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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTCACTTTAATATTTTTGTCGGTGACCTTAGTCCTGAGGTTACAGATGCCACATTGTATGCTTGCTTCTCTGTATATCCTAGTTGTTCgtaagtttttatataccctctatttttccttctcattgctattttgttttgtggtgtactatagatattttgttggaaatgcagatacctgaatttatat...

Basic information

species Glycine max
transcript GLYMA17G05530.1
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA17G05530.4 (Glycine max), 5'ss of exon 7
lower sequence: LOC_Os07g42380.1 (Oryza sativa), 5'ss of exon 6
GTCACTTTAATATTTTTGTCGGTGACCTTAGTCCTGAGGTTACAGATGCCACATTGTATGCTTGCTTCTCTGTATATCCTAGTTGTTCgtaagtttttat-----ataccctctatttttccttctcattg--ctattttgttttgtggtgtactatagatattttgttggaaatgcagatacctgaatttatat
  || || ||||||||||| ||||| ||||| || |||||||| ||| || |||| | ||| | |||||||| |||| | ||||| |||||||| |||||      || || ||| | ||   |  |||||  | | ||||  || |  |   | |    |||  | ||      |  |  | |||         
ACCATTTCAATATTTTTGTTGGTGATCTTAGCCCAGAGGTTACTGATTCCGCATTATTTGCATTCTTCTCTGGATATTCCAGTTGCTCgtaagtatttattacctttatccactagtgttttctgccattggcccaatttggcttttcctaccccagctttataatattttgtgcgttgtcagctgtc-------

upper sequence: GLYMA17G05530.4 (Glycine max), 5'ss of exon 7
lower sequence: Vv11s0016g00700.t01 (Vitis vinifera), 5'ss of exon 6
GTCACTTTAATATTTTTGTCGGTGACCTTAGTCCTGAGGTTACAGATGCCACATTGTATGCTTGCTTCTCTGTATATCCTAGTTGTTCgtaagtt---tttatataccctctatttttccttctcattgctattttgttttgtggtgtactatagatattttgttggaaatgcagatacctgaatttatat---
|||| |  ||||||||||| ||||| ||||| ||||||||||||||||| ||| ||| ||| || |||||||| |||||||| |||||||||| |   |||  ||  ||| | | ||| |||||  |   | | |  ||   |    | |  |   ||| |||     |||   ||| | ||   |  |||   
GTCATTACAATATTTTTGTTGGTGATCTTAGCCCTGAGGTTACAGATGCTACACTGTTTGCATGTTTCTCTGTTTATCCTAGCTGTTCgtaagctccgtttgcatggcctttttgttttcttctt-tgaatttgtgattgattaactttccttgtgtatgttgagactaattt-gatccgtgttctggtatcag

upper sequence: GLYMA17G05530.4 (Glycine max), 5'ss of exon 7
lower sequence: EFJ28907 (Selaginella moellendorffii), 5'ss of exon 6
GTCACTTTAATATTTTTGTCGGTGACCTTAGTCCTGAGGTTACAGATGCCACATTGTATGCTTGCTTCTCTGTATATCCTAGTTGTTCgtaagtttttatataccctctatttttccttctcattgcta-ttttgttttgtggtgtactatagatattttgttggaaatgcagatacctgaatttatat
| || |  ||||||||||| ||||| |||||||||||||| |||||||| ||| | || |||   ||||   | |||||| |||| |||||||| || ||||    ||     |||| |||   |   | |||| ||| |  |                                              
GACATTACAATATTTTTGTGGGTGATCTTAGTCCTGAGGTCACAGATGCAACACTCTACGCTGCTTTCTTCATGTATCCTGGTTGCTCgtaagtgttaatatggtttcctccattccatctttgtataacttttatttcgcag----------------------------------------------

upper sequence: GLYMA17G05530.4 (Glycine max), 5'ss of exon 7
lower sequence: EFJ13606 (Selaginella moellendorffii), 5'ss of exon 6
GTCACTTTAATATTTTTGTCGGTGACCTTAGTCCTGAGGTTACAGATGCCACATTGTATGCTTGCTTCTCTGTATATCCTAGTTGTTCgtaagtttttatataccctctatttttccttctcattgcta-ttttgttttgtggtgtactatagatattttgttggaaatgcagatacctgaatttatat
| || |  ||||||||||| ||||| |||||||||||||| |||||||| ||| | || |||   ||||   | |||||| ||||||||||||| || ||||    |      |||| |||   |   | ||||  || |  |                                              
GACATTACAATATTTTTGTGGGTGATCTTAGTCCTGAGGTCACAGATGCAACACTCTACGCTGCTTTCTTCATGTATCCTGGTTGTTCgtaagtgttaatatggttttctccattccatctttgtataacttttaattcgcag----------------------------------------------

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|193443462|gb|FK409208.1|FK409208
EST:     GTTACAGATGCCACATTGTATGCTTGCTTCTCTGTATATCCTAGTTGTTC                         TGATGCAAGGG
genomic: GTTACAGATGCCACATTGTATGCTTGCTTCTCTGTATATCCTAGTTGTTCgtaagttttt ... ttggttacagTGATGCAAGGG
EST: gi|208092308|gb|GD889373.1|GD889373
EST:     GTTACAGATGCCACATTGTATGCTTGCTTCTCTGTATATCCTAGTTGTTC                         TGATGCAAGGGTAA
genomic: GTTACAGATGCCACATTGTATGCTTGCTTCTCTGTATATCCTAGTTGTTCgtaagttttt ... ttggttacagTGATGCAAGGGTAA
EST: gi|11274392|gb|BF324745.1|BF324745
EST:     TTACAGATGCCACATTGTATGCTTGCTTCTGTGTATATGCCTA-TTGGTC                         TGATGCAAGGGTAATGTGGGATCAGAA
genomic: TTACAGATGCCACATTGTATGCTTGCTTCTCTGTATAT-CCTAGTTGTTCgtaagttttt ... ttggttacagTGATGCAAGGGTAATGTGGGATCAGAA
EST: gi|208171149|gb|GD967892.1|GD967892
EST:     GTTACAGATGCGACATTGTATGCTTGCTTCTCTGTATATCCTAGTTGTTC                         TGATGCAAGGGTAATGTGGGATCAGGAGACAGGCCGTTCCAGGGGATTTGG
genomic: GTTACAGATGCCACATTGTATGCTTGCTTCTCTGTATATCCTAGTTGTTCgtaagttttt ... ttggttacagTGATGCAAGGGTAATGTGGGATCAGAAGACAGGCCGTTCCAGGGGATTTGG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTCACTTTAATATTTTTGTCGGTGACCTTAGTCCTGAGGTTACAGATGCCACATTGTATGCTTGCTTCTCTGTATATCCTAGTTGTTCgtaagtttttatataccctctatttttccttctcattgctattttgttttgtggtgtactatagatattttgttggaaatgcagatacctgaatttatat

- - - - - - - - - - - - - - - - - - - - - CAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ccttctc