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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tttttatctatcttttgtggggattttagtaaacatgaattcaattagtttatcaactttcagtctttccaactcctatttttttgttcaaatttctcagTTGGAGCTTAAGCTTGGACTAGGGGGCACATCTTATGCAGATTTTATTGAAAGTGTGCATCTGCCTATGCAGCTGAG

Basic information

species Glycine max
transcript GLYMA09G36770.2
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA09G36770.2 (Glycine max), 3'ss of exon 4
lower sequence: Vv16s0013g00350.t01 (Vitis vinifera), 3'ss of exon 3
---tttttatctatcttttgtggggattttagtaaacatgaattcaat-tagtttat-caactttcagtctttccaactcctatttttttgttcaaatttctcagTTGGAGCTTAAGCTTGGACTAGGGGGCACATCTTATGCAGATTTTATTGAAAGTGTGCATCTGCCTATGCAGCTGAG
   |    |      | | |     ||||  || || | |  ||   | | ||| |  ||     ||   |||  ||  | | ||| ||| ||      |||||| ||||||||||| | ||| |||| |||||||| |||| |||||||||    ||||||||||| || |||||| ||||
tactgggcaatggaatctggacaaaatttctgtgaataagttttggttcttgttgagacatgaaccacagtttgtaatgcttttttctttctt-----gtctcagCTGGAGCTTAAGTTGGGATTAGGTGGCACATCATATGAAGATTTTATCCGCAGTGTGCATCTTCCAATGCAGTTGAG

upper sequence: GLYMA09G36770.2 (Glycine max), 3'ss of exon 4
lower sequence: Vv16s0013g00290.t01 (Vitis vinifera), 3'ss of exon 4
-----------------------------------------------------------------tttttatctatcttttgtggggattttagtaaacatgaattcaattagttt--atcaactttcagtctt---tccaactcctatttt--------tttgttcaaatttctcagTTGGAGCTTAAGCTTGGACTAGGGGGCACATCTTATGCAGATTTTATTGAAAGTGTGCATCTGCCTATGCAGCTGAG
                                                                 | || |  ||       | |    |  |  |||  |  ||  |||||||||   |     || || | |      || ||| | |||        |||  |    | |||||| ||||||||||| | ||| |||| |||||||| |||| |||||||||    ||||||||||| || |||||| ||||
gtaagttatcatccaatttggattatcataatcagtaacgcttcttacttttttcgggttggatgtcttcaaataatgggaatagaatctggaaaaaaattctatgaaattagttttggttcttgttgagacataaacataaatcccagtttgtaaacatttttctttcttatctcagCTGGAGCTTAAGTTGGGATTAGGTGGCACATCATATGAAGATTTTATCCGTAGTGTGCATCTTCCAATGCAGTTGAG
















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|23057217|gb|BU577892.1|BU577892
EST:     TTTCTCTTATTGCCGGGATAATTCTTTTTGGTGGCCTCCTTGCACCTAGC                         TTGGAGCTTAAGCTTGGACTAGGGGGCACATCTTATGCAGATTTTATTGAA
genomic: TTTCTCTTATTGCCGGGATAATTCTTTTTGGTGGCCTCCTTGCACCTAGCgtaagatttt ... aatttctcagTTGGAGCTTAAGCTTGGACTAGGGGGCACATCTTATGCAGATTTTATTGAA
EST: gi|9987763|gb|BE661871.1|BE661871
EST:     TTTCTCTTATTGNCGGGATAATTCTTTTTGGTGGCCTCCTTGC-CCTAGC                         TTGGAGCTTAAGCTTGGACTAGGGGGC-CATCTTATGCAGACTTTT
genomic: TTTCTCTTATTGCCGGGATAATTCTTTTTGGTGGCCTCCTTGCACCTAGCgtaagatttt ... aatttctcagTTGGAGCTTAAGCTTGGACTAGGGGGCACATCTTATGCAGA-TTTT
EST: gi|298165597|gb|HO011646.1|HO011646
EST:     TTTCTCTTATTGCCGGGATAATTCTTTTTGGTGGCCTCCTTGCACCTAGC                         TTGGAGCTTAAGCTTGGACTAGGGGGCACATCTTATGCAGACTTTAT
genomic: TTTCTCTTATTGCCGGGATAATTCTTTTTGGTGGCCTCCTTGCACCTAGCgtaagatttt ... aatttctcagTTGGAGCTTAAGCTTGGACTAGGGGGCACATCTTATGCAGATTTTAT
EST: gi|15813355|gb|BI785630.1|BI785630
EST:     TTTCTCTTATTGCCGGGATAATTCTTTTTGGTGGCCTCCTTGCACCTAGC                         TTGGAGCTTAAGCTTGGACTAGGGGGCACATCTTATGCAGATTTTATTGAA
genomic: TTTCTCTTATTGCCGGGATAATTCTTTTTGGTGGCCTCCTTGCACCTAGCgtaagatttt ... aatttctcagTTGGAGCTTAAGCTTGGACTAGGGGGCACATCTTATGCAGATTTTATTGAA
EST: gi|13791409|gb|BG654000.1|BG654000
EST:     TTTCTCTTATTGCCGGGATAATTCTTTTTGGTGGCCTCCTTGCACCTAGC                         TTGGAGCTTAAGCTTGGACTAGGGGGCACATCTTATGCAGACTTTATTGAA
genomic: TTTCTCTTATTGCCGGGATAATTCTTTTTGGTGGCCTCCTTGCACCTAGCgtaagatttt ... aatttctcagTTGGAGCTTAAGCTTGGACTAGGGGGCACATCTTATGCAGATTTTATTGAA
EST: gi|298195324|gb|HO039155.1|HO039155
EST:     TTTCTCATATTGCCGGGATAATTCTTTTTGGTGGCCTCCTTGCACCTAGC                         TTGGAGCTTAAGCTTGGAC
genomic: TTTCTCTTATTGCCGGGATAATTCTTTTTGGTGGCCTCCTTGCACCTAGCgtaagatttt ... aatttctcagTTGGAGCTTAAGCTTGGAC
EST: gi|27424921|gb|CA936441.1|CA936441
EST:     TTTCTCTTATTGCCGGGATAATTCTTTTTGGTGGCCTCCTTGCACCTAGC                         TTGGAGCTTAAGCTTGGA
genomic: TTTCTCTTATTGCCGGGATAATTCTTTTTGGTGGCCTCCTTGCACCTAGCgtaagatttt ... aatttctcagTTGGAGCTTAAGCTTGGA
EST: gi|5753292|gb|AI960579.1|AI960579
EST:     TTTCTCTTATTGCCGGGATAATTCTTTTTGGTGGCCTCCTTGCACCTAGC                         TTGGAGCTTAAGCTTGGACTAGGGGGCACATCTTATGCAGATTTTATTGAA
genomic: TTTCTCTTATTGCCGGGATAATTCTTTTTGGTGGCCTCCTTGCACCTAGCgtaagatttt ... aatttctcagTTGGAGCTTAAGCTTGGACTAGGGGGCACATCTTATGCAGATTTTATTGAA
EST: gi|254342695|gb|GR858857.1|GR858857
EST:     TTTCTCTTATTGCCGGGATAATTCTTTTTGGTGGCCTCCTTGCACCTAGC                         TTGGAGCTTAAGCTTGGACTAGGGGGCACATCTTATGCAGATTTTATTGAA
genomic: TTTCTCTTATTGCCGGGATAATTCTTTTTGGTGGCCTCCTTGCACCTAGCgtaagatttt ... aatttctcagTTGGAGCTTAAGCTTGGACTAGGGGGCACATCTTATGCAGATTTTATTGAA
EST: gi|193684207|gb|FK623471.1|FK623471
EST:     TTTCTCTTATTGCCGGGATAATTCTTTTTGGTGGCCTCCTTGCACCTAGC                         TTGGAGCTTAAGCTTGGACTAGGGGGCACATCTTATGCAGATTTTATTGAA
genomic: TTTCTCTTATTGCCGGGATAATTCTTTTTGGTGGCCTCCTTGCACCTAGCgtaagatttt ... aatttctcagTTGGAGCTTAAGCTTGGACTAGGGGGCACATCTTATGCAGATTTTATTGAA
EST: gi|21285677|gb|BQ473548.1|BQ473548
EST:     TTTCTCTTATTGCCGGGATAATTCTTTTTGGTGGCCTCCTTGCACCTAGC                         TTGGAGCTTAAGCTTGGACTAGGGGGCACATCTTATGCAGACTTTATTGAA
genomic: TTTCTCTTATTGCCGGGATAATTCTTTTTGGTGGCCTCCTTGCACCTAGCgtaagatttt ... aatttctcagTTGGAGCTTAAGCTTGGACTAGGGGGCACATCTTATGCAGATTTTATTGAA
EST: gi|15336929|gb|BI497585.1|BI497585
EST:     TTTCTCTTATTGCCGGGATAATTCTTTTTGGTGGCCTCCTTGCACCTAGC                         TTGGAGCTTAAGCTTGGACTAGGGGGCACATCTTATGCAGATTTTATTGAA
genomic: TTTCTCTTATTGCCGGGATAATTCTTTTTGGTGGCCTCCTTGCACCTAGCgtaagatttt ... aatttctcagTTGGAGCTTAAGCTTGGACTAGGGGGCACATCTTATGCAGATTTTATTGAA
EST: gi|151400607|gb|EV270421.1|EV270421
EST:     TTTCTCTTATTGCCGGGATAATTCTTTTTGGTGGCCTCCTTGCACCTAGC                         TTGGAGCTTAAGCTTGGACTAGGGGGCACATCTTATGCAGATTTTATTGAA
genomic: TTTCTCTTATTGCCGGGATAATTCTTTTTGGTGGCCTCCTTGCACCTAGCgtaagatttt ... aatttctcagTTGGAGCTTAAGCTTGGACTAGGGGGCACATCTTATGCAGATTTTATTGAA
EST: gi|193727963|gb|FK666693.1|FK666693
EST:     CCTTGCACCTAGC                         TTGGAGCTTAAGCTTGGACTAGGGGGCACATCTTATGCAGATTTTATTGAA
genomic: CCTTGCACCTAGCgtaagatttt ... aatttctcagTTGGAGCTTAAGCTTGGACTAGGGGGCACATCTTATGCAGATTTTATTGAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tagtttatcaactttcagtctttccaactcctatttttttgttcaaatttctcagTTGGAGCTTAAGCTTGGACTAGGGGGCACATCTTATGCAGATTTTATTGAAAGTGTGCATCTGCCTATGCAGCTGAG
                                               tttctc  CT-rich tract
                               tatttttttgttcaaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tttttatctatcttttgtggggattttagtaaacatgaattcaattagtttatcaactttcagtctttccaactcctatttttttgttcaaatttctcagTTGGAGCTTAAGCTTGGACTAGGGGGCACATCTTATGCAGATTTTATTGAAAGTGTGCATCTGCCTATGCAGCTGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA