTCAGCAACACCAGAGCACAGATCCAAGCCTACGTCTTTGATG                         TAATTAGAGCTAGTGTTCCGAAGTTAGACCTGGATTCAACCTTTGAACAGA
genomic: CTATAAGCTCAGCAACACCAGAGCACAGATCCAAGCCTACGTCTTTGATGgtatggacct ... attgctttagTAATTAGAGCTAGTGTTCCAAAGTTAGACCTGGATTCAACCTTTGAACAGA
EST: gi|71859260|gb|DT008315.1|DT008315
EST:     CTATAAGCTCAGCAACACCAGAGCACAGATCCAAGCCTACGTCTTTGATG                         TAATTAGAGCTAGTGTTCCGAAGTTAGACCTGGATTCAACCTTTGAACAGA
genomic: CTATAAGCTCAGCAACACCAGAGCACAGATCCAAGCCTACGTCTTTGATGgtatggacct ... attgctttagTAATTAGAGCTAGTGTTCCAAAGTTAGACCTGGATTCAACCTTTGAACAGA
EST: gi|110382334|gb|EC939189.1|EC939189
EST:     CTATAAGCTCAGCAACACCAGAGCACAGATCCAAGCCTATGTCTTTGATG                         TAATTAGAGCTAGTGTTCCAAAGTTAGACCTGGATTCAACCTTTGAACAGA
genomic: CTATAAGCTCAGCAACACCAGAGCACAGATCCAAGCCTACGTCTTTGATGgtatggacct ... attgctttagTAATTAGAGCTAGTGTTCCAAAGTTAGACCTGGATTCAACCTTTGAACAGA
EST: gi|110687599|gb|EE065191.1|EE065191
EST:     CTATAAGCTCAGCAACACCAGAGCACAGATCCAAGCCTACGTCTTTGATG                         TAATTAGAGCTAGTGTTCCAAAGTTAGACCTGGATTCAACCTTTGAACAGA
genomic: CTATAAGCTCAGCAACACCAGAGCACAGATCCAAGCCTACGTCTTTGATGgtatggacct ... attgctttagTAATTAGAGCTAGTGTTCCAAAGTTAGACCTGGATTCAACCTTTGAACAGA
EST: gi|110389091|gb|EC953904.1|EC953904
EST:     CCAGAGCACAGATCCAAGCCTATGTTTTTGATG                         TAATTAGAGCTAGTGTTCCAAAGTTAGACCTGGATTCAACCTTTGAACAGA
genomic: CCAGAGCACAGATCCAAGCCTACGTCTTTGATGgtatggacct ... attgctttagTAATTAGAGCTAGTGTTCCAAAGTTAGACCTGGATTCAACCTTTGAACAGA
EST: gi|161715489|gb|FC069052.1|FC069052
EST:     CTATAAGCTCAGCAACACCAGAGCACAGATCCAAGCCTATGTCTTTGATG                         TAATTAGAGCTAGTGTTCCAAAGTTAGACCTGGATTCAACCTTTGAACAGA
genomic: CTATAAGCTCAGCAACACCAGAGCACAGATCCAAGCCTACGTCTTTGATGgtatggacct ... attgctttagTAATTAGAGCTAGTGTTCCAAAGTTAGACCTGGATTCAACCTTTGAACAGA
EST: gi|110375966|gb|EC940998.1|EC940998
EST:     CTATAAGCTCAGCAACACCAGAGCACAGATCCAAGCCTACGTCTTTGATG                         TAATTAGAGCTAGTGTTCCGAAGTTAGACCTGGATTCAACCTTTGAACAGA
genomic: CTATAAGCTCAGCAACACCAGAGCACAGATCCAAGCCTACGTCTTTGATGgtatggacct ... attgctttagTAATTAGAGCTAGTGTTCCAAAGTTAGACCTGGATTCAACCTTTGAACAGA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTTGCATCTATTCAATATCGAGCCTTAGCAGAAAAGGCATCTGATGCTTTCTATAAGCTCAGCAACACCAGAGCACAGATCCAAGCCTACGTCTTTGATGgtatggacctgaatcttaagcttgtagcaaaattttcaaaaccttaatcatgttttttttttacttgatctgttctctatagacaattgagcatccatcc

- - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -agcaaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - atagacaa