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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...attgagattgaactcttgaataagagggttttgacttttggtgcatctcacaatgcgtgcattttggttaaaaagctttgcgtgatgactggctttgcagAAATTTGGATGAATTGCCTAACAGCAAGCGTAAACGTCTGAGACCTGGGAAAGTTTCTCCGCGGCGACAGGTGCCGAAGAATATACCGAGGCCTCCGTAT

Basic information

species Glycine max
transcript GLYMA01G39200.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA01G39200.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv07s0031g00820.t01 (Vitis vinifera), 3'ss of exon 2
----attgagat-tgaactcttgaataagagggttttgacttttggtgcatctcacaatgcgtgcattttggttaaaaagctttgcgtgatgactggctttgcagAAATTTGGATGAATTGCCTAACAGCAAGCGTAAACGTCTGAGACCTGGGAAAGTTTCTCCGCGGCGACAGGTGCCGAAGAATATACCGAGGCCTCCGTAT
||| | | | | | | ||| || || || | | | | | | | | || ||||| | | | | |||||||| |||| | |||||| |||||||||||||||||||| ||||| || ||| ||||||| | |||| ||| || | |||| ||||||| | |||
atgtatttatgtgtctatgcatatatatagacacttatacacatgatata----aagacttgagtgcatatatataacagcttagtattttt-tgaaaatagcagAAATCTGGAGGGATTGCCAAACAGCAAGCGTAAACGTCTAAGACCCGGAAAACTTTCTCCTTGTCGACCGGTTCCAGGTCACATACTGAGGCCTTCTTAT
















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|213615033|gb|DB960758.1|DB960758
EST:     CAGTTATCTAGAACACTTTCTGGCTTGACCAATCTCTTTTTTAATAGAAG                         AAATTTGGATGAATTGCCTAACAGCAAGCGTAAACGTCTGAGACCTGGGAA
genomic: CAGTTATCTAGAACACTTTCTGGCTTGACCAATCTCTTTTTTAATAGAAGgtatctgcgc ... ggctttgcagAAATTTGGATGAATTGCCTAACAGCAAGCGTAAACGTCTGAGACCTGGGAA
EST: gi|209704050|gb|BW673650.1|BW673650
EST:     CAGTTATCTAGAACACTTTCTGGCTTGACCAATCTCTTTTTTAATAGAAG                         AAATTTGGATGAATTGCCTAACAGCAAGCGTAAACGTCTGAGACCTGGGAA
genomic: CAGTTATCTAGAACACTTTCTGGCTTGACCAATCTCTTTTTTAATAGAAGgtatctgcgc ... ggctttgcagAAATTTGGATGAATTGCCTAACAGCAAGCGTAAACGTCTGAGACCTGGGAA
EST: gi|209710614|gb|BW676540.1|BW676540
EST:     CAGTTATCTAGAACACTTTCTGGCTTGACCAATCTCTTTTTTAATAGAAG                         AAATTTGGATGAATTGCCTAACAGCAAGCGTAAACGTCTGAGACCTGGGAA
genomic: CAGTTATCTAGAACACTTTCTGGCTTGACCAATCTCTTTTTTAATAGAAGgtatctgcgc ... ggctttgcagAAATTTGGATGAATTGCCTAACAGCAAGCGTAAACGTCTGAGACCTGGGAA
EST: gi|5509561|gb|AI856119.1|AI856119
EST:     CAGTTATCTAGAACACTTTCTGGCTTGACCAATCTCTTTTTTAATAGAAG                         AAATTTGGATGAATTGCCTAACAGCAAGCGTAAACGTCTGAGACCTGGGAA
genomic: CAGTTATCTAGAACACTTTCTGGCTTGACCAATCTCTTTTTTAATAGAAGgtatctgcgc ... ggctttgcagAAATTTGGATGAATTGCCTAACAGCAAGCGTAAACGTCTGAGACCTGGGAA
EST: gi|12691283|gb|BG157619.1|BG157619
EST:     CAGTTATCTAGAACACTTTCTGGCTTGACCAATCTCTTTTTTAATAGAAG                         AAATTTGGATGAATTGCCTAACAGCAAGCGTAAACGTCTGAGACCTGGGAA
genomic: CAGTTATCTAGAACACTTTCTGGCTTGACCAATCTCTTTTTTAATAGAAGgtatctgcgc ... ggctttgcagAAATTTGGATGAATTGCCTAACAGCAAGCGTAAACGTCTGAGACCTGGGAA
EST: gi|13125644|gb|BG316214.1|BG316214
EST:     CAGTTATCTAGAACACTTTCTGGCTTGACCAATCTCTTTTTTAATAGAAG                         AAATTTGGATGAATTGCCTAACAGCAAGCGTAAACGTCTGAGACCTGGGAA
genomic: CAGTTATCTAGAACACTTTCTGGCTTGACCAATCTCTTTTTTAATAGAAGgtatctgcgc ... ggctttgcagAAATTTGGATGAATTGCCTAACAGCAAGCGTAAACGTCTGAGACCTGGGAA
EST: gi|151401050|gb|EV270864.1|EV270864
EST:     CAGTTATCTAGAACACTTTCTGGCTTGACCAATCTCTTTTTTAATAGAAG                         AAATTTGGATGAATTGCCTAACAGCAAGCGTAAACGTCTGAGACCTGGGAA
genomic: CAGTTATCTAGAACACTTTCTGGCTTGACCAATCTCTTTTTTAATAGAAGgtatctgcgc ... ggctttgcagAAATTTGGATGAATTGCCTAACAGCAAGCGTAAACGTCTGAGACCTGGGAA
EST: gi|192305235|gb|FG993973.1|FG993973
EST:     CAGTTATCTAGAACACTTTCTGGCTTGACCAATCTCTTTTTTAATAGAAG                         AAATTTGGATGAATTGCCTAACAGCAAGCGTAAACGTCTGAGACCTGGGAA
genomic: CAGTTATCTAGAACACTTTCTGGCTTGACCAATCTCTTTTTTAATAGAAGgtatctgcgc ... ggctttgcagAAATTTGGATGAATTGCCTAACAGCAAGCGTAAACGTCTGAGACCTGGGAA
EST: gi|17023236|gb|BM094270.1|BM094270
EST:     CAGTTATCTAGAACACTTTCTGGCTTGACCAATCTCTTTTTTAATAGAAG                         AAATTTGGATGAATTGCCTAACAGCAAGCGTAAACGTCTGAGACCTGGGAA
genomic: CAGTTATCTAGAACACTTTCTGGCTTGACCAATCTCTTTTTTAATAGAAGgtatctgcgc ... ggctttgcagAAATTTGGATGAATTGCCTAACAGCAAGCGTAAACGTCTGAGACCTGGGAA
EST: gi|213589240|gb|DB957772.1|DB957772
EST:     CAGTTATCTAGAACACTTTCTGGCTTGACCAATCTCTTTTTTAATAGAAG                         AAATTTGGATGAATTGCCTAACAGCAAGCGTAAACGTCTGAGACCTGGGAA
genomic: CAGTTATCTAGAACACTTTCTGGCTTGACCAATCTCTTTTTTAATAGAAGgtatctgcgc ... ggctttgcagAAATTTGGATGAATTGCCTAACAGCAAGCGTAAACGTCTGAGACCTGGGAA
EST: gi|298197093|gb|HO041836.1|HO041836
EST:     CAGTTATCTAGAACACTTTCTGGCTTGACCAATCTCTTTTTTAATAGAAG                         AAATTTGGATGAATTGCCTAACAGCAAGCGTAAACGTCTGAGACCTGGGAA
genomic: CAGTTATCTAGAACACTTTCTGGCTTGACCAATCTCTTTTTTAATAGAAGgtatctgcgc ... ggctttgcagAAATTTGGATGAATTGCCTAACAGCAAGCGTAAACGTCTGAGACCTGGGAA
EST: gi|151410050|gb|EV279858.1|EV279858
EST:     CAGTTATCTAGAACACTTTCTGGCTTGACCAATCTCTTTTTTAATAGAAG                         AAATTTGGATGAATTGCCTAACAGCAAGCGTAAACGTCTGAGACCTGGGAA
genomic: CAGTTATCTAGAACACTTTCTGGCTTGACCAATCTCTTTTTTAATAGAAGgtatctgcgc ... ggctttgcagAAATTTGGATGAATTGCCTAACAGCAAGCGTAAACGTCTGAGACCTGGGAA
EST: gi|192300116|gb|FG991892.1|FG991892
EST:     CAGTTATCTAGAACACTTTCT-GCTTGACCAATCTCTTTTTTAATAGAAG                         AAATTTGGATGAATTGCCTAACAGCAAGCGTAAACGTCTGAGACCTGGGAA
genomic: CAGTTATCTAGAACACTTTCTGGCTTGACCAATCTCTTTTTTAATAGAAGgtatctgcgc ... ggctttgcagAAATTTGGATGAATTGCCTAACAGCAAGCGTAAACGTCTGAGACCTGGGAA
EST: gi|298189864|gb|HO038267.1|HO038267
EST:     CAGTTATCTAGAACACTTTCTGGCTTGACCAATCTCTTTTTTAATAGAAG                         AAATTTGGATGAATTGCCTAACAGCAAGCGTAAACGTCTGAGACCTGGGAA
genomic: CAGTTATCTAGAACACTTTCTGGCTTGACCAATCTCTTTTTTAATAGAAGgtatctgcgc ... ggctttgcagAAATTTGGATGAATTGCCTAACAGCAAGCGTAAACGTCTGAGACCTGGGAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tctcacaatgcgtgcattttggttaaaaagctttgcgtgatgactggctttgcagAAATTTGGATGAATTGCCTAACAGCAAGCGTAAACGTCTGAGACCTGGGAAAGTTTCTCCGCGGCGACAGGTGCCGAAGAATATACCGAGGCCTCCGTAT
 atctcac  putative branch site (score: 3)
 attttggttaaaaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
attgagattgaactcttgaataagagggttttgacttttggtgcatctcacaatgcgtgcattttggttaaaaagctttgcgtgatgactggctttgcagAAATTTGGATGAATTGCCTAACAGCAAGCGTAAACGTCTGAGACCTGGGAAAGTTTCTCCGCGGCGACAGGTGCCGAAGAATATACCGAGGCCTCCGTAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CGAAGA
- - - - - - - - - - - - - ggttttg
- - - - - - - - - - - - - - - - - - - tggtgca
- - - - - - - - - - - - - - - - - - - - - - - - -acaatgc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgcattt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgatgac