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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatacttttggataaactgctgcattcagtgccattctttctgctgtttctcctaaggaccttatgatgtctgattaactctttgacacattaaagGTGCTGGTGGCTGATATCAACATTGGATATGAAGATTTTGTGAACACCCAG

Basic information

species Glycine max
transcript GLYMA17G09970.1
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA17G09970.1 (Glycine max), 3'ss of exon 6
lower sequence: PP1S176_87V6.1 (Physcomitrella patens), 3'ss of exon 7
gtatacttttggataaactgctgcattcagtgcc-attctttctgctgtttctcctaaggaccttatgatgtctgattaact--ctttgacacattaa--agGTGCTGGTGGCTGATATCAACATTGGATATGAAGATTTTGTGAACACCCAG
  | | | |   | |         ||    |    ||||   |      | |   | |    | | |  || |  | |      | ||||     |    ||||||||||||| ||||||||||| || ||||||||| |||||||||| |||
--acattatacaacatttgaaaatatgtgatttggattcgaaccaaaaatacaaatcaatgtcgtctactgacgaacttgtcggcgttgatgaggttgtcagGTGCTGGTGGCGGATATCAACATAGGTTATGAAGATATTGTGAACACGCAG

upper sequence: GLYMA17G09970.1 (Glycine max), 3'ss of exon 6
lower sequence: PP1S1_203V6.1 (Physcomitrella patens), 3'ss of exon 6
gtatacttttggataaactgctgcattcagtgccattctttctgctgtttctcctaaggaccttatgatgtctga-ttaactctt-tgacacattaa--agGTGCTGGTGGCTGATATCAACATTGGATATGAAGATTTTGTGAACACCCAG
|  || |       ||| || | |  |   |   | | || |||  |    ||   ||  || |  | ||    | || || ||  ||   |   ||  |||| |||||||| |||||||||||||| ||||||||  ||||||| ||||||
gcttaatagataggaaaatgtttccgtttttagaagttttactga-gaagatcggtagtgccatgagctgatgaactttacgctggtggtgccaaaaccagGTTCTGGTGGCGGATATCAACATTGGTTATGAAGACATTGTGAATACCCAG

upper sequence: GLYMA17G09970.1 (Glycine max), 3'ss of exon 6
lower sequence: PP1S176_111V6.1 (Physcomitrella patens), 3'ss of exon 5
-----gtatacttttggataaactgctgcattcagtgccattctttctgctgtttctcctaaggaccttatgatgtctgattaactctttgacacattaaagGTGCTGGTGGCTGATATCAACATTGGATATGAAGATTTTGTGAACACCCAG
      || |   || || ||  ||     |  | |   |       | |   |     |      || | ||   ||  |   |  |    |   |   ||||||||||||| ||||||||||| || ||||||||| |||||||||| |||
acattatacaacatttgaaaatatgtgatttggattcgaaccaaaaatacaaatcaatgtcgtccactgacgaa--cttgtcggcgttgatgcgggtgtcagGTGCTGGTGGCGGATATCAACATAGGTTATGAAGATATTGTGAACACGCAG

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|22539997|gb|BU089840.1|BU089840
EST:     TGCATTCAATGCCACAATCACCGGATGAACAACTTGTCGTGGTCTCTCAG                         GTGCTGGTGGCTGATATCAACATTGGATATGAAGATTTTGTGAACACCCAG
genomic: TGCATTCAATGCCACAATCACCGGATGAACAACTTGTCGTGGTCTCTCAGgtatactttt ... cacattaaagGTGCTGGTGGCTGATATCAACATTGGATATGAAGATTTTGTGAACACCCAG
EST: gi|17964168|gb|BM270907.1|BM270907
EST:     TGCATTCAATGCCACAATCACCGGATGAACAACTTGTCGTGGTCTCTCAG                         GTGCTGGTGGCTGATATCAACATTGGATATGAAGATTTTGTGAACACCCAG
genomic: TGCATTCAATGCCACAATCACCGGATGAACAACTTGTCGTGGTCTCTCAGgtatactttt ... cacattaaagGTGCTGGTGGCTGATATCAACATTGGATATGAAGATTTTGTGAACACCCAG
EST: gi|6481804|gb|AW201075.1|AW201075
EST:     GCATTCAATGCCACAATCACCGGATGAACAACTTGTCGTGGTCTCTCCAG                         -TGCTGGTGGCTGATATCAACATTGGATATGAAGATTTTGTGAACACCCA
genomic: GCATTCAATGCCACAATCACCGGATGAACAACTTGTCGTGGTCTCTC-AGgtatactttt ... cacattaaagGTGCTGGTGGCTGATATCAACATTGGATATGAAGATTTTGTGAACACCCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgctgtttctcctaaggaccttatgatgtctgattaactctttgacacattaaagGTGCTGGTGGCTGATATCAACATTGGATATGAAGATTTTGTGAACACCCAG
                                              acattaaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatacttttggataaactgctgcattcagtgccattctttctgctgtttctcctaaggaccttatgatgtctgattaactctttgacacattaaagGTGCTGGTGGCTGATATCAACATTGGATATGAAGATTTTGTGAACACCCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA