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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ctgaacactggaattagaaaagggaaaatgacctaggtcttataatttttttcccatcataactaatgtgttgctgtaattcttcatgattttgtatcagATATGTCCTGAACTCACCTCGTATGAAGAAGTTTTTTGACTATATCCAACTTCCAAATTTTGACATTGCTGCAGATGCTGCAGCAACCTTTAAG

Basic information

species Glycine max
transcript GLYMA09G01370.2
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA09G01370.2 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os07g39630.1 (Oryza sativa), 3'ss of exon 4
---ctgaacactggaatt---agaaaagggaaaatgacctaggtcttataa-tttttttcccatcataactaatgtgttgctgtaattcttcatgattttgtatcagATATGTCCTGAACTCACCTCGTATGAAGAAGTTTTTTGACTATATCCAACTTCCAAATTTTGACATTGCTGCAGATGCTGCAGCAACCTTTAAG
   || |  | |    ||   | |||    |||||    |||   ||| || ||  | ||  |      || || | |    |||| | ||||        |  ||| || ||  |  | ||    |  ||||||||||| ||||||||||| |||||||||||||||||||||||  |||||||| | || |||||||||
caactaaggattctgttttacataaaccataaaatactgtagaaattagaaattcctgtcggaatggtgcttatttatcttggtaaatgttcac-------tcacagGTACGTTTTAGAGTCTGACCACATGAAGAAGTTCTTTGACTATATACAACTTCCAAATTTTGACATTGCATCAGATGCTTCTGCGACCTTTAAG

upper sequence: GLYMA09G01370.2 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G066051_T01 (Zea mays), 3'ss of exon 4
--ctgaacactg--gaattagaaaagggaaaatgacctaggtcttataatttttttcccatcataactaatgtgttgctgtaattcttcatgattttgtatcagATATGTCCTGAACTCACCTCGTATGAAGAAGTTTTTTGACTATATCCAACTTCCAAATTTTGACATTGCTGCAGATGCTGCAGCAACCTTTAAG
  ||  |||     ||   | ||  |  ||| |    | ||  ||  ||  |  |    |   |   |  | | ||  | ||   |||  | |||      ||| |||||  |  | ||    |  ||||||||||| ||||||||||| || ||||||||||||||||| ||| | |||||| | || |||||||||
agctagacatccatgatccataagtgcaaaatttttgttggagttggaagctcctgtggacttttggtgctattttcttatagaacttgttcatt----gacagGTATGTTTTAGAGTCTGAACACATGAAGAAGTTCTTTGACTATATACAGCTTCCAAATTTTGACATAGCTTCTGATGCTTCGGCTACCTTTAAG

upper sequence: GLYMA09G01370.2 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G351417_T02 (Zea mays), 3'ss of exon 3
----ctgaacactggaattagaaaagggaaaatgacctaggtcttataatttttttcccatcataactaatgtgttgctgtaattcttcatgattttgtatcagATATGTCCTGAACTCACCTCGTATGAAGAAGTTTTTTGACTATATCCAACTTCCAAATTTTGACATTGCTGCAGATGCTGCAGCAACCTTTAAG
    || |       |   | ||  |  |||||    | |    || |   |  |    |   |   |  | | ||  | ||     || | |||      ||| |||||  |  | ||    | |||||||||||| || |||||||| || ||||||||||||||||| ||| | |||||| | || |||||||||
attactaagttggacatccataagtgcaaaaatattgtcgaaactagaggctcatgtggacttttggtgctattttcttatagaatgtcttcatt----gacagGTATGTTTTAGAGTCCGAACATATGAAGAAGTTCTTCGACTATATACAGCTTCCAAATTTTGACATAGCTTCTGATGCTTCTGCTACCTTTAAG

upper sequence: GLYMA09G01370.2 (Glycine max), 3'ss of exon 4
lower sequence: AT5G47540.1 (Arabidopsis thaliana), 3'ss of exon 4
-----ctgaacactggaattagaaaagggaaaatgacctaggtcttataatttttttcccatcataactaatgtgttgctgtaattcttcatgattttgtat-cagATATGTCCTGAACTCACCTCGTATGAAGAAGTTTTTTGACTATATCCAACTTCCAAATTTTGACATTGCTGCAGATGCTGCAGCAACCTTTAAG
     |  | |  |  | ||     |      | |||||| |   ||    |   |||  |  |||||  |     || |      ||| ||   |||| || |||||||||  || | ||    | | ||||||| || ||||| || || || ||||||||||| ||||||||||| |||||||| || || ||||||
gtgagccaatcgtttcattttcttcatttt--acgacctatggagtaattatggattcagagaataacggaaaatgtgtttactaacttaatttctttggattcagATATGTTTTGGAGTCTGACCATGTGAAGAAATTCTTTGATTACATACAGCTTCCAAATTTCGACATTGCTGCCGATGCTGCTGCTACTTTTAAG

upper sequence: GLYMA09G01370.2 (Glycine max), 3'ss of exon 4
lower sequence: AT4G17270.1 (Arabidopsis thaliana), 3'ss of exon 4
---------ctgaacactggaattagaaaagggaaaatgacctaggtcttataatttttttc----ccatcataactaa---tgtgttgctgtaattcttcatgattttgta--tcagATATGTCCTGAACTCACCTCGTATGAAGAAGTTTTTTGACTATATCCAACTTCCAAATTTTGACATTGCTGCAGATGCTGCAGCAACCTTTAAG
             | | |    ||    | | ||  |   ||||  | ||  |||   |       | |||   |   |   | | | |    || |  |  |  || | |   ||||||||||  || ||||    |   |||||||||||||| |||| || || ||||| ||||| ||||||||||| |||||||| ||||| ||||||
gtgagcaaatcttatattttctttgattacgagattaaatcctatatgtttcaatccataaagagacaatctctatcgaatttatatagtgaaaactgcttctctttctatggttcagATATGTTTTGGACTCGGAGCACGTGAAGAAGTTTTTTTACTACATACAGCTTCCCAATTTCGACATTGCTGCTGATGCTGCTGCAACTTTTAAG

upper sequence: GLYMA09G01370.2 (Glycine max), 3'ss of exon 4
lower sequence: Vv10s0405g00020.t01 (Vitis vinifera), 3'ss of exon 4
ctgaacactgg-aattagaaaagggaaaatgacctaggtcttataatttttttcccatcataactaatgtgt-tgctgtaattcttcatgattttg-tatcagATATGTCCTGAACTCACCTCGTATGAAGAAGTTTTTTGACTATATCCAACTTCCAAATTTTGACATTGCTGCAGATGCTGCAGCAACCTTTAAG
|||  ||  || | || || ||    |  |    |   | |||| ||| || |       ||||| |  ||  |  | |||||  |  |  ||||  |  ||| || |||||| | ||| | |  ||||||||||||||||| ||||| ||||||||||||||||||||||||||||||||||| ||||| ||||||
ctgtccaaaggcagtttgacaa---tatcttttattattattattattattatatgggtttaactgagttgaattttctaatttatggtttttttcctgacagGTACGTCCTGGAATCAGCGCACATGAAGAAGTTTTTTGATTATATTCAACTTCCAAATTTTGACATTGCTGCAGATGCTGCTGCAACTTTTAAG

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|213599253|gb|DB962290.1|DB962290
EST:     GCCAGAAAAGATGCCACTCAAGTTGTTGCAAATTTACAAAGGCAACAGGTTCAGTTTAAGTTGATTGCATCTGATTACCTGGAGAAAAATATGGATCTTATGGATATT
genomic: GCCAGAAAAGATGCCACTCAAGTTGTTGCAAATTTACAAAGGCAACAGGTTCAGTTTAAGTTGATTGCATCTGATTACCTGGAGAAAAATATGGATCTTATGGATATT
EST: gi|207836097|gb|GD808754.1|GD808754
EST:     CACTATGGTGCGATGCTGAGGGAGTGCATAAGACACCAGATTGTTGCAAA                         ATATGTCCTGAACTCACCTCGTATGAAGAAGTTTTTTGACTATATCCAACT
genomic: CACTATGGTGCGATGCTGAGGGAGTGCATAAGACACCAGATTGTTGCAAAgtaagaaaaa ... tttgtatcagATATGTCCTGAACTCACCTCGTATGAAGAAGTTTTTTGACTATATCCAACT
EST: gi|27424482|gb|CA936002.1|CA936002
EST:     CCAGATTGTTGCAAA                         ATATGTCCTGAACTCACCTCGTATGAAGAAGTTTTTTGACTATATCCAACT
genomic: CCAGATTGTTGCAAAgtaagaaaaa ... tttgtatcagATATGTCCTGAACTCACCTCGTATGAAGAAGTTTTTTGACTATATCCAACT
EST: gi|208082045|gb|GD883411.1|GD883411
EST:     TATGGTGCGATGCTGAGGGAGTGCATAAGACACCAGATTGTTGCAAA                         ATATGTCCTGAACTCACATCGTATGAAGAAGTTTTTTGACTATATCCAACT
genomic: TATGGTGCGATGCTGAGGGAGTGCATAAGACACCAGATTGTTGCAAAgtaagaaaaa ... tttgtatcagATATGTCCTGAACTCACCTCGTATGAAGAAGTTTTTTGACTATATCCAACT
EST: gi|193447808|gb|FK414073.1|FK414073
EST:     CACTATGGTGCGATGCTGAGGGAGTGCATAAGACACCAGATTGTTGCAAA                         ATATGTCCTGAACTCACCTCGTATGAAGAAGTTTTTTGACTATATCCAACT
genomic: CACTATGGTGCGATGCTGAGGGAGTGCATAAGACACCAGATTGTTGCAAAgtaagaaaaa ... tttgtatcagATATGTCCTGAACTCACCTCGTATGAAGAAGTTTTTTGACTATATCCAACT
EST: gi|254314383|gb|GR831968.1|GR831968
EST:     GCCAGAAAAGATGCCACTCAACTTGTTGCAAATTTACAAAGGCAACAGGTTCAGTTTAAGTTGATTGCATCTGATTACCTGGAGAAAAATATGGATCTTATGGATATT
genomic: GCCAGAAAAGATGCCACTCAAGTTGTTGCAAATTTACAAAGGCAACAGGTTCAGTTTAAGTTGATTGCATCTGATTACCTGGAGAAAAATATGGATCTTATGGATATT
EST: gi|254314656|gb|GR829649.1|GR829649
EST:     CACTATGGTGCGATGCTGAGGGAGTGCATAAGACACCAGATTGTTGCAAA                         ATATGTCCTGAACTCACCTCGTATGAAGAAGTTTTTTGACTATATCCAACT
genomic: CACTATGGTGCGATGCTGAGGGAGTGCATAAGACACCAGATTGTTGCAAAgtaagaaaaa ... tttgtatcagATATGTCCTGAACTCACCTCGTATGAAGAAGTTTTTTGACTATATCCAACT
EST: gi|208120718|gb|GD916047.1|GD916047
EST:     GGAGGCCAGAAAAGATGCCACTCAAGTTGTTGCAAATTTACAAAGGCAACAGGTTCAGTTTAAGTTGATTGCATCTGATTACCTGGAGAAAAATATGGATCTTATGGATATT
genomic: GGAGGCCAGAAAAGATGCCACTCAAGTTGTTGCAAATTTACAAAGGCAACAGGTTCAGTTTAAGTTGATTGCATCTGATTACCTGGAGAAAAATATGGATCTTATGGATATT
EST: gi|15203298|gb|BI426066.1|BI426066
EST:     GCCAGAAAAGATGCCACTCAAGTTGTTGCAAATTTACAAAGGCAACAGGTTCAGTTTAAGTTGATTGCATCTGATTACCTGGAGAAAAATATGGATCTTATGGATATT
genomic: GCCAGAAAAGATGCCACTCAAGTTGTTGCAAATTTACAAAGGCAACAGGTTCAGTTTAAGTTGATTGCATCTGATTACCTGGAGAAAAATATGGATCTTATGGATATT
EST: gi|151397719|gb|EV267592.1|EV267592
EST:     GTCAGAAAAGATGCCACTCAAGTTGTTGCAAATTTACAAAGGCAACAGGTTCAGTTTAAGTTGATTGCATCTGATTACCTGGAGAAAAATATGGATCTTATGGATATT
genomic: GCCAGAAAAGATGCCACTCAAGTTGTTGCAAATTTACAAAGGCAACAGGTTCAGTTTAAGTTGATTGCATCTGATTACCTGGAGAAAAATATGGATCTTATGGATATT
EST: gi|18039695|gb|BM307989.1|BM307989
EST:     GCCAGAAAAGATGCCACTCAAGTTGTTGCAAATTTACAAAGGCAACAGGTTCAGTTTAAGTTGATTGCATCTGATTACCTGGAGAAAAATATGGATCTTATGGATATT
genomic: GCCAGAAAAGATGCCACTCAAGTTGTTGCAAATTTACAAAGGCAACAGGTTCAGTTTAAGTTGATTGCATCTGATTACCTGGAGAAAAATATGGATCTTATGGATATT
EST: gi|11414041|gb|BF425981.1|BF425981
EST:     CACTATGGTGCGATGCTGAGGGAGTGCATAAGACACCAGATTGTTGCAAA                         ATATGTCCTGAACTCACCTCGTATGAAGAAGTTTTTTGACTATATCCAACT
genomic: CACTATGGTGCGATGCTGAGGGAGTGCATAAGACACCAGATTGTTGCAAAgtaagaaaaa ... tttgtatcagATATGTCCTGAACTCACCTCGTATGAAGAAGTTTTTTGACTATATCCAACT
EST: gi|208241369|gb|GE039667.1|GE039667
EST:     GGAGTGCATAAGACACCAGATTGTTGCAAA                         ATATGTCCTGAACTCACCTCGTATGAAGAAGTTTTTTG
genomic: GGAGTGCATAAGACACCAGATTGTTGCAAAgtaagaaaaa ... tttgtatcagATATGTCCTGAACTCACCTCGTATGAAGAAGTTTTTTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttttttcccatcataactaatgtgttgctgtaattcttcatgattttgtatcagATATGTCCTGAACTCACCTCGTATGAAGAAGTTTTTTGACTATATCCAACTTCCAAATTTTGACATTGCTGCAGATGCTGCAGCAACCTTTAAG
               aactaat  putative branch site (score: 2)
             ataactaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ctgaacactggaattagaaaagggaaaatgacctaggtcttataatttttttcccatcataactaatgtgttgctgtaattcttcatgattttgtatcagATATGTCCTGAACTCACCTCGTATGAAGAAGTTTTTTGACTATATCCAACTTCCAAATTTTGACATTGCTGCAGATGCTGCAGCAACCTTTAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGCAG