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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tacattgttattgataacaaaaattataaatatttagaaatatgaatttgtaattcttaaagatttcttctgtgttgagtcattcttcaccttgttacagGGATGAGGAAGGACTCTATTATGCACTGGATCTTGGAGGCACAAACTTCCGTGTCCTTCGTGTACATTTAGGCGGGAAAGACAAAGGTGTTATCGGCCAG

Basic information

species Glycine max
transcript GLYMA05G35890.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA05G35890.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G058745_T02 (Zea mays), 3'ss of exon 1
tacattgttattgataacaaaaatta-taaatatttagaaatatgaatttgtaattcttaaagatttcttc-tgtgttgagtcattcttcaccttgttacagGGATGAGGAAGGACTCTATTATGCACTGGATCTTGGAGGCACAAACTTCCGTGTCCTTCGTGTACATTTAGGCGGGAAAGACAAAGGTGTTATCGGCCAG
  ||    | ||| |||   ||   | |    |    | ||| | || |  |||  |||        |||| | | |  |   ||   |     |  | ||| |||||  | || || | ||||||||||||||||||||| || ||||||||||| || || || ||  |||| || || || ||| ||||| ||   || 
accaccagt-ttgttaaggcaatccactcttcagcgtggaatgttaactc-taacacttgtgctgcacttcatttatccacatatgggttttgcttctgcagAGATGAACATGGGCTGTTTTATGCACTGGATCTTGGAGGGACCAACTTCCGTGTGCTGCGAGTCCAGCTAGGAGGAAAGGAGAAACGTGTTGTCAAACAA

upper sequence: GLYMA05G35890.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G432801_T01 (Zea mays), 3'ss of exon 1
tacattgttattgataacaaaaattataaat-atttagaaatatgaatttgtaattcttaaagatttcttc-tgtgttgagtcattcttcaccttgttacagGGATGAGGAAGGACTCTATTATGCACTGGATCTTGGAGGCACAAACTTCCGTGTCCTTCGTGTACATTTAGGCGGGAAAGACAAAGGTGTTATCGGCCAG
  ||    | ||| |||   ||   |    | | |  | ||||| || |  ||   |||        |||| |   |  |   ||   |     |  | ||| |||||  | || || | ||||||||||||||||||||| || ||||||||||| || || || ||  |||| || |  || ||| ||||| ||   || 
accaccagt-ttgttaatgcaatccactcctgagtgcggaatattaactc-tagcacttgtgctacacttcattcatcaacatatgggttttgcttctccagAGATGAACATGGGCTGTTTTATGCACTGGATCTTGGAGGGACCAACTTCCGTGTGCTGCGAGTCCAACTAGGAGGAAGGGAGAAACGTGTTGTCAAACAA

upper sequence: GLYMA05G35890.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv11s0016g03070.t01 (Vitis vinifera), 3'ss of exon 1
tacattgttattgataacaaaaattataaatatttagaaatatgaatttgtaat-tcttaaagatttcttctgtgttgagtcattcttcaccttgttacagGGATGAGGAAGGACTCTATTATGCACTGGATCTTGGAGGCACAAACTTCCGTGTCCTTCGTGTACATTTAGGCGGGAAAGACAAAGGTGTTATCGGCCAG
 || | |  || || ||    | || |  | || |   |   ||| |  |  || | | |        | |    |    ||  ||||    || ||  ||||||||| | ||  | | ||||||| |||| ||||| |||||||||||||||||| | ||||| || || || |||||||||||  ||||| |    || 
-acctggaaatggacaatttcagttgtccagatctgttacactgattaagagatatttcagctgaacatgccacttattctccctctttttttttttttagGGATGAGAAGGGTTTGTTTTATGCATTGGACCTTGGTGGCACAAACTTCCGTGTCTTGCGTGTGCAATTGGGTGGGAAAGACAAGCGTGTTGTTAAACAA

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|209714822|gb|BW674308.1|BW674308
EST:     GGTAGCAAGCTCAATATGTTGATCAGTTTTGTCGATAATCTCCCAACTGG                         GGATGAGGAAGGACTCTATTATGCACTGGATCTTGGAGGCACAAACTTCCG
genomic: GGTAGCAAGCTCAATATGTTGATCAGTTTTGTCGATAATCTCCCAACTGGgttcgtagat ... cttgttacagGGATGAGGAAGGACTCTATTATGCACTGGATCTTGGAGGCACAAACTTCCG
EST: gi|9986079|gb|BE660187.1|BE660187
EST:     GGTAGCAAGCTCAATATGTTGATCAGTTTTGTCGATAATCTCCCAACTGG                         GGATGAGGAAGGACTCTATTATGCACTGGATCTTGGAGGCACAAACTTCCG
genomic: GGTAGCAAGCTCAATATGTTGATCAGTTTTGTCGATAATCTCCCAACTGGgttcgtagat ... cttgttacagGGATGAGGAAGGACTCTATTATGCACTGGATCTTGGAGGCACAAACTTCCG
EST: gi|8284162|gb|BE021721.1|BE021721
EST:     GGTAGCAAGCTCAATATGTTGATCAGTTTTGTCGATAATCTCCCAACTGG                         GGATGAGGGAGGACTCTATTATGCACTGGATCTTGGAGGCACAAACTTTCG
genomic: GGTAGCAAGCTCAATATGTTGATCAGTTTTGTCGATAATCTCCCAACTGGgttcgtagat ... cttgttacagGGATGAGGAAGGACTCTATTATGCACTGGATCTTGGAGGCACAAACTTCCG
EST: gi|209717005|gb|BW679639.1|BW679639
EST:     GGTAGCAAGCTCAATATGTTGATCAGTTTTGTCGATAATCTCCCAACTGG                         GGATGAGGAAGGACTCTATTATGCACTGGATCTTGGAGGCACAAACTTCCG
genomic: GGTAGCAAGCTCAATATGTTGATCAGTTTTGTCGATAATCTCCCAACTGGgttcgtagat ... cttgttacagGGATGAGGAAGGACTCTATTATGCACTGGATCTTGGAGGCACAAACTTCCG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atttgtaattcttaaagatttcttctgtgttgagtcattcttcaccttgttacagGGATGAGGAAGGACTCTATTATGCACTGGATCTTGGAGGCACAAACTTCCGTGTCCTTCGTGTACATTTAGGCGGGAAAGACAAAGGTGTTATCGGCCAG
                                  tcattcttcacctt  CT-rich tract
     taattcttaaagattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tacattgttattgataacaaaaattataaatatttagaaatatgaatttgtaattcttaaagatttcttctgtgttgagtcattcttcaccttgttacagGGATGAGGAAGGACTCTATTATGCACTGGATCTTGGAGGCACAAACTTCCGTGTCCTTCGTGTACATTTAGGCGGGAAAGACAAAGGTGTTATCGGCCAG

- - - - - - - -aacaaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gtcattc