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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtgtttggtctatttattgtgtttggatataatccttgacttcttatgtataaatgatagtccttgctaattgtttccaatggtcatcatctatcagATGTTAGCAAAGAAGGTAGATACATTGACCAAAGCCATGGAAGTTGAGGCAAAGAAGATGAGAAGGGAAGTAGCTGCTATGGAGAAGGAGGTAGCTGCTA

Basic information

species Glycine max
transcript GLYMA02G09390.1
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA02G09390.1 (Glycine max), 3'ss of exon 9
lower sequence: LOC_Os02g50320.1 (Oryza sativa), 3'ss of exon 9
gtaagtgtttggtctatttattgtgtttggatataatccttgacttcttatgtataaatgatagtccttgctaattgtttccaatggtcatcatctatcagATGTTAGCAAAGAAGGTAGATACATTGACCAAAGCCATGGAAGTTGAGGCAAAGAAGATGAGAAGGGAAGTAGCTGCTATGGAGAAGGAGGTAGCTGCTA
||| |    | |  |   | ||   | ||||| ||||    |||   |  |||     | || | | ||||||| ||  ||         |  | || |||||||| ||||| |||||||||||||| ||||| || |||||||| ||||| || ||||||||  | || |||||||||||||||||||| || |||||||
gtatggcactagaattcctgtttattatggatttaatgg--gaccaatgctgtg--ggtcat-gcctttgctaactgcctc---------ttgttta-cagATGTTGGCAAAAAAGGTAGATACATTAACCAAGGCTATGGAAGTGGAGGCTAAAAAGATGAGGCGAGAGGTAGCTGCTATGGAGAAGGAAGTTGCTGCTA

upper sequence: GLYMA02G09390.1 (Glycine max), 3'ss of exon 9
lower sequence: GRMZM2G039325_T01 (Zea mays), 3'ss of exon 9
gtaagtgtttggtctatttattgtgtttggatataatccttgacttcttatgtataaatgatagtccttgctaattgtttccaatggtcatcatctatcagATGTTAGCAAAGAAGGTAGATACATTGACCAAAGCCATGGAAGTTGAGGCAAAGAAGATGAGAAGGGAAGTAGCTGCTATGGAGAAGGAGGTAGCTGCTA
||| | ||    |   ||  || |  | |   |   |  | ||    |      |||||  |  |  ||   || | |    |    |  |  |||  ||||||||||||||||| ||||| || || |||||||| |||||||| ||||| |  ||| | ||| | || || || || |||||||| || || || || |
gtatgcgtccatttctttccttat--tcgttcactttagtggatagttagc---taaatactgattattatgaagtttgcttatctattgttgtctggcagATGTTAGCAAAGAAAGTAGACACCTTAACCAAAGCAATGGAAGTGGAGGCTAGAAAGGTCAGACGAGAGGTTGCAGCCATGGAGAAAGAAGTTGCAGCAA

upper sequence: GLYMA02G09390.1 (Glycine max), 3'ss of exon 9
lower sequence: AT1G24764.1 (Arabidopsis thaliana), 3'ss of exon 9
gtaagtgtttggtctattta--ttgtgtttggatataatccttgacttcttatgtataaatgatagtccttgct--aattgtttccaatggtcat-catctat-----cagATGTTAGCAAAGAAGGTAGATACATTGACCAAAGCCATGGAAGTTGAGGCAAAGAAGATGAGAAGGGAAGTAGCTGCTATGGAGAAGGAGGTAGCTGCTA
||||| |||  || | ||||  || |||||   |||      | | | ||| | || | | ||   | |||| |  ||  |     | |  | || | |  ||      ||||| |||| |||||||| || ||||| || || || ||||| ||||| ||||||||||||||| ||||||||||||| ||||| || || || ||||| |
gtaagagttctgtttctttaagttctgtttctttatgccatattaat-cttgtttaaagaagaacattcttgttgtaaacggaggaagtaatgatacgttgatgttcgtagATGCTAGCGAAGAAGGTGGAAACATTAACAAAGGCAATGGAGGTTGAAGCAAAGAAGATGAGACGGGAAGTAGCTGCAATGGAAAAAGAAGTTGCTGCAA

upper sequence: GLYMA02G09390.1 (Glycine max), 3'ss of exon 9
lower sequence: AT2G01750.1 (Arabidopsis thaliana), 3'ss of exon 10
gtaagtgtttggtctatttattgtgtttggatataatccttgacttcttatgtataaatgatagtccttgct--aattgtttccaatggtcatcatctatcagATGTTAGCAAAGAAGGTAGATACATTGACCAAAGCCATGGAAGTTGAGGCAAAGAAGATGAGAAGGGAAGTAGCTGCTATGGAGAAGGAGGTAGCTGCTA
        || ||| |||  || |       |  ||     |  | ||||| | ||  | ||| ||  || |  || |  ||    | ||  |    | | ||||||| || |||||||| || ||| | || || || |||||||| || |||||||||||| |||| |||||||| || |||||||| |||||  | ||||
-------gttagtc-attagttttacacctttccaagaaacgtttgcttatatttattt-atattctctgatcaaaatacttgggcttgtgtttgctt-ttagATGTTGGCCAAGAAGGTTGAAACACTAACAAAGGCGATGGAAGTGGAAGCAAAGAAGATGCGAAGAGAAGTAGCAGCAATGGAGAAAGAGGTTTCAGCTA

upper sequence: GLYMA02G09390.1 (Glycine max), 3'ss of exon 9
lower sequence: AT1G14840.2 (Arabidopsis thaliana), 3'ss of exon 9
gtaagtgtttggtctatttattgtgtttggatataatccttgacttcttatgtataaatgatagtccttgctaattgtttcca-atggtcatcatctatc-agATGTTAGCAAAGAAGGTAGATACATTGACCAAAGCCATGGAAGTTGAGGCAAAGAAGATGAGAAGGGAAGTAGCTGCTATGGAGAAGGAGGTAGCTGCTA
      |||||  ||| |  |||   ||   |    | |||  |  | | | ||| ||   | ||      ||| | |    | ||||      | |||  ||||||| || |||||||| || ||||| || || || ||||| |||||||||||||||||| |||| ||||||||||  |||| ||| || || ||||| |
------gtttg--ctagtgtttggccttttttcctgttctttgccgcctttatatgaaatgttgtataatataagtctaaagatatgggttgtgtatatttagATGTTGGCCAAGAAGGTTGAAACATTAACAAAGGCGATGGACGTTGAGGCAAAGAAGATGCGAAGAGAAGTAGCTGTAATGGGGAAAGAAGTTGCTGCAA

upper sequence: GLYMA02G09390.1 (Glycine max), 3'ss of exon 9
lower sequence: AT1G68060.1 (Arabidopsis thaliana), 3'ss of exon 9
gtaagtgtttggtctatttattgtgtttggatataatccttgacttcttatgtataaatgatagtccttgctaattgtttccaatggtcatcatctatcagATGTTAGCAAAGAAGGTAGATACATTGACCAAAGCCATGGAAGTTGAGGCAAAGAAGATGAGAAGGGAAGTAGCTGCTATGGAGAAGGAGGTAGCTGCTA
                |  | | | | || || ||     | |  | || | || |||     ||   |  |    || |    || |  |  |||   ||||||||||||| ||||| || || || || || || ||||||||||| ||||||||||||||||||||||| ||||| |||||||| ||||| ||||| |
---------------gtaaaatctctctgaatgtaccatataaaatgttgt-taaaaagacgtgtttgtaatggaagtct----tgatatttttcttgtagATGTTAGCAAAAAAGGTTGAAACTTTAACAAAGGCAATGGAAGTTGAAGCAAAGAAGATGAGAAGGGAAGTGGCTGCAATGGAGAAAGAGGTTGCTGCAA

upper sequence: GLYMA02G09390.1 (Glycine max), 3'ss of exon 9
lower sequence: Vv01s0011g05790.t01 (Vitis vinifera), 3'ss of exon 9
gtaagtgtttggtctatttattgtgtttggatataatccttgacttcttatgtataaatgatagtccttgctaattgtttccaatggtcatcatctatcagATGTTAGCAAAGAAGGTAGATACATTGACCAAAGCCATGGAAGTTGAGGCAAAGAAGATGAGAAGGGAAGTAGCTGCTATGGAGAAGGAGGTAGCTGCTA
                 ||  | |  |||     |     || ||| | |||  | |||     |  ||||| || || |      || ||  | | ||||||| |||| ||||||||||||||||| ||||| || |||||||||||||| |||||||||||||||||||| ||||| |||||||||||||||||||| |
----------------gttggtattcttgtcctca---tctgtcttatgatgctttaattcatatttttgctcat-gtatttggatgtaattctttttcagATGCTAGCTAAGAAGGTAGATACATTAACCAAGGCAATGGAAGTTGAGGCTAAGAAGATGAGAAGGGAAGTTGCTGCCATGGAGAAGGAGGTAGCTGCCA

upper sequence: GLYMA02G09390.1 (Glycine max), 3'ss of exon 9
lower sequence: PP1S136_188V6.1 (Physcomitrella patens), 3'ss of exon 9
--------------------------------------------------------------------------------------gtaagtgtttggtctatttattgtgtttggatataatcctt--gacttcttatgtataaatgatagtc-------cttgctaattgtttccaatg-gtcatcatctat-cagATGTTAGCAAAGAAGGTAGATACATTGACCAAAGCCATGGAAGTTGAGGCAAAGAAGATGAGAAGGGAAGTAGCTGCTATGGAGAAGGAGGTAGCTGCTA
                                                                                       ||  | |    |  |  ||||||  ||   |   | | |   |  ||  | | | | |    || ||       |||  |   || ||| |||| ||  | || | | |||||| |  ||||||| || || || ||  | || ||  |||||||||||| ||||||||||||||| |||||    || ||||||||||| || ||  |  
gtgcgtatagggtaaactacatcttactagcatatgaatacttctctgcttagtgagttttgcattgatttttgaacaacttgattatatttatcgactgcagatattgttgttacctcgtaccttcccggtttgctgtttttgacatgtattcacgctggcttcgtggctgcttctaatgtgttctgatatgtgcagATGCTCTCAAAGAAAGTCGACACTTTATCTAAGGCTTTGGAAGTTGAGGGAAAGAAGATGAGAAGAGAAGTCCAAGCAATGGAGAAGGAAGTTGCCACCC

upper sequence: GLYMA02G09390.1 (Glycine max), 3'ss of exon 9
lower sequence: EFJ18059 (Selaginella moellendorffii), 3'ss of exon 9
gtaagtgtttggtctatttattgtgtttggatataatccttgacttcttatgtataaatgatagtccttgctaattgtttccaatggtcatcatctatcagATGTTAGCAAAGAAGGTAGATACATTGACCAAAGCCATGGAAGTTGAGGCAAAGAAGATGAGAAGGGAAGTAGCTGCTATGGAGAAGGAGGTAGCTGCTA
                                                ||||  |   |  | |  || | |  |  |  |    || | |   |   |||||| |  | |||||||| |||||  ||||||| || |||||||| ||||| ||||||||| | ||||| ||||| || |||||||||||||| || || |
---------------------------------------------gtatatgcgtgggtt-tggctctaggtgctcatgacagtcggacttttgcatgcagATGCTGTCCAAGAAGGTGGATACGCTGACCAAGGCAATGGAAGTAGAGGCGAAGAAGATGCGTAGGGAGGTAGCAGCAATGGAGAAGGAGGTGGCCGCGA

upper sequence: GLYMA02G09390.1 (Glycine max), 3'ss of exon 9
lower sequence: EFJ36655 (Selaginella moellendorffii), 3'ss of exon 9
gtaagtgtttggtctatttattgtgtttggatataatccttgacttcttatgtataaatgatagtccttgctaattgtttccaatggtcatcatctatcagATGTTAGCAAAGAAGGTAGATACATTGACCAAAGCCATGGAAGTTGAGGCAAAGAAGATGAGAAGGGAAGTAGCTGCTATGGAGAAGGAGGTAGCTGCTA
                                                ||||  |   |  | |  || | |  |  |  |    || | |   |   |||||| |  | |||||||| |||||  ||||||| || |||||||| ||||| ||||||||| | ||||| |||||  | |||||||||||||| || || |
---------------------------------------------gtatatgcgtgggtt-tggctctaggtgctcatgacagtcggacttttgcatgcagATGCTGTCCAAGAAGGTGGATACGCTGACCAAGGCAATGGAAGTAGAGGCGAAGAAGATGCGTAGGGAGGTAGCAACAATGGAGAAGGAGGTGGCCGCGA

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|208262955|gb|GE062431.1|GE062431
EST:     CTAAAAGATAAAGATGATGCTATTGAG                         ATGTTAGCAAAGAAGGTAGATACATTGACCAAAGCCATGGAAGTTGAGGCA
genomic: CTAAAAGATAAAGATGATGCTATTGAGgtaagtgttt ... catctatcagATGTTAGCAAAGAAGGTAGATACATTGACCAAAGCCATGGAAGTTGAGGCA
EST: gi|20075796|gb|BQ094579.1|BQ094579
EST:     CTGGTCACGAGAAAGATCAAAGCCTAAAAGATAAAGATGATGCTATTGAG                         ATGTTAGCAAAGAAGGTAGATACATTGACCAAAGCCATGGAAGTTGAGGCA
genomic: CTGGTCACGAGAAAGATCAAAGCCTAAAAGATAAAGATGATGCTATTGAGgtaagtgttt ... catctatcagATGTTAGCAAAGAAGGTAGATACATTGACCAAAGCCATGGAAGTTGAGGCA
EST: gi|23732761|gb|BU764555.1|BU764555
EST:     CTGGTCACGAGAAAGATCAAAGCCTAAAAGATAAAGATGATGCTATTGAG                         ATGTTAGCAAAGAAGGTAGATACATTGACCAAAGCCATGGAAGTTGAGGCA
genomic: CTGGTCACGAGAAAGATCAAAGCCTAAAAGATAAAGATGATGCTATTGAGgtaagtgttt ... catctatcagATGTTAGCAAAGAAGGTAGATACATTGACCAAAGCCATGGAAGTTGAGGCA
EST: gi|11274709|gb|BF325044.1|BF325044
EST:     CTGGTCACGAGAAAGATCAAAGCCTAAAAGATAAAGATGATGCTATTGAG                         ATGTTAGCAAAGAAGGTAGATACATTGACCAAAGCCATGGAAGTTGAGGCA
genomic: CTGGTCACGAGAAAGATCAAAGCCTAAAAGATAAAGATGATGCTATTGAGgtaagtgttt ... catctatcagATGTTAGCAAAGAAGGTAGATACATTGACCAAAGCCATGGAAGTTGAGGCA
EST: gi|298195439|gb|HO039270.1|HO039270
EST:     CTGGTCACGAGAAAGATCAAAGCCTAAAAGATAAAGATGATGCTATTGAG                         ATGTTAGCAAAGAAGGTAGATACATTGACCAAAGCCATGGAAGTTGAGGCA
genomic: CTGGTCACGAGAAAGATCAAAGCCTAAAAGATAAAGATGATGCTATTGAGgtaagtgttt ... catctatcagATGTTAGCAAAGAAGGTAGATACATTGACCAAAGCCATGGAAGTTGAGGCA
EST: gi|14011056|gb|BG725978.1|BG725978
EST:     CTGGTCACGAGAAAGATCAAAGCCTAAAAGATAAAGATGATGCTATTGAG                         ATGTTAGCAAAGAAGGTAGATACATTGACCAAAGCCATGGAAGTTGAGGCA
genomic: CTGGTCACGAGAAAGATCAAAGCCTAAAAGATAAAGATGATGCTATTGAGgtaagtgttt ... catctatcagATGTTAGCAAAGAAGGTAGATACATTGACCAAAGCCATGGAAGTTGAGGCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cttatgtataaatgatagtccttgctaattgtttccaatggtcatcatctatcagATGTTAGCAAAGAAGGTAGATACATTGACCAAAGCCATGGAAGTTGAGGCAAAGAAGATGAGAAGGGAAGTAGCTGCTATGGAGAAGGAGGTAGCTGCTA
                      tgctaat  putative branch site (score: 2)
      tataaatgata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagtgtttggtctatttattgtgtttggatataatccttgacttcttatgtataaatgatagtccttgctaattgtttccaatggtcatcatctatcagATGTTAGCAAAGAAGGTAGATACATTGACCAAAGCCATGGAAGTTGAGGCAAAGAAGATGAGAAGGGAAGTAGCTGCTATGGAGAAGGAGGTAGCTGCTA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT