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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCAATAGAAACTGGGGTAGGCTATGGGCAGTGGCTTCATGGAGAGGCTGTTGCAGCTGGCACGgtatttttttttaaaacaaaatatcgtgaattgtacttacatttgtgtttaatactaaagtctataggtctattttcatgaatctgtatgccaatgtacacag

Basic information

species Glycine max
transcript GLYMA11G08350.1
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA11G08350.1 (Glycine max), 5'ss of exon 6
lower sequence: AT5G66120.2 (Arabidopsis thaliana), 5'ss of exon 6
GCAATAGAAACTGGGGTAGGCTATGGGCAGTGGCTTCATGGAGAGGCTGTTGCAGCTGGCACGgtatttttttttaaaacaaaatatcgtgaattgtacttacatttgtgtttaatactaaagtctataggtctattttcatgaatctgtatgccaatgtacacag
|| |||||||||||  | || |||||  ||||||| |||||||| |||||||||||||||||||||| ||| | ||       |||| |  ||   |  |    | |          | ||| || |  | | | ||  |||   | | ||| |  |         
GCCATAGAAACTGGCTTTGGTTATGGAGAGTGGCTCCATGGAGAAGCTGTTGCAGCTGGCACGgtatctttctctatc-tgcgatattgctaaccatcttcttctct----------ccaaattcga--gatttgttcacattgttatatatactcag--------

upper sequence: GLYMA11G08350.1 (Glycine max), 5'ss of exon 6
lower sequence: Vv04s0023g03820.t01 (Vitis vinifera), 5'ss of exon 6
GCAATAGAAACTGGGGTAGGCTATGGGCAGTGGCTTCATGGAGAGGCTGTTGCAGCTGGCACGgtatttttttttaaaacaaaatatcgtgaattgtacttacatttgtgtttaat-actaaagtctataggtctattttcatgaatctgtatgccaatgtacacag-----------------------------------------------------------
||||||||||||||||| || |||||||||||||| |||||||| |||||||||||||||| |||||  | |       || ||| |  ||  ||   | | ||  |    ||  | | | |||||| ||    |         |   |||||||  |||     |                                                            
GCAATAGAAACTGGGGTTGGTTATGGGCAGTGGCTCCATGGAGAAGCTGTTGCAGCTGGCATGgtatggtatc------cacaattttctgttttcctcatccacctccccttgttcagtcaagtctgtatacatccgcatgcaagcatgtatgctcatgggtgtatttgtgtgtccttatctctttttttgatcactatcatgtgtattctgcaccaatgtttag
















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|57573973|gb|CX546948.1|CX546948
EST:     GGGTAGGCTATGGGCAGTGGCTTCATGGAGAGGCTGTTGCAGCTGGCACG                         GTAATGGCTGTTGACATGTCATATCGCCTAGGTTGGATTGATGATTCTCTT
genomic: GGGTAGGCTATGGGCAGTGGCTTCATGGAGAGGCTGTTGCAGCTGGCACGgtattttttt ... atgtacacagGTAATGGCTGTTGACATGTCATATCGCCTAGGTTGGATTGATGATTCTCTT
EST: gi|192314444|gb|FK008414.1|FK008414
EST:     GGGTAGGCTATGGGCAGTGGCTTCATGGAGAGGCTGTTGCAGCTGGCACG                         GTAATGGCTGTTGACATGTCATATCGCCTAGGTTGGATTGATGATTCTCTT
genomic: GGGTAGGCTATGGGCAGTGGCTTCATGGAGAGGCTGTTGCAGCTGGCACGgtattttttt ... atgtacacagGTAATGGCTGTTGACATGTCATATCGCCTAGGTTGGATTGATGATTCTCTT
EST: gi|151408017|gb|EV277832.1|EV277832
EST:     GGGTAGGCTATGGGCAGTGGCTTCATGGAGAGGCTGTTGCAGCTGGCACG                         ATAATGGCTGTTGACATGTCATATCGCCTAGGGTTGGATTGATGATTCTCT
genomic: GGGTAGGCTATGGGCAGTGGCTTCATGGAGAGGCTGTTGCAGCTGGCACGgtattttttt ... atgtacacagGTAATGGCTGTTGACATGTCATATCGCCTAGG-TTGGATTGATGATTCTCT
EST: gi|22541129|gb|BU090972.1|BU090972
EST:     GTTGCCGCTGGCACG                         GTAATGGCTGTTGACATGTCATATCGCCTAGGTTGGATTGATGATTCTCTT
genomic: GTTGCAGCTGGCACGgtattttttt ... atgtacacagGTAATGGCTGTTGACATGTCATATCGCCTAGGTTGGATTGATGATTCTCTT
EST: gi|151401299|gb|EV271113.1|EV271113
EST:     GGGTAGGCTATGGGCAGTGGCTTCATGGAGAGGCTGTTGCAGCTGGCACG                         GTAATGGCTGTTGACATGTCATATCGCCTAGGTTGGATTGATGATTCTCTT
genomic: GGGTAGGCTATGGGCAGTGGCTTCATGGAGAGGCTGTTGCAGCTGGCACGgtattttttt ... atgtacacagGTAATGGCTGTTGACATGTCATATCGCCTAGGTTGGATTGATGATTCTCTT
EST: gi|209711275|gb|BW665327.1|BW665327
EST:     GGGTAGGCTATGGGCAGTGGCTTCATGGAGAGGCTGTTGCAGCTGGCACG                         GTAATGGCTGTTGACATGTCATATCGCCTAGGTTGGATTGATGATTCTCTT
genomic: GGGTAGGCTATGGGCAGTGGCTTCATGGAGAGGCTGTTGCAGCTGGCACGgtattttttt ... atgtacacagGTAATGGCTGTTGACATGTCATATCGCCTAGGTTGGATTGATGATTCTCTT
EST: gi|14196069|gb|BE657919.2|BE657919
EST:     GGGTAGGCTATGGGCAGTGGCTTCATGGAGAGGCTGTTGCAGCTGGCACG                         GTAATGGCTGTTGACATGTCATATCGCCTAGGTTGGATTGATGATTCTCTT
genomic: GGGTAGGCTATGGGCAGTGGCTTCATGGAGAGGCTGTTGCAGCTGGCACGgtattttttt ... atgtacacagGTAATGGCTGTTGACATGTCATATCGCCTAGGTTGGATTGATGATTCTCTT
EST: gi|57574227|gb|CX547202.1|CX547202
EST:     GGGTAGGCTATGGGCAGTGGCTTCATGGAGAGGCTGTTGCAGCTGGCACG                         GTAATGGCTGTTGACATGTCATATCGCCTAGGTTGGATTGATGATTCTCTT
genomic: GGGTAGGCTATGGGCAGTGGCTTCATGGAGAGGCTGTTGCAGCTGGCACGgtattttttt ... atgtacacagGTAATGGCTGTTGACATGTCATATCGCCTAGGTTGGATTGATGATTCTCTT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GCAATAGAAACTGGGGTAGGCTATGGGCAGTGGCTTCATGGAGAGGCTGTTGCAGCTGGCACGgtatttttttttaaaacaaaatatcgtgaattgtacttacatttgtgtttaatactaaagtctataggtctattttcatgaatctgtatgccaatgtacacag

- - - - - - - - - - - - - - - - - - CATGGA
- - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - GAGAGG
- - - - - - - - - - - - - - - - - - - - - -  GCTGTT
- - - - - - - - - - - - - - - - - - - - - - - - -  GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTG