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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aattctatgagagactaaaaatatactagtatttaaaaaaaaaacaattggaggagtaaaaaagggtaattgggtagtgattgtgtgtggtgaaatgcagGAGAAGAACCATGGAAGCTATGACTTCATCTTTGTTGATGCGGACAAGGACAACTACCTCAACTACCACAAGAGGTTGATAGAGCTTGTAAAAGTTGGGG

Basic information

species Glycine max
transcript GLYMA07G33780.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA07G33780.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G127948_T04 (Zea mays), 3'ss of exon 6
-----aattctatgagagactaaaaatatactagtatttaaaaaaaaaacaattggaggagtaaaaaagggtaattgggtagtgattgtgtgtggtgaaatgcagGAGAAGAACCATGGAAGCTATGACTTCATCTTTGTTGATGCGGACAAGGACAACTACCTCAACTACCACAAGAGGTTGATAGAGCTTGTAAAAGTTGGGG------------------------------------------------
     || |      |   | | |  | | ||  |      | |   | | | | || |  | | |     |    |    |||  ||| ||         ||||||||||||||| ||    |  |||||| |||| || || || ||||||||||||||||||||||||||| || || || |  |||| || ||  | || |                                                
gtacgaaatggccaggccgccagatctgtgcttcttcgcctatatcgatcgagtagaagt-tgacatgacatctcggacccgtgtctgtctgcatctg--cgcaggagaagaaccacgggtcgttcgacttcgtcttcgtggacgccgacaagGACAACTACCTCAACTACCACGAGCGGCTGCTGAAGCTGGTGAAGCTGGGCGGCCTCATCGGCTACGACAACACGCTGTGGAACGGCTCCGTCGTGCTCC

upper sequence: GLYMA07G33780.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G127948_T02 (Zea mays), 3'ss of exon 5
-----aattctatgagagactaaaaatatactagtatttaaaaaaaaaacaattggaggagtaaaaaagggtaattgggtagtgattgtgtgtggtgaaatgcagGAGAAGAACCATGGAAGCTATGACTTCATCTTTGTTGATGCGGACAAGGACAACTACCTCAACTACCACAAGAGGTTGATAGAGCTTGTAAAAGTTGGGG
     || |      |   | | |  | | ||  |      | |   | | | | || |  | | |     |    |    |||  ||| ||         ||||||||||||||| ||    |  |||||| |||| || || || ||||||||||||||||||||||||||| || || || |  |||| || ||  | || |
gtacgaaatggccaggccgccagatctgtgcttcttcgcctatatcgatcgagtagaagt-tgacatgacatctcggacccgtgtctgtctgcatctg--cgcagGAGAAGAACCACGGGTCGTTCGACTTCGTCTTCGTGGACGCCGACAAGGACAACTACCTCAACTACCACGAGCGGCTGCTGAAGCTGGTGAAGCTGGGCG

upper sequence: GLYMA07G33780.1 (Glycine max), 3'ss of exon 4
lower sequence: AT4G34050.2 (Arabidopsis thaliana), 3'ss of exon 2
------------------------------------------------------------------------------------aattctatgagagactaaaaatatactagtatttaaaaaaaaaacaattggaggagtaaaaaagggtaattgggtagtgattgtgtgtggtgaaatgcagGAGAAGAACCATGGAAGCTATGACTTCATCTTTGTTGATGCGGACAAGGACAACTACCTCAACTACCACAAGAGGTTGATAGAGCTTGTAAAAGTTGGGG
                                                                                     |||  ||       | | ||| |     ||   |||       |  ||     || || |||| ||  |    |  | ||||||||||||    |||||||||||||||||||||  |||||||| || || |||||||| ||||| ||||||||| |||||||||||||| | ||||| || ||||| ||| |||| |
gtaagcattcttctttctgacgtaattaacaaaaaagatgatgaagataatgaaataattaaaaactcatggcctaattaggttgatttaatatcttgatgagaatttctgtatacgcaaatttgtttcctttttcatag-aagaaagtgtggt-aactgattattgtgtgtggttgggtgcagGAGAAGAACCATGGAACATATGACTTTATATTCGTTGATGCTGACAAAGACAACTACATCAACTACCACAAGCGTTTGATCGATCTTGTGAAAATTGGAG

upper sequence: GLYMA07G33780.1 (Glycine max), 3'ss of exon 4
lower sequence: PP1S16_28V6.1 (Physcomitrella patens), 3'ss of exon 4
aattctatgagagactaaaaa--tatactagtatttaaaaaaaaaacaattggaggagtaaaaaagggtaattgggtagt--gattgtgtgtggtgaaatg-cagGAGAAGAACCATGGAAGCTATGACTTCATCTTTGTTGATGCGGACAAGGACAACTACCTCAACTACCACAAGAGGTTGATAGAGCTTGTAAAAGTTGGGG
      | |  ||  ||| ||  | |||  |   |  ||| ||||||| ||   |   |    | | |        |  |  |||||        ||| || ||||| ||||| || |     |  ||||||||||| || || |||||||| |||||||| || ||||||||||||| | | ||  || | || |  || || |
-----caaggaagtgtaagaagctgtacagggtgtggaaagaaaaacagttattgacctgtctatgtgaggccaactcatcagattgcaaacttggaattggcagGACAAGAATCACGATTCTTTCGACTTCATCTTCGTAGACGCGGACAAAGACAACTATCTGAACTACCACAAGAAGCTCATGAAGTTGGTGAGGGTGGGAG

upper sequence: GLYMA07G33780.1 (Glycine max), 3'ss of exon 4
lower sequence: EFJ22516 (Selaginella moellendorffii), 3'ss of exon 4
aattctatgagagactaaaaatatactagtatttaaaaaaaaaacaattggaggagtaaaaaagggtaattgggtagtgattgtgtgtggtgaaatgcagGAGAAGAACCATGGAAGCTATGACTTCATCTTTGTTGATGCGGACAAGGACAACTACCTCAACTACCACAAGAGGTTGATAGAGCTTGTAAAAGTTGGGG
                           ||  || || | ||      ||       ||    |   | |          ||  ||     |     |||||||  ||| |||||    |  |||||||||||||| ||||| ||||||||||| ||| | ||||||||||||||||||||     | || ||||| || |
------------------------gtaagctttcaatacaacttttctt-------tatcttaccttgaaccaacgacaatgctgacactttcctcgcagGAGGCGAATCATGGCGCATTCGACTTCATCTTTGTGGATGCTGACAAGGACAATTACTTGAACTACCACAAGAGGTTGATCTCTTTGGTTAAAGTCGGAG

upper sequence: GLYMA07G33780.1 (Glycine max), 3'ss of exon 4
lower sequence: EFJ11728 (Selaginella moellendorffii), 3'ss of exon 4
aattctatgagagactaaaaatatactagtatttaaaaaaaaaacaattggaggagtaaaaaagggtaattgggtagtgattgtgtgtggtgaaatgcagGAGAAGAACCATGGAAGCTATGACTTCATCTTTGTTGATGCGGACAAGGACAACTACCTCAACTACCACAAGAGGTTGATAGAGCTTGTAAAAGTTGGGG
                           ||  || || | ||      ||       ||    |   | |          ||  ||     |     |||||||  ||| |||||    |  |||||||||||||| ||||| ||||||||||| ||| | ||||||||||||||||||||     | || ||||| || |
------------------------gtaagctttcaatacaacttttctt-------tatcttaccttgaaccaacgacaatgctgacactttcctcgcagGAGGCGAATCATGGCGCGTTCGACTTCATCTTTGTGGATGCTGACAAGGACAATTACTTGAACTACCACAAGAGGTTGATCTCTTTGGTTAAAGTCGGAG

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|58022625|gb|CX709366.1|CX709366
EST:     AATTCAGAGAAGGTCCTGCTCTACCAGTTCTTGATGAAATGATTAAAGAT                         GAGAAGAACCATGGAAGCTATGACTTCATCTTTGTTGATGCGGACAAGGAC
genomic: AATTCAGAGAAGGTCCTGCTCTACCAGTTCTTGATGAAATGATTAAAGATgtaagttttt ... tgaaatgcagGAGAAGAACCATGGAAGCTATGACTTCATCTTTGTTGATGCGGACAAGGAC
EST: gi|6665876|gb|AW277326.1|AW277326
EST:     AATTCAGAGAAGGTCCTGCTCTACCAGTTCTTGATGAAATGATTAAAGAT                         GAGAAGAACCATGGAAGCTATGACTTCATCTTTGTTGATGCGGACAAGGAC
genomic: AATTCAGAGAAGGTCCTGCTCTACCAGTTCTTGATGAAATGATTAAAGATgtaagttttt ... tgaaatgcagGAGAAGAACCATGGAAGCTATGACTTCATCTTTGTTGATGCGGACAAGGAC
EST: gi|16106075|gb|BI893815.1|BI893815
EST:     AATTCAGAGAAGGTCCTGCTCTACCAGTTCTTGATGAAATGATTAAAGAT                         GAGAAGAACCATGTTTTTTATGACTTCATCTTTGTTGATGCGGACAAGGAC
genomic: AATTCAGAGAAGGTCCTGCTCTACCAGTTCTTGATGAAATGATTAAAGATgtaagttttt ... tgaaatgcagGAGAAGAACCATGGAAGCTATGACTTCATCTTTGTTGATGCGGACAAGGAC
EST: gi|8403758|gb|BE059325.1|BE059325
EST:     AATTCAGAGAAGGTCCTGCTCTACCAGTTCTTGATGAAATGATTAAAGAT                         GAGAAGAACCATGGAAGCTATGACTTCATCTTTGTTGATGCGGACAAAGAC
genomic: AATTCAGAGAAGGTCCTGCTCTACCAGTTCTTGATGAAATGATTAAAGATgtaagttttt ... tgaaatgcagGAGAAGAACCATGGAAGCTATGACTTCATCTTTGTTGATGCGGACAAGGAC
EST: gi|13252073|gb|BG362976.1|BG362976
EST:     AATTCAGAGAAGGTCCTGCTCTACCAGTTCTTGATGAAATGATTAAAGAT                         GAGAAGAACCATGGAAGCTATGACTTCATCTTTGTTGATGCGGACAAGGAC
genomic: AATTCAGAGAAGGTCCTGCTCTACCAGTTCTTGATGAAATGATTAAAGATgtaagttttt ... tgaaatgcagGAGAAGAACCATGGAAGCTATGACTTCATCTTTGTTGATGCGGACAAGGAC
EST: gi|4395716|gb|AI494713.1|AI494713
EST:     AATTCAGAGAAGGTCCTGCTCTACCAGTTCTTGATGAAATGATTAAAGAT                         GAGAAGAACCATGGAAGCTATGACTTCATCTTTGTTGATGCGGACAAGGAC
genomic: AATTCAGAGAAGGTCCTGCTCTACCAGTTCTTGATGAAATGATTAAAGATgtaagttttt ... tgaaatgcagGAGAAGAACCATGGAAGCTATGACTTCATCTTTGTTGATGCGGACAAGGAC
EST: gi|58022356|gb|CX709097.1|CX709097
EST:     AATTCAGAGAAGGTCCTGCTCTACCAGTTCTTGATGAAATGATTAAAGAT                         GAGAAGAACCATGGAAGCTATGACTTCATCTTTGTTGATGCGGACAAGGAC
genomic: AATTCAGAGAAGGTCCTGCTCTACCAGTTCTTGATGAAATGATTAAAGATgtaagttttt ... tgaaatgcagGAGAAGAACCATGGAAGCTATGACTTCATCTTTGTTGATGCGGACAAGGAC
EST: gi|4301016|gb|AI443130.1|AI443130
EST:     AATTCAGAGAAGGTCCTGCTCTACCAGTTCTTGATGAAATGATTAAAGAT                         GAGAAGAACCATGGAAGCTATGACTTCATCTTTGTTGATGCGGACAAGGAC
genomic: AATTCAGAGAAGGTCCTGCTCTACCAGTTCTTGATGAAATGATTAAAGATgtaagttttt ... tgaaatgcagGAGAAGAACCATGGAAGCTATGACTTCATCTTTGTTGATGCGGACAAGGAC
EST: gi|26048143|gb|CA784719.1|CA784719
EST:     AATTCAGAGAAGGTCCTGCTCTACCAGTTCTTGATGAAATGATTAAAGAT                         GAGAAGAACCATGGAAGCTATGACTTCATCTTTGTTGATGCGGACAAGGAC
genomic: AATTCAGAGAAGGTCCTGCTCTACCAGTTCTTGATGAAATGATTAAAGATgtaagttttt ... tgaaatgcagGAGAAGAACCATGGAAGCTATGACTTCATCTTTGTTGATGCGGACAAGGAC
EST: gi|7145680|gb|AW507602.1|AW507602
EST:     AATTCAGAGAAGGTCCTGCTCTACCAGTTCTTGATGAAATGATTAAAGAT                         GAGAAGAACCATGGAAGCTATGACTTCATCTTTGTTGATGCGGACAAGGAC
genomic: AATTCAGAGAAGGTCCTGCTCTACCAGTTCTTGATGAAATGATTAAAGATgtaagttttt ... tgaaatgcagGAGAAGAACCATGGAAGCTATGACTTCATCTTTGTTGATGCGGACAAGGAC
EST: gi|7639897|gb|AW734209.1|AW734209
EST:     AATTCAGAGAAGGTCCTGCTCTACCAGTTCTTGATGAAATGATTAAAGAT                         GAGAAGAACCATGGAAGCTATGACTTCATCTTTGGTGATGCGGACCAGGAC
genomic: AATTCAGAGAAGGTCCTGCTCTACCAGTTCTTGATGAAATGATTAAAGATgtaagttttt ... tgaaatgcagGAGAAGAACCATGGAAGCTATGACTTCATCTTTGTTGATGCGGACAAGGAC
EST: gi|7042340|gb|AW472234.1|AW472234
EST:     AATTCAGAGAAGGTCCTGCTCTACCAGTTCTTGATGAAATGATTAAAGAT                         GAGAAGAACCATGGAAGCTATGACTTCATCTTTGTTGATGCGGACAAGGAC
genomic: AATTCAGAGAAGGTCCTGCTCTACCAGTTCTTGATGAAATGATTAAAGATgtaagttttt ... tgaaatgcagGAGAAGAACCATGGAAGCTATGACTTCATCTTTGTTGATGCGGACAAGGAC
EST: gi|15661667|gb|BI699038.1|BI699038
EST:     AATTCAGAGAAGGTCCTGCTCTACCAGTTCTTGATGAAATGATTAAAGAT                         GAGAAGAACCATGGAAGCTATGACTTCATCTTTGTTGATGCGGACAAGGAC
genomic: AATTCAGAGAAGGTCCTGCTCTACCAGTTCTTGATGAAATGATTAAAGATgtaagttttt ... tgaaatgcagGAGAAGAACCATGGAAGCTATGACTTCATCTTTGTTGATGCGGACAAGGAC
EST: gi|6200792|gb|AW152892.1|AW152892
EST:     AATTCAGAGAAGGTCCTGCTCTACCAGTTCTTGATGAAATGATTAAAGAT                         GAGAAGAACCATGGAAGCTATGACTTCATCTTTGTTGATGCGGACAAGGAC
genomic: AATTCAGAGAAGGTCCTGCTCTACCAGTTCTTGATGAAATGATTAAAGATgtaagttttt ... tgaaatgcagGAGAAGAACCATGGAAGCTATGACTTCATCTTTGTTGATGCGGACAAGGAC
EST: gi|13312671|gb|BG406322.1|BG406322
EST:     AATTCAGAGAAGGTCCTGCTCTACCAGTTCTTGATGAAATGATTAAAGAT                         GAGAAGAACCATGGAAGCTATTACCTT-ATCTTTGTTGATGCGGAC
genomic: AATTCAGAGAAGGTCCTGCTCTACCAGTTCTTGATGAAATGATTAAAGATgtaagttttt ... tgaaatgcagGAGAAGAACCATGGAAGCTATGAC-TTCATCTTTGTTGATGCGGAC
EST: gi|151395162|gb|EV265033.1|EV265033
EST:     AATTCAGAGAAGGTCCTGCTCTACCAGTTCTTGATGAAATGATTAAAGAT                         GAGAAGAACCATGGAAGCTATGACTTCATCTTTGTTGATGCGGACAAGGAC
genomic: AATTCAGAGAAGGTCCTGCTCTACCAGTTCTTGATGAAATGATTAAAGATgtaagttttt ... tgaaatgcagGAGAAGAACCATGGAAGCTATGACTTCATCTTTGTTGATGCGGACAAGGAC
EST: gi|151401262|gb|EV271076.1|EV271076
EST:     AATTCAGAGAAGGTCCTGCTCTACCAGTTCTTGATGAAATGATTAAAGAT                         GAGAAGAACCATGGAAGCTATGACTTCATCTTTGTTGATGCGGACAAGGAC
genomic: AATTCAGAGAAGGTCCTGCTCTACCAGTTCTTGATGAAATGATTAAAGATgtaagttttt ... tgaaatgcagGAGAAGAACCATGGAAGCTATGACTTCATCTTTGTTGATGCGGACAAGGAC
EST: gi|21677191|gb|BQ629542.1|BQ629542
EST:     TACCAGTTCTTGATGAAATGATTAAAGAT                         GAGAAGAACCATGGAAGCTATGACTTCATCTTTGTTGATGCGGACAAGGAC
genomic: TACCAGTTCTTGATGAAATGATTAAAGATgtaagttttt ... tgaaatgcagGAGAAGAACCATGGAAGCTATGACTTCATCTTTGTTGATGCGGACAAGGAC
EST: gi|20498741|gb|BQ273671.1|BQ273671
EST:     AATTCAGAGAAGGTCCTGCTCTACCAGTTCTTGATGAAATGATTAAAGAT                         GAGAAGAACCATGGAAGCTATGACTTCATCTTTGTTGATGCGGACAAGGAC
genomic: AATTCAGAGAAGGTCCTGCTCTACCAGTTCTTGATGAAATGATTAAAGATgtaagttttt ... tgaaatgcagGAGAAGAACCATGGAAGCTATGACTTCATCTTTGTTGATGCGGACAAGGAC
EST: gi|15000825|gb|BI321639.1|BI321639
EST:     AATTCAGAGAAGGTCCTGCTCTACCAGTTCTTGATGAAATGATTAAAGAT                         GAGAAGAACCATGGAAGCTATGACTTCATCTTTGTTGATGCGGACAAGGAC
genomic: AATTCAGAGAAGGTCCTGCTCTACCAGTTCTTGATGAAATGATTAAAGATgtaagttttt ... tgaaatgcagGAGAAGAACCATGGAAGCTATGACTTCATCTTTGTTGATGCGGACAAGGAC
EST: gi|151396345|gb|EV266222.1|EV266222
EST:     AATTCAGAGAAGGTCCTGCTCTACCAGTTCTTGATGAAATGATTAAAGAT                         GAGAAGAACCATGGAAGCTATGACTTCATCTTTGTTGATGCGGACAAGGAC
genomic: AATTCAGAGAAGGTCCTGCTCTACCAGTTCTTGATGAAATGATTAAAGATgtaagttttt ... tgaaatgcagGAGAAGAACCATGGAAGCTATGACTTCATCTTTGTTGATGCGGACAAGGAC
EST: gi|41145686|gb|CK605897.1|CK605897
EST:     AATTCAGAGAAGGTCCTGCTCTACCAGTTCTTGATGAAATGATTAAAGAT                         GAGAAGAACCATGGAAGCTATGACTTCATCTTTGTTGATGCGGACAAGGAC
genomic: AATTCAGAGAAGGTCCTGCTCTACCAGTTCTTGATGAAATGATTAAAGATgtaagttttt ... tgaaatgcagGAGAAGAACCATGGAAGCTATGACTTCATCTTTGTTGATGCGGACAAGGAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aattggaggagtaaaaaagggtaattgggtagtgattgtgtgtggtgaaatgcagGAGAAGAACCATGGAAGCTATGACTTCATCTTTGTTGATGCGGACAAGGACAACTACCTCAACTACCACAAGAGGTTGATAGAGCTTGTAAAAGTTGGGG
         agtaaaaaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aattctatgagagactaaaaatatactagtatttaaaaaaaaaacaattggaggagtaaaaaagggtaattgggtagtgattgtgtgtggtgaaatgcagGAGAAGAACCATGGAAGCTATGACTTCATCTTTGTTGATGCGGACAAGGACAACTACCTCAACTACCACAAGAGGTTGATAGAGCTTGTAAAAGTTGGGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGCTT
- - ctatgag
- - - - - - - - aaaaata
- - - - - - - - - - - - - - - - -taaaaaa
- - - - - - - - - - - - - - - - - aaaaaaa
- - - - - - - - - - - - - - - - - - - - - - - - -ggaggag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ggtagtg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gtgtgtg