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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tatcactgaatgctcccttcctctagttttcctattgactatatcttttatgtcaacttcttctcccatcattattatgtaactttccttcaatgtgcagACGAGGAGCCATAGTCACAACCTTCATTGTTTGCTATGCTCTCACATCTTTCATTTCTGGTTATGTGAGTGGGGGAATGTACTCACGTAATGGGG

Basic information

species Glycine max
transcript GLYMA08G20100.1
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA08G20100.1 (Glycine max), 3'ss of exon 8
lower sequence: LOC_Os12g07670.1 (Oryza sativa), 3'ss of exon 8
--tatcactgaatgctccc--ttcctctagttttcctattgact-atatcttttatgtcaacttcttctcccatcattattatgtaactttccttcaatgtgcagACGAGGAGCCATAGTCACAACCTTCATTGTTTGCTATGCTCTCACATCTTTCATTTCTGGTTATGTGAGTGGGGGAATGTACTCACGTAATGGGG
  | |     |  |||     ||  | |  ||||  ||     | | || || |   |  | ||  | | | | |    |||| || |   |  |   ||| ||| |||||  | ||  |||||||||||||||| ||||||||||| |||||||| |||||||| ||||| ||||| ||  | |||||| | ||||| |
tattttgaaaacagctttaagtttttttcttttttttagcatttcacattttgtgcatggatttgcttttctaac----ttatatagcgcgcgatatttgt-cagGCGAGGGTCTATCATCACAACCTTCATTGTGTGCTATGCTCTTACATCTTTTATTTCTGGCTATGTCAGTGGTGGCCTCTACTCAAGGAATGGTG

upper sequence: GLYMA08G20100.1 (Glycine max), 3'ss of exon 8
lower sequence: LOC_Os11g07910.1 (Oryza sativa), 3'ss of exon 8
tatcactgaatgctcccttcctctagttttcctattgacta-tatcttttatgtcaact---tcttctcccatcattattatgtaactttccttcaatgtg-cagACGAGGAGCCATAGTCACAACCTTCATTGTTTGCTATGCTCTCACATCTTTCATTTCTGGTTATGTGAGTGGGGGAATGTACTCACGTAATGGGG
      |  ||  | | || ||  | |     || | | || | | | ||  |  | ||     ||||     |  || ||  |    | | |   || || |||||||||||| ||  |||| |||||||| || ||||| || || ||||||||||||||||| ||||| ||||| ||  | |||||| | ||||| |
-----ttttatctttcatttctggattgacaataatcagtaatgtttgttcagctagctagtatttctttgcaccctactaaatgctgtacttcttatttgtcagACGAGGAGCTATCATCACGACCTTCATCGTGTGCTACGCCCTTACATCTTTCATTTCTGGATATGTTAGTGGTGGCCTCTACTCAAGGAATGGCG

upper sequence: GLYMA08G20100.1 (Glycine max), 3'ss of exon 8
lower sequence: LOC_Os02g34690.1 (Oryza sativa), 3'ss of exon 8
--tatcactgaatgctcc-cttcctctagttttcctat-tgactatatcttttatgtcaacttcttctcccatcattattatgtaactttccttcaatgtgcagACGAGGAGCCATAGTCACAACCTTCATTGTTTGCTATGCTCTCACATCTTTCATTTCTGGTTATGTGAGTGGGGGAATGTACTCACGTAATGGGG
   |  | |   ||  |  |||  |  ||  ||    | | |   ||  || |   || |        | ||||  |   |  | |  ||| |      || || |||||||| || |||||||| ||||||||||| ||||| || || || ||||| ||||| ||||| ||||| | | | || |||||  ||||||
ttcacaagtagctgaactactttatgaagcatttaagtctaatcgtactttctgattctatgcaaaagcgcatctctcacaccttatattcttat----tgtagGCGAGGAGCTATTGTCACAACATTCATTGTTTGTTATGCCCTTACTTCATTCATCTCTGGATATGTCAGTGGTGCACTTTATTCACGGCATGGGG

upper sequence: GLYMA08G20100.1 (Glycine max), 3'ss of exon 8
lower sequence: GRMZM2G420310_T01 (Zea mays), 3'ss of exon 8
tatcactgaatgctcccttcctctagttttcctattgactatatcttttatgtcaacttcttctcccatcattattatgtaactttccttcaatg-tg-----cagACGAGGAGCCATAGTCACAACCTTCATTGTTTGCTATGCTCTCACATCTTTCATTTCTGGTTATGTGAGTGGGGGAATGTACTCACGTAATGGGG
||  || || |  | | |      | ||   | ||| |           | |   | | |||  | ||   || ||   ||||||   ||  ||| ||     ||| ||||| || ||  |||||||||||||||| ||||||||||| |||||||| |||||||| ||||| ||||| ||  | |||||| | ||||| |
taatacagattatttcttcaacacatttgaacaatttaagcag------aagcataatcctttacacagtgtttttcgctaacttcaattggatggtgtttgtcagGCGAGGGGCTATCATCACAACCTTCATTGTGTGCTATGCTCTTACATCTTTTATTTCTGGATATGTTAGTGGTGGTCTTTACTCAAGGAATGGTG

upper sequence: GLYMA08G20100.1 (Glycine max), 3'ss of exon 8
lower sequence: GRMZM2G165631_T01 (Zea mays), 3'ss of exon 7
-tatcactgaatgctcccttcctctagttttcctat----tgactatatctt-ttatgtcaacttcttctcccatcattattatgtaactttccttcaatgtgcagACGAGGAGCCATAGTCACAACCTTCATTGTTTGCTATGCTCTCACATCTTTCATTTCTGGTTATGTGAGTGGGGGAATGTACTCACGTAATGGGG
  |  |   ||  ||   |     | |||||| |      | ||| ||  || |||||  |           | ||  | || ||||| | | || |      ||| |||||||| || |||||||| |||||||||||||||||||| || || ||||| ||||| ||||| ||||| | | | ||||||||| |||| |
gcaaaaaaaaaatctaattctactttgttttcttgaagcataactgtactttgttatgctactcaaaatgttcctcgcttttttgtaattattctgc------cagGCGAGGAGCTATTGTCACAACATTCATTGTTTGCTATGCTCTTACTTCATTCATCTCTGGATATGTCAGTGGTGCATTATACTCACGTCATGGAG

upper sequence: GLYMA08G20100.1 (Glycine max), 3'ss of exon 8
lower sequence: GRMZM2G087212_T01 (Zea mays), 3'ss of exon 8
tatcactgaatgctcccttcctct----agttttcctattgactatatcttt-tatgtcaacttcttctcccatcattattatgtaactttccttcaatgtgc-agACGAGGAGCCATAGTCACAACCTTCATTGTTTGCTATGCTCTCACATCTTTCATTTCTGGTTATGTGAGTGGGGGAATGTACTCACGTAATGGGG
      |  | ||| |  |  | |    |    |  | || ||  | | |   |   | ||| | ||   | | | ||  | |  |   ||  ||  || ||| || |||||||| ||  |||||||||||||||| ||||| ||||| ||||||||||| ||||| ||||| ||||| ||  | || ||| | ||||| |
------tagaggcttcaattttattaacaaggattttgttcaccttgtatgagtgcattaacattttgctcaagcctttatgtaaatactttgttgtatttgccagGCGAGGAGCTATCATCACAACCTTCATTGTGTGCTACGCTCTTACATCTTTCATCTCTGGATATGTTAGTGGTGGTCTCTATTCAAGGAATGGTG

upper sequence: GLYMA08G20100.1 (Glycine max), 3'ss of exon 8
lower sequence: GRMZM2G026231_T01 (Zea mays), 3'ss of exon 8
tatcactgaatgctcccttcctctagttttcctattgactatatcttttatgtcaacttcttctcccatcattattatgtaactttccttcaatgtg-------cagACGAGGAGCCATAGTCACAACCTTCATTGTTTGCTATGCTCTCACATCTTTCATTTCTGGTTATGTGAGTGGGGGAATGTACTCACGTAATGGGG
       ||  | ||  ||| |  | |  |   |   | |  |   |  | |   | | ||   |  |    | || | ||||||   || |  |||       ||| ||||| || ||  |||||||||||||||| ||||||||||| ||||| || |||||||| ||||| ||||| ||  | |||||| | |  || |
-----aagacagatcatttctttgactcatttgaacaatttaag--tagaagcataatcctgtacatagtgcttttctctaacttcaattgatggtgtgtttgtcagGCGAGGGGCTATCATCACAACCTTCATTGTGTGCTATGCTCTTACATCGTTTATTTCTGGATATGTTAGTGGTGGTCTTTACTCAAGGAGCGGTG

upper sequence: GLYMA08G20100.1 (Glycine max), 3'ss of exon 8
lower sequence: AT1G10950.1 (Arabidopsis thaliana), 3'ss of exon 8
-----tatcactgaatgctcccttcct----ctagttttcctattgactatatcttttatgtcaacttcttctcccatcattattatgtaactttccttcaatgtg---cagACGAGGAGCCATAGTCACAACCTTCATTGTTTGCTATGCTCTCACATCTTTCATTTCTGGTTATGTGAGTGGGGGAATGTACTCACGTAATGGGG
     ||| ||   || ||    || |    | | ||||    |    | |  | |  |||       ||| |    |   | ||    | || |  ||| |  |    |||  ||||||| || |||||||| ||||| || ||||||||||| || |||||  | |||||||||||||| || |||||||||||| | |  ||||
gtatgtattacactattcttttctcttgagaccaattttgtgttgttgttttccctacatgcggttggcttgtatattggattttgctcacctcttattctaattatttcagGAGAGGAGCAATCGTCACAACTTTCATAGTGTGCTATGCTCTGACTTCTTTTGTCTCTGGTTATGTGAGCGGTGGAATGTACTCAAGAAGCGGGG

upper sequence: GLYMA08G20100.1 (Glycine max), 3'ss of exon 8
lower sequence: Vv18s0041g00680.t01 (Vitis vinifera), 3'ss of exon 8
--tatcactgaatgctcccttcctctagttttccta-ttgactatatcttttatgtcaacttcttctcccatcattattatgtaactttccttcaatgtgcagACGAGGAGCCATAGTCACAACCTTCATTGTTTGCTATGCTCTCACATCTTTCATTTCTGGTTATGTGAGTGGGGGAATGTACTCACGTAATGGGG
   | || | | |       |  | | || |   ||  || ||  ||  ||    |||  ||| |      |  ||  | | |   | |  ||    || |||  ||||||| || ||||| || || || || || |||||||| ||||| |||||||| |||||||||||||| ||||||||||| || ||||| |
gtgagcattta-tatgtatatattttggtgtctataactgcctgcattgttctcctcattttcattaaaattactttctttattgatattatttg--gttcagGAGAGGAGCAATTGTCACGACTTTTATAGTGTGTTATGCTCTTACATCATTCATTTCGGGTTATGTGAGTGGTGGAATGTACTCCCGCAATGGTG

upper sequence: GLYMA08G20100.1 (Glycine max), 3'ss of exon 8
lower sequence: Vv12s0035g00280.t01 (Vitis vinifera), 3'ss of exon 8
tatcactgaatgctcccttcctctagttttcctattgactatatcttttatgtcaacttcttc-tcccatcattattatgtaactttccttcaatgtgcagACGAGGAGCCATAGTCACAACCTTCATTGTTTGCTATGCTCTCACATCTTTCATTTCTGGTTATGTGAGTGGGGGAATGTACTCACGTAATGGGG
  |     | |  |       | | ||||   | |    | |   | || ||    || |||| || |||||  |   | |    |   |     |  |||  ||||||| || |||||||| || || || || |||||||| ||||| |||||||| |||||||||||||| || ||||||||||| ||||| |
-gttttccagttgtattagtttgtcgtttgtgtttgttttcttgatattttgcttgctacttcatctcatcaccaaactatgctctgtttatgtggctcagGAGAGGAGCAATTGTCACAACTTTTATAGTATGTTATGCTCTGACATCATTCATTTCGGGTTATGTGAGTGGTGGGATGTACTCACGCAATGGTG

upper sequence: GLYMA08G20100.1 (Glycine max), 3'ss of exon 8
lower sequence: EFJ15096 (Selaginella moellendorffii), 3'ss of exon 8
tatcactgaatgctcccttcctctagttttcctattgactatatcttttatgtcaacttcttctcccatcattattatgtaactttccttcaatgtgcagACGAGGAGCCATAGTCACAACCTTCATTGTTTGCTATGCTCTCACATCTTTCATTTCTGGTTATGTGAGTGGGGGAATGTACTCACGTAATGGGG
                                   | | ||| | |       |  |       | ||||  |      |  |  |   |  |||  ||| || ||||| ||||| |||||||||||||| ||||| ||||| || || ||||| || |||||||| ||||| ||  | ||||| || || |  |
----------------------------------gtaagtatctgtcaccctgcggccgaggtgctcatcgct--cgcctcgccctgtgttgatg--cagGCGGGGAGCAATAGTGACAACCTTCATTGTATGCTACGCTCTTACGTCATTCATCTCCGGTTATGTCAGTGGCGGGTTTTACTCGCGAAACGATG

upper sequence: GLYMA08G20100.1 (Glycine max), 3'ss of exon 8
lower sequence: EFJ37593 (Selaginella moellendorffii), 3'ss of exon 8
tatcactgaatgctcccttcctctagttttcctattgactatatcttttatgtcaacttcttctcccatcattattatgtaactttccttcaatgtgcagACGAGGAGCCATAGTCACAACCTTCATTGTTTGCTATGCTCTCACATCTTTCATTTCTGGTTATGTGAGTGGGGGAATGTACTCACGTAATGGGG
                                   | | ||| | |       |  |       | ||||  |      |  |  |   |  |||  ||| || ||||| ||||| |||||||||||||| ||||| ||||| || || ||||| || |||||||| ||||| ||  | ||||| || || |  |
----------------------------------gtaagtatctgtcacgctgcggccgaggtgctcatcgct--cgcctcgccctttgttgatg--cagGCGGGGAGCAATAGTGACAACCTTCATTGTATGCTACGCTCTTACGTCATTCATCTCCGGTTATGTTAGTGGCGGGTTTTACTCGCGAAACGATG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttttatgtcaacttcttctcccatcattattatgtaactttccttcaatgtgcagACGAGGAGCCATAGTCACAACCTTCATTGTTTGCTATGCTCTCACATCTTTCATTTCTGGTTATGTGAGTGGGGGAATGTACTCACGTAATGGGG
                               atgtaac  putative branch site (score: 3)
                                     ctttccttc  CT-rich tract
                         attattatgtaacttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tatcactgaatgctcccttcctctagttttcctattgactatatcttttatgtcaacttcttctcccatcattattatgtaactttccttcaatgtgcagACGAGGAGCCATAGTCACAACCTTCATTGTTTGCTATGCTCTCACATCTTTCATTTCTGGTTATGTGAGTGGGGGAATGTACTCACGTAATGGGG

- - - -gaatgct
- - - - - - - - cttcctc
- - - - - - - - - - - - - - - cctattg