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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttttaaggctcattgccgtaccatcttattattttttgatatcttattgatctattttgattgttaactgtttgtctttcagtggtgaatttgttgtggtgaacaagCATTTACTTCATGACTTGACACAATCAAGAATAATATTATCTCTGAGGATG

Basic information

species Glycine max
transcript GLYMA08G15360.1
intron # 15
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA08G15360.1 (Glycine max), 3'ss of exon 15
lower sequence: GRMZM2G340527_T01 (Zea mays), 3'ss of exon 13
----gttttaaggctcattgccgtaccatcttatt-attttttgatat-cttattgatctatt-ttgattgttaactgtttgtctttcagtggtgaatttgttgtggtgaacaagCATTTACTTCATGACTTGACACAATCAAGAAT---AATATTATCTCTGAGGATG---------------------
    ||   ||  ||| || |      |   | || |  ||||||  | | | |  || |||  |||||  ||  || ||| | || |||||| |||||||||||||| ||||||||| | |||||||| |||||  ||    | ||    |      ||||||  |                       
gtctgtaacaatactctttacttctttagagtgtttacattttgacttacatgtgcatatatgattgatcttt--ctatttttattccagTGGGGAATTTGTTGTGGTTAACAAGCATCTTCTTCATGATTTGACTGAAATGGGCATTTGGACTCCTACTCTGAAAAACCAGATAATATATGATGATGGT

upper sequence: GLYMA08G15360.1 (Glycine max), 3'ss of exon 15
lower sequence: GRMZM2G304362_T01 (Zea mays), 3'ss of exon 13
----gttttaaggctcattgccgtaccatcttatt-attttttgatat-cttattgatctattttgattgttaactgtttgtctttcagtggtgaatttgttgtggtgaacaagCATTTACTTCATGACTTGACACAATCAAGAAT----AATATTATCTCTGAGGATG--------------------
    ||   ||  |||  | |      |   | || |  || |||| | | | |  |  | |  | | | ||     ||| | || |||||| |||||||||||||| ||||||||| | ||||||||  ||||  ||    | ||    | |  ||  |   |  |                      
gtctgtaacaatactccctacttctttagggtgtttacattgtgatgtacatgtgcacatgtgattaatctttctattttttgttccagTGGGGAATTTGTTGTGGTCAACAAGCATCTTCTTCATGATCTGACTGAAATGGGCATTTGGACTCCTACTTTGAAAAACCAGATAATATACGACGACGGT

upper sequence: GLYMA08G15360.1 (Glycine max), 3'ss of exon 15
lower sequence: Vv07s0031g01990.t01 (Vitis vinifera), 3'ss of exon 13
----gttttaaggctcattgccgtaccatcttattattttttgatatcttattg--atctat-tttgattgttaactgtttgtctttcagtggtgaatttgttgtggtgaacaagCATTTACTTCATGACTTGAC----------------------ACAATCAAGAATAATATTATCTCTGAGGATG--
    |||||    | | |  ||    ||| || | |  ||| |   | || |||  |||||  | |  |  ||   ||||| | | |||||||||||||||||||||| ||||||||| | ||||||||||| ||                      ||  | |||||  | || || | |||| |||  
gtttgttttgctaccc-taacctgttcattttctaagatttagtacttttgttgccatctaagtctcctctttccttgtttctttgtcagTGGTGAATTTGTTGTGGTAAACAAGCATCTTCTTCATGACTTAACTGAGATGGGTCTTTGGTCACCTACTCTTAAGAACCAGATAATTTATGAGAATGGC

upper sequence: GLYMA08G15360.1 (Glycine max), 3'ss of exon 15
lower sequence: EFJ20162 (Selaginella moellendorffii), 3'ss of exon 1
gttttaaggctcattgccgtaccatcttattattttttgatatcttattg-atctattttgattgtta-actgtttgtctttcagtggtgaatttgttgtggtgaacaagCATTTACTTCATGACTTGACACAATCAAGAATA---ATATTATCTCTGAGGATG-----------
                                   | ||   ||||  || |||   | ||||  |||   ||  ||   | ||||||||||||||||||||| ||||||||| | ||  | || |||||  | |   |||||   | |     |||||  ||            
----------------------------------gtatgccttctttctgtatcagctgtgatacttatgttgcctgc--tacagTGGTGAATTTGTTGTGGTTAACAAGCATCTGCTGAACGATTTGACTGATTTGGGAATATGGACACCGGATCTGAATATACAGGTTGGTTT

upper sequence: GLYMA08G15360.1 (Glycine max), 3'ss of exon 15
lower sequence: EFJ14283 (Selaginella moellendorffii), 3'ss of exon 12
gttttaaggctcattgccgtaccatcttattattttttgatatcttattg-atctattttgattgtta-actgtttgtctttcagtggtgaatttgttgtggtgaacaagCATTTACTTCATGACTTGACACAATCAAGAATA---ATATTATCTCTGAGGATG---------------------
                                   | ||   ||||  || |||   | ||||  |||   ||  || |   ||||||||||||||||||||| ||||||||||| ||  | || |||||  | |   |||||   | |     ||||| ||                       
----------------------------------gtatgccttctttctgtatcagctgtgatacttatgttgcctgcc--acagTGGTGAATTTGTTGTGGTTAACAAGCATTTGCTGAACGATTTGACCGATTTGGGAATATGGACACCGGATCTGAAGAACAAAGTAATGGCTTATAATGGC

upper sequence: GLYMA08G15360.1 (Glycine max), 3'ss of exon 15
lower sequence: EFJ20157 (Selaginella moellendorffii), 3'ss of exon 12
gttttaaggctcattgccgtaccatcttattattttttgatatcttattg-atctattttgattgtta-actgtttgtctttcagtggtgaatttgttgtggtgaacaagCATTTACTTCATGACTTGACACAATCAAGAATA---ATATTATCTCTGAGGATG---------------------
                                   | ||   ||||  || |||   | ||||  |||   ||  ||   | ||||||||||||||||||||| ||||||||||| ||  | || |||||  | |   |||||   | |     ||||| ||                       
----------------------------------gtatgccttctttctgtatcagctgtgatacttatgttgcctgc--tacagTGGTGAATTTGTTGTGGTTAACAAGCATTTGCTGAACGATTTGACCGATTTGGGAATATGGACACCGGATCTGAAGAACAAAGTAATGGCTTATAATGGC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tattttgattgttaactgtttgtctttcagtggtgaatttgttgtggtgaacaagCATTTACTTCATGACTTGACACAATCAAGAATAATATTATCTCTGAGGATG
         tgttaac  putative branch site (score: 2)
       attgttaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttttaaggctcattgccgtaccatcttattattttttgatatcttattgatctattttgattgttaactgtttgtctttcagtggtgaatttgttgtggtgaacaagCATTTACTTCATGACTTGACACAATCAAGAATAATATTATCTCTGAGGATG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGATG