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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...acaaatggactaaggtttcttaaagttgataatagttttgacttttggttatatgttataagacaatgaatctgataggccctcaatatgctaaatgcagACTTGCTGTAGAGGCATGGGGTTTGAAGAATTGCACCCAAAAGGAAGAGTGGTACAGTGACACTGTGACTGCTGTTCTTGTTCCTGCTTACATTGATAGT

Basic information

species Glycine max
transcript GLYMA18G14740.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA18G14740.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv06s0009g03740.t01 (Vitis vinifera), 3'ss of exon 3
acaaatggactaaggtttcttaaagttgataatagttttgacttttggttatatgttataagacaatgaatctgataggccctcaatatgctaaatgcagACTTGCTGTAGAGGCATGGGGTTTGAAGAATTGCACCCAAAAGGAAGAGTGGTACAGTGACACTGTGACTGCTGTTCTTGTTCCTGCTTACATTGATAGT
          | |   |||||     | | |  |  | ||| | || ||| ||  | |    |  || |||   || |||| ||  | || ||  ||||| |||||||| |||||||||||  |||||||||||||||||| ||| || |||| ||||||||| || ||||||||  |||| ||| | ||||| ||||||
---------gtgaatattcttcctcctaacacaa--tgtgaatgttcgttgtacctga----attataaattctatgggccttctct-tgatac-tgcagGCTTGCTGTGGAGGCATGGGGCCTGAAGAATTGCACCCAAAGGGAGGAATGGTTCAGTGACACCGTCACTGCTGTGGTTGTGCCTCCATACATCGATAGT
















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|192312355|gb|FK005359.1|FK005359
EST:     GGACTTGAAAATGTGATTGCAAGACACAGTCGTTTAGGCAAAGCAACCAG                         ACTTGCTGTAGAGGCATGGGGTTTGAAGAATTGCACCCAAAAGGAAGAGTG
genomic: GGACTTGAAAATGTGATTGCAAGACACAGTCGTTTAGGCAAAGCAACCAGgtaaggcaag ... ctaaatgcagACTTGCTGTAGAGGCATGGGGTTTGAAGAATTGCACCCAAAAGGAAGAGTG
EST: gi|105637492|gb|DY577144.1|DY577144
EST:     GGACTTGAAAATGTGATTGCAAGACACAGTCGTTTAGGCAAAGCAACCAG                         ACTTGCTGTAGAGGCATGGGGTTTGAAGAATTGCACCCAAAAGGAAGAGTG
genomic: GGACTTGAAAATGTGATTGCAAGACACAGTCGTTTAGGCAAAGCAACCAGgtaaggcaag ... ctaaatgcagACTTGCTGTAGAGGCATGGGGTTTGAAGAATTGCACCCAAAAGGAAGAGTG
EST: gi|192312356|gb|FK005360.1|FK005360
EST:     GGACTTGAAAATGTGATTGCAAGACACAGTCGTTTAGGCAAAGCAACCAG                         ACTTGCTGTAGAGGCATGGGGTTTGAAGAATTGCACCCAAAAGGAAGAGTG
genomic: GGACTTGAAAATGTGATTGCAAGACACAGTCGTTTAGGCAAAGCAACCAGgtaaggcaag ... ctaaatgcagACTTGCTGTAGAGGCATGGGGTTTGAAGAATTGCACCCAAAAGGAAGAGTG
EST: gi|5607145|gb|AI901243.1|AI901243
EST:     CGACTCGANAATGTGATTGCAAGACACAGTCGTCTATGCAAAGCAACCAG                         ACTTGCTGTAGAGGCATGG
genomic: GGACTTGAAAATGTGATTGCAAGACACAGTCGTTTAGGCAAAGCAACCAGgtaaggcaag ... ctaaatgcagACTTGCTGTAGAGGCATGG
EST: gi|7795420|gb|AW780745.1|AW780745
EST:     GGACTTGAAAATGTGATTGCAAGACACAGTCGTTTAGGCAAAGCAACCAG                         ACTTGCTGTAGAGGCATGGGGTTTGAAGAATTGCACCCAAAAGGAAGAGTG
genomic: GGACTTGAAAATGTGATTGCAAGACACAGTCGTTTAGGCAAAGCAACCAGgtaaggcaag ... ctaaatgcagACTTGCTGTAGAGGCATGGGGTTTGAAGAATTGCACCCAAAAGGAAGAGTG
EST: gi|120533482|gb|EH261615.1|EH261615
EST:     GGACTTGAAAATGTGATTGCCAGACACAGTCGTTTAGGCAAAGCAACCAG                         ACTTGCTGTAGAGGCCTGGGGTTTGAAGAATT
genomic: GGACTTGAAAATGTGATTGCAAGACACAGTCGTTTAGGCAAAGCAACCAGgtaaggcaag ... ctaaatgcagACTTGCTGTAGAGGCATGGGGTTTGAAGAATT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tggttatatgttataagacaatgaatctgataggccctcaatatgctaaatgcagACTTGCTGTAGAGGCATGGGGTTTGAAGAATTGCACCCAAAAGGAAGAGTGGTACAGTGACACTGTGACTGCTGTTCTTGTTCCTGCTTACATTGATAGT
                                           tgctaaa  putative branch site (score: 2)
     atatgttataa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
acaaatggactaaggtttcttaaagttgataatagttttgacttttggttatatgttataagacaatgaatctgataggccctcaatatgctaaatgcagACTTGCTGTAGAGGCATGGGGTTTGAAGAATTGCACCCAAAAGGAAGAGTGGTACAGTGACACTGTGACTGCTGTTCTTGTTCCTGCTTACATTGATAGT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -caatgaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ctgatag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ccctcaa