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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaattactcacatggtgacaaattattttataaaagttgtttaacatgctgaattgacattaccacaatattttatctcagGCTTCAGACTACAGAGAAAACAAAATTCACACAGGTTGGCTGGACAGTAGAATTGCAATGCGGGTTAGAGCAGAAAGGCCTGCCTGGTATCTTTCGGTCG

Basic information

species Glycine max
transcript GLYMA06G11120.1
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA06G11120.1 (Glycine max), 3'ss of exon 11
lower sequence: AC197672.3_FGT002 (Zea mays), 3'ss of exon 13
---------------------gtaaatt---actcacatggtgacaaattattttataaa-agttgtttaacatg-ctgaattgacattaccacaatatt-ttatctcagGCTTCAGACTACAGAGAAAACAAAATTCACACAGGTTGGCTGGACAGTAGAATTGCAATGCGGGTTAGAGCAGAAAGGCCTGCCTGGTATCTTTCGGTCG
                      | |||    | |   |   ||   | || | | ||      || |  |  ||| || ||       | |       || ||||  ||||||||||||| |||||||||||| || ||||| ||||||||||| |  ||||| || ||||| |||  ||| || |||||  | |||||| | || || |
gtaagaaatattgaccatcttttgaatccccattttgactatgttgatttgtctcatgtttgattttccattatggctaaacctgtggtgctgtttccttattattccagGCTTCAGACTTCAGAGAAAACAAGATCCACACTGGTTGGCTGGATACAAGAATAGCTATGCGTGTTCAAGCTGAGAGGCCCCCATGGTATATCTCAGTGG

upper sequence: GLYMA06G11120.1 (Glycine max), 3'ss of exon 11
lower sequence: GRMZM5G858094_T01 (Zea mays), 3'ss of exon 13
---------------------gtaaattac--tcacatggtgacaaattattttataaaagttg----tttaacatg-ctgaattgacattaccacaatatt-ttatctcagGCTTCAGACTACAGAGAAAACAAAATTCACACAGGTTGGCTGGACAGTAGAATTGCAATGCGGGTTAGAGCAGAAAGGCCTGCCTGGTATCTTTCGGTCG
                      ||||| ||  |  |||  ||   | | || | || ||  |||    | ||  ||| || ||       | | |   |  | ||||  |||||||||||||  ||||||||||| ||||| || |||||||| ||||  ||||| || ||||| |||  ||| || |||||  | |||||| |||| || |
gtaagaaatattaaccaccttttaaatcacattttcattatgttgattcatatcattaagtttgattttctattatggctaaacctgtggtgctattttcctattattccagGCTTCAGACTTTAGAGAAAACAAGATTCATACTGGTTGGCTCGACACCAGAATAGCTATGCGTGTTCAAGCTGAGAGGCCCCCATGGTATATTTCAGTGG

upper sequence: GLYMA06G11120.1 (Glycine max), 3'ss of exon 11
lower sequence: AT1G36160.1 (Arabidopsis thaliana), 3'ss of exon 12
gtaaattactcacatggtgacaaattattttataaaagttgtttaacatgctgaattgacattaccacaatattttatctcagGCTTCAGACTACAGAGAAAACAAAATTCACACAGGTTGGCTGGACAGTAGAATTGCAATGCGGGTTAGAGCAGAAAGGCCTGCCTGGTATCTTTCGGTCG
|||  || ||  | ||   |||||   ||  |       | |  || |  ||||    | || |   ||||  |  | |  ||||||| || ||| | || |||||||||||||| |||||| |||| ||||| ||||| |||||||| ||||| || |||||| | |||||||| || || |
gtacgtttctt-cttgcacacaaac--ttacactctgtgtatgcaataccctga--caagatcatttcaattgtcaacc--agGCTTCTGATTACCGTGATAACAAAATTCACACTGGTTGGTTGGATAGTAGGATTGCTATGCGGGTCAGAGCTGAGAGGCCTCCATGGTATCTCTCTGTTG

upper sequence: GLYMA06G11120.1 (Glycine max), 3'ss of exon 11
lower sequence: AT1G36180.1 (Arabidopsis thaliana), 3'ss of exon 12
gtaaattactcacatggtgacaaattattttataaaagttgtttaacatgctgaattgacattaccacaatattt-tatctcagGCTTCAGACTACAGAGAAAACAAAATTCACACAGGTTGGCTGGACAGTAGAATTGCAATGCGGGTTAGAGCAGAAAGGCCTGCCTGGTATCTTTCGGTCG
|||  || |   | |  |    |   |  |||||       | |||  | |     |||||  | ||     ||  ||   |||||||| || ||| | ||||||||||| ||||| |||||| |||||||||| ||||| |||||||| |||||||| || ||| | |||||||| || || |
gtatgtttccttcttcctacatacaaaagttatactgtgactgtaatgtacc---ctgacaagatcatttcgttgataaaccagGCTTCTGATTACCGGGAAAACAAAATACACACTGGTTGGTTGGACAGTAGGATTGCTATGCGGGTCAGAGCAGAGAGACCTCCATGGTATCTCTCTGTAG

upper sequence: GLYMA06G11120.1 (Glycine max), 3'ss of exon 11
lower sequence: Vv18s0001g04980.t01 (Vitis vinifera), 3'ss of exon 12
gtaaattactcacatggtgacaa----attat-tttataaaagttgtttaaca--tgctgaattgacattaccac------------aatattttatct-cagGCTTCAGACTACAGAGAAAACAAAATTCACACAGGTTGGCTGGACAGTAGAATTGCAATGCGGGTTAGAGCAGAAAGGCCTGCCTGGTATCTTTCGGTCG
||||| | || |  |  ||||||    |||   ||||| |   || || || |  |  | |  | | | ||| |             || |  || ||| |||||||| || |||||||| || ||||| ||||| |||||| |||||||||||||||| ||| |||||||||||||||||||  | ||||||||||| || |
gtaaagttctaatctattgacaatcaaattccatttatcatcctttttcaataatttttaaccttagaatacaaactaaagaaaagaaaaaccttttctgcagGCTTCTGATTACAGAGAGAATAAAATCCACACCGGTTGGTTGGACAGTAGAATTGCTATGAGGGTTAGAGCAGAAAGGCCGCCTTGGTATCTTTCTGTGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttataaaagttgtttaacatgctgaattgacattaccacaatattttatctcagGCTTCAGACTACAGAGAAAACAAAATTCACACAGGTTGGCTGGACAGTAGAATTGCAATGCGGGTTAGAGCAGAAAGGCCTGCCTGGTATCTTTCGGTCG
                         aattgac  putative branch site (score: 3)
                                            ttttatctc  putative PPT
                                      acaatattttatct  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaaattactcacatggtgacaaattattttataaaagttgtttaacatgctgaattgacattaccacaatattttatctcagGCTTCAGACTACAGAGAAAACAAAATTCACACAGGTTGGCTGGACAGTAGAATTGCAATGCGGGTTAGAGCAGAAAGGCCTGCCTGGTATCTTTCGGTCG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCAG