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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttgtatatcttagtgcatgcaatgggtaaatgtgcttttgtattcatgcataatagaaaacctaagtttgcttaatagttatttcaattttgctttgaagGCTTCTCCAGATATGGCTGTTACTCTTCTTCAAATTGCAAGAATATTTGCTACCAAAGTTCCCGGAAAGGTTGATGCTGATGTGTTGCAACTGCTCTGGA

Basic information

species Glycine max
transcript GLYMA05G36530.1
intron # 14
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA05G36530.1 (Glycine max), 3'ss of exon 14
lower sequence: LOC_Os03g15900.2 (Oryza sativa), 3'ss of exon 12
ttgtatat-cttagtgcatgcaatgggtaaatgtgcttttgtattcatgcataa--tagaaaacctaagtttgcttaatagttatttcaattttgctttgaagGCTTCTCCAGATATGGCTGTTACTCTTCTTCAAATTGCAAGAATATTTGCTACCAAAGTTCCCGGAAAGGTTGATGCTGATGTGTTGCAACTGCTCTGGA
||||  || | |  || |   | |   |  ||     ||  || || |  || |  |   |||   | | ||| || ||  ||  ||   | || | |   ||||  |||| |||||||| || ||||| ||| | ||||| ||||| ||||||||||||||||| || ||| | |||||||||||  | ||||| || ||||
ttgtgcatacattttgtagctattaatttgat---tattaataatcttttatcatttgctaaatacatggttgatttattattcgtttgttcttacatgatagGCAACTCCTGATATGGCCGTGACTCTGCTTGAGATTGCTAGAATTTTTGCTACCAAAGTTCCTGGCAAGATCGATGCTGATGTACTACAACTCCTGTGGA

upper sequence: GLYMA05G36530.1 (Glycine max), 3'ss of exon 14
lower sequence: GRMZM2G012319_T02 (Zea mays), 3'ss of exon 13
-ttgtatatcttagtgcatgcaatgggtaaatgtgcttttgtattcatgcataatagaaaacctaagtttgcttaatagttatttcaattttgctttgaagGCTTCTCCAGATATGGCTGTTACTCTTCTTCAAATTGCAAGAATATTTGCTACCAAAGTTCCCGGAAAGGTTGATGCTGATGTGTTGCAACTGCTCTGGA
 || |||   | | ||||   |        || |   || | ||   | | |       |    | | |||  | ||  || | |   | || | |   ||||  | || ||||||||||| ||||| ||| | ||||||||||| ||||| || |||||||| |||||| |||||||||||||  | ||  || | ||||
tttttatggttca-tgcacttatccttctgatttttattagcatgtgtccctttatctgatttcatgattgacttattattctgtttgtcttacatgatagGCAACCCCTGATATGGCTGTGACTCTGCTTGAGATTGCAAGAATTTTTGCCACTAAAGTTCCTGGAAAGATTGATGCTGATGTTCTACAGTTGTTATGGA

upper sequence: GLYMA05G36530.1 (Glycine max), 3'ss of exon 14
lower sequence: AT2G07360.2 (Arabidopsis thaliana), 3'ss of exon 15
ttgtatatcttagtgcatgcaatgggtaaatgtgcttttgtattcatgcataatagaaaacctaagtttgcttaatagtta-----tttcaattttgctttga-agGCTTCTCCAGATATGGCTGTTACTCTTCTTCAAATTGCAAGAATATTTGCTACCAAAGTTCCCGGAAAGGTTGATGCTGATGTGTTGCAACTGCTCTGGA
     ||||  | ||| |  ||   | | |    ||| | |||| | |  |||| |  |||     | | || | ||||||     ||| |||||| |||| | ||||  |||||||||||||||||| ||||||  ||||||| ||||||||||| ||||||||||| || ||  |||| |||||||| || || ||||| ||||
---cttatcc-attgcgttgaaactgaagaaaaacttgt-tattgaggagtaat-gttaactgttttcttctgactagttaactctttttaatttttctttcacagGCAACTCCAGATATGGCTGTTATTCTTCTCGAAATTGCCAGAATATTTGCCACCAAAGTTCCAGGGAAAATTGACGCTGATGTCTTACAGCTGCTATGGA

upper sequence: GLYMA05G36530.1 (Glycine max), 3'ss of exon 14
lower sequence: Vv07s0031g02090.t01 (Vitis vinifera), 3'ss of exon 15
--ttgtatatcttagtgcatgcaatgggtaaatgtgcttttgtattcatgcataatagaaaacctaagtttgcttaatagttatttcaattttgctttgaagGCTTCTCCAGATATGGCTGTTACTCTTCTTCAAATTGCAAGAATATTTGCTACCAAAGTTCCCGGAAAGGTTGATGCTGATGTGTTGCAACTGCTCTGGA
     ||||   | ||   |||      |     ||  | | ||           ||   || | |  |||  ||  |  || || |   || ||||   ||||  |||||||||||||||| ||||| ||| ||||||||||||| |||||||| |||||||| || ||| ||||||||||||| || ||||| || ||||
taccatataaaatggtttttgcttccttttgtactgtgtatatacctggtttgtgtacttaatcaatattttatt--ttctttttccttgttggcttattagGCAACTCCAGATATGGCTGTGACTCTCCTTGAAATTGCAAGAATTTTTGCTACTAAAGTTCCTGGGAAGATTGATGCTGATGTATTACAACTACTATGGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atgcataatagaaaacctaagtttgcttaatagttatttcaattttgctttgaagGCTTCTCCAGATATGGCTGTTACTCTTCTTCAAATTGCAAGAATATTTGCTACCAAAGTTCCCGGAAAGGTTGATGCTGATGTGTTGCAACTGCTCTGGA
                        gcttaat  putative branch site (score: 4)
                                          ttttgcttt  putative PPT
                          ttaatagttatttcaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttgtatatcttagtgcatgcaatgggtaaatgtgcttttgtattcatgcataatagaaaacctaagtttgcttaatagttatttcaattttgctttgaagGCTTCTCCAGATATGGCTGTTACTCTTCTTCAAATTGCAAGAATATTTGCTACCAAAGTTCCCGGAAAGGTTGATGCTGATGTGTTGCAACTGCTCTGGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGAT
- - - - - - - gcatgca
- - - - - - - - - - - - - - - - -gcttttg
- - - - - - - - - - - - - - - - - - - - - -tcatgca
- - - - - - - - - - - - - - - - - - - - - - - - - - - -gaaaacc