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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGTTGTAACAACCACGACACATAAGTCACTTCGTGGACCACGTGGGGCTATGATTTTCTTCAGGAAGGGTGTGAAAGAGATAAACAAACAAGGGAAGGAAgtgagtttaaaattataaatttaatgttttacggagataaggaattcaaaaatagggtaaaatacactttaactgcctgaattatagcactttcatgact...

Basic information

species Glycine max
transcript GLYMA14G36280.1
intron # 9
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA14G36280.2 (Glycine max), 5'ss of exon 9
lower sequence: LOC_Os03g52840.2 (Oryza sativa), 5'ss of exon 9
TGTTGTAACAACCACGACACATAAGTCACTTCGTGGACCACGTGGGGCTATGATTTTCTTCAGGAAGGGTGTGAAAGAGATAAACAAACAAGGGAAGGAAgtgagtttaaaattataaatttaatgttttacggagataaggaattcaaaaatagggtaaaatacactttaactgcctgaattatagcactttcatgact-----------------------
||| || || ||||| || || |||||||| |||||||||||||| || ||||| || | ||||||||| |||||||   ||||||| ||||| || || ||   |     |  | ||   ||      ||      || ||  ||   |       |     |  || | |||   |||  |  |  |   | |  |                         
TGTAGTGACTACCACTACTCACAAGTCACTCCGTGGACCACGTGGAGCCATGATCTTTTACAGGAAGGGGGTGAAAGGAGTAAACAAGCAAGGCAAAGAGgtatatacttgagcagaacaatagcaagatagtagcgtagggtgttggtactgtttcttctccatcctgtgactctgtgagcttcaaaaaaataaaaatgcctaatgaccctctaccgtctag

upper sequence: GLYMA14G36280.2 (Glycine max), 5'ss of exon 9
lower sequence: AT5G26780.3 (Arabidopsis thaliana), 5'ss of exon 9
TGTTGTAACAACCACGACACATAAGTCACTTCGTGGACCACGTGGGGCTATGATTTTCTTCAGGAAGGGTGTGAAAGAGATAAACAAACAAGGGAAGGAAgtgagtttaaaattataaatttaatgttttacggagataaggaattcaaaaatagggtaaaatacactttaactgcctgaattatagcactttcatgact-
|||||| || || || || || || || ||||| || ||  | ||||||||||| ||||| ||||||||  | |||||||| |||||||||||||| || |||| |      || |   ||  || || ||     || || || | |     ||      |   | ||||  || |    || || |  || | |||   
TGTTGTTACGACTACAACTCACAAATCGCTTCGCGGTCCTAGAGGGGCTATGATATTCTTTAGGAAGGGGTTAAAAGAGATTAACAAACAAGGGAAAGAGgtgaat------ttttcgtttctatattgtatatgaatgagtaaataacttccagttactgactaatttta--tgtc--gtttgtaac-tttacctgatag

upper sequence: GLYMA14G36280.2 (Glycine max), 5'ss of exon 9
lower sequence: Vv18s0001g07960.t01 (Vitis vinifera), 5'ss of exon 9
TGTTGTAACAACCACGACACATAAGTCACTTCGTGGACCACGTGGGGCTATGATTTTCTTCAGGAAGGGTGTGAAAGAGATAAACAAACAAGGGAAGGAAgtgagtttaaaattataa-atttaatgttttacggagataaggaattcaaaaatagggtaaaatacactttaactgcctgaatta--tagcactttcatgact-
| |||| |||||||| ||||||||||| || ||||| |||||||| || ||||| |||||||||||||| || |||||||| |||||||||||||| ||||||||| |  |  || || | | ||      ||  | |  || | ||    | |   |    | | || ||| ||||  | |||   || |  |   ||  || 
TATTGTGACAACCACAACACATAAGTCTCTACGTGGGCCACGTGGAGCAATGATATTCTTCAGGAAGGGGGTTAAAGAGATCAACAAACAAGGGAAAGAAgtgagtcttgatgtaaaataatgaaaagacaacaaacactagaagtt----actcatgctttagataccttagctgcaagcattgcttacccttactattgcta

upper sequence: GLYMA14G36280.2 (Glycine max), 5'ss of exon 9
lower sequence: EFJ32604 (Selaginella moellendorffii), 5'ss of exon 9
TGTTGTAACAACCACGACACATAAGTCACTTCGTGGACCACGTGGGGCTATGATTTTCTTCAGGAAGGGTGTGAAAGAGATAAACAAACAAGGGAAGGAAgtgagtttaaaattataaatttaatgttttacggagataaggaattcaaaaatagggtaaaatacactttaactgcctgaattatagcactttcatgact
 ||||| || || || || || || |||||| | || || ||||| || |||||||||||| | |||||||||||||| |  |||||||||||  |||| ||  |||||   |   || ||   |  || || | |    | |                                                         
CGTTGTCACCACTACCACGCACAAATCACTTAGAGGTCCTCGTGGAGCAATGATTTTCTTCCGCAAGGGTGTGAAAGAAACTAACAAACAAGGACAGGAGgtacgtttactttcccaagttacctccttgacagtgcctcgcag--------------------------------------------------------

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|19269481|gb|BM885737.1|BM885737
EST:     TGATTTTCTTCAGGAAGGGTGTGAAAGAGATAAACAAACAAGGGAAGGAA                         GTGTTGTATGACTATGAAGACAAAATAAACCAGGCTGTTTTTCCTGGACTT
genomic: TGATTTTCTTCAGGAAGGGTGTGAAAGAGATAAACAAACAAGGGAAGGAAgtgagtttaa ... catcttacagGTGTTGTATGACTATGAAGACAAAATAAACCAGGCTGTTTTTCCTGGACTT
EST: gi|192312199|gb|FK003920.1|FK003920
EST:     TGATTTTCTTCAGGAAGGGTGTGAAAGAGATAAACAAGCAAGGGAAGGAA                         GTGTTGTATGACTATGAAGACAAAATAAACCAGGCTGTTTTTCCTGGACTT
genomic: TGATTTTCTTCAGGAAGGGTGTGAAAGAGATAAACAAACAAGGGAAGGAAgtgagtttaa ... catcttacagGTGTTGTATGACTATGAAGACAAAATAAACCAGGCTGTTTTTCCTGGACTT
EST: gi|6915301|gb|AW396831.1|AW396831
EST:     AGAGATAAACAAATTTTGGAAGGAA                         GTGTTGTATGACTATGAAGACAAAATAAACCAGGCTGTTTTTCCTGGACTT
genomic: AGAGATAAACAAACAAGGGAAGGAAgtgagtttaa ... catcttacagGTGTTGTATGACTATGAAGACAAAATAAACCAGGCTGTTTTTCCTGGACTT
EST: gi|7796703|gb|AW782097.1|AW782097
EST:     TGATTTTCTTCAGGAAGGGTGTGAAAGAGATAAACAAACAAGGGAAGGAA                         GTGTTGTATGACTATGAAGACAAAATAAACCAGGCTGTTTTTCCTGGACTT
genomic: TGATTTTCTTCAGGAAGGGTGTGAAAGAGATAAACAAACAAGGGAAGGAAgtgagtttaa ... catcttacagGTGTTGTATGACTATGAAGACAAAATAAACCAGGCTGTTTTTCCTGGACTT
EST: gi|19348549|gb|BM893081.1|BM893081
EST:     TGATTTTCTTCAGGAAGGGTGTGAAAGAGATAAACAAACAAGGGAAGGAA                         GTGTTGTATGACTATGAAGACAAAATAAACCAGGCTGTTTTTCCTGGACTT
genomic: TGATTTTCTTCAGGAAGGGTGTGAAAGAGATAAACAAACAAGGGAAGGAAgtgagtttaa ... catcttacagGTGTTGTATGACTATGAAGACAAAATAAACCAGGCTGTTTTTCCTGGACTT
EST: gi|151409184|gb|EV278992.1|EV278992
EST:     AAGGGTGTGAAAGAGATAAACAAACAAGGGAAGGAA                         GTGTTGTATGACTATGAAGACAAAATAAACCAGGCTGTTTTTCCTGGACTT
genomic: AAGGGTGTGAAAGAGATAAACAAACAAGGGAAGGAAgtgagtttaa ... catcttacagGTGTTGTATGACTATGAAGACAAAATAAACCAGGCTGTTTTTCCTGGACTT
EST: gi|192315079|gb|FK010449.1|FK010449
EST:     TGATTTTCTTCAGGAAGGGTGTGAAAGAGATAAACAAACAAGGGAAGGAA                         GTGTTGTATGACTATGAAGACAAAATAAACCAGGCTGTTTTTCCTGGACTT
genomic: TGATTTTCTTCAGGAAGGGTGTGAAAGAGATAAACAAACAAGGGAAGGAAgtgagtttaa ... catcttacagGTGTTGTATGACTATGAAGACAAAATAAACCAGGCTGTTTTTCCTGGACTT
EST: gi|192312198|gb|FK003919.1|FK003919
EST:     TGATTTTCTTCAGGAAGGGTGTGAAAGAGATAAACAAGCAAGGGAAGGAA                         GTGTTGTATGACTATGAAGACAAAATAAACCAGGCTGTTTTTCCTGGACTT
genomic: TGATTTTCTTCAGGAAGGGTGTGAAAGAGATAAACAAACAAGGGAAGGAAgtgagtttaa ... catcttacagGTGTTGTATGACTATGAAGACAAAATAAACCAGGCTGTTTTTCCTGGACTT
EST: gi|192298247|gb|FG992067.1|FG992067
EST:     TGATTTTCTTCAGGAAGGGTGTGAAAGAGATAAACAAACAAGGGAAGGAA                         GTGTTGTATGACTATGAAGACAAAATAAACCAGGCTGTTTTTCCTGGACTT
genomic: TGATTTTCTTCAGGAAGGGTGTGAAAGAGATAAACAAACAAGGGAAGGAAgtgagtttaa ... catcttacagGTGTTGTATGACTATGAAGACAAAATAAACCAGGCTGTTTTTCCTGGACTT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGTTGTAACAACCACGACACATAAGTCACTTCGTGGACCACGTGGGGCTATGATTTTCTTCAGGAAGGGTGTGAAAGAGATAAACAAACAAGGGAAGGAAgtgagtttaaaattataaatttaatgttttacggagataaggaattcaaaaatagggtaaaatacactttaactgcctgaattatagcactttcatgact

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA