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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaactcccccaccaccacccaagttcttacctttattcacatttacacacatccatttgcatgctttcttagaattagttcttgctttgttgataatcctaataatattagGCTCTTATCGATGCCCCTGATATGGTGAGGTCCCAAGTCAATTTCAAAAGGCTTTCCCTAACCGACATTAAGATTGACATTAAGAGGGTCCCTAAGAAGA

Basic information

species Glycine max
transcript GLYMA16G08910.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA16G08910.1 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os02g40880.1 (Oryza sativa), 3'ss of exon 2
gtaactcccccaccaccacccaagttcttacctttattcacatttacacacatccatttgcatgctttcttagaattagttcttgctttgttgataatcctaataat-attagGCTCTTATCGATGCCCCTGATATGGTGAGGTCCCAAGTCAATTTCAAAAGGCTTTCCCTAACCGACATTAAGATTGACATTAAGAGGGTCCCTAAGAAGA
    ||        | | |    | || |   | || ||  | |||   | ||     ||| |   || || ||  |     |  || ||||     | ||   ||| |  |||| ||| | ||||| ||||| ||||| |||| |||  |||| ||||| ||||||||||| || ||||| ||||||||||| ||  | ||||| |||||||
----ctattatgttatcgct---gctcatttttctaatcggagttaattatattgtagtgctttgattattggatatcaca-taactctgtt-----ttctgtgaatcaccagGCACTTGTGGATGCTCCTGACATGGTCAGGTGCCAGATCAACTTCAAGAGGCTTTCCCTGACTGACATCAAGATTGACATCAAACGTGTCCCGAAGAAGA

upper sequence: GLYMA16G08910.1 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os04g43540.1 (Oryza sativa), 3'ss of exon 2
gtaactcccccaccaccacccaagttcttacctttattcacatttacacacatccatttgcatgctttcttagaattagttcttgctttgttgataatcctaataatattagGCTCTTATCGATGCCCCTGATATGGTGAGGTCCCAAGTCAATTTCAAAAGGCTTTCCCTAACCGACATTAAGATTGACATTAAGAGGGTCCCTAAGAAGA
         |     ||||   |  |||   |||  |   ||||   | | ||  |||    |   || | ||| ||         | ||    |  |  |  | || | |||| ||| | |||||||||||||||||  | | |||  | || |||||  ||||||| || || ||||||||||||||||| ||| | |||||||||||||
------tagctgtttccacttcatctctagacttgct---catt---ataaatttattactttatgttttgagattttaagtgctatatgcctttgctttttgtgatttcagGCACTTGTGGATGCCCCTGATATGGTCCGCTGCCAGATAAACTTCAAGCGGCTTTCTCTGACTGACATTAAGATTGACATCAAGCGTGTCCCTAAGAAGA

upper sequence: GLYMA16G08910.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G028883_T01 (Zea mays), 3'ss of exon 2
gtaactcccccaccaccacccaagttcttacctttattcacatttacacacat-ccatttgcatgctttcttagaattagttcttgctttgttgataatcctaataatattagGCTCTTATCGATGCCCCTGATATGGTGAGGTCCCAAGTCAATTTCAAAAGGCTTTCCCTAACCGACATTAAGATTGACATTAAGAGGGTCCCTAAGAAGA
          ||     | |  |  |  ||| | ||   |  || | | |     | ||    |||||||| |   ||  ||     |||||  ||  ||    |  |||||||||||| | |||||||| || |||||  | | |||| | || |||||  |||||||||| || ||||| ||||||||||||||  | ||||| |||||||
--------tacatgtgaatctgaaat--tacttctagctattttgagataatcgtcgttgatttgctttctgatg-ttgattgaaattttgt--attttctgtctggtattagGCTCTTGTTGATGCCCCCGACATGGTTCGTTGCCAAATGAACTTCAAGCGGCTTTCCCTGACTGACATCAAGATTGACATTAAACGTGTCCCAAAGAAGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgcatgctttcttagaattagttcttgctttgttgataatcctaataatattagGCTCTTATCGATGCCCCTGATATGGTGAGGTCCCAAGTCAATTTCAAAAGGCTTTCCCTAACCGACATTAAGATTGACATTAAGAGGGTCCCTAAGAAGA
                                        tcctaat  putative branch site (score: 2)
                                 ttgataatcctaataa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaactcccccaccaccacccaagttcttacctttattcacatttacacacatccatttgcatgctttcttagaattagttcttgctttgttgataatcctaataatattagGCTCTTATCGATGCCCCTGATATGGTGAGGTCCCAAGTCAATTTCAAAAGGCTTTCCCTAACCGACATTAAGATTGACATTAAGAGGGTCCCTAAGAAGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG