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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttgataaggtggtttgaactctggttgggtttctttgtgacaatcttcttgtagaattttgttgaggtcttggctccttacaatctttttcttgttgcagAATTTTGATGATGTCTTGGTTCCTGAAGACCATGTAAGTAGGAGCTATAATGATACTTACTACATAGACCCTCAGACTGTTTTGAGGTGCCACACAAGTG

Basic information

species Glycine max
transcript GLYMA18G52890.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA18G52890.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G078756_T02 (Zea mays), 3'ss of exon 2
ttgataaggtg-gtttgaactctggttgggtttctttgtgacaatcttcttgtagaattttgttgaggtcttggctc-cttacaatctttttcttgttgcagAATTTTGATGATGTCTTGGTTCCTGAAGACCATGTAAGTAGGAGCTATAATGATACTTACTACATAGACCCTCAGACTGTTTTGAGGTGCCACACAAGTG
    |   ||| |||||  ||   | |  ||   | |      |   |  | |    |  | ||  |    |||||  | || ||   || | | | ||||||||||||||||||||||||| |||   |||||||||||  |||| || ||||| || || ||  | ||   ||| || || || ||||| || || ||||
-atgtgctgtgtgtttgttcttcagattcgtacatcttcagggacaatggtatgtggtagtttttggtctctggctgacctataaatgttct-tcgctgcagAATTTTGATGATGTCTTGGTCCCTTCTGACCATGTAAGCCGGAGTTACAATGACACATATTATGTTGATGATCAAACAGTCTTAAGGTGTCATACCAGTG

upper sequence: GLYMA18G52890.1 (Glycine max), 3'ss of exon 3
lower sequence: AC211349.4_FGT001 (Zea mays), 3'ss of exon 2
---ttgataaggtggtttgaactctggttgggtttctttgtgacaatcttcttgtagaattttgttgaggtcttggctccttacaatctttttcttgttgcagAATTTTGATGATGTCTTGGTTCCTGAAGACCATGTAAGTAGGAGCTATAATGATACTTACTACATAGACCCTCAGACTGTTTTGAGGTGCCACACAAGTG
    |  |    || | |   ||     |  ||  ||||  |  ||   | | |||| | |||  || |    |||||       || | ||  ||| ||||||||||||||||||||||||| |||   |||||||||||  |||| || || || || || ||  | ||   ||| || || || ||||| || || ||||
tggcttcttccctgatatttgcttcaaattcgtgcctttacggaaacggtat-gtagtagttt--tgggcctctggctgacctatatatgttctttgctgcagAATTTTGATGATGTCTTGGTCCCTTCTGACCATGTAAGCCGGAGTTACAACGACACATATTATGTTGATGGTCAAACAGTCTTAAGGTGTCATACCAGTG

upper sequence: GLYMA18G52890.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv11s0103g00120.t01 (Vitis vinifera), 3'ss of exon 2
------ttgataaggtggtttgaactctggttgggtttctttgtgacaatcttcttgtagaattttgttgaggtcttggctccttacaatctttttcttgttgcagAATTTTGATGATGTCTTGGTTCCTGAAGACCATGTAAGTAGGAGCTATAATGATACTTACTACATAGACCCTCAGACTGTTTTGAGGTGCCACACAAGTG
      || |||      |  ||  | ||||     |    |   | |||  |  |  | | || | | ||  ||||    ||  | ||| |  |||||   |||||||||||||||||| |||||||||   || ||  | |||||||| || |||||||| |||||||| || ||||| ||||| |||||||| ||||| ||||
atcctatttatagcaca-tgagagatttggtcaatgtctgcttccaaaattcttattcatatttctat-gaattctta-tgccagaaaatatacttctt---gcagAATTTTGATGATGTTTTGGTTCCTCCTGATCACATCAGTAGGAGTTACAATGATACATACTACATTGATCCTCAAACTGTCTTGAGGTGTCACACCAGTG

upper sequence: GLYMA18G52890.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv19s0027g01380.t01 (Vitis vinifera), 3'ss of exon 2
------ttgataaggtggtttgaactctggttgggtttctttgtgacaatcttcttgtagaattttgttgaggtcttggctccttacaatctttttcttgttgcagAATTTTGATGATGTCTTGGTTCCTGAAGACCATGTAAGTAGGAGCTATAATGATACTTACTACATAGACCCTCAGACTGTTTTGAGGTGCCACACAAGTG
      || ||||||   |  ||  | ||||     |    |   | |||  |  |  | | || ||| ||  ||||   | |    |||  ||| ||| ||||||||||||||||||||||||||||||   || ||  | |||||||| || |||||||| |||||||| ||| |||| ||||| |||||||||||||| ||||
atcttatttataaggca-tgggagttttggtcaatgtctgcttccaaaattcttatccatatttctgt-gaattctta--tgccagaaat--tttacttcttgcagAATTTTGATGATGTCTTGGTTCCTCCTGATCACATCAGTAGGAGTTACAATGATACATACTACATTGACTCTCAAACTGTCTTGAGGTGCCACACTAGTG

upper sequence: GLYMA18G52890.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv19s0027g01220.t01 (Vitis vinifera), 3'ss of exon 2
-------ttgataaggtggtttgaactctggttgggtttctttgtgacaatcttcttgtagaattttgttgaggtcttggctccttacaatctttttcttgttgcagAATTTTGATGATGTCTTGGTTCCTGAAGACCATGTAAGTAGGAGCTATAATGATACTTACTACATAGACCCTCAGACTGTTTTGAGGTGCCACACAAGTG
       || ||||||    | ||| | ||||     |    |   |  ||  |  |  | | || | | ||  ||||    ||  | | |||  |||||   ||||||||||||||||||||||||||||   || || || ||||| || || |||||||| |||||||| ||| | || ||||| |||||||||||||| ||||
gatcctatttataaggca--tggaagtttggtcaatgtctgcttccaagattcttatccatatttctat-gaattctta-tgccagaaagtctacttctt---gcagAATTTTGATGATGTCTTGGTTCCTCCTGATCACGTCAGTAGAAGTTACAATGATACATACTACATTGACTCCCAAACTGTCTTGAGGTGCCACACTAGTG

upper sequence: GLYMA18G52890.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv19s0027g01200.t01 (Vitis vinifera), 3'ss of exon 1
------ttgataaggtggtttgaactctggttgggtttctttgtgacaatcttcttgtagaattttgttgaggtcttggctccttacaatctttttcttgttgcagAATTTTGATGATGTCTTGGTTCCTGAAGACCATGTAAGTAGGAGCTATAATGATACTTACTACATAGACCCTCAGACTGTTTTGAGGTGCCACACAAGTG
      || ||||||   |  ||  | ||||     |    |   | |||  |  |  | | || | | ||  ||||    ||  | | |||  |||||   ||||||||||||||||||||||||||||   || ||  | |||||||| || |||||||| |||||||| ||| |||| ||||| |||||||||||||| || |
atcctatttataaggca-tgggagttttggtcaatgtctgcttccaaaattcttatccatatttctat-gaattctta-tgccagaaagtctacttctt---gcagAATTTTGATGATGTCTTGGTTCCTCCTGATCACATCAGTAGGAGTTACAATGATACATACTACATTGACTCTCAAACTGTCTTGAGGTGCCACACTAGGG

upper sequence: GLYMA18G52890.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv19s0027g01150.t01 (Vitis vinifera), 3'ss of exon 3
------ttgataaggtggtttgaactctggttgggtttctttgtgacaatcttcttgtagaattttgttgaggtcttggctccttacaatctttttcttgttgcagAATTTTGATGATGTCTTGGTTCCTGAAGACCATGTAAGTAGGAGCTATAATGATACTTACTACATAGACCCTCAGACTGTTTTGAGGTGCCACACAAGTG
      || ||||||   |  ||  | |||||    |    |   | |||  |  |  | | || | | ||  ||||    ||  | | |||  |||||   ||||||||||||||||||||||||||||   || || || |||||||| || |||||||| |||||||| ||| |||| ||||| |||||||||||||| | ||
atcctatttataaggca-tgggagttttggtttatgtctgcttccaaaattcttatccatatttctat-gaattctta-tgccagaaagtctacttctt---gcagAATTTTGATGATGTCTTGGTTCCTCTTGATCACGTCAGTAGGAGTTACAATGATACATACTACATCGACTCTCAAACTGTCTTGAGGTGCCACACTACTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttcttgtagaattttgttgaggtcttggctccttacaatctttttcttgttgcagAATTTTGATGATGTCTTGGTTCCTGAAGACCATGTAAGTAGGAGCTATAATGATACTTACTACATAGACCCTCAGACTGTTTTGAGGTGCCACACAAGTG
                             tccttac  putative branch site (score: 2)
                                      tctttttcttgttgc  putative PPT
      tagaatttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttgataaggtggtttgaactctggttgggtttctttgtgacaatcttcttgtagaattttgttgaggtcttggctccttacaatctttttcttgttgcagAATTTTGATGATGTCTTGGTTCCTGAAGACCATGTAAGTAGGAGCTATAATGATACTTACTACATAGACCCTCAGACTGTTTTGAGGTGCCACACAAGTG

- - - -ggtggtt
- - - - - - - - - - - ggttggg
- - - - - - - - - - - - - - - - ctttgtg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gttgagg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ccttaca