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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TCCTTTAATTGGATCCTCTATTCAGTCAGCTACTGGGGTAGTGTATAATATTACTGGAGGAAAGGACATAACCCTGCAGGAAGTGAACAGGGTTTCTCAGgtatttaaagattgtcaccacttgcttaagaaacattttgttattcctttgatcttgtgaatttgttgcaaactaaccgtataatgtttcttgattttta...

Basic information

species Glycine max
transcript GLYMA02G46530.1
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA02G46530.1 (Glycine max), 5'ss of exon 5
lower sequence: LOC_Os04g56970.1 (Oryza sativa), 5'ss of exon 5
TCCTTTAATTGGATCCTCTATTCAGTCAGCTACTGGGGTAGTGTATAATATTACTGGAGGAAAGGACATAACCCTGCAGGAAGTGAACAGGGTTTCTCAGgt--atttaaagattgtcaccacttgcttaagaaacattttgttattcctttgatcttgtg----aatttgttgcaaactaaccgtataatgtttcttgattttta-----------------------------------------------------------------------------------------
||||||||| || || |||||| || | |||||||| || ||||| ||||| ||||| ||||||||||||||| |||| ||||| ||||  || ||||||||   | |||   || |  ||| |  |||  |||   | ||   |    | |||| | |      ||| ||||  |  | ||     |||  |    | ||    |                                                                                         
TCCTTTAATCGGGTCGTCTATTGAGGCGGCTACTGGTGTTGTGTACAATATCACTGGTGGAAAGGACATAACCTTGCAAGAAGTAAACAAAGTCTCTCAGgtgcgtgtaatatttcttgccattgtctt--gaactgtctttgaagaagtatgatatagcactgtaatatgtta-agtcgaaaaacttaagatgctattatcacgatcatactccacaatttagggctactggaattatgtggcctaggtgattgaagtgctttgttttgaccaatgcttatgcacgttttgcag

upper sequence: GLYMA02G46530.1 (Glycine max), 5'ss of exon 5
lower sequence: GRMZM2G119773_T01 (Zea mays), 5'ss of exon 5
TCCTTTAATTGGATCCTCTATTCAGTCAGCTACTGGGGTAGTGTATAATATTACTGGAGGAAAGGACATAACCCTGCAGGAAGTGAACAGGGTTTCTCAGgt--atttaaagattgtcaccacttgcttaagaaacattttgttattccttt---gatcttgtgaatt------tgttgcaaa--------ctaaccgtataatgtttcttgat--tttta------------------------
|||||| |||||||| || ||  || |||||||||| || ||||||||||||||||| || |||||||| ||  |||| |||||||||| ||| || |||||   | ||    |  | |  | ||  |||   |   |    |  |   ||    ||  ||  |||        |||  ||||        | ||   |||| |  || | |||  ||||                         
TCCTTTGATTGGATCATCCATCGAGGCAGCTACTGGCGTTGTGTATAATATTACTGGTGGGAAGGACATCACTTTGCAAGAAGTGAACAAGGTGTCCCAGgtgcgtgtaggattcattagaaattctttattgattctgcaatggtgttttaagagaagttaggaaacgttgggtgtctcaaatagaagaaccaaatatatagttgttttagatagttttgaccatatgtattcacctcttgcag

upper sequence: GLYMA02G46530.1 (Glycine max), 5'ss of exon 5
lower sequence: Vv19s0090g01320.t01 (Vitis vinifera), 5'ss of exon 5
TCCTTTAATTGGATCCTCTATTCAGTCAGCTACTGGGGTAGTGTATAATATTACTGGAGGAAAGGACATAACCCTGCAGGAAGTGAACAGGGTTTCTCAGgta-tttaaagattgtc-accacttgcttaagaaacattttgttattcctttgatcttgtgaatttgttgcaaactaaccgtataatgtttcttgattttta-
|||| |||||||||||||||| || || ||||| || || || || ||||||||||| ||||||||||||||| |||| ||||| || || || ||||||||| ||| || ||  |  |    ||| || ||   | ||   |  |   |||| |  |  |||   |||    |  ||  ||| | | |   |  |     | 
TCCTCTAATTGGATCCTCTATCCAATCTGCTACAGGTGTTGTCTACAATATTACTGGGGGAAAGGACATAACCTTGCAAGAAGTTAATAGAGTGTCTCAGgtagtttgaatatcatggaatttttgtttcagttcccttccctcttaaatttgctggta-gaacaagttatggaacaa--gtacattttgcataaaaccagac

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|207763655|gb|GD735692.1|GD735692
EST:     TTACTGGAGGAAAGGACATAACCCTGCAGGAAGTGAACAGGGTTTCTCAG                         GTTGTGACTAGTTTGGCTGATCCTTCTGCTAATATTATATTTGGGGCTGTC
genomic: TTACTGGAGGAAAGGACATAACCCTGCAGGAAGTGAACAGGGTTTCTCAGgtatttaaag ... atttttatagGTTGTGACTAGTTTGGCTGATCCTTCTGCTAATATTATATTTGGGGCTGTC
EST: gi|208083437|gb|GD880965.1|GD880965
EST:     TTACTGGAGGAAAGGACATAACCCTGCAGGAAGTGAACAGGGTTTCTCAG                         GTTGTGACTAGTTTGGCTGATCCTTCTGCTAATATTATATTTGGGGCTGTC
genomic: TTACTGGAGGAAAGGACATAACCCTGCAGGAAGTGAACAGGGTTTCTCAGgtatttaaag ... atttttatagGTTGTGACTAGTTTGGCTGATCCTTCTGCTAATATTATATTTGGGGCTGTC
EST: gi|208134341|gb|GD931392.1|GD931392
EST:     TTACTGGAGGAAAGGACATAACCCTGCAGGAAGTGAACAGGGTTTCTCAG                         GTTGTGACTAGTTTGGCTGATCCTTCTAGACTAAAATATTATATTTGGGG
genomic: TTACTGGAGGAAAGGACATAACCCTGCAGGAAGTGAACAGGGTTTCTCAGgtatttaaag ... atttttatagGTTGTGACTAGTTTGGCTGATCCTTCT-G-CTAA--TATTATATTTGGGG
EST: gi|208189254|gb|GD985632.1|GD985632
EST:     TTACTGGAGGAAAGGACATAACCCTGCAGGAAGTGAACAGGGTTTCTCAG                         GTTGTGACTAGTTTGGCTGATCCTTCTGCTAATATTATATTTGGGG
genomic: TTACTGGAGGAAAGGACATAACCCTGCAGGAAGTGAACAGGGTTTCTCAGgtatttaaag ... atttttatagGTTGTGACTAGTTTGGCTGATCCTTCTGCTAATATTATATTTGGGG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TCCTTTAATTGGATCCTCTATTCAGTCAGCTACTGGGGTAGTGTATAATATTACTGGAGGAAAGGACATAACCCTGCAGGAAGTGAACAGGGTTTCTCAGgtatttaaagattgtcaccacttgcttaagaaacattttgttattcctttgatcttgtgaatttgttgcaaactaaccgtataatgtttcttgattttta

- - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGCAG