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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tactttgatctctttctgagtttgagctttcaagtttcaacagtattattgtgctcatctctaaacatctgtggtaacttgttttttcctacaaatacagGCATTTGTGAATCTAGTTCTTACTCTCTGTGATCCGGGTGATTCCGTGGTTATGTTTGCTCCTTACTACTTCAATGCCTACATGTCCTTCCAGATGACTG

Basic information

species Glycine max
transcript GLYMA13G43830.2
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA13G43830.1 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os01g08270.1 (Oryza sativa), 3'ss of exon 5
tactttgatctctttctga--gtttgagctttcaagtttcaacagtattattgtgctcatctctaaacatctgtggtaacttgttttttcctacaaatacagGCATTTGTGAATCTAGTTCTTACTCTCTGTGATCCGGGTGATTCCGTGGTTATGTTTGCTCCTTACTACTTCAATGCCTACATGTCCTTCCAGATGACTG
  |||   | ||| | |||  | || | ||      | |  ||    |   |  ||  |     |  ||  |   || |  | || | ||  |      ||||| ||||| ||| | || || || || |||||| | || ||| | || || |||||||| || || ||||||||| |||||||||| ||||||||||| |
--cttacttttctgtatgactgcttcacctaaaccttgtttaccaactaggttagccaaataaaagtcaaataaagtgatgtcttctatcaaattttggcagGCCTTTGTAAATGTGGTCCTCACCCTTTGTGATGCTGGGGATGCAGTTGTCATGTTTGCACCATATTACTTCAATTCCTACATGTCATTCCAGATGACAG

upper sequence: GLYMA13G43830.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G107639_T01 (Zea mays), 3'ss of exon 4
------------------------------------------------------------------------tactttgatctctttctgagtttgagctttcaagtttcaacagtattattgtgctcatctctaaacatctgtggtaacttgttttttcctacaaata-------cagGCATTTGTGAATCTAGTTCTTACTCTCTGTGATCCGGGTGATTCCGTGGTTATGTTTGCTCCTTACTACTTCAATGCCTACATGTCCTTCCAGATGACTG
                                                                        |||||   |   || ||   |||| |    ||   |||     | ||    ||||   |  | | | | | |  |||  || | ||| |||  | |        ||||| ||||||||  | || || |||||||||||| | ||||||||||| || |||||||| || || || ||||||||||||||||| ||||||||||| |
gtaagttctgcctgcatttactacctattttgccttgtagtgttttccaaatgggccttatgtttcccaatttacttctgttaattacttc-tttgggggcacactcttctttcctgtttcactgctagaccttgatcttgtcttataatctggtcttttctaacattgattttttcagGCTTTTGTGAACTTGGTCCTCACTCTCTGTGATGCTGGTGATTCCGTTGTCATGTTTGCACCGTATTATTTCAATGCCTACATGTCATTCCAGATGACAG

upper sequence: GLYMA13G43830.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G029135_T01 (Zea mays), 3'ss of exon 4
tactttgatctctt-tctgagtttgagctttcaagtttcaacagtattattgtgctcatctctaaacatctgtggtaacttgttttttcctaca-----aatacagGCATTTGTGAATCTAGTTCTTACTCTCTGTGATCCGGGTGATTCCGTGGTTATGTTTGCTCCTTACTACTTCAATGCCTACATGTCCTTCCAGATGACTG
    |||||  ||| | || |      || |    || |     || |  ||  |     |||     ||| |  || || || ||||| ||||       | ||||| ||||||||  | || || ||||| |||||| | |||||||| || || |||||||| || || || ||||||||||||||||| ||||||||||| |
--tgttgattacttctttgggggcacactcttcctttcctgttttactcctgaaccttgatct---tgtct-tattatctggtcttttcttacattgatttttcagGCTTTTGTGAACTTGGTCCTCACTCTTTGTGATGCCGGTGATTCTGTTGTCATGTTTGCACCATATTATTTCAATGCCTACATGTCATTCCAGATGACAG

upper sequence: GLYMA13G43830.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv09s0002g05250.t01 (Vitis vinifera), 3'ss of exon 4
tactttgatctctttctgagtttgagctttcaagtttcaacagtatta--ttgtgctcatct--ctaaacatctgtggtaa---cttgttttttcctacaaatacagGCATTTGTGAATCTAGTTCTTACTCTCTGTGATCCGGGTGATTCCGTGGTTATGTTTGCTCCTTACTACTTCAATGCCTACATGTCCTTCCAGATGACTG
    | || |  ||||||  ||   ||| | |     ||| ||| |||  ||     ||| |  ||| || |||   | |    ||  || |||      |   ||||||||||||||||| ||||||||  | |||||| | || ||||  || ||||||||||| || |||||||||||||| |||||||||||||||||||| |
--tatagaacagtttctg--ttcttgctattag---ccaaaagtgttagcttccatccatttttctagacttctaaagcattgtctacttattttacttgatggcagGCATTTGTGAATCTCGTTCTTACATTATGTGATGCTGGAGATTTGGTTGTTATGTTTGCACCATACTACTTCAATGCATACATGTCCTTCCAGATGACAG

upper sequence: GLYMA13G43830.1 (Glycine max), 3'ss of exon 4
lower sequence: EFJ17703 (Selaginella moellendorffii), 3'ss of exon 4
tactttgatctctttctgagtttgagctttcaagtttcaacagtattattgtgctcatctctaaacatctgtggtaact-tgttttttcctacaaatacagGCATTTGTGAATCTAGTTCTTACTCTCTGTGATCCGGGTGATTCCGTGGTTATGTTTGCTCCTTACTACTTCAATGCCTACATGTCCTTCCAGATGACTG
                                    | |||      | | | |   ||  ||  ||| | | ||     || ||||| || |     ||||| | || |||| |||  || | | | |||||||| || ||||||||||| ||||||||||| || ||||||||||| |||| | | |||||||||||||
-----------------------------------gtgaactaacgcaatcttccgttccataggcatttattgttctagtgattttttctcc-----cagGCCTATGCGAATTTAGCACTCAGTTTGTGTGATCCAGGAGATTCCGTGGTAATGTTTGCTCCATATTACTTCAATGCGTACACGACATTCCAGATGACTG

upper sequence: GLYMA13G43830.1 (Glycine max), 3'ss of exon 4
lower sequence: EFJ16234 (Selaginella moellendorffii), 3'ss of exon 4
tactttgatctctttctgagtttgagctttcaagtttcaacagtattattgtgctcatctctaaacatctgtggtaact-tgttttttcctacaaatacagGCATTTGTGAATCTAGTTCTTACTCTCTGTGATCCGGGTGATTCCGTGGTTATGTTTGCTCCTTACTACTTCAATGCCTACATGTCCTTCCAGATGACTG
                                    | |||      | | | |   ||  ||  ||| | | ||     || ||||| || |     ||||| | || |||| |||  || | | | |||||||| || ||||||||||| ||||||||||| || ||||||||||| |||| | | ||||| |||||||
-----------------------------------gtgaactagcgcaatcttccgttccataggcatttattgttctagtgattttttctcc-----cagGCCTATGCGAATTTAGCACTCAGTTTGTGTGATCCAGGAGATTCCGTGGTAATGTTTGCTCCATATTACTTCAATGCGTACACGACATTCCAAATGACTG

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|23727838|gb|BU761954.1|BU761954
EST:     AAAATAATTTGCACAAATCTTCAGTAATGGTTACATCAGGTGCCAATCAG                         GCATTTGTGAATCTAGTTCTTACTCTCTGTGATCCGGGTGATTCCGTGGTC
genomic: AAAATAATTTGCACAAATCTTCAGTAATGGTTACATCAGGTGCCAATCAGgtgaggttaa ... acaaatacagGCATTTGTGAATCTAGTTCTTACTCTCTGTGATCCGGGTGATTCCGTGGTT
EST: gi|15816082|gb|BI788357.1|BI788357
EST:     AAAATAATTTGCACAAATCTTCAGTAATGGTTACATCAGGTGCCAATCAG                         GCATTTGTGAATCTAGTTCTTACTCTCTGTGATCCGGGTGATTCCGTGGTT
genomic: AAAATAATTTGCACAAATCTTCAGTAATGGTTACATCAGGTGCCAATCAGgtgaggttaa ... acaaatacagGCATTTGTGAATCTAGTTCTTACTCTCTGTGATCCGGGTGATTCCGTGGTT
EST: gi|5605984|gb|AI900082.1|AI900082
EST:     AAAATAATTTGCACAAATCTTCAGTAATGGTTACATCAGGTGCCAATCAG                         GCATTTGTGAATCTAGTTCTTACTCTCTGTGATCCGGGTGATTCCGTGGTT
genomic: AAAATAATTTGCACAAATCTTCAGTAATGGTTACATCAGGTGCCAATCAGgtgaggttaa ... acaaatacagGCATTTGTGAATCTAGTTCTTACTCTCTGTGATCCGGGTGATTCCGTGGTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttattgtgctcatctctaaacatctgtggtaacttgttttttcctacaaatacagGCATTTGTGAATCTAGTTCTTACTCTCTGTGATCCGGGTGATTCCGTGGTTATGTTTGCTCCTTACTACTTCAATGCCTACATGTCCTTCCAGATGACTG
                          tggtaac  putative branch site (score: 2)
                                cttgttttttcctac  CT-rich tract
                                 ttgtttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tactttgatctctttctgagtttgagctttcaagtttcaacagtattattgtgctcatctctaaacatctgtggtaacttgttttttcctacaaatacagGCATTTGTGAATCTAGTTCTTACTCTCTGTGATCCGGGTGATTCCGTGGTTATGTTTGCTCCTTACTACTTCAATGCCTACATGTCCTTCCAGATGACTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGATG
- - - - - -ctttctg
- - - - - - - - - - - - -gctttca
- - - - - - - - - - - - - - - - - - - - - - - - -tgtgctc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ctaaaca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tctgtgg