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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtctgttctcgatatcttttgagttttgcattcacctttcagtgcttgtctgagcaatttactttctaataacagAGCCTAACCTGGAGAGTCCTCTAAACAGCTATGCTGCAGCACTTTGGAATGACAAGGAAG

Basic information

species Glycine max
transcript GLYMA20G31920.2
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA20G31920.2 (Glycine max), 3'ss of exon 4
lower sequence: Vv13s0019g04090.t01 (Vitis vinifera), 3'ss of exon 4
------------------gtctgttctcgatatcttttgagttttgcattcacctttcagtgcttgt-ctgagcaatttactttctaataacagAGCCTAACCTGGAGAGTCCTCTAAACAGCTATGCTGCAGCACTTTGGAATGACAAGGAAG
                     |||| | | | | | |    |||| | |   | ||    |   ||| |   ||  |||  ||   |   |||||||| ||| | ||||||||||| ||||||||||||||| || | |||||  || | ||||
gtatgccaactttcccatacatgttttagctttttgtcctttttttcttgttcgttgttatcactgtgccttgctgtttgtttctgacatacagAGCCCAACATAGAGAGTCCTCTCAACAGCTATGCTGCATCATTATGGAACAACCAAGAAG
















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|208137624|gb|GD936328.1|GD936328
EST:     TTATGATTGCTAGAACTATTTCTTCTGTCTATTCAAAGTTTACTGGAAG                         AGCCTAACCTGGAGAGTCCTCTAAACAGCTATGCTGCAGCACTTTGGAATG
genomic: TTATGATTGC-AGAACTA-TTCTTCTGTCTATTCAAAGTTTACTGGAAGgtctgttctc ... ctaataacagAGCCTAACCTGGAGAGTCCTCTAAACAGCTATGCTGCAGCACTTTGGAATG
EST: gi|254328855|gb|GR833227.1|GR833227
EST:     AGCTTATGATTGCAGAACTATTCTTCTGTCTATTCAAAGTTTACTGGAAG                         AGCCTAACCTGGAGAGTCCTCTAAACAGCTATGCTGCAGCACTTTGGAATG
genomic: AGCTTATGATTGCAGAACTATTCTTCTGTCTATTCAAAGTTTACTGGAAGgtctgttctc ... ctaataacagAGCCTAACCTGGAGAGTCCTCTAAACAGCTATGCTGCAGCACTTTGGAATG
EST: gi|23731740|gb|BU764010.1|BU764010
EST:     AGCTTATGATTGCAGAACTATTCTTCTGTCTATTCAAAGTTTACTGGAAG                         AGCCTAACCTGGAGAGTCCTCTAAACAGCTATGCTGCAGCACTTTGGAATG
genomic: AGCTTATGATTGCAGAACTATTCTTCTGTCTATTCAAAGTTTACTGGAAGgtctgttctc ... ctaataacagAGCCTAACCTGGAGAGTCCTCTAAACAGCTATGCTGCAGCACTTTGGAATG
EST: gi|31307478|gb|CD392681.1|CD392681
EST:     AGCTTATGATTGCAGAACTATTCTTCTGTCTATTCAAAGTTTACTGGAAG                         AGCCTAACCTGGAGAGTCCTCTAAACAGCTATGCTGCAGCACTTTGGAATG
genomic: AGCTTATGATTGCAGAACTATTCTTCTGTCTATTCAAAGTTTACTGGAAGgtctgttctc ... ctaataacagAGCCTAACCTGGAGAGTCCTCTAAACAGCTATGCTGCAGCACTTTGGAATG
EST: gi|8285774|gb|BE023333.1|BE023333
EST:     AGCTTATGATTGCAGAACTATTCTTCTGTCTATTCAAAGTTTACTGGAAG                         AGCCTAACCTGGAGAGTCCTCTAAACAGCTATGCTGCAGCACTTTGGAATG
genomic: AGCTTATGATTGCAGAACTATTCTTCTGTCTATTCAAAGTTTACTGGAAGgtctgttctc ... ctaataacagAGCCTAACCTGGAGAGTCCTCTAAACAGCTATGCTGCAGCACTTTGGAATG
EST: gi|254328856|gb|GR833228.1|GR833228
EST:     AGCTTATGATTGCAGAACTATTCTTCTGTCTATTCAAAGTTTACTGGAAG                         AGCCTAACCTGGAGAGTCCTCTAAACAGCTATGCTGCAGCACTTTGGAATG
genomic: AGCTTATGATTGCAGAACTATTCTTCTGTCTATTCAAAGTTTACTGGAAGgtctgttctc ... ctaataacagAGCCTAACCTGGAGAGTCCTCTAAACAGCTATGCTGCAGCACTTTGGAATG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gagttttgcattcacctttcagtgcttgtctgagcaatttactttctaataacagAGCCTAACCTGGAGAGTCCTCTAAACAGCTATGCTGCAGCACTTTGGAATGACAAGGAAG
                                           ttctaat  putative branch site (score: 2)
                                     tttactttct  CT-rich tract
                                   aatttactttctaata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtctgttctcgatatcttttgagttttgcattcacctttcagtgcttgtctgagcaatttactttctaataacagAGCCTAACCTGGAGAGTCCTCTAAACAGCTATGCTGCAGCACTTTGGAATGACAAGGAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA