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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cttcagatgttagctggaaaaaagaaaagaaaacattgagcgattatgtttcttgattaatgacattttgatttttaaaattttgttaattattttgcagGTAGGTGTTGGTATGTGCATGGAAGGAATAGAACAGAACCCTATTGTTTATGAGTTGATGTCTGAAATGGCATTTCGTGATAAGAAAGTTAAAGTTTCG

Basic information

species Glycine max
transcript GLYMA10G11720.1
intron # 13
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA10G11720.2 (Glycine max), 3'ss of exon 13
lower sequence: GRMZM2G033592_T01 (Zea mays), 3'ss of exon 13
------cttcagatgttagctggaaaaaagaaaagaaaacattgagcgattatgtttcttgattaatgacattttgatttttaaaattttgttaattattttgcagGTAGGTGTTGGTATGTGCATGGAAGGAATAGAACAGAACCCTATTGTTTATGAGTTGATGTCTGAAATGGCATTTCGTGATAAGAAAGTTAAAGTTTCG
       ||||     ||  ||      ||||  ||     ||   |  |  ||| |||      |  || | |  | | ||  | | ||| |     || |  || | || ||||| ||||||||||| |||||||| || || ||  ||||||||||  | ||||||||||||||||||| | ||||||| ||| | |||  |
ttcatctttcatgatatacatgtgtttcagaactgatgtatttt--cagtgctgtatctaatccgactacttatgcagtgtttgactcttgctc----ttctctagATTGGCGTTGGCATGTGCATGGAGGGAATAGAGCACAATCCAGTTGTTTATGAACTTATGTCTGAAATGGCATTTCATAATAAGAAGGTTGAGGTTGAG

upper sequence: GLYMA10G11720.2 (Glycine max), 3'ss of exon 13
lower sequence: AT5G13690.1 (Arabidopsis thaliana), 3'ss of exon 13
cttcagatgttagctggaaaaaagaaaagaaa----acattgagcga-ttatgtttcttgatta-atgacattttgatttt-----taaaattttgttaattattttgca----gGTAGGTGTTGGTATGTGCATGGAAGGAATAGAACAGAACCCTATTGTTTATGAGTTGATGTCTGAAATGGCATTTCGTGATAAGAAAGTTAAAGTTTCG
    |  |  || ||   | |   | || |      |||||       |||||| | | | | | |  |  || |    ||     |  ||| |||||| |||| |||||    ||| ||||| || |||||||||||||||||||| ||||||||  | ||||| ||  | |  ||||||||||||||||| ||| |||||||| | ||   |
--gtaactcataactacgacattcacaatatgtttcacattttttatcttatgtctataggtgagactattttctccgcttagaaatggaatcttgttatttatgttgcacatagGTCGGTGTAGGAATGTGCATGGAAGGAATAGAGCAGAACCCGGTGGTTTACGAACTAACTTCTGAAATGGCATTTCGAGATGAGAAAGTTGATGTACAG

upper sequence: GLYMA10G11720.2 (Glycine max), 3'ss of exon 13
lower sequence: Vv13s0064g00370.t01 (Vitis vinifera), 3'ss of exon 13
cttcagatgttagctggaaaaaagaaaagaaaacatt-gagcgattatgtttcttgattaatgacattttgatttttaaaattttgttaat-tattttgcagGTAGGTGTTGGTATGTGCATGGAAGGAATAGAACAGAACCCTATTGTTTATGAGTTGATGTCTGAAATGGCATTTCGTGATAAGAAAGTTAAAGTTTCG
  | |  | || | ||   | |    |  | | |||| || |   |||||| |||||   | |  |||   ||   | |    || || || | |     |||| |||||||| ||||||||||||||||| || || |||||  ||| ||||||| ||||||||||||||||||||||   | | |||||| || ||  |
actaaacttttggatgtttatattccagtatatcatttgacctcctatgtt-cttgag-gaggttattgacatggctcactaattattgatgtttcccatagGTTGGTGTTGGCATGTGCATGGAAGGAATTGAGCAAAACCCAGTTGCTTATGAGCTGATGTCTGAAATGGCATTTCGCAGTGAAAAAGTTCAACTTGTG

upper sequence: GLYMA10G11720.2 (Glycine max), 3'ss of exon 13
lower sequence: PP1S329_23V6.1 (Physcomitrella patens), 3'ss of exon 13
---------cttcagatgttagctggaaaaaagaaaagaaaacattgagcgattatgtttcttgattaatgacattttgatttttaaaattttgttaattattttgcagGTAGGTGTTGGTATGTGCATGGAAGGAATAGAACAGAACCCTATTGTTTATGAGTTGATGTCTGAAATGGCATTTCGTGATAAGAAAGTTAAAGTTTCG
          |  |  | || | |||    || | |  |||  ||   |  ||   |     | ||||||    | ||   | || |   | |||| |   | | ||||||||||||||| ||||| |||||||| || || ||||||||  |||| ||||| |||||| |||||||||||||||   ||   |  ||    ||   |
gtaggattggtgaaagttttggttggttgtaatacagcaaagaat---gttatcggggcgtgt-attaatcgtctctt---tcttcactgtgtgttga--gtctggcagGTAGGTGTTGGCATGTGTATGGAAGGCATTGAGCAGAACCCAGTTGTGTATGACTTGATGGCTGAAATGGCATTTCACAATGCAACCGTCGTTGTCGAG

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|192322077|gb|FK012181.1|FK012181
EST:     CAATTTCTTCAGGGCCTGTTGATGCTCGTGTCAGTGCAAACTCAACAATG                         GTAGGTGTTGGTATGTGCATGGAAGGAATAGAACAGAACCCTATTGTTTAT
genomic: CAATTTCTTCAGGGCCTGTTGATGCTCGTGTCAGTGCAAACTCAACAATGgtactttcaa ... tattttgcagGTAGGTGTTGGTATGTGCATGGAAGGAATAGAACAGAACCCTATTGTTTAT






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atgtttcttgattaatgacattttgatttttaaaattttgttaattattttgcagGTAGGTGTTGGTATGTGCATGGAAGGAATAGAACAGAACCCTATTGTTTATGAGTTGATGTCTGAAATGGCATTTCGTGATAAGAAAGTTAAAGTTTCG
                                      tgttaat  putative branch site (score: 3)
                                            ttatttt  CT-rich tract
          attaatgacattttga  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
cttcagatgttagctggaaaaaagaaaagaaaacattgagcgattatgtttcttgattaatgacattttgatttttaaaattttgttaattattttgcagGTAGGTGTTGGTATGTGCATGGAAGGAATAGAACAGAACCCTATTGTTTATGAGTTGATGTCTGAAATGGCATTTCGTGATAAGAAAGTTAAAGTTTCG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA