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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...agtagaagtaatttggtgttttgttttagatggaacattgttgcactggcatgattttattgggaagtaacgagctatttgtttatgtctgtacaaacagATGATGATTTCAGGGAATTTGTTGATGGGGTGCCTAGAGGTTGCACGATCACAATTGTGTCTGATTCTTGCCACAGTGGTGGCCTACTTGAAGAAGCTAA

Basic information

species Glycine max
transcript GLYMA08G25170.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA08G25170.1 (Glycine max), 3'ss of exon 1
lower sequence: LOC_Os01g58580.1 (Oryza sativa), 3'ss of exon 1
agtagaagtaatttggtgttttgttttagatggaacattgttgcactggcatgattttattgggaagtaacgagcta-tttgtttat-gtctgtacaaacagATGATGATTTCAGGGAATTTGTTGATGGGGTGCCTAGAGGTTGCACGATCACAATTGTGTCTGATTCTTGCCACAGTGGTGGCCTACTTGAAGAAGCTAA
 |        ||||    ||||| | |  |    | | | |   |     |||| |  |        | |  |  || ||  ||  | ||   || |  ||||| | |||||||| ||| ||||  |   |||||| |  ||||||    | || || || ||||||||||||||||||||||||||| | ||    || ||
-gcgctccatatttctgcttttgatctgaa-aatatactctcatatcaagatgaatacaaacaattattataacttaattcattcgttgttgctatatgcagATCAAGATTTCAGAGAACTTGTGCAAAAGGTGCCCAATGGTTGCTTATTTACCATCGTCTCTGATTCTTGCCACAGTGGTGGCCTATTGGACAGCGCCAA
















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|209713857|gb|BW684050.1|BW684050
EST:     CACTGGCTTTGATGAATGCATTGTTCCGTCTGACATGAACCTCATCACTG                         ATGATGATTTCAGGGAATTTGTTGATGGGGTGCCTAGAGGTTTGCACGATC
genomic: CACTGGCTTTGATGAATGCATTGTTCCGTCTGACATGAACCTCATCACTGgttggttctc ... gtacaaacagATGATGATTTCAGGGAATTTGTTGATGGGGTGCCTAGAGGTT-GCACGATC
EST: gi|213607114|gb|DB966991.1|DB966991
EST:     CACTGGCTTTGATGAATGCATTGTTCCGTCTGACATGAACCTCATCACTG                         ATGATGATTTCAGGGAATTTGTTGATGGGGTGCCTAGAGGTTGCACGATCA
genomic: CACTGGCTTTGATGAATGCATTGTTCCGTCTGACATGAACCTCATCACTGgttggttctc ... gtacaaacagATGATGATTTCAGGGAATTTGTTGATGGGGTGCCTAGAGGTTGCACGATCA
EST: gi|298199297|gb|HO042660.1|HO042660
EST:     CACTGGCTTTGATGAATGCATTGTTCCGTCTGACATGAACCTCATCACTG                         ATGATGATTTCAGGGAATTTGTTGATGGGGTGCCTAGAGGTTGCACGATCA
genomic: CACTGGCTTTGATGAATGCATTGTTCCGTCTGACATGAACCTCATCACTGgttggttctc ... gtacaaacagATGATGATTTCAGGGAATTTGTTGATGGGGTGCCTAGAGGTTGCACGATCA
EST: gi|41145846|gb|CK606057.1|CK606057
EST:     CACTGGCTTTGATGAATGCATTGTTCCGTCTGACATGAACCTCATCACTG                         ATGATGATTTCAGGGAATTTGTTGATGGGGTGCCTAGAGGTTGCACGATCA
genomic: CACTGGCTTTGATGAATGCATTGTTCCGTCTGACATGAACCTCATCACTGgttggttctc ... gtacaaacagATGATGATTTCAGGGAATTTGTTGATGGGGTGCCTAGAGGTTGCACGATCA
EST: gi|298199367|gb|HO042730.1|HO042730
EST:     CACTGGCTTTGATGAATGCATTGTTCCGTCTGACATGAACCTCATCACTG                         ATGATGATTTCAGGGAATTTGTTGATGGGGTGCCTAGAGGTTGCACGATCA
genomic: CACTGGCTTTGATGAATGCATTGTTCCGTCTGACATGAACCTCATCACTGgttggttctc ... gtacaaacagATGATGATTTCAGGGAATTTGTTGATGGGGTGCCTAGAGGTTGCACGATCA
EST: gi|192322699|gb|FK014390.1|FK014390
EST:     ACTGGCTTTGATGAATGCATTTGTTCCGTCTGACATGAACCTCATCACTG                         ATGATGATTTCAGGGAATTTGTTGATGGGGTGCCTAGAGGTTGCACGATCA
genomic: ACTGGCTTTGATGAATGCA-TTGTTCCGTCTGACATGAACCTCATCACTGgttggttctc ... gtacaaacagATGATGATTTCAGGGAATTTGTTGATGGGGTGCCTAGAGGTTGCACGATCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctggcatgattttattgggaagtaacgagctatttgtttatgtctgtacaaacagATGATGATTTCAGGGAATTTGTTGATGGGGTGCCTAGAGGTTGCACGATCACAATTGTGTCTGATTCTTGCCACAGTGGTGGCCTACTTGAAGAAGCTAA
                   aagtaac  putative branch site (score: 2)
     atgattttatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
agtagaagtaatttggtgttttgttttagatggaacattgttgcactggcatgattttattgggaagtaacgagctatttgtttatgtctgtacaaacagATGATGATTTCAGGGAATTTGTTGATGGGGTGCCTAGAGGTTGCACGATCACAATTGTGTCTGATTCTTGCCACAGTGGTGGCCTACTTGAAGAAGCTAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGC
- - - - - - - - tgttttg
- - - - - - - - - - - - - - - - - - - - -tgcactg