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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...atttcagccattgtttatgccaaaatatctattctctttttgatttagtagagtttcaggatttgatttcaattcatcaagttttttacttaaatcgcagGCTACAATTTATCAACAAAAAGCTTTGGATATCAACGAGAGAGAGTTAGGTCTGGATCATCCTGATACCATGAAGAGCTATGGGGATCTTGCTGTTTTCT

Basic information

species Glycine max
transcript GLYMA07G06160.1
intron # 18
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA07G06160.1 (Glycine max), 3'ss of exon 18
lower sequence: LOC_Os07g23990.1 (Oryza sativa), 3'ss of exon 16
-atttcagccattgtttatgccaaaatatctattctctttttgatttagtagagtttcaggatttgatttcaattcatcaagttttttacttaaat--cgcagGCTACAATTTATCAACAAAAAGCTTTGGATATCAACGAGAGAGAGTTAGGTCTGGATCATCCTGATACCATGAAGAGCTATGGGGATCTTGCTGTTTTCT
 |        |||| |||    || |     |||     | ||||  | |  |||||    |  | |   ||| |||  | | || | |   |||    ||||||||| || ||||| ||||| ||  | || ||||| ||||| ||  | || || ||||| |||||||| |||||||| ||||| ||||||||||| ||||
caacatgagtattgattaattaaagaaga--attgagaatgtgatgaattgaagttttgaaaaat-accccaagtcaatatgcttatcatagaaaaaatgcagGCTACGATCTATCAGCAAAAGGCCCTAGACATCAATGAGAGGGAACTTGGGCTAGATCACCCTGATACAATGAAGAGTTATGGAGATCTTGCTGTGTTCT

upper sequence: GLYMA07G06160.1 (Glycine max), 3'ss of exon 18
lower sequence: AT1G01320.1 (Arabidopsis thaliana), 3'ss of exon 18
atttcagccattgtttatgccaaaatatctattctctttttgatttagtagagtttcaggatttgatttcaattcatcaagttttttacttaaatcgcagGCTACAATTTATCAACAAAAAGCTTTGGATATCAACGAGAGAGAGTTAGGTCTGGATCATCCTGATACCATGAAGAGCTATGGGGATCTTGCTGTTTTCT
            || | |   | | ||| |  |    || |||| |  |    ||  | ||    |||   |  |   ||| ||||   |||||   ||||||||||| ||||| ||||| ||||| || ||||| ||||| ||  | || || |||||||| ||||| |||||||| ||||| ||||||||||| ||||
------------gtctgtat-atattatatggttagattgtgatatctttcctttatatgac--aattgtgaaactaaaagattttg--ttaaa--acagGCTACAATATATCAGCAAAAGGCTTTAGACATCAATGAGAGGGAACTTGGACTTGATCATCCAGATACAATGAAGAGTTATGGTGATCTTGCTGTCTTCT

upper sequence: GLYMA07G06160.1 (Glycine max), 3'ss of exon 18
lower sequence: Vv00s0388g00080.t01 (Vitis vinifera), 3'ss of exon 3
--------atttcagccattgtttatgccaaaatatctattctctttttgatttagtagagtttcaggatttgatttcaattcatcaagttttttacttaaatcgcagGCTACAATTTATCAACAAAAAGCTTTGGATATCAACGAGAGAGAGTTAGGTCTGGATCATCCTGATACCATGAAGAGCTATGGGGATCTTGCTGTTTTCT
         |  || | |  ||||    |  || |||||| || |||||  |||  |  | ||   |    |  | | ||||||  |      ||     |||   |||| ||||||||||||||||| || ||||| ||||| ||||||||  |||| || |||||||| || || |||||||| ||||| ||||||||||| ||||
tatggtttttcccatctagggttttccacgtaa-atctatgctgtttttttttttttttacttgttg--cctattcttaattcaagag-----ttgtcccaattcaagGCCACAATTTATCAACAAAAGGCATTGGACATCAATGAGAGAGAACTAGGACTTGATCATCCAGACACGATGAAGAGTTATGGAGATCTTGCTGTGTTCT

upper sequence: GLYMA07G06160.1 (Glycine max), 3'ss of exon 18
lower sequence: Vv15s0046g00740.t01 (Vitis vinifera), 3'ss of exon 18
atttcagccattgtttatgccaaaatatctattctctttttgatttagtagagtttcaggatttgatttcaattcatcaagtttt----ttacttaaatcgcagGCTACAATTTATCAACAAAAAGCTTTGGATATCAACGAGAGAGAGTTAGGTCTGGATCATCCTGATACCATGAAGAGCTATGGGGATCTTGCTGTTTTCT
  | ||   |   | |||||     | | | || | ||||   | | |   | | |||   ||  ||  | ||      | ||      ||     |||  ||||| ||||||||||||||||| || ||||| ||||| ||||||||  |||| || |||||||| || || |||||||| ||||| ||||||||||| ||||
--tccatgtaa-atctatgctgtt-tttttttttttttttccttgttgcctattctcatttttccataactatatggttaattcaagagttgtcccaatttcagGCCACAATTTATCAACAAAAGGCGTTGGACATCAATGAGAGAGAACTAGGACTTGATCATCCAGACACAATGAAGAGTTATGGAGATCTTGCTGTGTTCT

upper sequence: GLYMA07G06160.1 (Glycine max), 3'ss of exon 18
lower sequence: EFJ26734 (Selaginella moellendorffii), 3'ss of exon 17
atttcagccattgtttatgccaaaatatctattctctttttgatttagtagagtttcaggatttgatttcaattcatcaagttttttacttaaatcgcagGCTACAATTTATCAACAAAAAGCTTTGGATATCAACGAGAGAGAGTTAGGTCTGGATCATCCTGATACCATGAAGAGCTATGGGGATCTTGCTGTTTTCT
                                      | || | | ||      |   | ||| ||  ||||  |  ||  ||| |       || |||||||| || || |||||||| ||||| || ||||| ||  | ||| | ||  |||| ||||| |||||||||||||||||||| ||||| ||||| || |
-------------------------------------gtctggtcttgtca---cttgcggttttata-caatcta--aacgtttgtcgacgcttctcagGCTACCATCTACCAACAAAAGGCTTTAGACATCAATGAACGCGAGCTTGGCTTGGACCATCCGGATACCATGAAGAGCTATGGAGATCTGGCTGTCTTTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tagtagagtttcaggatttgatttcaattcatcaagttttttacttaaatcgcagGCTACAATTTATCAACAAAAAGCTTTGGATATCAACGAGAGAGAGTTAGGTCTGGATCATCCTGATACCATGAAGAGCTATGGGGATCTTGCTGTTTTCT
               atttgat  putative branch site (score: 5)
                                    ttttttactt  putative PPT
                                 aagttttttacttaaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
atttcagccattgtttatgccaaaatatctattctctttttgatttagtagagtttcaggatttgatttcaattcatcaagttttttacttaaatcgcagGCTACAATTTATCAACAAAAAGCTTTGGATATCAACGAGAGAGAGTTAGGTCTGGATCATCCTGATACCATGAAGAGCTATGGGGATCTTGCTGTTTTCT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT
- -tcagcca
- - - - - - - -tatgcca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - ggatttg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -caattca