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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaccagacaaattatttttctttttactgttaaagttttatttagaaaataagtattacgtggaccatttttcctgatatatgtgattcactggtgacagGTGAAGGCGACCTTTTAACTGGTGGAGATTTATATGCT

Basic information

species Glycine max
transcript GLYMA08G23990.1
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA08G23990.1 (Glycine max), 3'ss of exon 5
lower sequence: Vv04s0008g02580.t01 (Vitis vinifera), 3'ss of exon 5
gtaccagacaaattatttttctttttactgttaaagttttatttagaaaataagtattacgtggaccatttttcctgatatatgtgattcactggtgacagGTGAAGGCGACCTTTTAACTGGTGGAGATTTATATGCT
||||      ||| ||  |  |   |  |  |    || |  |  |    ||| | |  | | ||    |  |     |   |     |||||| || |||||||||| || ||||||||||||||||| || ||||||
gtactgcttgaat-atgctaatacgtgatagttggtttgtggtctgtccttaactgtatcattgat-gctaataaaattgctttcctctcactgttg-cagGTGAAGGAGATCTTTTAACTGGTGGAGACTTGTATGCT
















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|19935049|gb|BQ080079.1|BQ080079
EST:     TCCAGCACTCGACAAAGATACACTTTGGGAATTTCAACCTAAGAAAATTG                         GTGAAGGCGACCTTTTAACTGGTGGAGATTTATATGCT
genomic: TCCAGCACTCGACAAAGATACACTTTGGGAATTTCAACCTAAGAAAATTGgtaccagaca ... ctggtgacagGTGAAGGCGACCTTTTAACTGGTGGAGATTTATATGCT
EST: gi|254333421|gb|GR841283.1|GR841283
EST:     TCCAGCACTCGACAAAGATACACTTTGGGAATTTCAACCTAAGAAAATTG                         GTGAAGGCGACCTTTTAACTGGTGGAGATTTATATGCT
genomic: TCCAGCACTCGACAAAGATACACTTTGGGAATTTCAACCTAAGAAAATTGgtaccagaca ... ctggtgacagGTGAAGGCGACCTTTTAACTGGTGGAGATTTATATGCT
EST: gi|213588728|gb|DB957708.1|DB957708
EST:     TCCAGCACTCGACAAAGATACACTTTGGGAATTTCAACCTAAGAAAATTG                         GTGAAGGCGACCTTTTAACTGGTGGAGATTTATATGCT
genomic: TCCAGCACTCGACAAAGATACACTTTGGGAATTTCAACCTAAGAAAATTGgtaccagaca ... ctggtgacagGTGAAGGCGACCTTTTAACTGGTGGAGATTTATATGCT
EST: gi|14126347|gb|BG790785.1|BG790785
EST:     TCCAGCACTCGACAAAGATACACTTTGGGAATTTCAACCTAAGAAAATTG                         GTGAAGGCGACCTTTTAACTGGTGGAGATTTATATGCT
genomic: TCCAGCACTCGACAAAGATACACTTTGGGAATTTCAACCTAAGAAAATTGgtaccagaca ... ctggtgacagGTGAAGGCGACCTTTTAACTGGTGGAGATTTATATGCT
EST: gi|209720598|gb|BW675045.1|BW675045
EST:     TCCAGCACTCGACAAAGATACACTTTGGGAATTTCAACCTAAGAAAATTG                         GTGAAGGCGACCTTTTAACTGGTGGAGATTTATATGCT
genomic: TCCAGCACTCGACAAAGATACACTTTGGGAATTTCAACCTAAGAAAATTGgtaccagaca ... ctggtgacagGTGAAGGCGACCTTTTAACTGGTGGAGATTTATATGCT
EST: gi|11413112|gb|BF425123.1|BF425123
EST:     TCCAGCACTCGACAAAGATACACTTTGGGAATTTCAACCTAAGAAAATTG                         GTGAAGGCGACCTTTTAACTGGTGGAGATTTATATGCT
genomic: TCCAGCACTCGACAAAGATACACTTTGGGAATTTCAACCTAAGAAAATTGgtaccagaca ... ctggtgacagGTGAAGGCGACCTTTTAACTGGTGGAGATTTATATGCT
EST: gi|19348868|gb|BM893400.1|BM893400
EST:     TCCAGCACTCGACAAAGATACACTTTGGGAATTTCAACCTAAGAAAAATG                         GCGAAGGCGACCTTTTAACTGGTGGAAGATT-ATATGCT
genomic: TCCAGCACTCGACAAAGATACACTTTGGGAATTTCAACCTAAGAAAATTGgtaccagaca ... ctggtgacagGTGAAGGCGACCTTTTAACTGGTGGA-GATTTATATGCT
EST: gi|209722703|gb|BW657957.1|BW657957
EST:     TCCAGCACTCGACAAAGATACACTTTGGGAATTTCAACCTAAGAAAATTG                         GTGAAGGCGACCTTTTAACTGGTGGAGATTTATATGCT
genomic: TCCAGCACTCGACAAAGATACACTTTGGGAATTTCAACCTAAGAAAATTGgtaccagaca ... ctggtgacagGTGAAGGCGACCTTTTAACTGGTGGAGATTTATATGCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aaaataagtattacgtggaccatttttcctgatatatgtgattcactggtgacagGTGAAGGCGACCTTTTAACTGGTGGAGATTTATATGCT
                          tcctgat  putative branch site (score: 3)
     aagtatta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaccagacaaattatttttctttttactgttaaagttttatttagaaaataagtattacgtggaccatttttcctgatatatgtgattcactggtgacagGTGAAGGCGACCTTTTAACTGGTGGAGATTTATATGCT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT