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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtccactagacttctatgtgtgtgcataaaatattagtaaagaggccactcctcttctatgctcctcattgtgactttgtattttagGGATGTCAAATACCATGAACCTGAGTTTTGGAAGTTTGGAGAAGAGGGGAACAAATACTTCCGACATGCAACTGGGCAGATATATGCAATCTCAAAGGAT

Basic information

species Glycine max
transcript GLYMA04G43340.2
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA04G43340.2 (Glycine max), 3'ss of exon 8
lower sequence: LOC_Os09g27950.1 (Oryza sativa), 3'ss of exon 8
---------gtaagtccactagacttctatgtgtgtgcataaaatattagtaaagaggccactcctcttctatgctcctcattgtgactttgtattttagGGATGTCAAATACCATGAACCTGAGTTTTGGAAGTTTGGAGAAGAGGGGAACAAATACTTCCGACATGCAACTGGGCAGATATATGCAATCTCAAAGGAT
          |     ||  | |   |||  | ||        ||  ||  |||        | ||  | |    |  ||  ||   |||| |||   ||  |||| |||||||| || |||||||| ||||||||||| ||||| |||||||| || ||||| ||||| ||||||||||||||||| ||||||||||| 
gtaaatattctggaaacaacataaaactacttctggaagctccatcgtatgaaatctctagatgctaatattcatttttccctgcatctttttatc--agAAATGTGAAATACCACGAGCCTGAGTTCTGGAAGTTTGGCGAAGACGGGAACAAGTATTTCCGCCATGCCACTGGGCAGATATATGCCATCTCAAAGGAC

upper sequence: GLYMA04G43340.2 (Glycine max), 3'ss of exon 8
lower sequence: LOC_Os02g35870.1 (Oryza sativa), 3'ss of exon 8
gtaagtccactagacttctatgtgtgtgcataaaatattagtaaagaggccactcctcttctatgctcctcattgtgactttgtattttagGGATGTCAAATACCATGAACCTGAGTTTTGGAAGTTTGGAGAAGAGGGGAACAAATACTTCCGACATGCAACTGGGCAGATATATGCAATCTCAAAGGAT
    ||    |  ||| |  | | |    ||  ||  ||       ||           | | ||||    | ||   | ||  ||   ||| |||| || ||||||||||||||||  ||||| ||||| || || ||||||||||||||||| ||||| |||||||||||||| || || ||||| || 
----gtaacgttaactcccctatcttgaaatttaaatttgacttgtagcttgaagtaaatgtctgcttga-actggctcctttcatac-agGAATGTGAAGTACCATGAACCTGAGTACTGGAAATTTGGGGAGGAAGGGAACAAATACTTCCGTCATGCTACTGGGCAGATATACGCGATTTCAAAAGAC

upper sequence: GLYMA04G43340.2 (Glycine max), 3'ss of exon 8
lower sequence: GRMZM2G133613_T01 (Zea mays), 3'ss of exon 8
--gtaagtccactagacttctatgt-gtgt-gcat---aaaatattagtaaagaggccactcctcttct----atgctcctcattgtgactttgtattttagGGATGTCAAATACCATGAACCTGAGTTTTGGAAGTTTGGAGAAGAGGGGAACAAATACTTCCGACATGCAACTGGGCAGATATATGCAATCTCAAAGGAT
   ||| | |    ||     | |  | |  ||||   ||   | | ||  | |  |||  | || | |    || |   |  |  |        |  | ||| |||  ||||||||||| |||||||| |||||||| ||||| || |||||||| |||||||| || || || ||||||||||| || ||||| ||||| 
gtataaattcctctgaaaaaaaagcagcgcagcattcgaattgaatcgtcgaaataccagccttcgttttgacatacatgttttctttttcccccacatcagGAATGCGAAATACCATGAGCCTGAGTTCTGGAAGTTCGGAGAGGACGGGAACAAGTACTTCCGCCACGCCACGGGGCAGATATACGCCATCTCCAAGGAC

upper sequence: GLYMA04G43340.2 (Glycine max), 3'ss of exon 8
lower sequence: GRMZM2G013079_T01 (Zea mays), 3'ss of exon 8
---gtaagtccactagacttctatgtgtgtgcataaaata--ttagtaaagaggccactcctcttctatgctcctcattgtgactt-tgtattt---tagGGATGTCAAATACCATGAACCTGAGTTTTGGAAGTTTGGAGAAGAGGGGAACAAATACTTCCGACATGCAACTGGGCAGATATATGCAATCTCAAAGGAT
     ||||    |    |||||      | || | |  |  | ||  |  ||          |  |     |||  |||   ||| | ||||    |||| |||| || ||||||||||||||||  ||||| ||||| || || || || ||||||||||| ||||| || |||||||||||||| || || || |||
atgacaagtaatgtttgtttctacactgttacaaacatgagttcagacactagattgaagtattaattgaggcctgcttgaaccttctctattcatatagGAATGTTAAGTACCATGAACCTGAGTACTGGAAATTTGGGGAGGAAGGAAATAAATACTTCCGTCATGCCACGGGGCAGATATATGCCATTTCGAAAGAT

upper sequence: GLYMA04G43340.2 (Glycine max), 3'ss of exon 8
lower sequence: GRMZM2G070708_T02 (Zea mays), 3'ss of exon 8
gtaagtccactagacttctatgtgtgtgcataaaatattagtaaagaggccactcctcttctatgct--cctcattgtgactttgtattttagGGATGTCAAATACCATGAACCTGAGTTTTGGAAGTTTGGAGAAGAGGGGAACAAATACTTCCGACATGCAACTGGGCAGATATATGCAATCTCAAAGGAT
    ||    |  |||||||    |||   || || || | |  |   || |    |  |  | ||   | | |   ||   |  |  | |||| |||| || ||||||||||||||||  ||||| ||||| || || || || || |||||||| ||||| || |||||||||||||| || || || |||
----gtaatgtttacttctacac-tgt---tacaacatgaattcaagcgctagatttgatagaggcctgcttgaacctgctctattcatatagGAATGTGAAGTACCATGAACCTGAGTACTGGAAATTTGGGGAGGAAGGAAATAAGTACTTCCGTCATGCTACAGGGCAGATATATGCCATTTCGAAAGAT

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|298180725|gb|HO022164.1|HO022164
EST:     CCCAGGGTCTACATTGGGTGTATGAAATCTGGACCTGTCCTTTCTAGAAA                         GGATGTCAAATACCATGAACCTGAGTTTTGGAAGTTTGGAGAAGAGGGGAA
genomic: CCCAGGGTCTACATTGGGTGTATGAAATCTGGACCTGTCCTTTCTAGAAAgtaagtccac ... tgtattttagGGATGTCAAATACCATGAACCTGAGTTTTGGAAGTTTGGAGAAGAGGGGAA
EST: gi|41146199|gb|CK606410.1|CK606410
EST:     GGGTGTATGAAATCTGGACCTGTCCTTTCTAGAAA                         GGATGTCAAATACCATGAACCTGAGTTTTGGAAGTTTGGAGAAGAGGGGAA
genomic: GGGTGTATGAAATCTGGACCTGTCCTTTCTAGAAAgtaagtccac ... tgtattttagGGATGTCAAATACCATGAACCTGAGTTTTGGAAGTTTGGAGAAGAGGGGAA
EST: gi|8827480|gb|BE211210.1|BE211210
EST:     CCCAGGGTCTACATTGGGTGTATGAAATCTGGACCTGTCCTTTCTAGAAA                         GGATGTCAAATACCATGAACCTGAGTTTTGGAAGTTTGGAGAAGAGGGGAA
genomic: CCCAGGGTCTACATTGGGTGTATGAAATCTGGACCTGTCCTTTCTAGAAAgtaagtccac ... tgtattttagGGATGTCAAATACCATGAACCTGAGTTTTGGAAGTTTGGAGAAGAGGGGAA
EST: gi|151395197|gb|EV265068.1|EV265068
EST:     CCCAGGGTCTACATTGGGTGTATGAAATCTGGACCTGTCCTTTCTAGAAA                         GGATGTCAAATACCATGAACCTGAGTTTTGG
genomic: CCCAGGGTCTACATTGGGTGTATGAAATCTGGACCTGTCCTTTCTAGAAAgtaagtccac ... tgtattttagGGATGTCAAATACCATGAACCTGAGTTTTGG
EST: gi|51337140|gb|CO981006.1|CO981006
EST:     CCCAGGGTCTACATTGGGTGTATGAAATCTGGACCTGTCCTTTCTAGAAA                         GGATGTCAAATACCATGAACCTGAGTTTTGGAAGTTTGGAGAAGAGGGGAA
genomic: CCCAGGGTCTACATTGGGTGTATGAAATCTGGACCTGTCCTTTCTAGAAAgtaagtccac ... tgtattttagGGATGTCAAATACCATGAACCTGAGTTTTGGAAGTTTGGAGAAGAGGGGAA
EST: gi|151412778|gb|EV282590.1|EV282590
EST:     CCCAGGGTCTACATTGGGTGTATGAAATCTGGACCTGTCCTTTCTAGAAA                         GGATGTCAAATACCATGAACCTGAGTTTTGGAAGTTTGGAGAAGAGGGGAA
genomic: CCCAGGGTCTACATTGGGTGTATGAAATCTGGACCTGTCCTTTCTAGAAAgtaagtccac ... tgtattttagGGATGTCAAATACCATGAACCTGAGTTTTGGAAGTTTGGAGAAGAGGGGAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

attagtaaagaggccactcctcttctatgctcctcattgtgactttgtattttagGGATGTCAAATACCATGAACCTGAGTTTTGGAAGTTTGGAGAAGAGGGGAACAAATACTTCCGACATGCAACTGGGCAGATATATGCAATCTCAAAGGAT
                                           tttgtatttta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagtccactagacttctatgtgtgtgcataaaatattagtaaagaggccactcctcttctatgctcctcattgtgactttgtattttagGGATGTCAAATACCATGAACCTGAGTTTTGGAAGTTTGGAGAAGAGGGGAACAAATACTTCCGACATGCAACTGGGCAGATATATGCAATCTCAAAGGAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGAT