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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagtgttttactcgtgctcaaatatggcaagagattgactagttgttccaattagaagtttagaacagtgatgggaaacacgaatatgatccttctctggatatatttctgtagGGAGCAATAATGGCTGTTGGAGCATCGGAGCCCACTGTTGTGGCTACAAAGGATGGTCGCATTGGAATGAAGAACCAAATGCAG

Basic information

species Glycine max
transcript GLYMA10G35960.1
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA10G35960.1 (Glycine max), 3'ss of exon 5
lower sequence: Vv18s0072g01000.t01 (Vitis vinifera), 3'ss of exon 4
gtgagtgtttta-ctc-gtgctcaaatatggcaa------gagattgactagttgttccaattagaagtttag--------aacagtgatgggaaacacgaatatgatccttctctggatatattt-ctgtagGGAGCAATAATGGCTGTTGGAGCATCGGAGCCCACTGTTGTGGCTACAAAGGATGGTCGCATTGGAATGAAGAACCAAATGCAG
|| ||| ||| | ||| |   |  ||  |  | |       | ||| |    |||   ||  ||     | ||        ||  ||    ||| | ||  | || ||  |  | || || | ||| ||| |||||||||| ||||| ||||||||||| || || || ||||| || || ||||||||||| ||||| ||||||| ||| ||||||
gtaagtatttaaactcagaatttgaacctctccactctgcaaaattcatagcttggggcagatatggaatgagggggactaaattgtatcaggataaacata-attatgttgatttgcatgttttttctgcagGGAGCAATCATGGCGGTTGGAGCATCAGAACCAACCGTTGTTGCCACCAAGGATGGTCGGATTGGCATGAAGAGCCAGATGCAG
















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|193397613|gb|FK365075.1|FK365075
EST:     GCCACCTGGAACT                         GGTAGCAATAATGGCTGTTGGAGCATCGGAGCCCACTGTTGTGGCTACAAA
genomic: GCCACCTGGAACTgtgagtgttt ... atttctgtagGG-AGCAATAATGGCTGTTGGAGCATCGGAGCCCACTGTTGTGGCTACAAA
EST: gi|13790727|gb|BG653318.1|BG653318
EST:     TGGGAATGTTTGGTGTTGATCGCTTTGATGCTATTCTGCCACCTGGAACT                         GGAGCAATAATGGCTGTTGGAGCATCGGAGCCCACTGTT
genomic: TGGGAATGTTTGGTGTTGATCGCTTTGATGCTATTCTGCCACCTGGAACTgtgagtgttt ... atttctgtagGGAGCAATAATGGCTGTTGGAGCATCGGAGCCCACTGTT
EST: gi|193417002|gb|FK382036.1|FK382036
EST:     TGGGAATGTTTGGTGTTGATCGCTTTGATGCTATTCTGCCACCTGGAACT                         GGAGCAATAATGGCTGTTGGAGCATCGGAGCCCACTGTTGTGGCTACAAAG
genomic: TGGGAATGTTTGGTGTTGATCGCTTTGATGCTATTCTGCCACCTGGAACTgtgagtgttt ... atttctgtagGGAGCAATAATGGCTGTTGGAGCATCGGAGCCCACTGTTGTGGCTACAAAG
EST: gi|193609247|gb|FK561159.1|FK561159
EST:     AATGTTTGGTGTTGATCGCTTTGATGCTATTCTGCCACCTGGAACT                         GGAGCAATAATGGCTGTTGGAGCATCGGAGCCCACTGTTGTGGCTACAAAG
genomic: AATGTTTGGTGTTGATCGCTTTGATGCTATTCTGCCACCTGGAACTgtgagtgttt ... atttctgtagGGAGCAATAATGGCTGTTGGAGCATCGGAGCCCACTGTTGTGGCTACAAAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttagaacagtgatgggaaacacgaatatgatccttctctggatatatttctgtagGGAGCAATAATGGCTGTTGGAGCATCGGAGCCCACTGTTGTGGCTACAAAGGATGGTCGCATTGGAATGAAGAACCAAATGCAG
                                            tatttct  CT-rich tract
                                         atatatttct  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagtgttttactcgtgctcaaatatggcaagagattgactagttgttccaattagaagtttagaacagtgatgggaaacacgaatatgatccttctctggatatatttctgtagGGAGCAATAATGGCTGTTGGAGCATCGGAGCCCACTGTTGTGGCTACAAAGGATGGTCGCATTGGAATGAAGAACCAAATGCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAC