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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttacttttcttctcatctctcataatcaactttctttttaatggaatgtgacctatgtcatgatattgattcaatcgctttagGAAGCTTTCTGAGGATGTTTCTGGGTCCTATCAATGTTCGTGCCTCCAGGAAGGACGTTCAGCTCAAGGTCAAAGAGGAATACAACAGTTACAGG

Basic information

species Glycine max
transcript GLYMA20G38960.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA20G38960.2 (Glycine max), 3'ss of exon 2
lower sequence: Vv02s0025g03210.t01 (Vitis vinifera), 3'ss of exon 2
-------------------------gttacttttctt--ctcatctctcataatcaactttctttttaatggaatgtgacctatgtcatgatat---tgattcaatcgctt------tagGAAGCTTTCTGAGGATGTTTCTGGGTCCTATCAATGTTCGTGCCTCCAGGAAGGACGTTCAGCTCAAGGTCAAAGAGGAATACAACAGTTACAGG
                          ||| || ||||   |    | |   ||    ||    || |  | |  |  |   ||| |  || |||   || ||  ||    |       |||  | |||||||| ||||||||||||||||| ||||| | |||| | ||||||||||||||| | || || |||||||| |||||||||||||| 
gtgatttgtttgatctgatagatctattaattctcttgattttcttatgggaagtgtctcgtattctgtttgtttccgttgtatttattgttatcattgtttgtatgatgtgatgcacagGTGGGTTTCTGAGAATGTTTCTGGGTCCTATAAATGTGCATGCCACTAGGAAGGACGTTCAGTTGAAAGTTAAAGAGGAGTACAACAGTTACAGA
















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|14259702|gb|BG882610.1|BG882610
EST:     CATCATCGTTGACGGTGACTCCTCTTCGCTTCTCCCTGGCCATGCACAAG                         GAAGCTTTCTGAGGATGTTTCTGGGTCCTATCAATGTTCGTGCCTCCAGGA
genomic: CATCATCGTTGACGGTGACTCCTCTTCGCTTCTCCCTGGCCATGCACAAGgttacttttc ... atcgctttagGAAGCTTTCTGAGGATGTTTCTGGGTCCTATCAATGTTCGTGCCTCCAGGA
EST: gi|298182431|gb|HO026606.1|HO026606
EST:     CATCATCGTTGACGGTGACTCCTCTTCGCTTCTCCCTGGCCATGCACAAG                         GAAGCTTTCTGAGGATGTTTCTGGGTCCTATCAATGTTCGTGCCTCCAGGA
genomic: CATCATCGTTGACGGTGACTCCTCTTCGCTTCTCCCTGGCCATGCACAAGgttacttttc ... atcgctttagGAAGCTTTCTGAGGATGTTTCTGGGTCCTATCAATGTTCGTGCCTCCAGGA
EST: gi|207843228|gb|GD816830.1|GD816830
EST:     CATCATCGTTGACGGTGACTCCTCTTCGCTTCTCCCTGGCCATGCACAAG                         GAAGCTTTCTGAGGAT
genomic: CATCATCGTTGACGGTGACTCCTCTTCGCTTCTCCCTGGCCATGCACAAGgttacttttc ... atcgctttagGAAGCTTTCTGAGGAT
EST: gi|14258798|gb|BG881706.1|BG881706
EST:     CATCATCGTTGACGGTGACTCCTCTTCGCTTCTCCCTGGCCATGCACAAG                         GAAGCTNTCTGAGGATGTTTCTGGGTCCTATCAATGTTCGTGCCTCCAGGA
genomic: CATCATCGTTGACGGTGACTCCTCTTCGCTTCTCCCTGGCCATGCACAAGgttacttttc ... atcgctttagGAAGCTTTCTGAGGATGTTTCTGGGTCCTATCAATGTTCGTGCCTCCAGGA
EST: gi|213590375|gb|DB963896.1|DB963896
EST:     CATCATCGTTGACGGTGACTCCTCTTCGCTTCTCCCTGGCCATGCACAAG                         GAAGCTTTCTGAGGATGTTTCTGGGTCCTATCAATGTTCGTGCCTCCAGGA
genomic: CATCATCGTTGACGGTGACTCCTCTTCGCTTCTCCCTGGCCATGCACAAGgttacttttc ... atcgctttagGAAGCTTTCTGAGGATGTTTCTGGGTCCTATCAATGTTCGTGCCTCCAGGA
EST: gi|298199045|gb|HO042408.1|HO042408
EST:     CATCATCGTTGACGGTGACTCCTCTTCGCTTCTCCTTGGCCATGCACAAG                         GAAGCTTTCTGAGGATGTTTCTGGGTCCTATCAATGTTCGTGCCTCCAGGA
genomic: CATCATCGTTGACGGTGACTCCTCTTCGCTTCTCCCTGGCCATGCACAAGgttacttttc ... atcgctttagGAAGCTTTCTGAGGATGTTTCTGGGTCCTATCAATGTTCGTGCCTCCAGGA
EST: gi|192319099|gb|FK010635.1|FK010635
EST:     CATCATCGTTGACGGTGACTCCACTTCGCTTCTCCCTGGCCATGCACAAG                         GAAGCTTTCTGAGGATGTTTCTGGGTCCTATCAATGTTCGTGCCTCCAGGA
genomic: CATCATCGTTGACGGTGACTCCTCTTCGCTTCTCCCTGGCCATGCACAAGgttacttttc ... atcgctttagGAAGCTTTCTGAGGATGTTTCTGGGTCCTATCAATGTTCGTGCCTCCAGGA
EST: gi|192320395|gb|FK012253.1|FK012253
EST:     CATCATCGTTGACGGTGACTCCTCTTCGCTTCTCCCTGGCCATGCACAAG                         GAAGCTTTCTGAGGATGTTTCTGGGTCCTATCAATGTTCGTGCCTCCAGGA
genomic: CATCATCGTTGACGGTGACTCCTCTTCGCTTCTCCCTGGCCATGCACAAGgttacttttc ... atcgctttagGAAGCTTTCTGAGGATGTTTCTGGGTCCTATCAATGTTCGTGCCTCCAGGA
EST: gi|209701984|gb|BW664584.1|BW664584
EST:     CATCATCGTTGACGGTGACTCCTCTTCGCTTCTCCCTGGCCATGCACAAG                         GAAGCTTTCTGAGGATGTTTCTGGGTCCTATCAATGTTCGTGCCTCCAGGA
genomic: CATCATCGTTGACGGTGACTCCTCTTCGCTTCTCCCTGGCCATGCACAAGgttacttttc ... atcgctttagGAAGCTTTCTGAGGATGTTTCTGGGTCCTATCAATGTTCGTGCCTCCAGGA
EST: gi|213594582|gb|DB958001.1|DB958001
EST:     CATCATCGTTGACGGTGACTCCTCTTCGCTTCTCCCTGGCCATGCACAAG                         GAAGCTTTCTGAGGATGTTTCTGGGTCCTATCAATGTTCGTGCCTCCAGGA
genomic: CATCATCGTTGACGGTGACTCCTCTTCGCTTCTCCCTGGCCATGCACAAGgttacttttc ... atcgctttagGAAGCTTTCTGAGGATGTTTCTGGGTCCTATCAATGTTCGTGCCTCCAGGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

actttctttttaatggaatgtgacctatgtcatgatattgattcaatcgctttagGAAGCTTTCTGAGGATGTTTCTGGGTCCTATCAATGTTCGTGCCTCCAGGAAGGACGTTCAGCTCAAGGTCAAAGAGGAATACAACAGTTACAGG
                                   tattgat  putative branch site (score: 3)
                                              tcgcttt  putative PPT
      tttttaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttacttttcttctcatctctcataatcaactttctttttaatggaatgtgacctatgtcatgatattgattcaatcgctttagGAAGCTTTCTGAGGATGTTTCTGGGTCCTATCAATGTTCGTGCCTCCAGGAAGGACGTTCAGCTCAAGGTCAAAGAGGAATACAACAGTTACAGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGGA