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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttccaaatcagtaatttttttttgttgaaataatctctaatttgccaattatctttccaaaaattgttatattcttcatgaaactgcaaattgaatgcagGAATATGTACTGCTTTAGCTATCAATCTGGCAAATTGGAGCATCTAATGAAG

Basic information

species Glycine max
transcript GLYMA05G30430.1
intron # 14
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA05G30430.1 (Glycine max), 3'ss of exon 14
lower sequence: LOC_Os01g21940.1 (Oryza sativa), 3'ss of exon 13
ttccaaatcagtaatttttttttgttgaaataatctctaatttgccaattatctttccaaaaattgttatattcttcatgaaactgcaaattgaatgcagGAATATGTACTGCTTTAGCTATCAATCTGGCAAATTGGAGCATCTAATGAAG
          ||||   |  | || | || |  |   |    |    || |||||     |  |||  |    | ||||||  | | |  |    |||||||| ||||| ||||||||||| || || || ||| |||||||||||||||||
----------gtaaggatactgtgataaagttcttcattgcattttcatcatcttagtttattttg--agtgccatcatgactc-gtacttattttgcagGAACATGTATTGCTTTAGCTACCAGTCCGGTAAACTGGAGCATCTAATGAAG

upper sequence: GLYMA05G30430.1 (Glycine max), 3'ss of exon 14
lower sequence: GRMZM2G037683_T01 (Zea mays), 3'ss of exon 13
ttccaaatcagtaatttttttttgttgaaataatctctaatttgccaattatctttccaaaaa-ttgttatattcttcatgaaactgcaaattgaat-gcagGAATATGTACTGCTTTAGCTATCAATCTGGCAAATTGGAGCATCTAATGAAG
 |    ||     |  | | ||| ||| | |    ||||||    | ||| | | |     |  ||| | | |    |||  || |   | |||  | ||||||| ||||| ||||||||||| |||||||| ||| |||||||||| ||||||
gtgaggatatactagatatatttcttgcattg---tctaatgcttcgattttgtgtttgttatcttggtctgtatgacatctaaattggagttgttttgcagGAACATGTATTGCTTTAGCTACCAATCTGGTAAACTGGAGCATCTGATGAAG

upper sequence: GLYMA05G30430.1 (Glycine max), 3'ss of exon 14
lower sequence: Vv17s0000g08930.t01 (Vitis vinifera), 3'ss of exon 14
ttccaaatcagtaatttttttttgttgaaataatctctaatttgccaattatctttccaaaaattgttatattcttcatgaa----actgcaaattgaatgcagGAATATGTACTGCTTTAGCTATCAATCTGGCAAATTGGAGCATCTAATGAAG
    |  | ||||  |  ||    |     |  |||    | |||    | |  | |        ||| || | ||    ||    ||||   ||   ||| |||||||| |||||||| ||||| ||||| || ||||| |||||||||||||||
----actttagtatatgattcccatgtgcctgttcttgtctctgctggatttactgcaggtgtcggttctactattagctaactgaactgttgatcatatgtagGAATATCTACTGCTTCAGCTACCAATCGGGTAAATTAGAGCATCTAATGAAG

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|193366687|gb|FK332423.1|FK332423
EST:     GCCTGTGTTTCACCTAAAGGAGAATGGATTTACTGTGTTGGTGAAGACAG                         GAATATGTACTGCTTTAGCTATCAATCTGGCAAATTGGAGCATCTAATGAA
genomic: GCCTGTGTTTCACCTAAAGGAGAATGGATTTACTGTGTTGGTGAAGACAGgtatcctaat ... ttgaatgcagGAATATGTACTGCTTTAGCTATCAATCTGGCAAATTGGAGCATCTAATGAA
EST: gi|207778029|gb|GD747094.1|GD747094
EST:     GCCTGTGTTTCACCTAAAGGAGAATGGATTTACTGTGTTGGTGAAGACAG                         GAATATGTACTGCTTTAGCTATCAATCTGGCAAATTGGAGCATCTAATGAA
genomic: GCCTGTGTTTCACCTAAAGGAGAATGGATTTACTGTGTTGGTGAAGACAGgtatcctaat ... ttgaatgcagGAATATGTACTGCTTTAGCTATCAATCTGGCAAATTGGAGCATCTAATGAA
EST: gi|213619985|gb|DB976961.1|DB976961
EST:     GCCTGTGTTTCACCTAAAGGAGAATGGATTTACTGTGTTGGTGAAGACAG                         GAATATGTACTGCTTTAGCTATCAATCTGGCAAATTGGAGCATCTAATGAA
genomic: GCCTGTGTTTCACCTAAAGGAGAATGGATTTACTGTGTTGGTGAAGACAGgtatcctaat ... ttgaatgcagGAATATGTACTGCTTTAGCTATCAATCTGGCAAATTGGAGCATCTAATGAA
EST: gi|209727602|gb|BW669926.1|BW669926
EST:     ACTGTGTTGGTGAAGACAG                         GAATATGTACTGCTTTAGCTATCAATCTGGCAAATTGGAGCATCTAATGAA
genomic: ACTGTGTTGGTGAAGACAGgtatcctaat ... ttgaatgcagGAATATGTACTGCTTTAGCTATCAATCTGGCAAATTGGAGCATCTAATGAA
EST: gi|208302631|gb|GE097876.1|GE097876
EST:     CTGTGTTGGTGAAGACAG                         GAATATGTACTGCTTTAGCTATCAATCTGGCAAATTGGAGCATCTAATGAA
genomic: CTGTGTTGGTGAAGACAGgtatcctaat ... ttgaatgcagGAATATGTACTGCTTTAGCTATCAATCTGGCAAATTGGAGCATCTAATGAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

caattatctttccaaaaattgttatattcttcatgaaactgcaaattgaatgcagGAATATGTACTGCTTTAGCTATCAATCTGGCAAATTGGAGCATCTAATGAAG
             aaaaattgttatattc  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttccaaatcagtaatttttttttgttgaaataatctctaatttgccaattatctttccaaaaattgttatattcttcatgaaactgcaaattgaatgcagGAATATGTACTGCTTTAGCTATCAATCTGGCAAATTGGAGCATCTAATGAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCA
- ccaaatc
- - - - - - - - - - - tgttgaa
- - - - - - - - - - - - - - - - - - - - tttgcca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - catgaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ctgcaaa