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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtaccaagccgtgttggtctatctctttacccaaatttgtttgtatgatttatcaatcttcgttacctttgttttccagCTATGGATTGGTGAAGAGCTATGATATGCCCTGCACTATCGAATCAGTTTCTCTGGAACCTAAGTATGGGAACAAGTTTGTTGCCGGGGGAGAAGATATG

Basic information

species Glycine max
transcript GLYMA17G12770.3
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA17G12770.3 (Glycine max), 3'ss of exon 5
lower sequence: LOC_Os02g11060.1 (Oryza sativa), 3'ss of exon 5
gtaagtaccaagccgtgttggtctatctctttacc--caaatttgtttgtatgatttatcaatcttcgttacctttgttttccagCTATGGATTGGTGAAGAGCTATGATATGCCCTGCACTATCGAATCAGTTTCTCTGGAACCTAAGTATGGGAACAAGTTTGTTGCCGGGGGAGAAGATATG
|||||       |  |      |  | |   ||     || |  | ||   | |||||| ||  |   |     || || | |||||  ||| | || ||||||||| ||||||| |||| | | ||||||| |||||| ||||| |||||||||||||| ||  |||| || |||||||| |||
gtaagatattttctattcaaagcgttgttggtagtattaattgggattagctcatttattaaaatatttcctggttattcttcagCTTCGGACTTGTTAAGAGCTATAATATGCCATGCAATGTGGAATCAGCTTCTCTTGAACCAAAGTATGGGAACAAATTCATTGCTGGTGGAGAAGACATG

upper sequence: GLYMA17G12770.3 (Glycine max), 3'ss of exon 5
lower sequence: LOC_Os06g39760.1 (Oryza sativa), 3'ss of exon 5
---------gtaagtaccaa-gccgtgttggtctatctctttacccaaatttgtttg-tatgatttatcaatcttcgttacct--ttgttttccagCTATGGATTGGTGAAGAGCTATGATATGCCCTGCACTATCGAATCAGTTTCTCTGGAACCTAAGTATGGGAACAAGTTTGTTGCCGGGGGAGAAGATATG
          |   || ||      |   | | |      | |  |||| || ||   |    |  | ||| | |  ||  ||  || |||| ||||| |||  | || || |||||||||||||| |||||| | || |||| ||| |||||||| || | ||||| ||| ||| |||  |||||||||||||||
gtacgtattatttctatcatcattataccgttgttctgtgtcatacaaaattattaaatcctttgcaacaaacattttttgctggttattttgcagCTTTGGGCTTGTTAAAAGCTATGATATGCCTTGCACTGTGGAGTCAGCTTCCCTGGAACCAAAATCTGGGAGCAAATTTATTGTTGGGGGAGAAGATATG
















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|208336897|gb|GE135581.1|GE135581
EST:     TATATAACAACTGCTGATGGTTCTACTGTAAAGTTTTGGGATGCAAATTA                         CTATGGATTGGTGAAGAGCTATGATATGCCCTGCACTNTCGAATCAGTTT
genomic: TATATAACAACTGCTGATGGTTCTACTGTAAAGTTTTGGGATGCAAATTAgtaagtacca ... tgttttccagCTATGGATTGGTGAAGAGCTATGATATGCCCTGCACTATCGAATCAGTTT
EST: gi|193382095|gb|FK345754.1|FK345754
EST:     TATATAACAACTGCTGATGGTTCTACTGTAAAGTTTTGGGATGCAAATTA                         CTATGGATTGGTGAAGAGCTATGATATGCCCTGCACTATCGAATCAGTTTC
genomic: TATATAACAACTGCTGATGGTTCTACTGTAAAGTTTTGGGATGCAAATTAgtaagtacca ... tgttttccagCTATGGATTGGTGAAGAGCTATGATATGCCCTGCACTATCGAATCAGTTTC
EST: gi|193363152|gb|FK328300.1|FK328300
EST:     ATATAACAACTGCTGATGGTTCTACTGTAAAGTTTTGGGATTGCAAATTA                         CTATGGATTGGTGAAGAGCTATGATATGCCCTGCACTATCGAATCAGTTT
genomic: ATATAACAACTGCTGATGGTTCTACTGTAAAGTTTTGGGAT-GCAAATTAgtaagtacca ... tgttttccagCTATGGATTGGTGAAGAGCTATGATATGCCCTGCACTATCGAATCAGTTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctttacccaaatttgtttgtatgatttatcaatcttcgttacctttgttttccagCTATGGATTGGTGAAGAGCTATGATATGCCCTGCACTATCGAATCAGTTTCTCTGGAACCTAAGTATGGGAACAAGTTTGTTGCCGGGGGAGAAGATATG
                                tcttcgttacctttgt  CT-rich tract
        aaatttgtttgtatga  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagtaccaagccgtgttggtctatctctttacccaaatttgtttgtatgatttatcaatcttcgttacctttgttttccagCTATGGATTGGTGAAGAGCTATGATATGCCCTGCACTATCGAATCAGTTTCTCTGGAACCTAAGTATGGGAACAAGTTTGTTGCCGGGGGAGAAGATATG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAA