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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttttgcctcagttttgacaagttttctttccccctgtggctgtacgatgactatatagattgatggcattttaagcttttctttctttgcaataatgcagGCCTATTCTACAGTTGGAACACCTGATTATATTGCTCCAGAAGTTCTTCTGAAGAAAGGATATGGCGTGGAATGTGATTG

Basic information

species Glycine max
transcript GLYMA10G00830.1
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA10G00830.1 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G088245_T01 (Zea mays), 3'ss of exon 5
ttttgcctcagttttgacaagttttctttccccctgtggctgtacgatgactatatagattgatggcattttaagcttttctttctttgcaataatgcagGCCTATTCTACAGTTGGAACACCTGATTATATTGCTCCAGAAGTTCTTCTGAAGAAAGGATATGGCGTGGAATGTGATTG
             |    ||   || |||  ||   ||      ||||  ||  |||     ||    ||   |  |  || ||||          |||||| || || || || |||||||| || || || |||||||||||||||||||||||||| || ||  |||||||||| ||
------------gtcagtaatcatttttttaccacttgatgactcgatctcttgatatgcaaatctttttgacaagtgatcattct----ggctgcgcagGCTTACTCGACCGTCGGAACACCAGACTACATCGCTCCAGAAGTTCTTCTGAAGAAAGGCTACGGGATGGAATGTGACTG

upper sequence: GLYMA10G00830.1 (Glycine max), 3'ss of exon 5
lower sequence: AT4G14350.3 (Arabidopsis thaliana), 3'ss of exon 6
------------------------------------ttttgcctcagttt----tgacaagttttctttccccctgtggctgtacgatgactatatagattgatggc-attttaagcttttctttct---ttgcaataatg-----cagGCCTATTCTACAGTTGGAACACCTGATTATATTGCTCCAGAAGTTCTTCTGAAGAAAGGATATGGCGTGGAATGTGATTG
                                     | ||    |||      |  | ||| |  ||      ||       |   |  | ||  | || ||   | || |||    |  ||| ||   ||    | ||      ||||| ||||| |||||||| || ||||| |||||||| |||||||||||  |||| |||||||||||  |||||||||||||
gtaagtttcacttattcctcatcttttcttccagagatgtggagtagtccacagtatccagtatatttcgttattgaaagcaaattctctccattgatatagacatctatgttagatatgacttactaggttaaggtcattactttcagGCTTATTCCACAGTTGGCACTCCTGACTATATTGCCCCAGAAGTTCTGTTGAAAAAAGGATATGGAATGGAATGTGATTG

upper sequence: GLYMA10G00830.1 (Glycine max), 3'ss of exon 5
lower sequence: AT3G23310.1 (Arabidopsis thaliana), 3'ss of exon 6
--------------------------------ttttgcct--cagttttgacaagttttctttccccctgtggctgtacgatgactatatagattgatg---gcattttaagctt--------ttctttctttgcaat-------aatgcagGCCTATTCTACAGTTGGAACACCTGATTATATTGCTCCAGAAGTTCTTCTGAAGAAAGGATATGGCGTGGAATGTGATTG
                                || | | |  ||| ||  |||| |  || || |     |     || |     | |    | ||||       ||||  | |          |  ||   || |||       | ||||||| ||||||||||||||||| ||||| |||||||||||||||||| |  ||||||||||||||||| |||||||||||||
gtgagtttatcgttcttttcttgttctgagatttctacttgccagattgaacaaatcatcattactttattcatcttatggaagtttttctcactgatatataagttttctgttcaaatacagcttattaagtgaaatgctatcaattgcagGCTTATTCTACAGTTGGAACTCCTGACTATATTGCTCCAGAAGTTTTGTTGAAGAAAGGATATGGCATGGAATGTGATTG

upper sequence: GLYMA10G00830.1 (Glycine max), 3'ss of exon 5
lower sequence: Vv05s0049g01220.t01 (Vitis vinifera), 3'ss of exon 5
---ttttgcctcagttttgacaagttttctttccccctgtggctgtacgatgactatatagattgatggcattttaagcttttctttctttgcaataatgcagGCCTATTCTACAGTTGGAACACCTGATTATATTGCTCCAGAAGTTCTTCTGAAGAAAGGATATGGCGTGGAATGTGATTG
    ||||  ||   | | | |||   | |||   |  |   |||  | |     |||  | || ||  ||  | || |||||  |   ||| |||| |||||||||||||||| ||||| || ||||| || |||||||||||||| || || ||||||||||||||  |||| ||||||||
tcactttgtttcctctgttataagaaatgtttatgcaggaccctgcgctaactgcataagggtttatatcaact-aaacttttgata--ttggaatactgcagGCCTATTCTACTGTTGGTACCCCTGACTACATTGCTCCAGAAGTGCTGCTTAAGAAAGGATATGGGATGGAGTGTGATTG

upper sequence: GLYMA10G00830.1 (Glycine max), 3'ss of exon 5
lower sequence: PP1S87_129V6.1 (Physcomitrella patens), 3'ss of exon 5
---------------------------------------------------------ttttgcctcagttttgacaagttttctttccccctgtggctgtacga-tg--actatatagattgatggcattttaagcttttctttctttgcaata-atgcagGCCTATTCTACAGTTGGAACACCTGATTATATTGCTCCAGAAGTTCTTCTGAAGAAAGGATATGGCGTGGAATGTGATTG
                                                          |||| |  || | | |     |   ||| |       |  || | | ||  |||  || |||     | | | | |  | ||    |   |      || ||||| ||||| ||||| || || || |||||||||||||| ||||| || ||||||||||| |||||  |||| ||||| ||
gtaatcttctttgcattccattttgcagtagctcttcgtcctcttcacaatttctgcctttgtcatagatgtcatcttctaggtttgcatacagaggagtgcaagtggcactccattgatcatctgtaatctcaagtattgacacaaagtttcgcattcagGCATATTCAACAGTCGGCACTCCAGATTATATTGCTCCTGAAGTACTGCTGAAGAAAGGCTATGGGATGGAGTGTGACTG

upper sequence: GLYMA10G00830.1 (Glycine max), 3'ss of exon 5
lower sequence: EFJ28086 (Selaginella moellendorffii), 3'ss of exon 5
ttttgcctcagttttgacaagttttctttccccctgtggctgtacgatgactatatagattgatggcattttaagcttttctttctttgcaataatgcagGCCTATTCTACAGTTGGAACACCTGATTATATTGCTCCAGAAGTTCTTCTGAAGAAAGGATATGGCGTGGAATGTGATTG
                                         || ||  |  | ||     |  ||    |      |||| | |   ||   |    ||||| ||||| || || || || || |||||||||||||| |||||||| |||||||| ||||| ||  |||| ||||||||
-----------------------------------------gtgcgtagcttgtacttccttttg----tcccgatttttatctaagtgttctttaacagGCTTATTCAACTGTCGGGACGCCAGATTATATTGCTCCCGAAGTTCTACTGAAGAAGGGATACGGGATGGAGTGTGATTG

upper sequence: GLYMA10G00830.1 (Glycine max), 3'ss of exon 5
lower sequence: EFJ29515 (Selaginella moellendorffii), 3'ss of exon 5
ttttgcctcagttttgacaagttttctttccccctgtggctgtacgatgactatatagattgatggcattttaagcttt-tctttctttgcaataatgcagGCCTATTCTACAGTTGGAACACCTGATTATATTGCTCCAGAAGTTCTTCTGAAGAAAGGATATGGCGTGGAATGTGATTG
                                         || ||  |  | ||    ||  |    |    |  ||| |||   ||| |  |||  ||||| ||||| || || || || || |||||||||||||| |||||||| |||||||| ||||| ||  |||| ||||||||
-----------------------------------------gtgcgtagcttgtac---ttccttttgtcccgatttttatctaagtttcctttaa--cagGCTTATTCAACTGTCGGGACGCCAGATTATATTGCTCCCGAAGTTCTACTGAAGAAGGGATACGGGATGGAGTGTGATTG

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|254348922|gb|GR852601.1|GR852601
EST:     GAACCCAACAGGAACAACTGCAGCATTGGCAGAAAAATCGACGAATGCTT                         GCCTATTCTACAGTTGGAACACCTGATTATATTGCTCCAGAAGTTCTTCTG
genomic: GAACCCAACAGGAACAACTGCAGCATTGGCAGAAAAATCGACGAATGCTTgtaagcctct ... aataatgcagGCCTATTCTACAGTTGGAACACCTGATTATATTGCTCCAGAAGTTCTTCTG
EST: gi|31561374|gb|CD487212.1|CD487212
EST:     GAACCCAACAGGAACAACTGCAGCATTGGCAGAAAAATCGACGAATGCTT                         GCCTATTCTACAGTTGGAACA
genomic: GAACCCAACAGGAACAACTGCAGCATTGGCAGAAAAATCGACGAATGCTTgtaagcctct ... aataatgcagGCCTATTCTACAGTTGGAACA
EST: gi|208130018|gb|GD930647.1|GD930647
EST:     GAACCCAACAGGAACAACTGCAGCATTGGCAGAAAAATCGACGAATGCTT                         GCCTATTCTACAGTTGGAACACCTGATTAT
genomic: GAACCCAACAGGAACAACTGCAGCATTGGCAGAAAAATCGACGAATGCTTgtaagcctct ... aataatgcagGCCTATTCTACAGTTGGAACACCTGATTAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gatgactatatagattgatggcattttaagcttttctttctttgcaataatgcagGCCTATTCTACAGTTGGAACACCTGATTATATTGCTCCAGAAGTTCTTCTGAAGAAAGGATATGGCGTGGAATGTGATTG
            gattgat  putative branch site (score: 4)
                              cttttctttctttgca  putative PPT
      tatatagatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttttgcctcagttttgacaagttttctttccccctgtggctgtacgatgactatatagattgatggcattttaagcttttctttctttgcaataatgcagGCCTATTCTACAGTTGGAACACCTGATTATATTGCTCCAGAAGTTCTTCTGAAGAAAGGATATGGCGTGGAATGTGATTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA
- -tgcctca
- - - - - - - tgacaag
- - - - - - - - - - - - - -ttccccc
- - - - - - - - - - - - - - - - - - tggctgt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgatggc