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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gtatctggttgtcatgtgcctttaaacgcatctctgggctttcaattagtatttttcttgtcccactgttttcttaattgaattcttgttgcatccaaagCCAGGAGAATCCTTGAAGGATTTCTACAGGCGTACAAATATGTATTGGCAAATGGCAGCCCATGAACATACTCAACACACTGGAAAA

Basic information

species Glycine max
transcript GLYMA04G36770.1
intron # 17
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA04G36770.1 (Glycine max), 3'ss of exon 17
lower sequence: GRMZM2G100815_T01 (Zea mays), 3'ss of exon 14
-------------------------------------------------------------------------gtatctg-gttgtcatgtgcct----ttaaacgcatct---ctgggctttca--attagtatttttcttgtcc----cactgtttt-ctta-attgaattcttgttgcatccaaagCCAGGAGAATCCTTGAAGGATTTCTACAGGCGTACAAATATGTATTGGCAAATGGCAGCCCATGAACATACTCAACACACTGGAAAA
                                                                          | ||    |  |||| || ||    |  |||  |||    |    | |||   |   | | ||  |    ||     | |||||| |||| |||   || |  ||      |||||| ||||||||  |||  |||||||||| | | ||||||||||| ||||||||||| ||| |||| || ||||||||||||||||| 
gtaatgttgtacttagttttgtttattttctgtcacttctagatttattgctttccttttcattagctggctcctgtccatatcatcatatgtctgttctcgaacaaatcatggccaaccattcgttacctgcagttaacaaaaccaagatattgttttgcttatattttcttttgtttattctgaaagCCTGGAGAATCACTGAGAGATTTCTACAAGAGGACAAATATGTACTGGCAAATGGCTGCCTATGAGCACACTCAACACACTGGAAAG

upper sequence: GLYMA04G36770.1 (Glycine max), 3'ss of exon 17
lower sequence: AT5G50310.1 (Arabidopsis thaliana), 3'ss of exon 17
gtatctggttgtcatgtgcctttaaacgcatctctgggctttcaattagtatttttcttgtcccactgttttcttaattgaattcttgttgcatccaaagCCAGGAGAATCCTTGAAGGATTTCTACAGGCGTACAAATATGTATTGGCAAATGGCAGCCCATGAACATACTCAACACACTGGAAAA
   |  | ||||| |   | |||      ||      |  |   |     ||| |  |||   | |   |   ||  |     | ||||||  |   ||||| |||||| | |||||||||||||| | ||| ||||||||||| ||||||||||| ||| | || ||||| ||||| ||||| || 
--gtaagattgtcttcgccatttccttttattctgttgtctgagaaggagattctgtttgaagctcaactaatttggtca---tgttgttgtctttgaagCCTGGAGAAACTTTGAAGGATTTCTATAAGCGCACAAATATGTACTGGCAAATGGCTGCCTACGAGCATACCCAACATACTGGCAAG

upper sequence: GLYMA04G36770.1 (Glycine max), 3'ss of exon 17
lower sequence: Vv17s0000g10130.t01 (Vitis vinifera), 3'ss of exon 17
gtatctggttgtcatgtgcctttaaacgcatctctgggctttcaattagtatttttcttgtcccactgttttcttaattgaattcttgt----tgcatcc---aaagCCAGGAGAATCCTTGAAGGATTTCTACAGGCGTACAAATATGTATTGGCAAATGGCAGCCCATGAACATACTCAACACACTGGAAAA
        ||||  ||||| | |||| |||  | |   ||  || |   |   | || |    || |  ||| | || ||| | ||| |    || ||      ||||| |||||| |||||||||| ||||| | |||||| ||| |||| |||||||||||||| ||||| || ||||||||||||||||| 
------ttttgtgttgtgcatctaaaggcacatttaaactc-cattcttttcatctcatccatcattactttgtcaactgattgcttatcatttgtattttgtgaagCCTGGAGAAACCTTGAAGGACTTCTATAAGCGTACCAATTTGTACTGGCAAATGGCAGCACATGAGCACACTCAACACACTGGAAAG

upper sequence: GLYMA04G36770.1 (Glycine max), 3'ss of exon 17
lower sequence: PP1S15_393V6.2 (Physcomitrella patens), 3'ss of exon 18
-----------------------------gtatctgg-ttgtcatgtgcctttaaacgcatctctgggctttcaat-----tagtatttttcttgtcccactgttttcttaat-tgaattcttgttgcatccaaa--------gCCAGGAGAATCCTTGAAGGATTTCTACAGGCGTACAAATATGTATTGGCAAATGGCAGCCCATGAACATACTCAACACACTGGAAAA-------------
                              | || || || ||   ||||| ||||        |    ||||||      |||| | |||| | || || |  |     ||  |||| |    ||  |   |||        ||||||||||  |||||||||||| |     || ||||| ||||||||||||||||||||| | || || |||||||| ||||| |||             
gtacgtgcactattagttgacatttatgtttctccggcttatctgctgcctgtaaagagggggataatttttcaacgaagctagtttatttcgtttctcattactggagcaacatgaactgacattagaatgaaatgactgcagCCAGGAGAAAGCTTGAAGGATTTTTTTGCTCGAACAAACATGTATTGGCAAATGGCAGCCTACGAGCACACTCAACATACTGGCAAAGAACTACGGAAGG

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|9903008|gb|BE611976.1|BE611976
EST:     AGCAGATTAGAGCTAGTCTTGGCTTGTCAGATTCACAGAGAACACCCTCG                         CCAGGAGAATCCTTGAAGGATTTCTACAGGCGTACAAATATGTATTGGCAA
genomic: AGCAGATTAGAGCTAGTCTTGGCTTGTCAGATTCACAGAGAACACCCTCGgtaatatatt ... gcatccaaagCCAGGAGAATCCTTGAAGGATTTCTACAGGCGTACAAATATGTATTGGCAA
EST: gi|193480934|gb|FK444373.1|FK444373
EST:     GGCAGATTAGAGCTAGTCTTGGCTTGTCAGATTCACAGAGAACACCCTCG                         CCAGGAGAATCCTTGAAGGATTTCTACAGGCGTACAAATATGTATTGGCAA
genomic: AGCAGATTAGAGCTAGTCTTGGCTTGTCAGATTCACAGAGAACACCCTCGgtaatatatt ... gcatccaaagCCAGGAGAATCCTTGAAGGATTTCTACAGGCGTACAAATATGTATTGGCAA
EST: gi|11688791|gb|BF596467.1|BF596467
EST:     CTAGTCTCGGCTTGTCAGATTCACAGAGAACACCCTCG                         CCAGGAGAATCCTTGAAGGATTTCTACAGGCGTACAAATATGTATTGGCAA
genomic: CTAGTCTTGGCTTGTCAGATTCACAGAGAACACCCTCGgtaatatatt ... gcatccaaagCCAGGAGAATCCTTGAAGGATTTCTACAGGCGTACAAATATGTATTGGCAA
EST: gi|21286225|gb|BQ474096.1|BQ474096
EST:     AGCAGATTAGAGCTAGTCTTGGCTTGTCAGATTCACAGAGAACACCCTCG                         CCAGGAGAATCCTTGAAGGATTTCTACAGGCGTACAAATATGTATTGGCAA
genomic: AGCAGATTAGAGCTAGTCTTGGCTTGTCAGATTCACAGAGAACACCCTCGgtaatatatt ... gcatccaaagCCAGGAGAATCCTTGAAGGATTTCTACAGGCGTACAAATATGTATTGGCAA
EST: gi|26048263|gb|CA784790.1|CA784790
EST:     AGCAGATTAGAGCTAGTCTTGGCTTGTCAGATTCACAGAGAACACCCTCG                         CCAGGAGAATCCTTGAAGGATTTCTACAGGCGTACAAATATGTATTGGCAA
genomic: AGCAGATTAGAGCTAGTCTTGGCTTGTCAGATTCACAGAGAACACCCTCGgtaatatatt ... gcatccaaagCCAGGAGAATCCTTGAAGGATTTCTACAGGCGTACAAATATGTATTGGCAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttagtatttttcttgtcccactgttttcttaattgaattcttgttgcatccaaagCCAGGAGAATCCTTGAAGGATTTCTACAGGCGTACAAATATGTATTGGCAAATGGCAGCCCATGAACATACTCAACACACTGGAAAA
                          tcttaat  putative branch site (score: 3)
                       ttttcttaattgaatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatctggttgtcatgtgcctttaaacgcatctctgggctttcaattagtatttttcttgtcccactgttttcttaattgaattcttgttgcatccaaagCCAGGAGAATCCTTGAAGGATTTCTACAGGCGTACAAATATGTATTGGCAAATGGCAGCCCATGAACATACTCAACACACTGGAAAA

- -tctggtt
- - - - - - catgtgc
- - - - - - - - - - - - - - - - - - -gctttca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgaattc