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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgcttgttttgagcttgatgctcccttaatttaaaccttatccctttatctttctaagagattcactctgccacaattaataatacttttaacatattttccagTCTGCCTTGCTTGCCTTAGCTGCTCATGCATCTGATCCATCTGAAGCTGATCGACTAAGACATCTTGCCTCACCTGCTGGAAAG

Basic information

species Glycine max
transcript GLYMA17G07050.2
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA17G07050.2 (Glycine max), 3'ss of exon 10
lower sequence: AT4G30210.2 (Arabidopsis thaliana), 3'ss of exon 10
-gtgcttgttttgagcttgatgctcccttaatttaaaccttatccctttatctttctaagagattcactctgccacaattaataatacttttaacatattttccagTCTGCCTTGCTTGCCTTAGCTGCTCATGCATCTGATCCATCTGAAGCTGATCGACTAAGACATCTTGCCTCACCTGCTGGAAAG
  || |||  || |  ||     |    |  ||  || |   |   ||| ||||  || ||||||||  ||    |||||| |   |  ||||   | | || |||||||| ||  |||| || ||||||||||||||||||||  | ||||| || ||| ||| ||| ||||| |||||||||||||||
gttggttggattca-tttaccattagactggttataatcagttttgtttctcttcata-gagattcaaact----caattattttcatgttta--ttttcttgcagTCTGCTTTAGTTGCGTTGGCTGCTCATGCATCTGATCCTACCGAAGCAGAACGATTAAAACACCTTGCTTCACCTGCTGGAAAG

upper sequence: GLYMA17G07050.2 (Glycine max), 3'ss of exon 10
lower sequence: AT4G30210.1 (Arabidopsis thaliana), 3'ss of exon 10
-gtgcttgttttgagcttgatgctcccttaatttaaaccttatccctttatctttctaagagattcactctgccacaattaataatacttttaacatattttccagTCTGCCTTGCTTGCCTTAGCTGCTCATGCATCTGATCCATCTGAAGCTGATCGACTAAGACATCTTGCCTCACCTGCTGGAAAG---
  || |||  || |  ||     |    |  ||  || |   |   ||| ||||  || ||||||||  ||    |||||| |   |  ||||   | | || |||||||| ||  |||| || ||||||||||||||||||||  | ||||| || ||| ||| ||| ||||| |||||||||||||||   
gttggttggattca-tttaccattagactggttataatcagttttgtttctcttcata-gagattcaaact----caattattttcatgttta--ttttcttgcagTCTGCTTTAGTTGCGTTGGCTGCTCATGCATCTGATCCTACCGAAGCAGAACGATTAAAACACCTTGCTTCACCTGCTGGAAAGGTT
















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|14125979|gb|BG790417.1|BG790417
EST:     TAAGAACAGCACTTACACGATATGCAGATGTTTTGAGTTCACCCAAAAAG                         TCTGCCTTGCTTGCCTTAGCTGCTCATGCATCTGATCCATCTGAAGCTGAT
genomic: TAAGAACAGCACTTACACGATATGCAGATGTTTTGAGTTCACCCAAAAAGgtgcttgttt ... tattttccagTCTGCCTTGCTTGCCTTAGCTGCTCATGCATCTGATCCATCTGAAGCTGAT
EST: gi|105633831|gb|DW247194.1|DW247194
EST:     TAAGAACAGCACTTACACGATATGCAGATGTCTTGAGTTCACCCAAAAAG                         TCTGCCTTGCTTGCCTTAGCTGCTCATGCATCTGATCCATCTGAAGCTGAT
genomic: TAAGAACAGCACTTACACGATATGCAGATGTTTTGAGTTCACCCAAAAAGgtgcttgttt ... tattttccagTCTGCCTTGCTTGCCTTAGCTGCTCATGCATCTGATCCATCTGAAGCTGAT
EST: gi|254332042|gb|GR846245.1|GR846245
EST:     TAAGAACAGCACTTACACGATATGCAGATGTTTTGAGTTCACCCAAAAAG                         TCTGCCTTGCTTGCCTTAGCTGCTCATGCATCTGATCCATCTGAAGCTGAT
genomic: TAAGAACAGCACTTACACGATATGCAGATGTTTTGAGTTCACCCAAAAAGgtgcttgttt ... tattttccagTCTGCCTTGCTTGCCTTAGCTGCTCATGCATCTGATCCATCTGAAGCTGAT
EST: gi|254341892|gb|GR853029.1|GR853029
EST:     TAAGAACAGCACTTACACGATATGCAGATGTTTTGAGTTCACCCAAAAAG                         TCTGCCTTGCTTGCCTTAGCTGCTCATGCATCTGATCCATCTGAAGCTGAT
genomic: TAAGAACAGCACTTACACGATATGCAGATGTTTTGAGTTCACCCAAAAAGgtgcttgttt ... tattttccagTCTGCCTTGCTTGCCTTAGCTGCTCATGCATCTGATCCATCTGAAGCTGAT
EST: gi|21887259|gb|BQ740472.1|BQ740472
EST:     TAAGAACAGCACTTACACGATATGCAGATGTTTTGAGTTCACCCAAAAAG                         TCTGCCTTGCTTGCCTTAGCTGCTCATGCATCTGATCCATCTGAAGCTGAT
genomic: TAAGAACAGCACTTACACGATATGCAGATGTTTTGAGTTCACCCAAAAAGgtgcttgttt ... tattttccagTCTGCCTTGCTTGCCTTAGCTGCTCATGCATCTGATCCATCTGAAGCTGAT
EST: gi|105633448|gb|DW246811.1|DW246811
EST:     TAAGAACAGCACTTACACGATATGCAGATGTTTTGAGTTCACCCAAAAAG                         TCTGCCTTGCTTGCCTTAGCTGCTCATGCATCCGATCCATCTGAAGCTGAT
genomic: TAAGAACAGCACTTACACGATATGCAGATGTTTTGAGTTCACCCAAAAAGgtgcttgttt ... tattttccagTCTGCCTTGCTTGCCTTAGCTGCTCATGCATCTGATCCATCTGAAGCTGAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctttctaagagattcactctgccacaattaataatacttttaacatattttccagTCTGCCTTGCTTGCCTTAGCTGCTCATGCATCTGATCCATCTGAAGCTGATCGACTAAGACATCTTGCCTCACCTGCTGGAAAG
                                     ttttaac  putative branch site (score: 2)
                                             tattttcc  CT-rich tract
                       acaattaataatactt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgcttgttttgagcttgatgctcccttaatttaaaccttatccctttatctttctaagagattcactctgccacaattaataatacttttaacatattttccagTCTGCCTTGCTTGCCTTAGCTGCTCATGCATCTGATCCATCTGAAGCTGATCGACTAAGACATCTTGCCTCACCTGCTGGAAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA