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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tctagggagtttagtcatgctaaatgttttatgattaatcgcatttgtctctggttattagtctatgaattgaagtgacacataatttaatgttttgcagTGAAATTGCAAAGCATCTTTCACTTCCACCAGTCAAGCTTCACTGCAGCATGCTTGCTGAGGATGCTATAAAAGCAGCTGTTAAAGATTATGAAGCTAAG

Basic information

species Glycine max
transcript GLYMA06G19310.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA06G19310.1 (Glycine max), 3'ss of exon 2
lower sequence: PP1S76_212V6.1 (Physcomitrella patens), 3'ss of exon 4
tctagggagtttagtcatgctaaatgttttatgattaatcgcatttgtctctggttattagtctatgaattgaagtg-acacataatttaatgttttgcagTGAAATTGCAAAGCATCTTTCACTTCCACCAGTCAAGCTTCACTGCAGCATGCTTGCTGAGGATGCTATAAAAGCAGCTGTTAAAGATTATGAAGCTAAG
  | |   |  | |     |  | ||| |  |      ||  |      | || |  | ||  ||| | || ||  |     ||   | ||  || |||||||| || || ||||| || || || ||||| || ||| | |||||||||||||||||||| |||||||| ||||| || || || || ||  |  | |||
attggttggcatggattaccgcagtgtgtcttaggccctcagaac-aaatgtgttcctaaggatataagttaaatggtggggatgtgtgaactttctgcagTGACATCGCCAAGCACCTATCTCTGCCACCTGTGAAGTTGCACTGCAGCATGCTTGCTGAAGATGCTATCAAAGCGGCGGTGAAGGACTACAAGTCCAAG

upper sequence: GLYMA06G19310.1 (Glycine max), 3'ss of exon 2
lower sequence: PP1S39_352V6.2 (Physcomitrella patens), 3'ss of exon 4
-tctagggagtttagtcatgctaaatgttttatgattaatcgcat-ttgtctctggttattagtctatgaattgaagtgacacataatttaatgttttgcagTGAAATTGCAAAGCATCTTTCACTTCCACCAGTCAAGCTTCACTGCAGCATGCTTGCTGAGGATGCTATAAAAGCAGCTGTTAAAGATTATGAAGCTAAG
 | ||    |  |  |  || | | |  ||||||  |  |  | | || ||  |  |  ||     || ||   | |||         ||  | ||||||||||| ||||| || ||| | ||  | ||||| || ||| | ||||||||||||||||||||||||||||| ||||| ||||| || || ||  | ||||| 
gtgtacaaggcattat-gtg-tgagtactttatgggtgttgacctattttccattatgcttgaaagattaaagcatgtggtgtgggtattttttttttgcagTGATATTGCCAAACATTTGTCTTTGCCACCTGTGAAGTTGCACTGCAGCATGCTTGCTGAGGATGCTATTAAAGCGGCTGTGAAGGACTACAAGGCTAAA

upper sequence: GLYMA06G19310.1 (Glycine max), 3'ss of exon 2
lower sequence: EFJ10697 (Selaginella moellendorffii), 3'ss of exon 2
tctagggagtttagtcatgctaaatgttttatgattaatcgcatttgtctctggttattagtctatgaattgaagtgacacataatttaatgttttgcagTGAAATTGCAAAGCATCTTTCACTTCCACCAGTCAAGCTTCACTGCAGCATGCTTGCTGAGGATGCTATAAAAGCAGCTGTTAAAGATTATGAAGCTAAG
                                      |  | ||| |   ||        |||  ||    |||   | |     ||  |  || ||||||| || || |||||||| || || || ||||| ||||| ||||||||||||||||| |||||||| || ||||| ||  | |||||||| || || |||
-------------------------------------gtaacttttcttcttgagaggatttctccgaggctaagct-ctctcctctttcttcttcgcagTGACATCGCCAAGCATCTGTCGCTGCCGCCAGTGAAGCTCCACTGCAGCATGCTTGCCGAGGATGCGATCAAAGCCGCGATCAAAGATTACGACGCGAAG

upper sequence: GLYMA06G19310.1 (Glycine max), 3'ss of exon 2
lower sequence: EFJ35746 (Selaginella moellendorffii), 3'ss of exon 2
tctagggagtttagtcatgctaaatgttttatgattaatcgcatttgtctctggttattagtctatgaattgaagtgacacataatttaatgttttgcagTGAAATTGCAAAGCATCTTTCACTTCCACCAGTCAAGCTTCACTGCAGCATGCTTGCTGAGGATGCTATAAAAGCAGCTGTTAAAGATTATGAAGCTAAG
                                      |    ||| |   ||        | |  ||    |||   ||      ||  |  || ||||||| || || |||||||| || || || ||||| ||||| ||||||||||||||||| |||||||| || ||||| ||  | |||||||| || || |||
-------------------------------------gtaatttttcttcttgagaggatttttccgaggctaagct-cattcctctttcttcttcgcagTGACATCGCCAAGCATCTGTCGCTACCGCCAGTGAAGCTCCACTGCAGCATGCTTGCCGAGGATGCGATCAAAGCCGCGATCAAAGATTACGACGCCAAG

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|6725217|gb|AW309616.1|AW309616
EST:     TGGGTGAAGGGAAAGCAAATGGAGGAAGTTTTGACCA-TAAAAAC-C                         TGAATTTGCAAAGCATCTTTCACTT-CACCCAGTCAAGCTTCACTGCAGCA
genomic: TGGGTGAAGGGAAAGCAAATGGAGGAAGTTTTGACCATTAAAAACACgtgagtgcta ... tgttttgcagTGAAATTGCAAAGCATCTTTCACTTCCA-CCAGTCAAGCTTCACTGCAGCA
EST: gi|6566871|gb|AW234503.1|AW234503
EST:     GAATGGGTGAAGGGAAAGCAAATGGAGGAAGTTTTGACCATTAAAAACAC                         TGAAATTGCAAAGCATCTGTCACTTCCACCAGTCAAGCTTCACTGCAGCAT
genomic: GAATGGGTGAAGGGAAAGCAAATGGAGGAAGTTTTGACCATTAAAAACACgtgagtgcta ... tgttttgcagTGAAATTGCAAAGCATCTTTCACTTCCACCAGTCAAGCTTCACTGCAGCAT
EST: gi|193363052|gb|FK328816.1|FK328816
EST:     GAATGGGTGAAGGGAAAGCAAATGGAGGAAGTTTTGACCATCAAAAACAC                         TGAAATTGCAAAGCATCTTTCACTTCCACCAGTCAAGCTTCACTGCAGCAT
genomic: GAATGGGTGAAGGGAAAGCAAATGGAGGAAGTTTTGACCATTAAAAACACgtgagtgcta ... tgttttgcagTGAAATTGCAAAGCATCTTTCACTTCCACCAGTCAAGCTTCACTGCAGCAT
EST: gi|31305918|gb|CD391121.1|CD391121
EST:     GGGAAAGCAAATGGAGGAAGTTTTGACCATTAAAAACAC                         TGAAATTGCAAAGCATCTTTCACTTCCACCAGTCAAGCTTCACTGCAGCAT
genomic: GGGAAAGCAAATGGAGGAAGTTTTGACCATTAAAAACACgtgagtgcta ... tgttttgcagTGAAATTGCAAAGCATCTTTCACTTCCACCAGTCAAGCTTCACTGCAGCAT
EST: gi|16105635|gb|BI893375.1|BI893375
EST:     GAATGGGTGAAGGGAAAGCAAATGGAGGAAGTTTTGACCATTAAAAACAC                         TGAAATTGCAAAGCATCTTTCACTTCCACCAGTCAAGCTTCACTGCAGCAT
genomic: GAATGGGTGAAGGGAAAGCAAATGGAGGAAGTTTTGACCATTAAAAACACgtgagtgcta ... tgttttgcagTGAAATTGCAAAGCATCTTTCACTTCCACCAGTCAAGCTTCACTGCAGCAT
EST: gi|298167282|gb|HO010721.1|HO010721
EST:     GAATGGGTGAAGGGAAAGCAAATGGAGGAAGTTTTGACCATTAAAAACAC                         TGAAATTGCAAAGCATCTTTCACTTCCACCAGTCAAGCTTCACTGCAGCAT
genomic: GAATGGGTGAAGGGAAAGCAAATGGAGGAAGTTTTGACCATTAAAAACACgtgagtgcta ... tgttttgcagTGAAATTGCAAAGCATCTTTCACTTCCACCAGTCAAGCTTCACTGCAGCAT
EST: gi|31561265|gb|CD487103.1|CD487103
EST:     GGGAAAGCAAATGGAGGAGAGTTTTGACCATTAAAAACAC                         TGAAACTGCAAAGCATCTTTCACTTCCACCAGTCAAGCTTCACTGCAGCAT
genomic: GGGAAAGCAAATGGAGGA-AGTTTTGACCATTAAAAACACgtgagtgcta ... tgttttgcagTGAAATTGCAAAGCATCTTTCACTTCCACCAGTCAAGCTTCACTGCAGCAT
EST: gi|6566522|gb|AW234165.1|AW234165
EST:     GAATGGGTGAAGGGAAAGCAAATGGAGGAAGTTTTGACCATTAAAAACAC                         TGAAATTGCAAAGCATCTTTCACTTCCACCAGTCAAGCTTCACTGCAGCAT
genomic: GAATGGGTGAAGGGAAAGCAAATGGAGGAAGTTTTGACCATTAAAAACACgtgagtgcta ... tgttttgcagTGAAATTGCAAAGCATCTTTCACTTCCACCAGTCAAGCTTCACTGCAGCAT
EST: gi|31460265|gb|CD402233.1|CD402233
EST:     GAATGGGTGAAGGGAAAGCAAATGGAGGAAGTTTTGACCATTAAAAACAC                         TGAAATTGCAAAGCATCTTTCACTTCCACCAGTCAAGCTTCACTGCAGCAT
genomic: GAATGGGTGAAGGGAAAGCAAATGGAGGAAGTTTTGACCATTAAAAACACgtgagtgcta ... tgttttgcagTGAAATTGCAAAGCATCTTTCACTTCCACCAGTCAAGCTTCACTGCAGCAT
EST: gi|298174719|gb|HO014750.1|HO014750
EST:     GAATGGGTGAAGGGAAAGCAAATGGAGGAAGTTTTGACCATTAAAAACAC                         TGAAATTGCAAAGCATCTTTCACTTCCACCAGTCAAGCTTCACTGCAGCAT
genomic: GAATGGGTGAAGGGAAAGCAAATGGAGGAAGTTTTGACCATTAAAAACACgtgagtgcta ... tgttttgcagTGAAATTGCAAAGCATCTTTCACTTCCACCAGTCAAGCTTCACTGCAGCAT
EST: gi|254313658|gb|GR831287.1|GR831287
EST:     GAATGGGTGAAGGGAAAGCAAATGGAGGAAGTTTTGACCATTAAAAACAC                         TGAAATTGCAAAGCATCTTTCACTTCCACCAGTCAAGCTTCACTGCAGCAT
genomic: GAATGGGTGAAGGGAAAGCAAATGGAGGAAGTTTTGACCATTAAAAACACgtgagtgcta ... tgttttgcagTGAAATTGCAAAGCATCTTTCACTTCCACCAGTCAAGCTTCACTGCAGCAT
EST: gi|16343105|gb|BI968700.1|BI968700
EST:     GAATGGGTGAAGGGAAAGCAAATGGAGGAAGTTTTGACCATTAAAAACAC                         TGAAATTGCAAAGCATCTTTCACTTCCACCAGTCAAGCTTCACTGCAGCAT
genomic: GAATGGGTGAAGGGAAAGCAAATGGAGGAAGTTTTGACCATTAAAAACACgtgagtgcta ... tgttttgcagTGAAATTGCAAAGCATCTTTCACTTCCACCAGTCAAGCTTCACTGCAGCAT
EST: gi|20449069|gb|BQ253193.1|BQ253193
EST:     GAATGGGTGAAGGGAAAGCAAATGGAGGAAGTTTTGACCATTAAAAACAC                         TGAAATTGCAAAGCATCTTTCACTTCCACCAGTCAAGCTTCACTGCAGCAT
genomic: GAATGGGTGAAGGGAAAGCAAATGGAGGAAGTTTTGACCATTAAAAACACgtgagtgcta ... tgttttgcagTGAAATTGCAAAGCATCTTTCACTTCCACCAGTCAAGCTTCACTGCAGCAT
EST: gi|31459833|gb|CD401861.1|CD401861
EST:     GAATGGGTGAAGGGAAAGCAAATGGAGGAAGTTTTGACCATTAAAGACAC                         TGAAATGGCAAAGCATCTTTCACTTCCACCAGTCAAGCTTCACTGCAGCAT
genomic: GAATGGGTGAAGGGAAAGCAAATGGAGGAAGTTTTGACCATTAAAAACACgtgagtgcta ... tgttttgcagTGAAATTGCAAAGCATCTTTCACTTCCACCAGTCAAGCTTCACTGCAGCAT
EST: gi|192314955|gb|FK010773.1|FK010773
EST:     GGGTGAAGGGAAAGCAAATGGAGGAAGTTTTGACCATTAAAAACAC                         TGAAATTGCAAAGCATCTTTCACTTCCACCAGTCAAGCTTCACTGCAGCAT
genomic: GGGTGAAGGGAAAGCAAATGGAGGAAGTTTTGACCATTAAAAACACgtgagtgcta ... tgttttgcagTGAAATTGCAAAGCATCTTTCACTTCCACCAGTCAAGCTTCACTGCAGCAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgtctctggttattagtctatgaattgaagtgacacataatttaatgttttgcagTGAAATTGCAAAGCATCTTTCACTTCCACCAGTCAAGCTTCACTGCAGCATGCTTGCTGAGGATGCTATAAAAGCAGCTGTTAAAGATTATGAAGCTAAG
                                       atttaat  putative branch site (score: 4)
                                  acataatttaatgttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tctagggagtttagtcatgctaaatgttttatgattaatcgcatttgtctctggttattagtctatgaattgaagtgacacataatttaatgttttgcagTGAAATTGCAAAGCATCTTTCACTTCCACCAGTCAAGCTTCACTGCAGCATGCTTGCTGAGGATGCTATAAAAGCAGCTGTTAAAGATTATGAAGCTAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC
- - - - - - - tcatgct
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gtctatg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgacaca