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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgttttaactttacagtcagaaaaaaaaacttgtttccacttcattgctgatactttctcaagtgaactgatgtataccttaatatattcatgcttgcagTCAGGTTTACATGGCTAAAGAGATCAAAACTGGTGAAATTGTTGCTCTGAAGAAAATACGAATGGACAATGAGAGAGAGGGG

Basic information

species Glycine max
transcript GLYMA14G04410.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA14G04410.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv06s0009g01800.t01 (Vitis vinifera), 3'ss of exon 2
--tgttttaactttacag----tcagaaaaaaaaacttgtttccacttcattgctgatactttctcaagtgaactgatgtataccttaatatattcatgcttgcagTCAGGTTTACATGGCTAAAGAGATCAAAACTGGTGAAATTGTTGCTCTGAAGAAAATACGAATGGACAATGAGAGAGAGGGG
  | |||    |  | ||       |       || ||||| ||  |   ||  ||||  | ||   ||  |  |||| | |   || || | |  ||   |||||||| || |||||||||| ||| |||||||| || |||||||||||| ||||||||||||||||||||||||| |||||||||
tttatttgggttcaaaagaactctggtttcttgaatttgttccctttaagtttgtgatgttatccgcaggaacttgat-tgt---ttcatctgtgtata--tgcagTCAAGTGTACATGGCTAGAGAAATCAAAACAGGGGAAATTGTTGCTTTGAAGAAAATACGAATGGACAATGAAAGAGAGGGG
















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|208125981|gb|GD921641.1|GD921641
EST:     AGTGTTGATTGCTTCGAGAAATTGGAGCAAATTGGCGAGGGCACATATGG                         TCAGGTTTACATGGCTAAAGAGATCAAAACTGGTGAAATTGTTGCTCTGAA
genomic: AGTGTTGATTGCTTCGAGAAATTGGAGCAAATTGGCGAGGGCACATATGGgtttgtttca ... atgcttgcagTCAGGTTTACATGGCTAAAGAGATCAAAACTGGTGAAATTGTTGCTCTGAA
EST: gi|213617624|gb|DB969336.1|DB969336
EST:     AGTGTTGATTGCTTCGAGAAATTGGAGCAAATTGGCGAGGGCACATATGG                         TCAGGTTTACATGGCTAAAGAGATCAAAACTGGTGAAATTGTTGCTCTGAA
genomic: AGTGTTGATTGCTTCGAGAAATTGGAGCAAATTGGCGAGGGCACATATGGgtttgtttca ... atgcttgcagTCAGGTTTACATGGCTAAAGAGATCAAAACTGGTGAAATTGTTGCTCTGAA
EST: gi|193350835|gb|FK314157.1|FK314157
EST:     AGTGTTGATTGCTTCGAGAAATTGGAGCAAATTGGCGAGGGCACATATGG                         TCAGGTTTTACATGGCTAAAGAGATCAAAAACTGGTG
genomic: AGTGTTGATTGCTTCGAGAAATTGGAGCAAATTGGCGAGGGCACATATGGgtttgtttca ... atgcttgcagTCAGGTTT-ACATGGCTAAAGAGATCAAAA-CTGGTG
EST: gi|193350783|gb|FK314133.1|FK314133
EST:     AGTGTTGATTGCTTCGAGAAATTGGAGCAAATTGGCGAGGGCACATATGG                         TCAGGTTTACATGGCTAAAGAGATCAAAACTGGTGAAATTGTTGCTCTGAA
genomic: AGTGTTGATTGCTTCGAGAAATTGGAGCAAATTGGCGAGGGCACATATGGgtttgtttca ... atgcttgcagTCAGGTTTACATGGCTAAAGAGATCAAAACTGGTGAAATTGTTGCTCTGAA
EST: gi|11275076|gb|BF325399.1|BF325399
EST:     AGTGTTGATTGCTTCGAGAAATTGGAGCAAATTGGCGAGGGCACATATGG                         TCAGGTTTACATGGCTAAAGAGATCAAAACTGGTGAAATTGTTGCTCTGAA
genomic: AGTGTTGATTGCTTCGAGAAATTGGAGCAAATTGGCGAGGGCACATATGGgtttgtttca ... atgcttgcagTCAGGTTTACATGGCTAAAGAGATCAAAACTGGTGAAATTGTTGCTCTGAA
EST: gi|208052340|gb|GD855235.1|GD855235
EST:     AGTGTTGATTGCTTCGAGAAATTGGAGCAAATTGGCGAGGGCACATATGG                         TCAGGTTTACATGGCTAAAGAGATCAAAACTGGTGAAATTGTTGCTCTGAA
genomic: AGTGTTGATTGCTTCGAGAAATTGGAGCAAATTGGCGAGGGCACATATGGgtttgtttca ... atgcttgcagTCAGGTTTACATGGCTAAAGAGATCAAAACTGGTGAAATTGTTGCTCTGAA
EST: gi|19348210|gb|BM892742.1|BM892742
EST:     AGTGTTGATTGCTTCGAGAAATTGGAGCAAATTGGCGAGGGCACATATGG                         TCAGGTTTACATGGCTAAAGAGATCAAAACTGGTGAAATTGTTGCTCTGAA
genomic: AGTGTTGATTGCTTCGAGAAATTGGAGCAAATTGGCGAGGGCACATATGGgtttgtttca ... atgcttgcagTCAGGTTTACATGGCTAAAGAGATCAAAACTGGTGAAATTGTTGCTCTGAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgctgatactttctcaagtgaactgatgtataccttaatatattcatgcttgcagTCAGGTTTACATGGCTAAAGAGATCAAAACTGGTGAAATTGTTGCTCTGAAGAAAATACGAATGGACAATGAGAGAGAGGGG
                            tataccttaatatatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgttttaactttacagtcagaaaaaaaaacttgtttccacttcattgctgatactttctcaagtgaactgatgtataccttaatatattcatgcttgcagTCAGGTTTACATGGCTAAAGAGATCAAAACTGGTGAAATTGTTGCTCTGAAGAAAATACGAATGGACAATGAGAGAGAGGGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGAGG
- - - - - - - - - - aaaaaaa
- - - - - - - - - - - - - - - - - - ccacttc
- - - - - - - - - - - - - - - - - - - - - - ttgctga
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - actgatg