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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cacaaagtcaaagaaaaaagccattatttttctaaaataagttgaaccagacatactcttattccagtactgtatggtattaatttcttcacttttttagGTTGTTGGGTTGGATTTGGTGGATGATGAAAGCAAACCTGAAAGACGGCCAACAAAACACATGCCTACACCGGAGCAATGGACTAATGTATTCAATCCAG

Basic information

species Glycine max
transcript GLYMA03G07460.1
intron # 12
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA03G07460.1 (Glycine max), 3'ss of exon 12
lower sequence: LOC_Os05g28180.3 (Oryza sativa), 3'ss of exon 4
-cacaaagtcaaagaaaaaagccattatttttctaaaataagttga-accagacatactcttattccagtactgtatggtattaatttcttcacttttttagGTTGTTGGGTTGGATTTGGTGGATGATGAAAGCAAACCTGAAAGACGGCCAACAAAACACATGCCTACACCGGAGCAATGGACTAATGTATTCAATCCAG
  || | || |     |       |||    |   ||||| ||| | | |  ||| |     |       ||| || | || |   || ||     ||  ||||||| ||||| |||||||| |||||||| || ||||||||||| || |||||||| || ||||||||||| || |||||||| ||||| ||||| ||||
ggactaggtaatttttatttttatttaaaactactaaatatgttaatatcgcacacatcacaagcaggcaactttaggatact--cttttttggccttgcagGTTGTAGGGTTAGATTTGGTTGATGATGAGAGTAAACCTGAAAGGCGTCCAACAAAGCATATGCCTACACCTGAACAATGGACCAATGTCTTCAACCCAG

upper sequence: GLYMA03G07460.1 (Glycine max), 3'ss of exon 12
lower sequence: GRMZM2G416667_T01 (Zea mays), 3'ss of exon 12
cacaaagtcaaagaaaaaagccattatttttctaaaataagttgaaccagacatactcttattccagtactgtatggtattaatttcttcact------tttttagGTTGTTGGGTTGGATTTGGTGGATGATGAAAGCAAACCTGAAAGACGGCCAACAAAACACATGCCTACACCGGAGCAATGGACTAATGTATTCAATCCAG
       | |        ||  || ||  ||   ||||| |||       |  ||       | ||  |    |     | ||||   ||  |       ||  ||||||| ||||||||  |||| ||||||||||| ||||| ||||| || |||||||| |||||||| ||||| || || ||||| ||||| ||||| || |
------attagttttttcagtaatgataattgagaaatacgttcgcatgtatttatctcagatacatgatatcacaacttcaattgactctttctgggccttgcagGTTGTAGGGTTGGACCTGGTTGATGATGAAAGTAAACCAGAAAGGCGTCCAACAAAGCACATGCCCACACCTGAACAGTGGACCAATGTGTTCAACCCTG

upper sequence: GLYMA03G07460.1 (Glycine max), 3'ss of exon 12
lower sequence: AT2G38280.1 (Arabidopsis thaliana), 3'ss of exon 12
cacaaagtcaaagaaaaaagccattatttttctaaaataagttgaaccagacatactcttattccagt---actgtatggtattaatttcttcacttttttagGTTGTTGGGTTGGATTTGGTGGATGATGAAAGCAAACCTGAAAGACGGCCAACAAAACACATGCCTACACCGGAGCAATGGACTAATGTATTCAATCCAG
      || |      | | |    | |   ||  |||  |     |   ||| | |         ||   ||||  || | |    || ||  || ||| |||||||||| || |||||||| |||||||||||||||||||||||||| || |||||||||||||| || || |  ||||||||||| | ||||||||| |
------gttagcattcatatcttcaaataacctctaatccgcatgtctttacacaataaagagttggtttgactggttgctgtct-cttgtttgctatttcagGTTGTTGGATTTGATTTGGTTGATGATGAAAGCAAACCTGAAAGACGTCCCACAAAACACATGCCCACTCCAGCTCAATGGACTAACGCATTCAATCCTG

upper sequence: GLYMA03G07460.1 (Glycine max), 3'ss of exon 12
lower sequence: Vv08s0105g00570.t01 (Vitis vinifera), 3'ss of exon 12
---cacaaagtcaaagaaaaaagccattatttttctaaaataagttgaaccagacatactcttattccagtact-gtatggtattaatttcttcacttttttagGTTGTTGGGTTGGATTTGGTGGATGATGAAAGCAAACCTGAAAGACGGCCAACAAAACACATGCCTACACCGGAGCAATGGACTAATGTATTCAATCCAG
   |     ||  |    | |  |     |  || |    |    |||| ||   ||   |||  |   ||| | |  |     | ||||| |    |||| ||||||||||  |||| || |||||||||||||||||||| |||||||| || |||||||| |||||||| || |  || ||||| ||||  |||||||| |
ttgcttttggtttacattagatcctggcttactttttccct---ctgaatcaagaat-tacttgctatggtatttgagtaactattatttcattggattttcagGTTGTTGGCCTGGACTTAGTGGATGATGAAAGCAAACCAGAAAGACGTCCTACAAAACATATGCCTACTCCAGCTCAGTGGACCAATGCTTTCAATCCTG

upper sequence: GLYMA03G07460.1 (Glycine max), 3'ss of exon 12
lower sequence: PP1S307_76V6.1 (Physcomitrella patens), 3'ss of exon 12
-----cacaaa-gtcaaagaaaaaagccattatttttctaaaataagttgaaccagacatactcttattccagtactgtatggtattaatttcttcacttttttagGTTGTTGGGTTGGATTTGGTGGATGATGAAAGCAAACCTGAAAGACGGCCAACAAAACACATGCCTACACCGGAGCAATGGACTAATGTATTCAATCCAG
     |||||  |  | | |  |||   |  | | |||   |  |||  ||      |||  |||| ||    | || ||     ||  | |            |||| || ||||| ||| ||||||||||||| || || ||||||||  |||| |||||||||||||  || || |   ||||||  ||    ||||| ||||
aatatcacaattgatataaagtaaaattac-agtcttcattagcaaggagatttgttcatgttctttttaatttgctttaactctttggtgtggggggc-----agGTGGTAGGGTTTGATATGGTGGATGATGAGAGTAAGCCTGAAAGGAGGCCCACAAAACACATGCAGACTCCTGCAGAATGGAACAACCCCTTCAACCCAG

upper sequence: GLYMA03G07460.1 (Glycine max), 3'ss of exon 12
lower sequence: PP1S168_82V6.1 (Physcomitrella patens), 3'ss of exon 12
-----------------------------------------------------------cacaaagtcaaagaaaaaagccattattt----ttctaaaataagttgaac-cagacatactcttattccagtactgta--tggtattaatttcttcactttt-ttagGTTGTTGGGTTGGATTTGGTGGATGATGAAAGCAAACCTGAAAGACGGCCAACAAAACACATGCCTACACCGGAGCAATGGACTAATGTATTCAATCCAG
                                                           ||||    | |    ||   | |||   |    | ||     | |  |  | | | |||||     |     |||| |   | |||    || |||      |  ||||| || || || ||  ||||||||||||||||||| |||||||| ||||||||||| |||||||   |||| |   |||||   ||    || ||||| |
gtgagttgaaaaaactactaaattactgttcttctcagttttgcatcttcattcttgcacacattagccatctgaactacgattgcatgaggtgctccttcatgcggtgctctgtcatacaaaagtcatgatactatggtttgtacgctttcctttgtgcgtactagGTGGTGGGATTTGACATGGTGGATGATGAAAGCAAGCCTGAAAGGCGGCCAACAAAGCACATGCAACCACCTGCAAAATGGGACAACCCTTTTAATCCGG

upper sequence: GLYMA03G07460.1 (Glycine max), 3'ss of exon 12
lower sequence: PP1S77_89V6.1 (Physcomitrella patens), 3'ss of exon 12
------------------------------------------------------------cacaaagtcaaagaaaaaagccattatttttctaaaata--agttgaa----ccagacatactcttattccagtactgtatggtattaatttctt-cacttttt----------tagGTTGTTGGGTTGGATTTGGTGGATGATGAAAGCAAACCTGAAAGACGGCCAACAAAACACATGCCTACACCGGAGCAATGGACTAATGTATTCAATCCAG
                                                            | |    || ||    | |    ||  |||| |    ||   || |||    || || |   |  | | ||| |    |    |  |  |||| | || |||||          ||||||||||| || ||| ||||||||||||| ||||| |||||||| |||||||| || |||||||   |||| | | |||||  ||||   ||||||||||
gttggtcaaaagcaaaaccaaacccccagcgtcatgcgtcttttcgtttacattcttgtccgctttctccaactggatacgatttgcttttgtcgcgtattggtcgaaataacctgataatttgctttcccattgggtttcaatccttctttcatgcattttttgttaaatgaatagGTTGTTGGATTCGATATGGTGGATGATGAGAGCAAGCCTGAAAGGCGGCCAACGAAGCACATGCAACCACCTGCGAAATGGGATAATCCTTTCAATCCAG

upper sequence: GLYMA03G07460.1 (Glycine max), 3'ss of exon 12
lower sequence: EFJ30909 (Selaginella moellendorffii), 3'ss of exon 11
cacaaagtcaaagaaaaaagccattatttttctaaaataagttgaaccagacatactcttattccagtactgtatggta-ttaatttcttcacttttt-tagGTTGTTGGGTTGGATTTGGTGGATGATGAAAGCAAACCTGAAAGACGGCCAACAAAACACATGCCTACACCGGAGCAATGGACTAATGTATTCAATCCAG
                                                 |   |||| |   | ||   |    | |   |||||  ||  ||||| |  ||||||| || || ||  ||||||| |||||||||||||| |||||||||||||| || || ||||  || || || || |||   | |   ||||||||||
-------------------------------------------------gtattactttgtgttcatctcgaactagagcttaatcactgaactttatgcagGTTGTCGGTTTTGACATGGTGGACGATGAAAGCAAACCCGAAAGACGGCCAACTAAGCATATGCAGACTCCCGAACAGTGGCAAATTTCTTTCAATCCAG

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|15813627|gb|BI785902.1|BI785902
EST:     TCACTGTCAACCCAGATTCACATCCTCAGCTGCATGTTTTCCTGAAACAG                         GTTGTTGGGTTGGATTTGGTGGATGATGAAAGCAAACCTGAAAGACGGCCA
genomic: TCACTGTCAACCCAGATTCACATCCTCAGCTGCATGTTTTCCTGAAACAGgtgtgttatt ... acttttttagGTTGTTGGGTTGGATTTGGTGGATGATGAAAGCAAACCTGAAAGACGGCCA
EST: gi|9565697|gb|BE475206.1|BE475206
EST:     TCACTGTCAACCCAGATTCACATCCTCAGCTGCATGTTTTCCTGAAACAG                         GTTGTTGGGTTGGATTTGGTGGATGATGAAAGCAAACCTGAAAGACGGCCA
genomic: TCACTGTCAACCCAGATTCACATCCTCAGCTGCATGTTTTCCTGAAACAGgtgtgttatt ... acttttttagGTTGTTGGGTTGGATTTGGTGGATGATGAAAGCAAACCTGAAAGACGGCCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

accagacatactcttattccagtactgtatggtattaatttcttcacttttttagGTTGTTGGGTTGGATTTGGTGGATGATGAAAGCAAACCTGAAAGACGGCCAACAAAACACATGCCTACACCGGAGCAATGGACTAATGTATTCAATCCAG
                                tattaat  putative branch site (score: 2)
                                      tttcttcactttttt  CT-rich tract
                                tattaatttcttcact  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
cacaaagtcaaagaaaaaagccattatttttctaaaataagttgaaccagacatactcttattccagtactgtatggtattaatttcttcacttttttagGTTGTTGGGTTGGATTTGGTGGATGATGAAAGCAAACCTGAAAGACGGCCAACAAAACACATGCCTACACCGGAGCAATGGACTAATGTATTCAATCCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCA
- - - - - aagaaaa
- - - - - - - - - agccatt
- - - - - - - - - - - - - - - - -aaaataa
- - - - - - - - - - - - - - - - - - - - - - - ccagaca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgtatgg