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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttttttctctttccttttccttttggccttgttgacacttattttgtgcttgaattaaattagatgctgcaatttggttatgacttgtgattatttacagGTACAAATCTGCACTGGGAGGACTGTGGGTAGTTTCCATACTATTTTCTTGCTATACATTAACAGAAGTTCTTCGAATTTCAAGTAGCACATGGTTAAGT

Basic information

species Glycine max
transcript GLYMA06G46940.1
intron # 22
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA06G46940.1 (Glycine max), 3'ss of exon 22
lower sequence: LOC_Os04g52900.1 (Oryza sativa), 3'ss of exon 20
-----------------------------ttttttctctttccttttccttttggccttgttgacac------------------ttattttgtgcttgaat-taaatta-gatg--ctgcaa--tttggttatgacttgtgatta--tttacagGTACAAATCTGCACTGGGAGGACTGTGGGTAGTTTCCATACTATTTTCTTGCTATACATTAACAGAAGTTCTTCGAATTTCAAGTAGCACATGGTTAAGT
                              | | | || |   |  | |   | |       || ||                  | || ||   | |   | || || | ||||  ||| ||  | || |||     |    |||  ||| ||| ||||||  |||| |||||||  | ||||| || ||  | || |||| ||||||| || | || ||||||||||| |||||||||||||||||||| || 
gtaaaagattgttgtctcattgtatggtagtatatttcatgtataatacagatagaagaaaggaaacaggagagggagggaggcataatattaaacatatttatagatcatgatgacctggaatatctgcttacttaatacctttacctttgcagCTACAAAAATGCATTGGGAGGGATCTGGGTGGTATCTGTTCTCTTTTTTTGCTATGCACTCACTGAAGTTCTTCGCATTTCAAGTAGCACATGGTTGAGC

upper sequence: GLYMA06G46940.1 (Glycine max), 3'ss of exon 22
lower sequence: GRMZM2G084181_T01 (Zea mays), 3'ss of exon 20
ttttttctctttccttttccttttggccttgttgacacttattttgtgcttgaattaaattagatgctgcaatttggttatgacttgtgattatttacagGTACAAATCTGCACTGGGAGGACTGTGGGTAGTTTCCATACTATTTTCTTGCTATACATTAACAGAAGTTCTTCGAATTTCAAGTAGCACATGGTTAAGT
          |         ||||||  ||||    | |  ||||| |||  |  |||  ||| ||       |  ||  ||   | ||||  ||  ||| ||||||  ||||||||||||  | ||||| || |||||||| || | ||||||| || | || ||||||||||| |||||||||||||||||||| || 
---------gtaagagaaaattttgggattgtccttagt-gttttgagctgcatataatatag-tgtgatttctgagtattgtggtctgatc-ttcgcagTTACAAAAATGCACTGGGAGGGATATGGGTGGTGTCCATACTCTTCTTTTGCTATGCACTGACTGAAGTTCTTCGCATTTCAAGTAGCACATGGTTGAGC

upper sequence: GLYMA06G46940.1 (Glycine max), 3'ss of exon 22
lower sequence: AT1G30410.1 (Arabidopsis thaliana), 3'ss of exon 22
----------------------------------------------------------------ttttttctctttccttttccttttggccttgttgacacttattttgtgcttgaattaaat-tagatgctgcaatttggttatgact--tgtgatt----atttacagGTACAAATCTGCACTGGGAGGACTGTGGGTAGTTTCCATACTATTTTCTTGCTATACATTAACAGAAGTTCTTCGAATTTCAAGTAGCACATGGTTAAGT
                                                                     |   |   ||       ||   |      ||| ||  ||| |  ||  || |||   | | | ||||  |      ||  |  |||| ||    |||| |||||| |||   ||| | || ||  | |||||||||   || ||| |  | ||||||  |  ||| |||||||| ||| |||||||||||||||||||||||
gtactttacctcaccatttttttatggctacaaagagatcaactttgatcgttcaaccgaaatgaaaaatagttgagctaacatagtttaacaaaagaaca-ttgctttatatttatataaaaaacaaaagatgcagatgaacagtgcttaatgtggtttccaattttcagGTATAAAGAAGCAGTAGGCGGCTTATGGGTAGTTATGATTCTACTGGCATGCTATTTAGCAACTGAAGTTCTCCGAGTTTCAAGTAGCACATGGTTAAGT

upper sequence: GLYMA06G46940.1 (Glycine max), 3'ss of exon 22
lower sequence: Vv10s0003g04460.t01 (Vitis vinifera), 3'ss of exon 2
ttttttctctttccttttccttttggccttgttgacacttattttgtgcttgaattaaattagatgctgca-----atttggttatgacttgtgattatttacagGTACAAATCTGCACTGGGAGGACTGTGGGTAGTTTCCATACTATTTTCTTGCTATACATTAACAGAAGTTCTTCGAATTTCAAGTAGCACATGGTTAAGT
     |||||||  |  ||  ||| |  | | |  || || ||       | ||    ||   ||  | ||     |  ||| | |   ||||   | ||| |||||| |||  |||| | || || || |||||||||    |||| ||| | ||||||   || ||||||||||||||||||  ||||||||| |||||||| 
----gtctcttttgtagtctctttagaat-gctttcatttgttggacagctaaacatgatcctatagtccatgaacagatgggttttctttgttcctttttgcagGTATAAAGATGCATTAGGCGGCCTATGGGTAGTTGTGGTACTCTTTGCATGCTATGTGTTGACAGAAGTTCTTCGAATTGGAAGTAGCACCTGGTTAAGC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtgcttgaattaaattagatgctgcaatttggttatgacttgtgattatttacagGTACAAATCTGCACTGGGAGGACTGTGGGTAGTTTCCATACTATTTTCTTGCTATACATTAACAGAAGTTCTTCGAATTTCAAGTAGCACATGGTTAAGT
     tgaattaaattagat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttttttctctttccttttccttttggccttgttgacacttattttgtgcttgaattaaattagatgctgcaatttggttatgacttgtgattatttacagGTACAAATCTGCACTGGGAGGACTGTGGGTAGTTTCCATACTATTTTCTTGCTATACATTAACAGAAGTTCTTCGAATTTCAAGTAGCACATGGTTAAGT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGT
- - - - - - - - - ccttttg
- - - - - - - - - - - - - - -tgttgac
- - - - - - - - - - - - - - - - - - - - - - - tgcttga
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -atgctgc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ggttatg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - acttgtg