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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...agcctttcattagcaactccccttgcacctcttttaaattgtagcaatgtgtgccatattctttgtaacaagattttgattatttgtttgtatcatgcagACTGACACCAAGAAGATATCGGCTGTATCTATATTCTTTGAAACAATGCCATACAGATTGAATGAGAGCACTGGTTATATCGATTATGACCAG

Basic information

species Glycine max
transcript GLYMA14G36280.1
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA14G36280.1 (Glycine max), 3'ss of exon 6
lower sequence: LOC_Os03g52840.2 (Oryza sativa), 3'ss of exon 6
agcctttcattagcaactccccttgcacctcttttaaattgtagcaatgtgtgccatattctttgtaacaagatt---ttgattatttgtttgtatcatgcagACTGACACCAAGAAGATATCGGCTGTATCTATATTCTTTGAAACAATGCCATACAGATTGAATGAGAGCACTGGTTATATCGATTATGACCAG
 |  |||| |   |  |||   |   |  | | || |  | ||    | | ||  |   || |  |  || |  |   ||| | |  |  |||     |||||||||| || |||||||| || || || || ||||||||||| |||||||| ||||||||| |||| |||||||| |  || |||||||| |||
tgagtttcttcccc--ctcaattcttagttatgttcagatataatgctct-tggtactctcatcctcccatggcttagttgttcaacttcttgatggttgcagACTGATACTAAGAAGATTTCAGCAGTTTCGATATTCTTTGAGACAATGCCCTACAGATTGGATGAAAGCACTGGCTTGATTGATTATGATCAG

upper sequence: GLYMA14G36280.1 (Glycine max), 3'ss of exon 6
lower sequence: GRMZM2G135283_T02 (Zea mays), 3'ss of exon 6
---agcctttcattagcaactccccttgcacctcttttaaattgtagcaatg-tgtgccatattctttgtaacaagattttgattatttgtttgtatcatgcagACTGACACCAAGAAGATATCGGCTGTATCTATATTCTTTGAAACAATGCCATACAGATTGAATGAGAGCACTGGTTATATCGATTATGACCAG
    ||   | | |  ||  | ||| |  |    |  |||  |  ||  ||| ||  | | || ||       |    |   |   | |   |      ||||||||||||| ||||||||||| ||    || ||||| ||||| |||||||| ||||||||| |||| |||||||| |  || ||||| || |||
atctgcaaatgaatgacattttcccataaattcttagtaacattcagatatgatgctctagatactcc----tatagctcaaaggttctacctactgtttgcagACTGACACTAAGAAGATATCTGCAACTTCAATATTTTTTGAGACAATGCCTTACAGATTGGATGAAAGCACTGGATTGATTGATTACGATCAG

upper sequence: GLYMA14G36280.1 (Glycine max), 3'ss of exon 6
lower sequence: GRMZM2G135283_T01 (Zea mays), 3'ss of exon 6
---agcctttcattagcaactccccttgcacctcttttaaattgtagcaatg-tgtgccatattctttgtaacaagattttgattatttgtttgtatcatgcagACTGACACCAAGAAGATATCGGCTGTATCTATATTCTTTGAAACAATGCCATACAGATTGAATGAGAGCACTGGTTATATCGATTATGACCAG-------
    ||   | | |  ||  | ||| |  |    |  |||  |  ||  ||| ||  | | || ||       |    |   |   | |   |      ||||||||||||| ||||||||||| ||    || ||||| ||||| |||||||| ||||||||| |||| |||||||| |  || ||||| || |||       
atctgcaaatgaatgacattttcccataaattcttagtaacattcagatatgatgctctagatactcc----tatagctcaaaggttctacctactgtttgcagACTGACACTAAGAAGATATCTGCAACTTCAATATTTTTTGAGACAATGCCTTACAGATTGGATGAAAGCACTGGATTGATTGATTACGATCAGGTCATTT

upper sequence: GLYMA14G36280.1 (Glycine max), 3'ss of exon 6
lower sequence: AT5G26780.3 (Arabidopsis thaliana), 3'ss of exon 6
-------------agcctttca---ttagcaactccccttgcacctcttttaaattgtagcaatgtgtgcc--atattct-ttgtaacaagattttgattatttgtttgtatcatgcagACTGACACCAAGAAGATATCGGCTGTATCTATATTCTTTGAAACAATGCCATACAGATTGAATGAGAGCACTGGTTATATCGATTATGACCAG
             || || ||    || |  | ||    |    || | ||   |  |  |  ||||      ||||| | |  |  |   ||||   ||||||| |    |  ||||||||||||| ||||| |||||||||||||| || || ||||| |||||||||||||||||| |||||| ||||||||| || ||||||||||||
gtacttgggttctagtctctctagcttggtcagtcagtatttgactttcttttctcatctctttgtggaattgatattgtatcttttcctcatttcttttatttgctc---ttgtgcagACTGACACGAAGAAAATATCGGCTGTATCCATCTTTTTTGAGACAATGCCATACAGATTGGATGAGAACACTGGTTACATTGATTATGACCAG

upper sequence: GLYMA14G36280.1 (Glycine max), 3'ss of exon 6
lower sequence: Vv18s0001g07960.t01 (Vitis vinifera), 3'ss of exon 6
agcctttcattagcaactccccttgcacctcttttaaattgtagcaa---tgtgtgccatattctttgtaacaagattttgattatttgtttg-tatcatgcagACTGACACCAAGAAGATATCGGCTGTATCTATATTCTTTGAAACAATGCCATACAGATTGAATGAGAGCACTGGTTATATCGATTATGACCAG
    ||| |  |  || | |   | |   | ||||   |||    ||   ||| | |  |||    |||  | || |||| || |||  |||   ||  ||||||| ||||||||||||||||| ||||| |||||||| ||||| |||||||||||||||||| |||| |  ||||| ||||| || |||||||||
---atttgaggaataatttcttcttcctttttttttttttgataaaagcttgtcttcagtatctgatgtg-ctagcttttcatcattcttttaacattttgcagACCGACACCAAGAAGATATCTGCTGTGTCTATATTTTTTGAGACAATGCCATACAGATTGGATGAAAAAACTGGATATATTGACTATGACCAG

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|192312199|gb|FK003920.1|FK003920
EST:     TTATGGCACTTGATCTTCCCCATGGTGGGCATCTATCGCATGGTTATCAG                         ACTGACACCAAGAAGATATCGGCTGTATCTATATTCTTTGAAACAATGCCA
genomic: TTATGGCACTTGATCTTCCCCATGGTGGGCATCTATCGCATGGTTATCAGgttaagttct ... tatcatgcagACTGACACCAAGAAGATATCGGCTGTATCTATATTCTTTGAAACAATGCCA
EST: gi|151396057|gb|EV265934.1|EV265934
EST:     TTATGGCACTTGATCTTCCCCATGGTGGGCATCTATCGCATGGTTATCAG                         ACTGACACCAAGAAGATATCGGCTGTATCTATATTCTTTGAAACAATGCCA
genomic: TTATGGCACTTGATCTTCCCCATGGTGGGCATCTATCGCATGGTTATCAGgttaagttct ... tatcatgcagACTGACACCAAGAAGATATCGGCTGTATCTATATTCTTTGAAACAATGCCA
EST: gi|298187285|gb|HO034434.1|HO034434
EST:     TTATGGCACTTGATCTTCCCCATGGTGGGCATCTATCGCATGGTTATCAG                         ACTGACACCAAGAAGATATCGGCTGTATCTATATTCTTTGAAACAATGCCA
genomic: TTATGGCACTTGATCTTCCCCATGGTGGGCATCTATCGCATGGTTATCAGgttaagttct ... tatcatgcagACTGACACCAAGAAGATATCGGCTGTATCTATATTCTTTGAAACAATGCCA
EST: gi|27426205|gb|CA937725.1|CA937725
EST:     TTATGGCACTTGATCTTCCCCATGGTGGGCATCTATCGCATGGTTATCAG                         ACTGACACCAAGAAGATATCGGCTGTATCTATATTCTTTGAAACAATGCCA
genomic: TTATGGCACTTGATCTTCCCCATGGTGGGCATCTATCGCATGGTTATCAGgttaagttct ... tatcatgcagACTGACACCAAGAAGATATCGGCTGTATCTATATTCTTTGAAACAATGCCA
EST: gi|192312198|gb|FK003919.1|FK003919
EST:     TTATGGCACTTGATCTTCCCCATGGTGGGCATCTATCGCATGGTTATCAG                         ACTGACACCAAGAAGATATCGGCTGTATCTATATTCTTTGAAACAATGCCA
genomic: TTATGGCACTTGATCTTCCCCATGGTGGGCATCTATCGCATGGTTATCAGgttaagttct ... tatcatgcagACTGACACCAAGAAGATATCGGCTGTATCTATATTCTTTGAAACAATGCCA
EST: gi|209724640|gb|BW651425.1|BW651425
EST:     TTATGGCACTTGATCTTCCCCATGGTGGGCATCTATCGCATGGTTATCAG                         ACTGACACCAAGAAGATATCGGCTGTATCTATATTCTTTGAAACAATGCCA
genomic: TTATGGCACTTGATCTTCCCCATGGTGGGCATCTATCGCATGGTTATCAGgttaagttct ... tatcatgcagACTGACACCAAGAAGATATCGGCTGTATCTATATTCTTTGAAACAATGCCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aatgtgtgccatattctttgtaacaagattttgattatttgtttgtatcatgcagACTGACACCAAGAAGATATCGGCTGTATCTATATTCTTTGAAACAATGCCATACAGATTGAATGAGAGCACTGGTTATATCGATTATGACCAG
                           attttgattatttgtt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
agcctttcattagcaactccccttgcacctcttttaaattgtagcaatgtgtgccatattctttgtaacaagattttgattatttgtttgtatcatgcagACTGACACCAAGAAGATATCGGCTGTATCTATATTCTTTGAAACAATGCCATACAGATTGAATGAGAGCACTGGTTATATCGATTATGACCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCA