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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ccaaacttattgactttgtggccaaatgttcattaattcctttgaagtttgcttaaacttttacaagctaataactagaatgttttggcctttttcacagCTTGATGGTCGTGTCAAAACTTTGCACCCTAACATACATGGGGGTATCCTTGCCCGAAGGGACCAAAAACATCACATTGACGCCCTCAGTGCTCATGGGA

Basic information

species Glycine max
transcript GLYMA04G16670.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA04G16670.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv01s0011g01460.t01 (Vitis vinifera), 3'ss of exon 4
ccaaacttattgactttgtg--gccaaatgttcattaatt---cctttgaagtttgcttaaacttttacaagctaataactagaatgttttggcctttttcacagCTTGATGGTCGTGTCAAAACTTTGCACCCTAACATACATGGGGGTATCCTTGCCCGAAGGGACCAAAAACATCACATTGACGCCCTCAGTGCTCATGGGA
   |  || |  |    ||      ||||  || ||  ||   ||| |   |  ||    |    ||   || |   ||  |  || ||||    | ||| |||||||||||| ||||| |||||||| || || ||||||||||||||||| |||||  |||| |||||||| | |||||| || || || | ||  ||||| |
---attttgtccatcaagtattattaaatcctcttttctttcacctcttgcgagtgacacatggcttttgagttttgaa--aatatttttttagttattttacagCTTGATGGCCGTGTGAAAACTTTACATCCAAACATACATGGGGGTATTCTTGCTAGAAGAGACCAAAAGCTTCACATGGAAGCTCTTAATGAGCATGGAA
















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|192323163|gb|FK017389.1|FK017389
EST:     CTGGAGTAGCTGTTACTAAAGTTGAAAAGCTCACTAAGTTCCCTGAAATG                         CTTGATGGTCGTGTCAAAACTTTGCACCCTAACATACATGGGGGTATCCTT
genomic: CTGGAGTAGCTGTTACTAAAGTTGAAAAGCTCACTAAGTTCCCTGAAATGgtgtgttgga ... tttttcacagCTTGATGGTCGTGTCAAAACTTTGCACCCTAACATACATGGGGGTATCCTT
EST: gi|20812255|gb|BQ296725.1|BQ296725
EST:     CTGGAGTAGCTGTTACTAAAGTTGAAAAGCTCACTAAGTTCCCTGAAATG                         CTTGATGGTCGTGTCAAAACTTTGCACCCTAACATACATGGGGGTATCCTT
genomic: CTGGAGTAGCTGTTACTAAAGTTGAAAAGCTCACTAAGTTCCCTGAAATGgtgtgttgga ... tttttcacagCTTGATGGTCGTGTCAAAACTTTGCACCCTAACATACATGGGGGTATCCTT
EST: gi|151410033|gb|EV279841.1|EV279841
EST:     CTGGAGTAGCTGTTACTAAAGTTGAAAAGCTCACTAAGTTCCCTGAAATG                         CTTGATGGTCGTGTCAAAACTTTGCACCCTAACATACATGGGGGTATCCTT
genomic: CTGGAGTAGCTGTTACTAAAGTTGAAAAGCTCACTAAGTTCCCTGAAATGgtgtgttgga ... tttttcacagCTTGATGGTCGTGTCAAAACTTTGCACCCTAACATACATGGGGGTATCCTT
EST: gi|20812245|gb|BQ296723.1|BQ296723
EST:     CTGGAGTAGCTGTTACTAAAGTTGAAAAGCTCACTAAGTTCCCTGAAATG                         CTTGATGGTCGTGTCAAAACTTTGCACCCTAACATACATGGGGGTATCCTT
genomic: CTGGAGTAGCTGTTACTAAAGTTGAAAAGCTCACTAAGTTCCCTGAAATGgtgtgttgga ... tttttcacagCTTGATGGTCGTGTCAAAACTTTGCACCCTAACATACATGGGGGTATCCTT
EST: gi|193366619|gb|FK331949.1|FK331949
EST:     CTGGAGTAGCTGTTACTAAAGTTGAAAAGCTCACTAAGTTCCCTGAAATG                         CTTGATGGTCGTGTCAAAACTTTGCACCCTAACATACATGGGGGGTATCCT
genomic: CTGGAGTAGCTGTTACTAAAGTTGAAAAGCTCACTAAGTTCCCTGAAATGgtgtgttgga ... tttttcacagCTTGATGGTCGTGTCAAAACTTTGCACCCTAACATACATGGGGG-TATCCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agtttgcttaaacttttacaagctaataactagaatgttttggcctttttcacagCTTGATGGTCGTGTCAAAACTTTGCACCCTAACATACATGGGGGTATCCTTGCCCGAAGGGACCAAAAACATCACATTGACGCCCTCAGTGCTCATGGGA
                       taataac  putative branch site (score: 1)
                                     ttttggcctttttc  putative PPT
       ttaaacttttacaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ccaaacttattgactttgtggccaaatgttcattaattcctttgaagtttgcttaaacttttacaagctaataactagaatgttttggcctttttcacagCTTGATGGTCGTGTCAAAACTTTGCACCCTAACATACATGGGGGTATCCTTGCCCGAAGGGACCAAAAACATCACATTGACGCCCTCAGTGCTCATGGGA

ccaaact
- - - - - -gactttg
- - - - - - - - - - gccaaat
- - - - - - - - - - - - - - - - - - -tcctttg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tacaagc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgttttg