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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagattatttgttccatgtgttttacttaccattgactgaaattttctgaaattgatgtgttggaattttgtttgccgtgaatgcagGTAAATACGCTCAGGTCACAAATAACCCAGAAAATGATGGTTGTATAAATGCCGTTTTGCTTGTTTAAGGTCATAGCAAGCATCAGGGTTCCAGCTTGAT

Basic information

species Glycine max
transcript GLYMA10G10000.1
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA10G10000.1 (Glycine max), 3'ss of exon 8
lower sequence: LOC_Os07g47580.1 (Oryza sativa), 3'ss of exon 8
gtaagattatttgttccatgtgttttacttaccattgactgaaatttt---ctgaaattgatgtgttggaattttgtttgccgtgaatgcagGTAAATACGCTCAGGTCACAAATAACCCAGAAAATGATGGTTGTATAAATGCCGTTTTGCTTGTTTAAGGTCATAGCAAGCATCAGGGTTCCAGCTTGAT--
|||||   || ||||  ||||  | | ||||   |    |  || ||    ||| || |  |    |  ||    |||      |  |||||||||||| || || || ||||| |||||||| |||||||| ||||| ||||| || || || || ||||| |  |    ||   |   |||   |||     
gtaaggc-atctgttgaatgt--tctgcttattttgctttttaacttctccctggaacttgttccataaaacagcgttcttgtcg--tgcagGTAAATATGCACAAGTTACAAACAACCCAGAGAATGATGGCTGTATCAATGCTGTCTTACTCGTGTAAGGACGCAAT--GCTATACACTTCATTCTTCTCGT

upper sequence: GLYMA10G10000.1 (Glycine max), 3'ss of exon 8
lower sequence: Vv08s0105g00280.t01 (Vitis vinifera), 3'ss of exon 8
gtaagattatttgttccatgtgttttacttaccattgactgaaattttctgaaattgatgtgttggaattttgt------------ttgccgtgaatgcagGTAAATACGCTCAGGTCACAAATAACCCAGAAAATGATGGTTGTATAAATGCCGTTTTGCTTGTTTAAGG---TCATAGCAAGCATCAGGGTTCCAGCTTGAT
||||||   ||| | | || |||  || ||  |||||  |    ||| ||  |  ||  |  ||   ||||| |             ||  ||| ||| ||| |||||||| || || |||||||||||||| |||||||| ||||||||||| ||||||||||| ||||    | ||    |||| || |  |   |      
gtaagaaattttttactatttgtactattt-tcattgttttgtgtttgcttcatctgcagcttttttattttttattttttgaattctgtggtggatgtagGGAAATACGCACAAGTGACAAATAACCCAGAGAATGATGGATGTATAAATGCTGTTTTGCTTGTGTAAGAGGATTATCAACAGCAACAAGAATATGGTGG---
















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|208320447|gb|GE122462.1|GE122462
EST:     GAATGTCAGNGAACTTGGTCTTGTCACACCTGCTGGGAAAGTTGTGTGGG                         GTAAATACGCTCAGGTCACAAATAACCCAGAAAATGATGGTTGTATAAATG
genomic: GAATGTCAGTGAACTTGGTCTTGTCACACCTGCTGGGAAAGTTGTGTGGGgtaagattat ... gtgaatgcagGTAAATACGCTCAGGTCACAAATAACCCAGAAAATGATGGTTGTATAAATG
EST: gi|14258675|gb|BG881583.1|BG881583
EST:     GAATGTCAGTGAACTTGGTCTTGTCACACCTGCTGGGAAAGTTGTGTGGG                         GTAAATACGCTCAGGTCACAAATAACCCAGAAAATGATGGTTGTATAAATG
genomic: GAATGTCAGTGAACTTGGTCTTGTCACACCTGCTGGGAAAGTTGTGTGGGgtaagattat ... gtgaatgcagGTAAATACGCTCAGGTCACAAATAACCCAGAAAATGATGGTTGTATAAATG
EST: gi|207682562|gb|GD664877.1|GD664877
EST:     GAATGTCAGTGAACTTGGTCTTGTCACACCTGCTGGGAAAGTTGTGTGGG                         GTAAATACGCTCAGGTCACAAATAACCCAGAAAATGATGGTTGTATAAATG
genomic: GAATGTCAGTGAACTTGGTCTTGTCACACCTGCTGGGAAAGTTGTGTGGGgtaagattat ... gtgaatgcagGTAAATACGCTCAGGTCACAAATAACCCAGAAAATGATGGTTGTATAAATG
EST: gi|31459692|gb|CD401720.1|CD401720
EST:     GAATGTCAGTGAACTTGGTCTTGTCACACCTGCTGGGAAAGTTGTGTGGG                         GTAAATACGCTCAGGTCACAAATAACCCAGAAAATGATGGTTGTATAAATG
genomic: GAATGTCAGTGAACTTGGTCTTGTCACACCTGCTGGGAAAGTTGTGTGGGgtaagattat ... gtgaatgcagGTAAATACGCTCAGGTCACAAATAACCCAGAAAATGATGGTTGTATAAATG
EST: gi|22931857|gb|BU548996.1|BU548996
EST:     GAATGTCAGTGAACTTGGTCTTGTCACACCTGCTGGGAAAGTTGTGTGGG                         GTAAATACGCTCAGGTCACAAATAACCCAGAAAATGATGGTTGTATAAATG
genomic: GAATGTCAGTGAACTTGGTCTTGTCACACCTGCTGGGAAAGTTGTGTGGGgtaagattat ... gtgaatgcagGTAAATACGCTCAGGTCACAAATAACCCAGAAAATGATGGTTGTATAAATG
EST: gi|151408011|gb|EV277826.1|EV277826
EST:     GAATGTCAGTGAACTTGGTCTTGTCACACCTGCTGGGAAAGTTGTGTGGG                         GTAAATACGCTCACGTCACA
genomic: GAATGTCAGTGAACTTGGTCTTGTCACACCTGCTGGGAAAGTTGTGTGGGgtaagattat ... gtgaatgcagGTAAATACGCTCAGGTCACA
EST: gi|23730169|gb|BU763189.1|BU763189
EST:     GAATGTCAGTGAACTTGGTCTTGTCACACCTGCTGGGAAAGTTGTGTGGG                         GTAAATACGCTCAGGTCACAAATAACCCAGAAAATGATGGTTGTATAAATG
genomic: GAATGTCAGTGAACTTGGTCTTGTCACACCTGCTGGGAAAGTTGTGTGGGgtaagattat ... gtgaatgcagGTAAATACGCTCAGGTCACAAATAACCCAGAAAATGATGGTTGTATAAATG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgactgaaattttctgaaattgatgtgttggaattttgtttgccgtgaatgcagGTAAATACGCTCAGGTCACAAATAACCCAGAAAATGATGGTTGTATAAATGCCGTTTTGCTTGTTTAAGGTCATAGCAAGCATCAGGGTTCCAGCTTGAT
       aaattttctgaaatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagattatttgttccatgtgttttacttaccattgactgaaattttctgaaattgatgtgttggaattttgtttgccgtgaatgcagGTAAATACGCTCAGGTCACAAATAACCCAGAAAATGATGGTTGTATAAATGCCGTTTTGCTTGTTTAAGGTCATAGCAAGCATCAGGGTTCCAGCTTGAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCAAG