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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...agcttagtcatgctaaaggttttattattaatcacatttgtctccacctctccggttattagtttatgaattgaagtgacacataatgaatgtttttcagTGAAATTGCAAAGCATCTTTCACTTCCACCAGTCAAGCTTCACTGCAGCATGCTTGCTGAGGATGCTATAAAAGCAGCTGTTAAAGATTATGAAGCTAAG

Basic information

species Glycine max
transcript GLYMA13G21010.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA13G21010.1 (Glycine max), 3'ss of exon 2
lower sequence: PP1S76_212V6.1 (Physcomitrella patens), 3'ss of exon 4
agcttagtcatgctaaaggttttattattaatcacatttgtctccacctctccggttattagtttatgaattgaa--gtgacacataatgaatgtttttcagTGAAATTGCAAAGCATCTTTCACTTCCACCAGTCAAGCTTCACTGCAGCATGCTTGCTGAGGATGCTATAAAAGCAGCTGTTAAAGATTATGAAGCTAAG
   |   |       |       | | |   | |      ||   ||   |  | |  | ||  ||| | || ||  |||        ||||  || | |||||| || || ||||| || || || ||||| || ||| | |||||||||||||||||||| |||||||| ||||| || || || || ||  |  | |||
-attggttggcatggattaccgcagtgtgtcttaggccc-tcagaacaaatgtgttcctaaggatataagttaaatggtggggatgtgtgaactttctgcagTGACATCGCCAAGCACCTATCTCTGCCACCTGTGAAGTTGCACTGCAGCATGCTTGCTGAAGATGCTATCAAAGCGGCGGTGAAGGACTACAAGTCCAAG

upper sequence: GLYMA13G21010.1 (Glycine max), 3'ss of exon 2
lower sequence: PP1S39_352V6.2 (Physcomitrella patens), 3'ss of exon 4
agcttagtcatgctaaaggttttattattaatcacattt---gtctccacctctccggttattagtttatgaattgaagtgacacataatgaatgttttt------cagTGAAATTGCAAAGCATCTTTCACTTCCACCAGTCAAGCTTCACTGCAGCATGCTTGCTGAGGATGCTATAAAAGCAGCTGTTAAAGATTATGAAGCTAAG
          ||   ||||  ||||   | |  || ||    || |  |||| |       |  | ||   |  | ||   |       ||  | |||||      |||||| ||||| || ||| | ||  | ||||| || ||| | ||||||||||||||||||||||||||||| ||||| ||||| || || ||  | ||||| 
---------gtgtacaaggcattatgtgtgagtactttatgggtgttgacctattttccattatgcttgaaagattaaagcatgtggtgtgggtattttttttttgcagTGATATTGCCAAACATTTGTCTTTGCCACCTGTGAAGTTGCACTGCAGCATGCTTGCTGAGGATGCTATTAAAGCGGCTGTGAAGGACTACAAGGCTAAA

upper sequence: GLYMA13G21010.1 (Glycine max), 3'ss of exon 2
lower sequence: EFJ10697 (Selaginella moellendorffii), 3'ss of exon 2
agcttagtcatgctaaaggttttattattaatcacatttgtctccacctctccggttattagtttatgaattgaagtgacacataatgaatgtttttcagTGAAATTGCAAAGCATCTTTCACTTCCACCAGTCAAGCTTCACTGCAGCATGCTTGCTGAGGATGCTATAAAAGCAGCTGTTAAAGATTATGAAGCTAAG
                                      |  ||   | |||   |    |  | |  ||    |||          |   |  ||  |||||| || || |||||||| || || || ||||| ||||| ||||||||||||||||| |||||||| || ||||| ||  | |||||||| || || |||
-------------------------------------gtaacttttcttcttgagaggatt-tctccgaggctaagctctctcctctttcttcttcgcagTGACATCGCCAAGCATCTGTCGCTGCCGCCAGTGAAGCTCCACTGCAGCATGCTTGCCGAGGATGCGATCAAAGCCGCGATCAAAGATTACGACGCGAAG

upper sequence: GLYMA13G21010.1 (Glycine max), 3'ss of exon 2
lower sequence: EFJ35746 (Selaginella moellendorffii), 3'ss of exon 2
agcttagtcatgctaaaggttttattattaatcacatttgtctccacctctccggttattagtttatgaattgaagtgacacataatgaatgtttttcagTGAAATTGCAAAGCATCTTTCACTTCCACCAGTCAAGCTTCACTGCAGCATGCTTGCTGAGGATGCTATAAAAGCAGCTGTTAAAGATTATGAAGCTAAG
                                      |   |   | |||   |    |  ||       | |  | |  | |  |   |  ||  |||||| || || |||||||| || || || ||||| ||||| ||||||||||||||||| |||||||| || ||||| ||  | |||||||| || || |||
-------------------------------------gtaatttttcttcttgagaggatttttccgaggctaagctcattcctctttc-ttcttcgcagTGACATCGCCAAGCATCTGTCGCTACCGCCAGTGAAGCTCCACTGCAGCATGCTTGCCGAGGATGCGATCAAAGCCGCGATCAAAGATTACGACGCCAAG

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|17023300|gb|BM094334.1|BM094334
EST:     GAATGGGTTAAGGAAAAGCAAATAGAGGAAGTTTTGACCATTAAAAACAC                         TGAAATTGCAAAGCATCTTTCACTTCCACCAGTCAAGCTTCACTGCAGCAT
genomic: GAATGGGTTAAGGAAAAGCAAATAGAGGAAGTTTTGACCATTAAAAACACgtgagtactt ... tgtttttcagTGAAATTGCAAAGCATCTTTCACTTCCACCAGTCAAGCTTCACTGCAGCAT
EST: gi|298182640|gb|HO031375.1|HO031375
EST:     GAATGGGTTAAGGAAAAGCAAATAGAGGAAGTTTTGACCATTAAAAACAC                         TGAAATTGCAAAGCATCTTTCACTTCCACCAGTCAAGCTTCACTGCAGCAT
genomic: GAATGGGTTAAGGAAAAGCAAATAGAGGAAGTTTTGACCATTAAAAACACgtgagtactt ... tgtttttcagTGAAATTGCAAAGCATCTTTCACTTCCACCAGTCAAGCTTCACTGCAGCAT
EST: gi|17400360|gb|BM177142.1|BM177142
EST:     GAATGGGTTAAGGAAAAGCAAATAGAGGAAGTTTTGACCATTAAAAACAC                         TGAAATTGCAAAGCATCTTTCACTTCCACCAGTCAAGCTTCACTGCAGCAT
genomic: GAATGGGTTAAGGAAAAGCAAATAGAGGAAGTTTTGACCATTAAAAACACgtgagtactt ... tgtttttcagTGAAATTGCAAAGCATCTTTCACTTCCACCAGTCAAGCTTCACTGCAGCAT
EST: gi|26269121|gb|CA820184.1|CA820184
EST:     GAATGGGTTAAGGAAAAGCAAATAGAGGAAGTTTTGACCATTAAAAACAC                         TGAAATTGCAAAGCATCTTTCACTTCCACCAGTCAAGCTTCACTGCAGCAT
genomic: GAATGGGTTAAGGAAAAGCAAATAGAGGAAGTTTTGACCATTAAAAACACgtgagtactt ... tgtttttcagTGAAATTGCAAAGCATCTTTCACTTCCACCAGTCAAGCTTCACTGCAGCAT
EST: gi|16106168|gb|BI893908.1|BI893908
EST:     GAATGGGTTAAGGAAAAGCAAATAGAGGAAGTTTTGACCATTAAAAACAC                         TGAAATTGCAAAGCATCTTTCACTTCCACCAGTCAAGCTTCACTGCAGCAT
genomic: GAATGGGTTAAGGAAAAGCAAATAGAGGAAGTTTTGACCATTAAAAACACgtgagtactt ... tgtttttcagTGAAATTGCAAAGCATCTTTCACTTCCACCAGTCAAGCTTCACTGCAGCAT
EST: gi|17963703|gb|BM270449.1|BM270449
EST:     GAATGGGTTAAGGAAAAGCAAATAGAGGAAGTTTTGACCATTAAAAACAC                         TGAAATTGCAAAGCATCTTTCACTTCCACCAGTCAAGCTTCACTGCAGCAT
genomic: GAATGGGTTAAGGAAAAGCAAATAGAGGAAGTTTTGACCATTAAAAACACgtgagtactt ... tgtttttcagTGAAATTGCAAAGCATCTTTCACTTCCACCAGTCAAGCTTCACTGCAGCAT
EST: gi|10232595|gb|BE801483.1|BE801483
EST:     GAATGGGTTAAGGAAAAGCAAATAGAGGAAGTTTTGACCATTAAAAACAC                         TGAAATTGCAAAGCATCTTTCACTTCCACCAGTCAAGCTTCACTGCAGCAT
genomic: GAATGGGTTAAGGAAAAGCAAATAGAGGAAGTTTTGACCATTAAAAACACgtgagtactt ... tgtttttcagTGAAATTGCAAAGCATCTTTCACTTCCACCAGTCAAGCTTCACTGCAGCAT
EST: gi|120533245|gb|EH261378.1|EH261378
EST:     GAATGGGTTAAGGAAAAGCAAATAGAGGAAGTTTTGACCATTAAAAACAC                         TGAAATTGCAAAGCATCTTTCACTTCCACCAGTCAAGCTTCACTGCAGCAT
genomic: GAATGGGTTAAGGAAAAGCAAATAGAGGAAGTTTTGACCATTAAAAACACgtgagtactt ... tgtttttcagTGAAATTGCAAAGCATCTTTCACTTCCACCAGTCAAGCTTCACTGCAGCAT
EST: gi|298192270|gb|HO036352.1|HO036352
EST:     GAATGGGTTAAGGAAAAGCAAATAGAGGAAGTTTTGACCATTAAAAACAC                         TGAAATTGCAAAGCATCTTTCACTTCCACCAGTTAAGCTTCACTGCAGCAT
genomic: GAATGGGTTAAGGAAAAGCAAATAGAGGAAGTTTTGACCATTAAAAACACgtgagtactt ... tgtttttcagTGAAATTGCAAAGCATCTTTCACTTCCACCAGTCAAGCTTCACTGCAGCAT
EST: gi|16344571|gb|BI970166.1|BI970166
EST:     GAATGGGTTAAGGAAAAGCAAATAGAGGAAGTTTTGACCATTAAAAACAC                         TGAAATTGCAAAGCATCTTTCACTTCCACCAGTCAAGCTTCACTGCAGCAT
genomic: GAATGGGTTAAGGAAAAGCAAATAGAGGAAGTTTTGACCATTAAAAACACgtgagtactt ... tgtttttcagTGAAATTGCAAAGCATCTTTCACTTCCACCAGTCAAGCTTCACTGCAGCAT
EST: gi|298179071|gb|HO027542.1|HO027542
EST:     GAATGGGTTAAGGAAAAGCAAATAGAGGAAGTTTTGACCATTAAAAACAC                         TGAAATTGCAAAGCATCTTTCGCTTCCACCAGTCAAGCTTCACTGCAGCAT
genomic: GAATGGGTTAAGGAAAAGCAAATAGAGGAAGTTTTGACCATTAAAAACACgtgagtactt ... tgtttttcagTGAAATTGCAAAGCATCTTTCACTTCCACCAGTCAAGCTTCACTGCAGCAT
EST: gi|14206283|gb|BG839961.1|BG839961
EST:     GAATGGGTTAAGGAAAAGCAAATAGAGGAAGTTTTGACCATTAAAAACAC                         TGAAATTGCAAAGCATCTTTCACTTCCACCAGTCAAGCTTCACTGCAGCAT
genomic: GAATGGGTTAAGGAAAAGCAAATAGAGGAAGTTTTGACCATTAAAAACACgtgagtactt ... tgtttttcagTGAAATTGCAAAGCATCTTTCACTTCCACCAGTCAAGCTTCACTGCAGCAT
EST: gi|18734724|gb|BM528349.1|BM528349
EST:     GAATGGGTTAAGGAAAAGCAAATAGAGGAAGTTTTGACCATTAAAAACAC                         TGAAATTGCAAAGCATCTTTCACTTCCACCAGTCAAGCTTCACTGCAGCAT
genomic: GAATGGGTTAAGGAAAAGCAAATAGAGGAAGTTTTGACCATTAAAAACACgtgagtactt ... tgtttttcagTGAAATTGCAAAGCATCTTTCACTTCCACCAGTCAAGCTTCACTGCAGCAT
EST: gi|14259781|gb|BG882689.1|BG882689
EST:     GAATGAGTTAAGGAAAAGCAAATCTAGGAAGTTTTGACCATTAAAAACAC                         TGAAATTGCAAAGCATCTTTCACTTCCACCATTCAAGCTTCACTGCAGCAT
genomic: GAATGGGTTAAGGAAAAGCAAATAGAGGAAGTTTTGACCATTAAAAACACgtgagtactt ... tgtttttcagTGAAATTGCAAAGCATCTTTCACTTCCACCAGTCAAGCTTCACTGCAGCAT
EST: gi|7924422|gb|AW830448.1|AW830448
EST:     GAATGGGTTAAGGAAAAGCAAATAGAGGAAGTTTTGACCATTAAAAACAC                         TGAAATTGCAAAGCATCTTTCACTTCCACCAGTCAAGCTTCACTGCAGCAT
genomic: GAATGGGTTAAGGAAAAGCAAATAGAGGAAGTTTTGACCATTAAAAACACgtgagtactt ... tgtttttcagTGAAATTGCAAAGCATCTTTCACTTCCACCAGTCAAGCTTCACTGCAGCAT
EST: gi|14991180|gb|BI316853.1|BI316853
EST:     GAATGGGTTAAGGAAAAGCCAATAGAGGAAGTTTTGACCATTAAAAACAC                         TGAAATTGCAAAGCATCTTTCACTTCCACCAGTCAAGCTTCACTGCAGCAT
genomic: GAATGGGTTAAGGAAAAGCAAATAGAGGAAGTTTTGACCATTAAAAACACgtgagtactt ... tgtttttcagTGAAATTGCAAAGCATCTTTCACTTCCACCAGTCAAGCTTCACTGCAGCAT
EST: gi|24135728|gb|BU926238.1|BU926238
EST:     GAATGGGTTAAGGAAAAGCAAATAGAGGAAGTTTTGACCATTAAAAACAC                         TGAAATTGCAAAGCATCTTTCACTTCCACCAGTCAAGCTTCACTGCAGCAT
genomic: GAATGGGTTAAGGAAAAGCAAATAGAGGAAGTTTTGACCATTAAAAACACgtgagtactt ... tgtttttcagTGAAATTGCAAAGCATCTTTCACTTCCACCAGTCAAGCTTCACTGCAGCAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

acctctccggttattagtttatgaattgaagtgacacataatgaatgtttttcagTGAAATTGCAAAGCATCTTTCACTTCCACCAGTCAAGCTTCACTGCAGCATGCTTGCTGAGGATGCTATAAAAGCAGCTGTTAAAGATTATGAAGCTAAG
                                             tgtttttc  CT-rich tract
          ttattagtttatgaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
agcttagtcatgctaaaggttttattattaatcacatttgtctccacctctccggttattagtttatgaattgaagtgacacataatgaatgtttttcagTGAAATTGCAAAGCATCTTTCACTTCCACCAGTCAAGCTTCACTGCAGCATGCTTGCTGAGGATGCTATAAAAGCAGCTGTTAAAGATTATGAAGCTAAG

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