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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CTTTTATGGAAGGGGCTTACAATCGTGTCTTGAGTGCACGACAGACAGTGCCACATGATACATACGTTTATTTTATGGATCTTTTGGCAAAGACTGTCAGgtaataattgttattgttgttttattttaatagcccagtggatggttgaactctagtgataaactagaggaaactggaactactgcttgatttcttcaga...

Basic information

species Glycine max
transcript GLYMA05G25730.1
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA05G25730.1 (Glycine max), 5'ss of exon 4
lower sequence: Vv02s0025g02010.t01 (Vitis vinifera), 5'ss of exon 4
CTTTTATGGAAGGGGCTTACAATCGTGTCTTGAGTGCACGACAGACAGTGCCACATGATACATACGTTTATTTTATGGATCTTTTGGCAAAGACTGTCAGgtaataattgttattgttgttttattttaatagcccagtggatggttg-aactctagtgataaactagaggaaactggaactactg--cttg-atttcttcaga
|||| |||||||| |||||||||||||| ||||||||  ||||||||||||| ||||| || || |||||||| ||||||||  |||| ||||| ||||||||| || | | | |  ||      |  ||  |   | |  ||    | || | ||     | |    |  | ||   | | || |   ||| || | |||   
CTTTCATGGAAGGAGCTTACAATCGTGTGTTGAGTGCTAGACAGACAGTGCCCCATGAAACTTATGTTTATTTCATGGATCTGCTGGCGAAGACAGTCAGgtaaaaactttgact--tgagcctctagaaggggttaataaatttcaggaaatttaaaacgataaccaaccacacacaagccaccgactttgcatattttcc--

upper sequence: GLYMA05G25730.1 (Glycine max), 5'ss of exon 4
lower sequence: PP1S48_71V6.1 (Physcomitrella patens), 5'ss of exon 5
CTTTTATGGAAGGGGCTTACAATCGTGTCTTGAGTGCACGACAGACAGTGCCACATGATACATACGTTTATTTTATGGATCTTTTGGCAAAGACTGTCAGgta--------ataattgttattgttgttttatttta------atagcccagtggatggttgaactctagtgataaactagaggaaactggaactactgc---ttgatt-tcttcaga-----
|||| ||||| || ||||||||||||||  |||||||||| ||  | || |||||||| || ||||| || |||||||| ||| | || ||||||||||||||        |||  | | || ||| | |   ||||      | |  |   |   ||   | | | |  |  |    | | | | | ||| | |  ||    || ||| || ||        
CTTTCATGGAGGGTGCTTACAATCGTGTGCTGAGTGCACGTCAAGCTGTTCCACATGAAACTTACGTGTACTTTATGGACCTTCTTGCTAAGACTGTCAGgtatgattcctatatatataatggttttctgggtttattgcgtacattctgttctttgcaaggaatatgctcttgttttcgggaatattggtaatgatgtactttcattatcatcgtgcacag
















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|192324155|gb|FK017886.1|FK017886
EST:     CCACATGATACATACGTTTATTTTATGGATCTTTTGGCAAAGACTGTCAG                         AGATGAAATAGCTGGTTGCAGTGAGAAGGCCTATGACTATCTTTCAATTAA
genomic: CCACATGATACATACGTTTATTTTATGGATCTTTTGGCAAAGACTGTCAGgtaataattg ... aaacattcagAGATGAAATAGCTGGTTGCAGTGAGAAGGCCTATGACTATCTTTCAATTAA
EST: gi|298178308|gb|HO024043.1|HO024043
EST:     CCACATGATACATACGTTTATTTTATGGATCTTTTGGCAAAGACTGTCAG                         AGATGAAATAGCTGGTTGCAGTGAGAAGGCCTATGACTATCTTTCAATTAA
genomic: CCACATGATACATACGTTTATTTTATGGATCTTTTGGCAAAGACTGTCAGgtaataattg ... aaacattcagAGATGAAATAGCTGGTTGCAGTGAGAAGGCCTATGACTATCTTTCAATTAA
EST: gi|193721599|gb|FK658755.1|FK658755
EST:     CCACATGATACATACGTTTATTTTATGGATCTTTTGGCAAAGACTGTCAG                         AGATGAAATAGCTGGTTGCAGTGAGAAGGCCTATGACTATCTTTCAATTAA
genomic: CCACATGATACATACGTTTATTTTATGGATCTTTTGGCAAAGACTGTCAGgtaataattg ... aaacattcagAGATGAAATAGCTGGTTGCAGTGAGAAGGCCTATGACTATCTTTCAATTAA
EST: gi|4307283|gb|AI444025.1|AI444025
EST:     CTTTTGGCAAAGACTGTCAG                         AGATGAAATAGCTGGTTGCAGTGAGAAGGCCTATGACTATCTTTCAATTAA
genomic: CTTTTGGCAAAGACTGTCAGgtaataattg ... aaacattcagAGATGAAATAGCTGGTTGCAGTGAGAAGGCCTATGACTATCTTTCAATTAA
EST: gi|58022693|gb|CX709434.1|CX709434
EST:     CCACATGATACATACGTTTATTTTATGGATCTTTTGGCAAAGACTGTCAG                         AGATGAAATAGCTGGTTGCAGTGAGAAGGCCTATGACTATCTTTCAATTAA
genomic: CCACATGATACATACGTTTATTTTATGGATCTTTTGGCAAAGACTGTCAGgtaataattg ... aaacattcagAGATGAAATAGCTGGTTGCAGTGAGAAGGCCTATGACTATCTTTCAATTAA
EST: gi|58019686|gb|CX706428.1|CX706428
EST:     CCACATGATACATACGTTTATTTTATGGATCTTTTGGCAAAGACTGTCAG                         AGATGAAATAGCTGGTTGCAGTGAGAAGGCCTATGACTATCTTTCAATTAA
genomic: CCACATGATACATACGTTTATTTTATGGATCTTTTGGCAAAGACTGTCAGgtaataattg ... aaacattcagAGATGAAATAGCTGGTTGCAGTGAGAAGGCCTATGACTATCTTTCAATTAA
EST: gi|7234655|gb|AW569991.1|AW569991
EST:     CCACATGATACATACGTTTATTTTATGGATCTTTTGGCAAAGACTGTCAG                         AGATGAAATAGCTGGTTGCAGTGAGAAGGCCTATGACTATCTTTCAATTAA
genomic: CCACATGATACATACGTTTATTTTATGGATCTTTTGGCAAAGACTGTCAGgtaataattg ... aaacattcagAGATGAAATAGCTGGTTGCAGTGAGAAGGCCTATGACTATCTTTCAATTAA
EST: gi|193561614|gb|FK520623.1|FK520623
EST:     CCACATGATACATACGTTTATTTTATGGATCTTTTGGCAAAGACTGTCAG                         AGATGAAATAGCTGGTTGACAAGTAGAAGAAGGCCTATGA
genomic: CCACATGATACATACGTTTATTTTATGGATCTTTTGGCAAAGACTGTCAGgtaataattg ... aaacattcagAGATGAAATAGCTGGTTG-CA-GT-GA-GAAGGCCTATGA
EST: gi|33389688|gb|CA852895.1|CA852895
EST:     CCACATGATACATACGTTTATTTTATGGATCTTTTGGCAAAGACTGTCAG                         AGATGAAATAGCTGGTTGCAGTGAGAAGGCCTATGACTATCTTTCAATTAA
genomic: CCACATGATACATACGTTTATTTTATGGATCTTTTGGCAAAGACTGTCAGgtaataattg ... aaacattcagAGATGAAATAGCTGGTTGCAGTGAGAAGGCCTATGACTATCTTTCAATTAA
EST: gi|23729081|gb|BU762625.1|BU762625
EST:     CCACATGATACATACGTTTATTTTATGGATCTTTTGGCAAAGACTGTCAG                         AGATGAAATAGCTGGTTGCAGTGAGAAGGCCTATGACTATCTTTCAATTAA
genomic: CCACATGATACATACGTTTATTTTATGGATCTTTTGGCAAAGACTGTCAGgtaataattg ... aaacattcagAGATGAAATAGCTGGTTGCAGTGAGAAGGCCTATGACTATCTTTCAATTAA
EST: gi|58014496|gb|CX701238.1|CX701238
EST:     CCACATGATACATACGTTTATTTTATGGATCTTTTGGCAAAGACTGTCAG                         AGATGAAATAGCTGGTTGCAGTGAGAAGGCCTATGACTATCTTTCAATTAA
genomic: CCACATGATACATACGTTTATTTTATGGATCTTTTGGCAAAGACTGTCAGgtaataattg ... aaacattcagAGATGAAATAGCTGGTTGCAGTGAGAAGGCCTATGACTATCTTTCAATTAA
EST: gi|9820179|gb|BE555689.1|BE555689
EST:     CCACATGATACATACGTTTATTTTATGGATCTTTTGGCAAAGACTGTCAG                         AGATGAAATAGCTGGTTGCAGTGAGAAGGCCTATGACTATCTTTCAATTAA
genomic: CCACATGATACATACGTTTATTTTATGGATCTTTTGGCAAAGACTGTCAGgtaataattg ... aaacattcagAGATGAAATAGCTGGTTGCAGTGAGAAGGCCTATGACTATCTTTCAATTAA
EST: gi|151401431|gb|EV271245.1|EV271245
EST:     CCACATGATACATACGTTTATTTTATGGATCTTTTGGCAAAGACTGTCAG                         AGATGAAATAGCTGGTTGCAGTGAGAAGGCCTATGACTATCTTTCAATTAA
genomic: CCACATGATACATACGTTTATTTTATGGATCTTTTGGCAAAGACTGTCAGgtaataattg ... aaacattcagAGATGAAATAGCTGGTTGCAGTGAGAAGGCCTATGACTATCTTTCAATTAA
EST: gi|192306503|gb|FG996207.1|FG996207
EST:     CCACATGATACATACGTTTATTTTATGGATCTTTTGGCAAAGACTGTCAG                         AGATGAAATAGCTGGTTGCAGTGAGAAGGCCTATGACTATCTTTCAATTAA
genomic: CCACATGATACATACGTTTATTTTATGGATCTTTTGGCAAAGACTGTCAGgtaataattg ... aaacattcagAGATGAAATAGCTGGTTGCAGTGAGAAGGCCTATGACTATCTTTCAATTAA
EST: gi|6845858|gb|AW348148.1|AW348148
EST:     TTTGGCAAAGACTGTCAG                         AGATGAAATAGCTGGTTGCAGTGAGAAGGCCTATGACTATCTTTCAATTAA
genomic: TTTGGCAAAGACTGTCAGgtaataattg ... aaacattcagAGATGAAATAGCTGGTTGCAGTGAGAAGGCCTATGACTATCTTTCAATTAA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CTTTTATGGAAGGGGCTTACAATCGTGTCTTGAGTGCACGACAGACAGTGCCACATGATACATACGTTTATTTTATGGATCTTTTGGCAAAGACTGTCAGgtaataattgttattgttgttttattttaatagcccagtggatggttgaactctagtgataaactagaggaaactggaactactgcttgatttcttcaga

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG