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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ttagtgtcatacttgaatttaaagttgtgtgcagtcatgttatttatttcacaagaaataggttgacaaatttacacgttgacttactatctatatatgtcagaTACAATGGCGTGCACTTGATGAGATAAACGCAGGGGTGTGTGATGGTATGACATATGCAGAAATCAAGAAAAACATGCCAGAGGAGTATGAG

Basic information

species Glycine max
transcript GLYMA18G06770.1
intron # 20
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA18G06770.1 (Glycine max), 3'ss of exon 20
lower sequence: LOC_Os05g07130.2 (Oryza sativa), 3'ss of exon 18
ttagtgtcatacttgaatttaaagttgtgtgcagtcatgttatttatttcacaagaaataggttgacaaatttacacgttgacttactatctatatatgtcagaTACAATGGCGTGCACTTGATGAGATAAACGCAGGGGTGTGTGATGGTATGACATATGCAGAAATCAAGAAAAACATGCCAGAGGAGTATGAG
         || |       |||||| ||     |  | |||  ||  ||     |  ||| |  |   || |   |||||  | || ||   | | || ||||||||||||||||| ||||||||||||||| | |||||||||||||| ||||| |||| ||| || ||||||   ||||| ||||| | ||| 
--------gtaatcagg---aaagttttggagtatt-tcttacataactcttgcaaggtagtt--atttatatgggcgttgcttaacaattgttgtttg-cagATACAATGGCGTGCTCTTGATGAGATAAACTCTGGGGTGTGTGATGGGATGACGTATGAAGAGATAAAGAAAGTTATGCCCGAGGAATTTGA-

upper sequence: GLYMA18G06770.1 (Glycine max), 3'ss of exon 20
lower sequence: LOC_Os03g18310.1 (Oryza sativa), 3'ss of exon 17
-ttagtgtcatacttgaatttaaagttgtgtgcagtcatgttatttatttcacaagaaataggttgacaaatttacacgttgacttactatctatatatgtc--agaTACAATGGCGTGCACTTGATGAGATAAACGCAGGGGTGTGTGATGGTATGACATATGCAGAAATCAAGAAAAACATGCCAGAGGAGTATGAG
 | ||| |  |    ||| |||          ||   | |  | || | || |||    |||  |  ||||  |  ||  || | |  | || || | |     ||||||||||||||||||||||||| |||||||| ||  | |||||||| ||||| ||||  ||||| |||||||  |  || || || ||||| 
gtcagtttgctctaggaaatta---ccaaactcaagtaagaaaattttgtctcaacttttag-ctatcaaacctg-acactggcatgttttccatgtgtcctctagATACAATGGCGTGCACTTGATGAAATAAACGCTGGCATCTGTGATGGGATGACGTATGATGAAATAAAGAAAATTAAACCTGAAGAATATGA-

upper sequence: GLYMA18G06770.1 (Glycine max), 3'ss of exon 20
lower sequence: LOC_Os03g18310.3 (Oryza sativa), 3'ss of exon 16
-ttagtgtcatacttgaatttaaagttgtgtgcagtcatgttatttatttcacaagaaataggttgacaaatttacacgttgacttactatctatatatgt--cagaTACAATGGCGTGCACTTGATGAGATAAACGCAGGGGTGTGTGATGGTATGACATATGCAGAAATCAAGAAAAACATGCCAGAGGAGTATGAG-------
 | ||| |  |    ||| |||          ||   | |  | || | || |||    |||  |  ||||  |  ||  || | |  | || || | |     ||||||||||||||||||||||||| |||||||| ||  | |||||||| ||||| ||||  ||||| |||||||  |  || || || ||||||       
gtcagtttgctctaggaaatta---ccaaactcaagtaagaaaattttgtctcaacttttag-ctatcaaacctg-acactggcatgttttccatgtgtcctctagATACAATGGCGTGCACTTGATGAAATAAACGCTGGCATCTGTGATGGGATGACGTATGATGAAATAAAGAAAATTAAACCTGAAGAATATGAGTACGCAA

upper sequence: GLYMA18G06770.1 (Glycine max), 3'ss of exon 20
lower sequence: GRMZM2G021846_T01 (Zea mays), 3'ss of exon 18
ttagtgtcatacttgaatttaaagttgtgtgcagtcatgttatttatttcacaagaaataggt-tgacaaatttacacgttgacttactatctatatatgtcagaTACAATGGCGTGCACTTGATGAGATAAACGCAGGGGTGTGTGATGGTATGACATATGCAGAAATCAAGAAAAACATGCCAGAGGAGTATGAG
         || |||  |  |   ||  |   |||| | |||   |  |      |  || ||    |||  || |   | |||||  | |   ||| ||| |||||||||||||||| ||||||||||| ||  | || ||||||||||| ||||| |||| ||| || ||||||| |||||| ||||| | ||| 
--------gtatttggttacacgatttagg--agtcttcttaaagaactgttgctatgtaagtacagcaagattgc---tcgacttg-tgt---tatttgt-agATACAATGGCGTGCTCTTGATGAGATCAATTCTGGAGTGTGTGATGGGATGACTTATGAAGAGATAAAGAAAATCATGCCCGAGGAATTTGA-

upper sequence: GLYMA18G06770.1 (Glycine max), 3'ss of exon 20
lower sequence: GRMZM5G824405_T02 (Zea mays), 3'ss of exon 16
-ttag-tgtcatacttgaatttaaagttgtgtgcagtcatgttatttatttcacaagaaataggttgacaaatttacacgttgacttactatctatatatgtcagaTACAATGGCGTGCACTTGATGAGATAAACGCAGGGGTGTGTGATGGTATGACATATGCAGAAATCAAGAAAAACATGCCAGAGGAGTATGAG
 |||| | |||||  |||   |||| | | |   ||  |   |  |   | |  |   ||   |||  ||||  || || |||  |  |    | | | |   |||||||||||||||| ||||||||||| || || ||||| |||||||| |||||||| |  ||||| |||||||  |  || || || ||||| 
gttagctatcataggtga---taaaatag-gcctagcaagactgctctctacttatagaa-gtgttaccaaaacta-ac-ttgtttctcctcatgt-tcttctagATACAATGGCGTGCTCTTGATGAGATCAATGCTGGGGTCTGTGATGGGATGACATACGATGAAATAAAGAAAAGTAAACCTGAAGAATATGA-

upper sequence: GLYMA18G06770.1 (Glycine max), 3'ss of exon 20
lower sequence: Vv06s0004g06920.t01 (Vitis vinifera), 3'ss of exon 18
ttagtgtcatacttgaatttaaagttgtgtgcagtcatgttattta----tttcacaagaaataggttgacaaatttacacgttgacttactatctatatatgtcagaTACAATGGCGTGCACTTGATGAGATAAACGCAGGGGTGTGTGATGGTATGACATATGCAGAAATCAAGAAAAACATGCCAGAGGAGTATGAG
 |||  |   | || |    ||  | |||   |  ||    || ||    |||     |||||  ||  | ||| ||  |   | ||||  |   ||  | ||  ||||||||||||||||||||||||||||||| || || ||||||||||| |||||||||| ||| || ||||| |||||||| ||||| || || 
-tagcttttgaatttagaaaaatttggtggataaccaacaaatctaggaatttgtgtggaaatgagtatagaaaattcta---taacttttt---tacttttggtagATACAATGGCGTGCACTTGATGAGATAAATGCTGGAGTGTGTGATGGAATGACATATGAAGAGATAAAGAAGAACATGCCTGAGGAATACGA-

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|8669465|gb|BE190572.1|BE190572
EST:     ACTACAACGAACAATTCTGACAGCCAGTCCAATTGTTGGATTTCCCAAGA                         TACAATGGCGTGCACTTGATGAGATAAACGCAGGGGTGTGTGATGGTATGA
genomic: ACTACAACGAACAATTCTGACAGCCAGTCCAATTGTTGGATTTCCCAAGGttagtgtcat ... atatgtcagaTACAATGGCGTGCACTTGATGAGATAAACGCAGGGGTGTGTGATGGTATGA
EST: gi|7691217|gb|AW759348.1|AW759348
EST:     ACTACAACGAACAATTCTGACAGCCAGTCCAATTGTTGGATTTNCCAAGA                         TACAATGGCGTGCACTTGATGAGATAAACGCAGGGGTGTGTGATGGTATGA
genomic: ACTACAACGAACAATTCTGACAGCCAGTCCAATTGTTGGATTTCCCAAGGttagtgtcat ... atatgtcagaTACAATGGCGTGCACTTGATGAGATAAACGCAGGGGTGTGTGATGGTATGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cacaagaaataggttgacaaatttacacgttgacttactatctatatatgtcagaTACAATGGCGTGCACTTGATGAGATAAACGCAGGGGTGTGTGATGGTATGACATATGCAGAAATCAAGAAAAACATGCCAGAGGAGTATGAG
                               gacttac  putative branch site (score: 2)
                                  ttactatctatatat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttagtgtcatacttgaatttaaagttgtgtgcagtcatgttatttatttcacaagaaataggttgacaaatttacacgttgacttactatctatatatgtcagaTACAATGGCGTGCACTTGATGAGATAAACGCAGGGGTGTGTGATGGTATGACATATGCAGAAATCAAGAAAAACATGCCAGAGGAGTATGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG