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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tcaatgattatatatcatttatagtgaatctgctaaacagcatgtataagcaagtattaaagggaatgatgatttgtgatatttgtaacttcttgtctagATATGGACTAGTACACTGCAACGAACAATTCTGACAGCCACTCCAATTGTTGGATTTCCCAAG

Basic information

species Glycine max
transcript GLYMA11G27870.1
intron # 18
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA11G27870.1 (Glycine max), 3'ss of exon 18
lower sequence: GRMZM2G021846_T02 (Zea mays), 3'ss of exon 17
tcaatgattatatatcatttatagtgaatctgctaaacagcatgtataagcaagtattaaagggaatgatgatttgtgatatttgtaacttcttgtctagATATGGACTAGTACACTGCAACGAACAATTCTGACAGCCACTCCAATTGTTGGATTTCCCAAG-------------------------------------
          ||  |  |||    ||| |      ||       | | | || | || | | ||  |||  |||||  ||  | | |     |||| ||||||||||| ||||| || ||  |||||||| ||||||| | ||||||||||||||| ||||||                                     
---------gtaagtattttcccatgattt-----aatgatggatctgacca-gcataacatgggctgaaaatttgcaattatcgaa-----ttgtttagATATGGACCAGTACCCTTCAGAGAACAATTTTGACAGCAAGTCCAATTGTTGGATTCCCCAAGGTATTTGGTTACACGATTTAGGAGTCTTCTTAAAGAA

upper sequence: GLYMA11G27870.1 (Glycine max), 3'ss of exon 18
lower sequence: GRMZM2G021846_T01 (Zea mays), 3'ss of exon 17
tcaatgattatatatcatttatagtgaatctgctaaacagcatgtataagcaagtattaaagggaatgatgatttgtgatatttgtaacttcttgtctagATATGGACTAGTACACTGCAACGAACAATTCTGACAGCCACTCCAATTGTTGGATTTCCCAAG
          ||  |  |||    ||| |      ||       | | | || | || | | ||  |||  |||||  ||  | | |     |||| ||||||||||| ||||| || ||  |||||||| ||||||| | ||||||||||||||| ||||||
---------gtaagtattttcccatgattt-----aatgatggatctgacca-gcataacatgggctgaaaatttgcaattatcgaa-----ttgtttagATATGGACCAGTACCCTTCAGAGAACAATTTTGACAGCAAGTCCAATTGTTGGATTCCCCAAG
















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|51336524|gb|CO980390.1|CO980390
EST:     AGCTTGCCAAGTTTGTTGGAAAGCGTCTCAAATCAGAACGGGCTGCTTCT                         ATATGGACTAGTACACTGCAACGAACAATTCTGACAGCCACTCCAATTGTT
genomic: AGCTTGCCAAGTTTGTTGGAAAGCGTCTCAAATCAGAACGGGCTGCTTCTgtaagcgtta ... tcttgtctagATATGGACTAGTACACTGCAACGAACAATTCTGACAGCCACTCCAATTGTT
EST: gi|51336471|gb|CO980337.1|CO980337
EST:     AGCTTGCCAAGTTTGTTGGNNNGCGTCTCAAATCAGAACGGGCTGCTTCT                         ATATGGACTAGTACACTGCAACGAACAATTCTGACAGCCACTCCAATTGTT
genomic: AGCTTGCCAAGTTTGTTGGAAAGCGTCTCAAATCAGAACGGGCTGCTTCTgtaagcgtta ... tcttgtctagATATGGACTAGTACACTGCAACGAACAATTCTGACAGCCACTCCAATTGTT
EST: gi|20448750|gb|BQ252874.1|BQ252874
EST:     AGCTTGCCAAGTTTGTTGGAAAGCGTCTCAAATCAGAACGGGCTGCTTCT                         ATATGGACTAGTACACTGCAACGAACAATTCTGACAGCCACTCCAATTGTT
genomic: AGCTTGCCAAGTTTGTTGGAAAGCGTCTCAAATCAGAACGGGCTGCTTCTgtaagcgtta ... tcttgtctagATATGGACTAGTACACTGCAACGAACAATTCTGACAGCCACTCCAATTGTT
EST: gi|22930234|gb|BU547373.1|BU547373
EST:     AGCTTGCCAAATTTGTTGGAAAGCGTCTCAAATCAGAACGGGCTGCTTCT                         ATATGGACTAGTACACTGCAACGAACAATTCTGACAGCCACTCCAATTGTT
genomic: AGCTTGCCAAGTTTGTTGGAAAGCGTCTCAAATCAGAACGGGCTGCTTCTgtaagcgtta ... tcttgtctagATATGGACTAGTACACTGCAACGAACAATTCTGACAGCCACTCCAATTGTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ataagcaagtattaaagggaatgatgatttgtgatatttgtaacttcttgtctagATATGGACTAGTACACTGCAACGAACAATTCTGACAGCCACTCCAATTGTTGGATTTCCCAAG
                                     ttgtaac  putative branch site (score: 2)
                                           cttcttgtct  CT-rich tract
      aagtattaaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tcaatgattatatatcatttatagtgaatctgctaaacagcatgtataagcaagtattaaagggaatgatgatttgtgatatttgtaacttcttgtctagATATGGACTAGTACACTGCAACGAACAATTCTGACAGCCACTCCAATTGTTGGATTTCCCAAG

- - - - - - - - - - - - - - tctgcta
- - - - - - - - - - - - - - - - - - - -gcatgta
- - - - - - - - - - - - - - - - - - - - - - - - -gcaagta
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ggaatga
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgatttg