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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...catgtcaatgcctttttatactgctatattatatttcgactggtacaatggtgaatttttctattgcaatatcttacaatcatacatattatattggcagGAAAAGTATGAAGAAGCAACTGCTGCACTTGCTGAAATGGAGAAGAGGGCAGTTATGGCAGAATCTATGCTGGAGGCTACATTGCAGTACCAATCTGGCC

Basic information

species Glycine max
transcript GLYMA20G38810.1
intron # 15
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA20G38810.1 (Glycine max), 3'ss of exon 15
lower sequence: LOC_Os01g61860.2 (Oryza sativa), 3'ss of exon 15
catgtcaatgcctttttatactgctatat-tatatttcgactggtacaatggtgaatttttctattgcaatatcttacaatcatacat-attatattggcagGAAAAGTATGAAGAAGCAACTGCTGCACTTGCTGAAATGGAGAAGAGGGCAGTTATGGCAGAATCTATGCTGGAGGCTACATTGCAGTACCAATCTGGCC
 |   || |    | | ||  |  |  |  |||| |    |   |||| ||     |   | || || | | ||||   || | |  | | | | |  ||||||||||||||| ||||| |  ||| |||| ||  |||||||||| || ||||| ||||||||| |||||||||| || ||| ||||||| |||||  |||
gactccattttgctgtcattttttttgacatataatctagcaaataca-tgcctgttcaatataatg-attctcttgttataacatttgactttgtatgcagGAAAAGTATGAGGAAGCTATGGCTTCACTAGCACAAATGGAGAACAGAGCAGTCATGGCAGAAACTATGCTGGAAGCAACACTGCAGTATCAATCAAGCC

upper sequence: GLYMA20G38810.1 (Glycine max), 3'ss of exon 15
lower sequence: LOC_Os05g38950.2 (Oryza sativa), 3'ss of exon 15
catgtca-atgcct-ttttatactgctatattatatttcgactggtacaatggtgaatttttctattgcaatatcttacaatcatacatattatattggcagGAAAAGTATGAAGAAGCAACTGCTGCACTTGCTGAAATGGAGAAGAGGGCAGTTATGGCAGAATCTATGCTGGAGGCTACATTGCAGTACCAATCTGGCC
  || || || | | | || | |   || |  ||||||  |    ||   |  |  |||||| || |         | ||      | |   | ||  ||||||||||||||| ||||| |  ||| |||| ||  |||||||||| ||||| || ||||||||  | ||| ||||||| ||| ||||||| ||| || |||
tgtgacatatacatatgttgtgcccttaaaacatatttgtatacttattttc-tatatttttgtaatattgggctct-catcggatcctgacacatatgcagGAAAAGTATGAGGAAGCTATGGCTTCACTCGCGAAAATGGAGAACAGGGCTGTAATGGCAGAGACAATGTTGGAGGCCACACTGCAGTATCAAACTAGCC

upper sequence: GLYMA20G38810.1 (Glycine max), 3'ss of exon 15
lower sequence: GRMZM2G051050_T01 (Zea mays), 3'ss of exon 15
--catgtcaatgcctttttatactgctatattatatttcgactggtacaatggtgaatttttcta--ttgcaatat-cttacaatcatacatattatattggcagGAAAAGTATGAAGAAGCAACTGCTGCACTTGCTGAAATGGAGAAGAGGGCAGTTATGGCAGAATCTATGCTGGAGGCTACATTGCAGTACCAATCTGGCC
  | | | |  |  |||||||     | || ||| | ||   || |   |   |   |||  |||  |||    |  ||||||      |||   ||||  |||||||||||| || ||||| |  ||| |||||||  |||||||||| || || || ||||||||| | ||| ||||||||||| |||||||||||||| |||
tgcttattatcgtttttttatcaaaat-tagtatgtgtc--ttgtttttactcttcttttccctagcttgttccacgcttacag--gatcatgacatatatgcagGAAAAGTACGAGGAAGCTATGGCTTCACTTGCCCAAATGGAGAACAGAGCTGTAATGGCAGAAACAATGTTGGAGGCTACACTGCAGTACCAATCTAGCC

upper sequence: GLYMA20G38810.1 (Glycine max), 3'ss of exon 15
lower sequence: GRMZM2G096470_T01 (Zea mays), 3'ss of exon 15
--catgtcaatgcctttttatactgctatattatatttcgactggtacaatggtgaatttttc-tattgcaatatcttacaatcatacatattatattggcagGAAAAGTATGAAGAAGCAACTGCTGCACTTGCTGAAATGGAGAAGAGGGCAGTTATGGCAGAATCTATGCTGGAGGCTACATTGCAGTACCAATCTGGCC
   ||||    || |   |||   ||   ||  || |    |  ||| | |  ||  | ||   | ||   ||    | |     ||| || | ||||  ||||| ||||| || | ||| |  ||| |||||||| |||||||||| || ||||||||||||||| ||||| | ||||| ||  | |||||||||||| | |
ttaatgtttgggcatgaatatgtcgcagcat-gtaatgaagcaagtaaatttttgcttgttcagttttatgatccgctgcttgtgtacttactctatt--cagGAGAAGTACGAGGGAGCTATGGCTTCACTTGCTCAAATGGAGAACAGAGCAGTTATGGCAGAAACTATGTTAGAGGCAACCATTCAGTACCAATCTAGTC

upper sequence: GLYMA20G38810.1 (Glycine max), 3'ss of exon 15
lower sequence: GRMZM2G094951_T02 (Zea mays), 3'ss of exon 1
catgtcaatgcctttttatactgctatattatatttcgactggtacaatggtgaatttttctattgcaatatctta---caatcataca----tattatattggcagGAAAAGTATGAAGAAGCAACTGCTGCACTTGCTGAAATGGAGAAGAGGGCAGTTATGGCAGAATCTATGCTGGAGGCTACATTGCAGTACCAATCTGGCC
        |  | ||||   | |   ||  | | || |   |   |     || | | |||| || |  || |||    ||  | ||||     || | ||  |||||||||||| || ||||| |  ||| |||||||  ||||||||||  | || || ||||||||| | ||| | ||||||||| |||||||||||||| |||
-------ttatcgtttttaccagaattagcaaaattagcacgtgtcttctttgtactcttcttttaccctagcttgttccacgcttacaggatcatgacatgtgcagGAAAAGTACGAGGAAGCTATGGCTTCACTTGCCCAAATGGAGAACCGAGCTGTAATGGCAGAAACAATGTTAGAGGCTACACTGCAGTACCAATCTAGCC

upper sequence: GLYMA20G38810.1 (Glycine max), 3'ss of exon 15
lower sequence: AT3G55020.1 (Arabidopsis thaliana), 3'ss of exon 15
catgtcaatgcctttttatactgctatattatat--ttcgactggtacaatggtgaatttttctattgcaatatcttacaatcatacatattata-ttggc--agGAAAAGTATGAAGAAGCAACTGCTGCACTTGCTGAAATGGAGAAGAGGGCAGTTATGGCAGAATCTATGCTGGAGGCTACATTGCAGTACCAATCTGGCC
        ||| |  ||  | ||| |  ||||||  ||   ||  |    |  |    | ||||||   |     || |  | |   |||| |||  |||   ||||||| || || |||||   ||||||||| ||||||||||||||||| ||||| |||||||| || ||||| ||||| || |||||||| ||||||||||
-----agctgcgtgatttgaatgcaactttatatccttttcctttttttgtattctcctgttctatcttagatcgtttctgtaacgaatatgataactggtctagGAAAAATACGAGGAAGCTGTTGCTGCACTGGCTGAAATGGAGAAGAGAGCAGTGATGGCAGAGTCCATGCTCGAGGCAACTTTGCAGTATCAATCTGGCC

upper sequence: GLYMA20G38810.1 (Glycine max), 3'ss of exon 15
lower sequence: AT2G39280.1 (Arabidopsis thaliana), 3'ss of exon 15
-catgtcaatgcctttttatactgctatattatatttcgactggtacaatggtgaatttttctattgcaatatctt-acaatcatacatattatattggcagGAAAAGTATGAAGAAGCAACTGCTGCACTTGCTGAAATGGAGAAGAGGGCAGTTATGGCAGAATCTATGCTGGAGGCTACATTGCAGTACCAATCTGGCC
  |||   ||| | | || |     | | || | | ||       ||      ||        |      |||| | |  || ||| ||  ||     | |||||||||||||||| ||   ||| || || || || |||||| ||||||||||||||||||| || ||| ||||||| || |||||||| ||||||||||
ttatgaggatgtcatcttgttagagtttctt-tgtctcagtatacacttattcgaggcgacacaaaaagttatcctcagtatgata-atgctaatggtgtagGAAAAGTATGAAGAGGCTGTTGCAGCTCTCGCGGAGATGGAGGAGAGGGCAGTTATGGCAGAGTCCATGTTGGAGGCGACTTTGCAGTATCAATCTGGCC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

caatggtgaatttttctattgcaatatcttacaatcatacatattatattggcagGAAAAGTATGAAGAAGCAACTGCTGCACTTGCTGAAATGGAGAAGAGGGCAGTTATGGCAGAATCTATGCTGGAGGCTACATTGCAGTACCAATCTGGCC
                         atcttac  putative branch site (score: 3)
                      aatatcttacaatcat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
catgtcaatgcctttttatactgctatattatatttcgactggtacaatggtgaatttttctattgcaatatcttacaatcatacatattatattggcagGAAAAGTATGAAGAAGCAACTGCTGCACTTGCTGAAATGGAGAAGAGGGCAGTTATGGCAGAATCTATGCTGGAGGCTACATTGCAGTACCAATCTGGCC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG
- - -caatgcc
- - - - - - - - - tactgct
- - - - - - - - - - - - - - - - - - - -ctggtac
- - - - - - - - - - - - - - - - - - - - - - - aatggtg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - catacat