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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ggtatggaaaaaatgtcatatttccatctgtagttcatcaaagttagtaaataattttttaaaaaataaatttaatttttaactaatttcttttatgtagGTGGGTCTGCCAGCCCGAGGTAAAACTTTCACTGCAGCTAAACTTACAAGATATCTTCGATGGTTAGGTCATAATACCAAACACTTCAATGTTGGGAAG

Basic information

species Glycine max
transcript GLYMA18G06770.1
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA18G06770.1 (Glycine max), 3'ss of exon 8
lower sequence: LOC_Os05g07130.1 (Oryza sativa), 3'ss of exon 6
-ggtatggaaaaaatgtcatatttccatctgtagttcatcaaagttagtaaataattttttaaaaaataaatttaatttttaactaa--tttcttttatgtagGTGGGTCTGCCAGCCCGAGGTAAAACTTTCACTGCAGCTAAACTTACAAGATATCTTCGATGGTTAGGTCATAATACCAAACACTTCAATGTTGGGAAG
  ||||   ||  || |  |||| |    |    |||||     | | |   ||   |||| ||||  | ||||  ||  |||  |    | |||  |   |||| || || ||||| || ||||||||||| || |||||||| |||||||| || ||||| |||||||||||| | |||| ||| ||||||||||| |||
tagtataataattatttgttattgcatcttaagattcatttgtatcactgctta---ttttgaaaagcagattttcttcctaaacatgtctacttgcaaacagGTTGGCCTACCAGCTCGTGGTAAAACTTTTACCGCAGCTAAGCTTACAAGGTACCTTCGTTGGTTAGGTCATGAAACCAGACATTTCAATGTTGGAAAG

upper sequence: GLYMA18G06770.1 (Glycine max), 3'ss of exon 8
lower sequence: LOC_Os03g18310.1 (Oryza sativa), 3'ss of exon 5
ggtatggaaaaaatgtcatatttccatctgtagttcatcaaagttagtaaataattttttaaaaaataaatttaatttttaactaatttcttttatg------tagGTGGGTCTGCCAGCCCGAGGTAAAACTTTCACTGCAGCTAAACTTACAAGATATCTTCGATGGTTAGGTCATAATACCAAACACTTCAATGTTGGGAAG
   ||   || ||||    |||||  ||   | |   |  || | | |  || ||  || |||  |    |  | || ||   |||    | |  ||      ||||| ||  ||||||| || ||||| || || || || ||||| |||||||| || |||||||||||||||||| | || ||||||||||||||||| |||
--catatgaagaatgaataatttctgtc---aatgtgttgaaat-actttattatgcttcaaattacctttgcagttcttctgtaaccattgtgctgccattctagGTTGGGTTGCCAGCTCGTGGTAAGACCTTTACAGCGGCTAAGCTTACAAGGTACCTTCGATGGTTAGGTCATGAAACAAAACACTTCAATGTTGGAAAG

upper sequence: GLYMA18G06770.1 (Glycine max), 3'ss of exon 8
lower sequence: GRMZM5G824405_T01 (Zea mays), 3'ss of exon 6
ggtatggaaaaaatgtcatatttccatctgtagttcatcaaagttagtaaataattttttaaaaaataaatttaatttttaactaatttcttttatg-tagGTGGGTCTGCCAGCCCGAGGTAAAACTTTCACTGCAGCTAAACTTACAAGATATCTTCGATGGTTAGGTCATAATACCAAACACTTCAATGTTGGGAAG
    |||||  | |    |   |||||    |  || |      |       |  |   ||   |   | ||   |||||||  |  | ||  |||  ||||| || || ||||| |||||||| || || || ||||||||||||||||||||||| ||||||||||||||| | || ||||||||||||||||| |||
-agctggaactattccagttaatccattgagatgtctttctttctttctttcagataagtatgcatgcagttctttttttaatcatctgctgatattctagGTTGGGCTACCAGCTCGAGGTAAGACCTTTACAGCAGCTAAACTTACAAGATATCTCCGATGGTTAGGTCATGAAACAAAACACTTCAATGTTGGAAAG

upper sequence: GLYMA18G06770.1 (Glycine max), 3'ss of exon 8
lower sequence: GRMZM2G021846_T02 (Zea mays), 3'ss of exon 6
ggtatggaaaaaatgtcatatttccatctgtagttcatcaaagttagtaaataatt--ttttaaaaaataaat-ttaatttttaactaatttcttttatgt-agGTGGGTCTGCCAGCCCGAGGTAAAACTTTCACTGCAGCTAAACTTACAAGATATCTTCGATGGTTAGGTCATAATACCAAACACTTCAATGTTGGGAAG
    |||  |||   | || | |          |||   |   ||  | | |  ||  ||  || |  |  || |  || |  || || || ||    | | |||| || || ||||| || |||||||| |||||||||| ||| |||||||| || ||||| ||||| || ||| | || | ||| |||||||||||||||
----tggtcaaatgcttatctgtttgaacaagtttctaaacttttcttcagtccttgtttccaacagttggatctccatctgaaaatatttactcccgtatcagGTTGGCCTACCAGCTCGTGGTAAAACCTTCACTGCAGTTAAGCTTACAAGGTACCTTCGTTGGTTGGGCCATGAAACTAGACATTTCAATGTTGGGAAG

upper sequence: GLYMA18G06770.1 (Glycine max), 3'ss of exon 8
lower sequence: Vv06s0004g06920.t01 (Vitis vinifera), 3'ss of exon 6
----ggtatggaaaaaatgtcatatttccatctgtagttcatcaaagtt-agtaaataattttttaaaaaataaatttaatttttaactaatttcttttatgtagGTGGGTCTGCCAGCCCGAGGTAAAACTTTCACTGCAGCTAAACTTACAAGATATCTTCGATGGTTAGGTCATAATACCAAACACTTCAATGTTGGGAAG
      |   | || |      || |||||| ||| |  | | ||| || | | |  |||||| | |||||| |||     || |||| ||||| | ||    |||| ||  ||||||| |||||||||||||| ||||||||||||||||||||||||||||| ||||| |||||| | |||||||||||||||||||| |||
gcaacttccagtaacagcaggttaattccatttgttgcacctaaaaattcatttaccaattttgttaaaaatgaat---ggttgtaacaaatttatattt--cagGTTGGCTTGCCAGCTCGAGGTAAAACTTTTACTGCAGCTAAACTTACAAGATATCTTCGCTGGTTGGGTCATGAGACCAAACACTTCAATGTTGGAAAG

upper sequence: GLYMA18G06770.1 (Glycine max), 3'ss of exon 8
lower sequence: PP1S215_89V6.1 (Physcomitrella patens), 3'ss of exon 7
ggtatggaaaaaatgtcatatttccatctgtagttcatcaaagttagtaaataattttttaaaaaataaatttaatttttaactaatttctttta--tgtagGTGGGTCTGCCAGCCCGAGGTAAAACTTTCACTGCAGCTAAACTTACAAGATATCTTCGATGGTTAGGTCATAATACCAAACACTTCAATGTTGGGAAG
  |        | |    ||||       |||     | |  ||    ||||      |   ||  ||   |     || ||  | | |||  |   |  |||| ||  | || || || || || || ||||||||||||||||| || |||||| | || |||||||||||| | ||||| |||||||||||||| |||
--tgctttcctagtagtgtattgttgagcgtataatgtgattgtggccaaattcacgctgttaagctacgctgggagttgaatgagtctctgatggtttcagGTTGGGTTACCGGCTCGTGGAAAGACATTCACTGCAGCTAAACTGACCAGATATTTGCGGTGGTTAGGTCATGACACCAAGCACTTCAATGTTGGCAAG

upper sequence: GLYMA18G06770.1 (Glycine max), 3'ss of exon 8
lower sequence: PP1S242_66V6.1 (Physcomitrella patens), 3'ss of exon 7
ggtatggaaaaaatgtcat-atttccatctgtagttcatcaaagttagtaaataattttttaaaaaataaatttaatttttaactaatttctttta-tgtagGTGGGTCTGCCAGCCCGAGGTAAAACTTTCACTGCAGCTAAACTTACAAGATATCTTCGATGGTTAGGTCATAATACCAAACACTTCAATGTTGGGAAG
     ||        | || ||       | || |   |    ||    || |  |   |   ||  ||  ||     || ||| | ||    | | |  |||| ||  |||| || || || || ||||||||||||||||| || ||  ||||| | |||||| |||||||| ||||||| ||||| ||||| || |||
--atcggggtgcccattattatggttggatatattatcttgctgtagccaagttctcaatatcaagctatgttgggagttgaacaagttctagtgactacagGTTGGGTTGCCGGCGCGTGGAAAGACTTTCACTGCAGCTAAGCTGACCCGATATTTGCGATGGCTAGGTCATGATACCAAGCACTTTAATGTCGGCAAG

upper sequence: GLYMA18G06770.1 (Glycine max), 3'ss of exon 8
lower sequence: EFJ07288 (Selaginella moellendorffii), 3'ss of exon 2
ggtatggaaaaaatgtcatatttccatctgtagttcatcaaagttagtaaataattttttaaaaaataaatttaatttttaactaatttcttttatgtagGTGGGTCTGCCAGCCCGAGGTAAAACTTTCACTGCAGCTAAACTTACAAGATATCTTCGATGGTTAGGTCATAATACCAAACACTTCAATGTTGGGAAG
                                              ||| ||  | |  | |    ||| | | || ||| | |    |  |      |||||||  | |||||  | || |||||||||||||| |  || || |||||||||||||| ||| | |||||| | || ||||||||||| ||||| || 
----------------------------------------------gtagat--tgtcgtcattcttaactcttatctttgaatcgggttct----acagGTGGGCTTACCAGCAAGGGGGAAAACTTTCACTGCTGTCAAGCTAACAAGATATCTTCGTTGGCTTGGTCATGACACTAAACACTTCAACGTTGGAAAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agtaaataattttttaaaaaataaatttaatttttaactaatttcttttatgtagGTGGGTCTGCCAGCCCGAGGTAAAACTTTCACTGCAGCTAAACTTACAAGATATCTTCGATGGTTAGGTCATAATACCAAACACTTCAATGTTGGGAAG
                                   aactaat  putative branch site (score: 2)
                                         tttcttttat  CT-rich tract
     ataattttttaaaaaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ggtatggaaaaaatgtcatatttccatctgtagttcatcaaagttagtaaataattttttaaaaaataaatttaatttttaactaatttcttttatgtagGTGGGTCTGCCAGCCCGAGGTAAAACTTTCACTGCAGCTAAACTTACAAGATATCTTCGATGGTTAGGTCATAATACCAAACACTTCAATGTTGGGAAG

- - - -aaaaaat
- - - - - - - - - - - -ccatctg