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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttgtttgatcattctttactatcttactctgttctttctagttttctgtttttgtgatacgtttatttcagttatattgatttctcctttaactggtcagGCACACCTGGCGATTGGAGTCACATTATCAAACAGATTGGAATGTTTACTTTCACTGGATTGAATGCGGAACAAGTTTCCTTCATGACTAAAGAGTTCCA

Basic information

species Glycine max
transcript GLYMA06G08670.2
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA06G08670.2 (Glycine max), 3'ss of exon 9
lower sequence: LOC_Os01g55540.2 (Oryza sativa), 3'ss of exon 10
ttgtttgatcattctttactatcttactctgttctttctagttttctgtttttgtgatacgtttatttcagttatattgatttctcctttaac-----tggtcagGCACACCTGGCGATTGGAGTCACATTATCAAACAGATTGGAATGTTTACTTTCACTGGATTGAATGCGGAACAAGTTTCCTTCATGACTAAAGAGTTCCA
      |    || | | |  | || ||   | | ||||   |  ||     || | ||| ||      | |  || | |||  |    | |          |||  || ||||| || ||||||||||| || || ||||| |||||||| |||||||||||  | ||    || |||||  | |||||||   | || | |||
-----aggagtttttcttccctttttctgaatccattctctatggctaaaagtgaggtacattgtcagaaatattaatcattgttgacatgataacatcatgcagAAACTCCTGGAGACTGGAGTCACATCATTAAGCAGATCGGAATGTTCACTTTCACTGGGCTCAACAGTGATCAAGTGGCTTTCATGAGGCAGGAATACCA

upper sequence: GLYMA06G08670.2 (Glycine max), 3'ss of exon 9
lower sequence: PP1S132_95V6.1 (Physcomitrella patens), 3'ss of exon 11
ttgtttgatcattctttactatcttac-tctgttctttctagttttctgtttttgtgatacgtttatt--tcagttatattgatttctcctttaactggtcagGCACACCTGGCGATTGGAGTCACATTATCAAACAGATTGGAATGTTTACTTTCACTGGATTGAATGCGGAACAAGTTTCCTTCATGACTAAAGAGTTCCA
     |||  |  |   |  |  |||  | | ||||    |  | | || |       | | || | |  |  | | | ||  |||||    ||      ||||||||||||||||||||| |||| || | || |||||||||||||| |||||||| ||||||||   |   |||||    ||||||||     | |  ||
acacatga--aagcgacaaaactttatgtgtattctgctcaagtatgtggtccaact-tgcattaagtgatttggtctctttttttctttgatattcatgcagGCACACCTGGCGATTGGACTCACGTTCTGAAGCAGATTGGAATGTTCACTTTCACGGGATTGAACAAGTCTCAAGTCGAGTTCATGACCCGTCAATATCA
















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|8285275|gb|BE022834.1|BE022834
EST:     TCGCATCATCAGTATGCGCCAAGAACTTTTCGATGCTTTATGTTCCAGAG                         GCACACCTGGCGATTGGAGTCACATTATCAAACAGATTGGAATGTTTACTT
genomic: TCGCATCATCAGTATGCGCCAAGAACTTTTCGATGCTTTATGTTCCAGAGgtcagcgtct ... aactggtcagGCACACCTGGCGATTGGAGTCACATTATCAAACAGATTGGAATGTTTACTT
EST: gi|17963124|gb|BM269877.1|BM269877
EST:     TCGCATCATCAGTATGCGCCAAGAACTTTTCGATGCTTTATGTTCCAGAG                         GCACACCTGGCGATTGGAGTCACATTATCAAACAGATTGGAATGTTTACTT
genomic: TCGCATCATCAGTATGCGCCAAGAACTTTTCGATGCTTTATGTTCCAGAGgtcagcgtct ... aactggtcagGCACACCTGGCGATTGGAGTCACATTATCAAACAGATTGGAATGTTTACTT
EST: gi|209719287|gb|BW679816.1|BW679816
EST:     TCGCATCATCAGTATGCGCCAAGAACTTTTCGATGCTTTATGTTCCAGAG                         GCACACCTGGCGATTGGAGTCACATTATCAAACAGATTGGAATGTTTACTT
genomic: TCGCATCATCAGTATGCGCCAAGAACTTTTCGATGCTTTATGTTCCAGAGgtcagcgtct ... aactggtcagGCACACCTGGCGATTGGAGTCACATTATCAAACAGATTGGAATGTTTACTT
EST: gi|192307221|gb|FK001221.1|FK001221
EST:     TCGCATCATCAGTATGCGCCAAGAACTTTTCAATGCTTTATGTTCCAGAG                         GCACACCTGGCGATTGGAGTCACATTATCAAACAGATTGGAATGTTTACTT
genomic: TCGCATCATCAGTATGCGCCAAGAACTTTTCGATGCTTTATGTTCCAGAGgtcagcgtct ... aactggtcagGCACACCTGGCGATTGGAGTCACATTATCAAACAGATTGGAATGTTTACTT
EST: gi|21995197|gb|BQ786725.1|BQ786725
EST:     TCGCATCATCAGTATGCGCCAAGAACTTTTCGATGCTTTATGTTCCAGAG                         GCACACCTGGCGATTGGAGTCACATTATCAAACAGATTGGAATGCTTACTT
genomic: TCGCATCATCAGTATGCGCCAAGAACTTTTCGATGCTTTATGTTCCAGAGgtcagcgtct ... aactggtcagGCACACCTGGCGATTGGAGTCACATTATCAAACAGATTGGAATGTTTACTT
EST: gi|4293232|gb|AI442018.1|AI442018
EST:     TCGCATCATCAGTATGCGCCAAGAACTTTTCGATGCTTTATGTTCCAGAG                         GCACACCTGGCGATTGGAGTCACATTATCAAACAGATTGGAATGTTTACTT
genomic: TCGCATCATCAGTATGCGCCAAGAACTTTTCGATGCTTTATGTTCCAGAGgtcagcgtct ... aactggtcagGCACACCTGGCGATTGGAGTCACATTATCAAACAGATTGGAATGTTTACTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctgtttttgtgatacgtttatttcagttatattgatttctcctttaactggtcagGCACACCTGGCGATTGGAGTCACATTATCAAACAGATTGGAATGTTTACTTTCACTGGATTGAATGCGGAACAAGTTTCCTTCATGACTAAAGAGTTCCA
                                         ctttaac  putative branch site (score: 3)
                                   tttctcctttaact  CT-rich tract
                tttatttcagttatat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttgtttgatcattctttactatcttactctgttctttctagttttctgtttttgtgatacgtttatttcagttatattgatttctcctttaactggtcagGCACACCTGGCGATTGGAGTCACATTATCAAACAGATTGGAATGTTTACTTTCACTGGATTGAATGCGGAACAAGTTTCCTTCATGACTAAAGAGTTCCA

ttgtttg