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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...atcaaatagaaattcatctgtattaaagataccagacaaatgaactttatctattatgtcggtaaattttggtggtcacaatacatttttgaacttgcagGAACAACAAATGGTAATGCCTGGACACCGTGAGTCAAACTTGCAGAAAGAGCTGAACCGATACATTCCCACGGCCGCAGCATTTGGAGGCATCTGTATCG

Basic information

species Glycine max
transcript GLYMA13G34370.1
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA13G34370.1 (Glycine max), 3'ss of exon 6
lower sequence: LOC_Os09g17830.1 (Oryza sativa), 3'ss of exon 5
atcaaatagaaattcatctgtattaaagataccagacaaatgaactttatctattatgtcggtaaattttggtggtcacaatacatttttgaacttg-cagGAACAACAAATGGTAATGCCTGGACACCGTGAGTCAAACTTGCAGAAAGAGCTGAACCGATACATTCCCACGGCCGCAGCATTTGGAGGCATCTGTATCG
   | ||| |     || | || |   ||    |  | |||   || |||   ||   ||        |   |   | | ||   | | | |   |  |||||||| |||||||| |||||||| || |||||||||||||||||||| ||  ||||| ||||||| ||||| ||||| |||||||| ||  | || || |
tctatatatagtgggatatttagtgttgaggtgat-ctaatagtctatattggtttactcaaaggccatctataaactccatttctatgtcactataacagGAACAGCAAATGGTGATGCCTGGCCATCGTGAGTCAAACTTGCAGAAGGAATTGAACAGATACATCCCCACTGCCGCTGCATTTGGTGGAGTGTGCATTG

upper sequence: GLYMA13G34370.1 (Glycine max), 3'ss of exon 6
lower sequence: LOC_Os09g17840.1 (Oryza sativa), 3'ss of exon 5
atcaaatagaaattcatctgtattaaagataccagacaaatgaac-tttatctatt-------atgtcggtaaatt--ttggtggtcacaatacatttttgaacttg-cagGAACAACAAATGGTAATGCCTGGACACCGTGAGTCAAACTTGCAGAAAGAGCTGAACCGATACATTCCCACGGCCGCAGCATTTGGAGGCATCTGTATCG
        || ||| |   || || | |  | |  |  | |  |  ||| | ||         ||||   ||| |   |   ||  | | ||   |||   ||  |  ||||||||||||||||| |||||||| || |||||||||||||||||||| ||  ||||| ||||||| ||||| || || |||||||| ||  | || || |
--------gatattta---gtgttgaggtgatctaattagtctatatttgtttacatacagaaatgttactaagtccatctatgaactccatttctttgccaatataacagGAACAACAAATGGTGATGCCTGGCCATCGTGAGTCAAACTTGCAGAAGGAATTGAACAGATACATCCCCACTGCTGCTGCATTTGGTGGAGTGTGCATTG

upper sequence: GLYMA13G34370.1 (Glycine max), 3'ss of exon 6
lower sequence: LOC_Os03g11440.1 (Oryza sativa), 3'ss of exon 6
atcaaatagaaattcatctgtattaaagataccagacaaatgaactttatctattatgtcggtaaattttggtggtcacaatacatttttgaacttgcagGAACAACAAATGGTAATGCCTGGACACCGTGAGTCAAACTTGCAGAAAGAGCTGAACCGATACATTCCCACGGCCGCAGCATTTGGAGGCATCTGTATCG
 | ||||| ||   ||    ||||    ||| | |       |     |  ||| |||   |       |      ||| | || |||   |  |  ||||| ||||||||||| ||||| || || |||||||| || || ||||||||  ||||| ||||||| || || || || |||||||| ||  |||| || |
gtaaaataaaa---caaaactattttctatatctggtctggaatgcagaattatcatgcaagagctacctttaaaccacca-acctttgcaatttaacagGAGCAACAAATGGTGATGCCAGGCCATCGTGAGTCGAATTTACAGAAAGAATTGAACAGATACATCCCTACAGCTGCTGCATTTGGTGGAGTCTGCATTG

upper sequence: GLYMA13G34370.1 (Glycine max), 3'ss of exon 6
lower sequence: GRMZM2G073498_T02 (Zea mays), 3'ss of exon 5
atcaaatagaaattcatctgtattaaagataccagacaaatgaactttatctattatgt--cggtaaattttggtggtcacaatacatttttgaacttgcagGAACAACAAATGGTAATGCCTGGACACCGTGAGTCAAACTTGCAGAAAGAGCTGAACCGATACATTCCCACGGCCGCAGCATTTGGAGGCATCTGTATCG
 | |  |    |   | |||| ||| |  |  |  || ||| |     |   | ||||   |  | |  | || |  ||     ||| |    |   ||||||||||||||||||| ||||| ||||| |||||||||||||||||||| || |||||||||||||| ||||| || || |||||||| ||  | || ||||
-taacgtgttgagcta-ctgttttatatttggctcactaattatgcaaactcactatgcaacaattacctgtgatcatcctctgacactggatattctgcagGAACAACAAATGGTGATGCCAGGACATCGTGAGTCAAACTTGCAGAAGGAACTGAACCGATACATCCCCACTGCTGCTGCATTTGGTGGAGTATGCATCG

upper sequence: GLYMA13G34370.1 (Glycine max), 3'ss of exon 6
lower sequence: GRMZM2G130987_T04 (Zea mays), 3'ss of exon 5
atcaaatagaaattcatctgtattaaagataccagacaaatgaactt----tatctattatgtcggtaaattttggtggtcacaatacatttttgaacttgcagGAACAACAAATGGTAATGCCTGGACACCGTGAGTCAAACTTGCAGAAAGAGCTGAACCGATACATTCCCACGGCCGCAGCATTTGGAGGCATCTGTATCG
 |  |||| ||  | |    | ||  | || ||   ||  ||||  |    |||  |  |  | | |||  | || |  | ||| |  || ||   |  ||||||||||||||||||| ||||| || || |||||||| ||||||||||| || || ||||||||||| ||||| || || |||||||| ||  | || || |
-tacaatataatcttaatgatttttcacatgcctatcagttgaagatttggtatggagcagtttgctaacctgtgatcctgacactggatatt---atatgcagGAACAACAAATGGTGATGCCAGGCCATCGTGAGTCGAACTTGCAGAAGGAACTTAACCGATACATCCCCACTGCTGCTGCATTTGGTGGTGTATGCATTG

upper sequence: GLYMA13G34370.1 (Glycine max), 3'ss of exon 6
lower sequence: GRMZM2G307252_T02 (Zea mays), 3'ss of exon 6
atcaaatagaaattcatctgtattaaagataccaga-----caaatgaactttatctattatgtcggtaaattttggtggtcacaatacatttttgaacttgcagGAACAACAAATGGTAATGCCTGGACACCGTGAGTCAAACTTGCAGAAAGAGCTGAACCGATACATTCCCACGGCCGCAGCATTTGGAGGCATCTGTATCG
    | | | | |  |   || ||||     ||| |     || ||| |   | || ||  |   | | |  |||  |     |  |||  |    |     ||||| ||||||||||| ||||| || || |||||||||||| |||| |  || |||||| ||||||| || || || ||||||||||||||  | || || |
--ggagttggact--actggtgttaatagggccatagttttcacatgcaagatttccatgctagtg-tgagctttatttaaacccttaccctggcaattcaacagGAGCAACAAATGGTGATGCCAGGCCATCGTGAGTCAAACCTGCAAAGGGAACTGAACAGATACATCCCAACTGCTGCAGCATTTGGAGGAGTGTGCATTG

upper sequence: GLYMA13G34370.1 (Glycine max), 3'ss of exon 6
lower sequence: PP1S323_56V6.1 (Physcomitrella patens), 3'ss of exon 6
-----------------atcaaatagaaattcatctgtattaaagataccagacaaatgaactttatc-tatt--atgtcggtaaattttggtggtcacaatacatttttgaacttgcagGAACAACAAATGGTAATGCCTGGACACCGTGAGTCAAACTTGCAGAAAGAGCTGAACCGATACATTCCCACGGCCGCAGCATTTGGAGGCATCTGTATCG
                 ||  ||| |         |||| |   | ||     ||||| |  | |||  ||||  | | |   | |||    ||  | || | |  |||||   |  ||||||||||||||| | |||||||| |||||||| || ||| | ||||  ||  ||||||| ||||||||||| || || || |||||||| || ||||| |
gtaattgatttgaaacgatttaattgccgcgtgattgtagttgggttagacagcaaattaggtctattatattgaaggccttgatattccactgaactcagt-cgcttttggtttaacagGAACAACAAATGTTCATGCCTGGCCACCGTGAATCCAACCTTCAGAGGGAATTGAACCGGTACATTCCCACAGCAGCTGCTTTTGGAGGTATGTGTATTG

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|6455535|gb|AW186218.1|AW186218
EST:     GGATTGAAGTCTCTGGTTCATCTGCTAAAGATGTTGCCAAGCAGCTTAAG                         GAACAACAAATGGTAATGCCTGGACACCGTGAGTCAAACTTGCAGAAAGAG
genomic: GGATTGAAGTCTCTGGTTCATCTGCTAAAGATGTTGCCAAGCAGCTTAAGgtactgacta ... gaacttgcagGAACAACAAATGGTAATGCCTGGACACCGTGAGTCAAACTTGCAGAAAGAG
EST: gi|13788204|gb|BG650796.1|BG650796
EST:     GGATTGAAGTCTCTGGTTCATCTGCTAAAGATGTTGCCAAGCAGCTTAAG                         GAACAACAAATGGTAATGCCTGGACACCGTGAG
genomic: GGATTGAAGTCTCTGGTTCATCTGCTAAAGATGTTGCCAAGCAGCTTAAGgtactgacta ... gaacttgcagGAACAACAAATGGTAATGCCTGGACACCGTGAG
EST: gi|192302460|gb|FG994796.1|FG994796
EST:     GGATTGAAGTCTCTGGTTCATCTGCTAAAGATGTTGCCAAGCAGCTTAAG                         GAACAACAAATGGTAATGCCTGGACACCGTGAGTCAAACTTGCAGAAAGAG
genomic: GGATTGAAGTCTCTGGTTCATCTGCTAAAGATGTTGCCAAGCAGCTTAAGgtactgacta ... gaacttgcagGAACAACAAATGGTAATGCCTGGACACCGTGAGTCAAACTTGCAGAAAGAG
EST: gi|209699070|gb|BW652863.1|BW652863
EST:     CTGCTAAAGATGTTGCCAAGCAGCTTAAG                         GAACAACAAATGGTAATGCCTGGACACCGTGAGTCAAACTTGCAGAAAGAG
genomic: CTGCTAAAGATGTTGCCAAGCAGCTTAAGgtactgacta ... gaacttgcagGAACAACAAATGGTAATGCCTGGACACCGTGAGTCAAACTTGCAGAAAGAG
EST: gi|209721282|gb|BW665776.1|BW665776
EST:     GGATTGAAGTCTCTGGTTCATCTGCTAAAGATGTTGCCAAGCAGCTTAAG                         GAACAACAAATGGTAATGCCTGGACACCGTGAGTCAAACTTGCAGAAAGAG
genomic: GGATTGAAGTCTCTGGTTCATCTGCTAAAGATGTTGCCAAGCAGCTTAAGgtactgacta ... gaacttgcagGAACAACAAATGGTAATGCCTGGACACCGTGAGTCAAACTTGCAGAAAGAG
EST: gi|58019929|gb|CX706671.1|CX706671
EST:     GGATTGAAGTCTCTGGTTCATCTGCTAAAGATGTTGCCAAGCAGCTTAAG                         GAACAACAAATGGTAATGCCTGGACACCGTGAGTCAAACTTGCAGAAAGAG
genomic: GGATTGAAGTCTCTGGTTCATCTGCTAAAGATGTTGCCAAGCAGCTTAAGgtactgacta ... gaacttgcagGAACAACAAATGGTAATGCCTGGACACCGTGAGTCAAACTTGCAGAAAGAG
EST: gi|17964561|gb|BM271294.1|BM271294
EST:     GGATTGAAGTCTCTGGTTCATCTGCTAAAGATGTTGCCAAGCAGCTTAAG                         GAACAACAAATGGTAATGCCTGGACACCGTGAGTCAAACTTGCAGAAAGAG
genomic: GGATTGAAGTCTCTGGTTCATCTGCTAAAGATGTTGCCAAGCAGCTTAAGgtactgacta ... gaacttgcagGAACAACAAATGGTAATGCCTGGACACCGTGAGTCAAACTTGCAGAAAGAG
EST: gi|13789823|gb|BG652414.1|BG652414
EST:     GGATTGAAGTCTCTGGTTCATCTGCTAAAGATGTTGCCAAGCAGCTTAAG                         GAACAACAAATGGTAATGCCTGGACACCGTGAGTCAAACTTGCAGAAAGAG
genomic: GGATTGAAGTCTCTGGTTCATCTGCTAAAGATGTTGCCAAGCAGCTTAAGgtactgacta ... gaacttgcagGAACAACAAATGGTAATGCCTGGACACCGTGAGTCAAACTTGCAGAAAGAG
EST: gi|298188471|gb|HO035164.1|HO035164
EST:     GGATTGAAGTCTCTGGTTCATCTGCCAAAGATGTTGCCAAGCAGCTTAAG                         GAACAACAAATGGTAATGCCTGGACACCGTGAGTCAAACTTGCAGAAAGAG
genomic: GGATTGAAGTCTCTGGTTCATCTGCTAAAGATGTTGCCAAGCAGCTTAAGgtactgacta ... gaacttgcagGAACAACAAATGGTAATGCCTGGACACCGTGAGTCAAACTTGCAGAAAGAG
EST: gi|7691868|gb|AW759987.1|AW759987
EST:     GGATTGAAGTCTCTGGTTCATCTGCTAAAGATGTTGCCAAGCAGCTTAAG                         GAACAACAAATGGTAATGCCTGGACACCGTGAGTCAAACTTGCAGAAAGAG
genomic: GGATTGAAGTCTCTGGTTCATCTGCTAAAGATGTTGCCAAGCAGCTTAAGgtactgacta ... gaacttgcagGAACAACAAATGGTAATGCCTGGACACCGTGAGTCAAACTTGCAGAAAGAG
EST: gi|26058357|gb|CA801271.1|CA801271
EST:     GGATTGAAGTCTCTGGTTCATCTGCTAAAGATGTTGCCAAGCAGCTTAAG                         GAACAACAAATGGTAATGCCTGGACACCGTGAGTCAAACTTGCAGAAAGAG
genomic: GGATTGAAGTCTCTGGTTCATCTGCTAAAGATGTTGCCAAGCAGCTTAAGgtactgacta ... gaacttgcagGAACAACAAATGGTAATGCCTGGACACCGTGAGTCAAACTTGCAGAAAGAG
EST: gi|214004008|gb|DB984914.1|DB984914
EST:     CTGCTAAAGATGTTGCCAAGCAGCTTAAG                         GAACAACAAATGGTAATGCCTGGACACCGTGAGTCAAACTTGCAGAAAGAG
genomic: CTGCTAAAGATGTTGCCAAGCAGCTTAAGgtactgacta ... gaacttgcagGAACAACAAATGGTAATGCCTGGACACCGTGAGTCAAACTTGCAGAAAGAG
EST: gi|17020953|gb|BM091987.1|BM091987
EST:     GGATTGAAGTCTCTGGTTCATCTGCTAAAGATGTTGCCAAGCAGCTTAAG                         GAACAACAAATGGTAATGCCTGGACACCGTGAGTCAAACTTGCAGAAAGAG
genomic: GGATTGAAGTCTCTGGTTCATCTGCTAAAGATGTTGCCAAGCAGCTTAAGgtactgacta ... gaacttgcagGAACAACAAATGGTAATGCCTGGACACCGTGAGTCAAACTTGCAGAAAGAG
EST: gi|13252241|gb|BG363144.1|BG363144
EST:     GGATTGAAGTCTCTGGTTCATCTGCTAAAGATGTTGCCAAGCAGCTTAAG                         GAACAACAAATGGTAATGCCTGGACACCGTGAGTCAAACTTGCAGAAAGAG
genomic: GGATTGAAGTCTCTGGTTCATCTGCTAAAGATGTTGCCAAGCAGCTTAAGgtactgacta ... gaacttgcagGAACAACAAATGGTAATGCCTGGACACCGTGAGTCAAACTTGCAGAAAGAG
EST: gi|17964577|gb|BM271310.1|BM271310
EST:     GGATTGAAGTCTCTGGTTCATCTGCTAAAGATGTTGCCAAGCAGCTTAAG                         GAACAACAAATGGTAATGCCTGGACACCGTGAGTCAAACTTGCAGAAAGAG
genomic: GGATTGAAGTCTCTGGTTCATCTGCTAAAGATGTTGCCAAGCAGCTTAAGgtactgacta ... gaacttgcagGAACAACAAATGGTAATGCCTGGACACCGTGAGTCAAACTTGCAGAAAGAG
EST: gi|17964777|gb|BM271506.1|BM271506
EST:     GGATTGAAGTCTCTGGTTCATCTGCTAAAGATGTTGCCAAGCAGCTTAAG                         GAACAACAAATGGTAATGCCTGGACACCGTGAGTCAAACTTGCAGAAAGAG
genomic: GGATTGAAGTCTCTGGTTCATCTGCTAAAGATGTTGCCAAGCAGCTTAAGgtactgacta ... gaacttgcagGAACAACAAATGGTAATGCCTGGACACCGTGAGTCAAACTTGCAGAAAGAG
EST: gi|8827474|gb|BE211204.1|BE211204
EST:     GGATTGAAGTCTCTGGTTCATCTGCTAAAGATGTTGCCAAGCAGCTTAAG                         GAACAACAAATGGTAATGCCTGGACACCGTGAGTCAAACTTGCAGAAAGAG
genomic: GGATTGAAGTCTCTGGTTCATCTGCTAAAGATGTTGCCAAGCAGCTTAAGgtactgacta ... gaacttgcagGAACAACAAATGGTAATGCCTGGACACCGTGAGTCAAACTTGCAGAAAGAG
EST: gi|18690777|gb|BM519625.1|BM519625
EST:     GGATTGAAGTCTCTGGTTCATCTGCTAAAGATGTTGCCAAGCAGCTTAAG                         GAACAACAAATGGTAATGCCTGGACACCGTGAGTCAAACTTGCAGAAAGAG
genomic: GGATTGAAGTCTCTGGTTCATCTGCTAAAGATGTTGCCAAGCAGCTTAAGgtactgacta ... gaacttgcagGAACAACAAATGGTAATGCCTGGACACCGTGAGTCAAACTTGCAGAAAGAG
EST: gi|57575142|gb|CX548117.1|CX548117
EST:     GGATTGAAGTCTCTGGTTCATCTGCTAAAGATGTTGCCAAGCAGCTTAAG                         GAACAACAAATGGTAATGCCTGGACACCGTGAGTCAAACTTGCAGAAAGAG
genomic: GGATTGAAGTCTCTGGTTCATCTGCTAAAGATGTTGCCAAGCAGCTTAAGgtactgacta ... gaacttgcagGAACAACAAATGGTAATGCCTGGACACCGTGAGTCAAACTTGCAGAAAGAG
EST: gi|20813072|gb|BQ297550.1|BQ297550
EST:     GGATTGAAGTCTCTGGTTCATCTGCTAAAGATGTTGCCAAGCAGCTTAAG                         GAACAACAAATGGTAATGCCTGGACACCGTGAGTCAAACTTGCAGAAAGAG
genomic: GGATTGAAGTCTCTGGTTCATCTGCTAAAGATGTTGCCAAGCAGCTTAAGgtactgacta ... gaacttgcagGAACAACAAATGGTAATGCCTGGACACCGTGAGTCAAACTTGCAGAAAGAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttatctattatgtcggtaaattttggtggtcacaatacatttttgaacttgcagGAACAACAAATGGTAATGCCTGGACACCGTGAGTCAAACTTGCAGAAAGAGCTGAACCGATACATTCCCACGGCCGCAGCATTTGGAGGCATCTGTATCG
                                  aatacatttttgaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
atcaaatagaaattcatctgtattaaagataccagacaaatgaactttatctattatgtcggtaaattttggtggtcacaatacatttttgaacttgcagGAACAACAAATGGTAATGCCTGGACACCGTGAGTCAAACTTGCAGAAAGAGCTGAACCGATACATTCCCACGGCCGCAGCATTTGGAGGCATCTGTATCG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGG
- - aatagaaa
- - - - - - - catctgt
- - - - - - - - - - - - - - - -ccagaca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tggtggt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - caataca