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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagttctttctttgaggaaagctatttttctgtgtatcaattatgtacaaagggattactcctcgttgctcataggcacaacaatttgacttccttctttggttcccagGCTGTTAGAAAACTGAATGATGCAAAGAAACTTGAATCCAGTGCTCACTACAGTGCTGATTTTGGCAAAGACTAAAGGCTATTATAAAATTCTGAGCCAT

Basic information

species Glycine max
transcript GLYMA14G07750.1
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA14G07750.1 (Glycine max), 3'ss of exon 9
lower sequence: Vv18s0001g13090.t01 (Vitis vinifera), 3'ss of exon 9
-------------------------------------------gtgagttctttctttgaggaaagct-----atttttctgtgtatcaattatgtacaaagggattactc--ctcgttgctcat--aggcacaacaatttgacttccttct-ttggttc---------------ccagGCTGTTAGAAAACTGAATGATGCAAAGAAACTTGAATCCAGTGCTCACTACAGTGCTGATTTTGGCAAAGACTAAAGGCTAT--TATAAAATTCTGAGCCAT
                                            | |  ||| | ||  |  | |  |     ||  ||||   | ||||    |   ||| | |  | |   || | |  | ||  ||    ||    |   ||||  ||| ||  ||                |||||||||| | ||||||||||| ||||||||||||||||| ||||||||||||| |||||||||||| |||||||| |    ||  |||   |||   ||    
gtgagcttttcttcggggcattggcttccagtaattaataagcctcatctctgtattgaacaataaattttatatcattcttcttgtcaaaagggggaaaatgaaacaatttgcttggtcttgatgaagttgaaatggctgatcttctgtctgttcatttttatcttgtatcattccagGCTGTTCGGAAACTGAATGAAGCAAAGAAACTTGAATCTAGTGCTCACTACAATGCTGATTTTGGGAAAGACTAGAACACATGTTATTCCATTTCAAGAG--
















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|22931717|gb|BU548856.1|BU548856
EST:     CAGCAATTCGTGCAGAACGCGATTATGTGATCCATGAAGATTTTATGAAG                         GCTGTTAGAAAACTGAATGATGCAAAGAAACTTGAATCCAGTGCTCACTAC
genomic: CAGCAATTCGTGCAGAACGCGATTATGTGATCCATGAAGATTTTATGAAGgtgagttctt ... tggttcccagGCTGTTAGAAAACTGAATGATGCAAAGAAACTTGAATCCAGTGCTCACTAC
EST: gi|193523096|gb|FK479511.1|FK479511
EST:     GATTATGTGATCCATGAAGATTTTATGAAG                         GCTGTTAGAAAACCGAATGATGCAAAGAAACTTGAATCCAGTGCTCACTAC
genomic: GATTATGTGATCCATGAAGATTTTATGAAGgtgagttctt ... tggttcccagGCTGTTAGAAAACTGAATGATGCAAAGAAACTTGAATCCAGTGCTCACTAC
EST: gi|57574105|gb|CX547080.1|CX547080
EST:     CAGCAATTCGTGCAGAACGCGATTATGTGATCCATGAAGATTTTATGAAG                         GCTGTTAGAAAACTGAATGATGCAAAGAAACTTGAATCCAGTGCTCACTAC
genomic: CAGCAATTCGTGCAGAACGCGATTATGTGATCCATGAAGATTTTATGAAGgtgagttctt ... tggttcccagGCTGTTAGAAAACTGAATGATGCAAAGAAACTTGAATCCAGTGCTCACTAC
EST: gi|15664798|gb|BI702177.1|BI702177
EST:     CAGCAATTCGTGCAGAACGCGATTATGTGATCCATGAAGATTTTATGAAG                         GCTGTTAGAAAACTGAATGATGCAAAGAAACTTGAATCCAGTGCTCACTAC
genomic: CAGCAATTCGTGCAGAACGCGATTATGTGATCCATGAAGATTTTATGAAGgtgagttctt ... tggttcccagGCTGTTAGAAAACTGAATGATGCAAAGAAACTTGAATCCAGTGCTCACTAC
EST: gi|31467046|gb|CD409074.1|CD409074
EST:     CAGCAATTCGTGCAGAACGCGATTATGTGATCCATGAAGATTTTATGAAG                         GCTGTTAGAAAACTGAATGATGCAAAGAAACTTGAATCCAGTGCTCACTAC
genomic: CAGCAATTCGTGCAGAACGCGATTATGTGATCCATGAAGATTTTATGAAGgtgagttctt ... tggttcccagGCTGTTAGAAAACTGAATGATGCAAAGAAACTTGAATCCAGTGCTCACTAC
EST: gi|192308351|gb|FK001337.1|FK001337
EST:     CAGCAATTCGTGCAGAACGCGATTATGTGATCCATGAAGATTTTATGAAG                         GCTGTTAGAAAACTGAATGATGCAAAGAAACTTGAATCCAGTGCTCACTAC
genomic: CAGCAATTCGTGCAGAACGCGATTATGTGATCCATGAAGATTTTATGAAGgtgagttctt ... tggttcccagGCTGTTAGAAAACTGAATGATGCAAAGAAACTTGAATCCAGTGCTCACTAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

attactcctcgttgctcataggcacaacaatttgacttccttctttggttcccagGCTGTTAGAAAACTGAATGATGCAAAGAAACTTGAATCCAGTGCTCACTACAGTGCTGATTTTGGCAAAGACTAAAGGCTATTATAAAATTCTGAGCCAT
                             atttgac  putative branch site (score: 4)
                                   cttccttctttggttc  CT-rich tract
                         aacaattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagttctttctttgaggaaagctatttttctgtgtatcaattatgtacaaagggattactcctcgttgctcataggcacaacaatttgacttccttctttggttcccagGCTGTTAGAAAACTGAATGATGCAAAGAAACTTGAATCCAGTGCTCACTACAGTGCTGATTTTGGCAAAGACTAAAGGCTATTATAAAATTCTGAGCCAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAAG