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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttattattgtctcaaatagtcatttgagtactaatggtaagtcaaaaatatgattcttatgagattttttgttacagGGAGAAAATAAAGGATTTCTTGTCTGCAAGAAAAAGATGGCCACTTCTCCTGAAACTTTGTGTTGCTTGTGTCCTCAACCATTTCGGCAATTTGTTGAAT

Basic information

species Glycine max
transcript GLYMA04G09070.1
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA04G09070.1 (Glycine max), 3'ss of exon 9
lower sequence: LOC_Os01g10150.1 (Oryza sativa), 3'ss of exon 9
gttattattgtctcaaatagtcatttgagtactaatggtaagtcaaaaatatgattcttatgagattttttgttacagGGAGAAAATAAAGGATTTCTTGTCTGCAAGAAAAAGATGGCCACTTCTCCTGAAACTTTGTGTTGCTTGTGTCCTCAACCATTTCGGCAATTTGTTGAAT
|||| | |||  | |  |  | | ||   |  |  |   | |    || |  | ||  ||    ||   |      ||||||| |||||||| |||||||| ||||||||||||||||| || ||||| ||| |||| ||| || |  |||| | ||||||||| ||||||||||| |
gttaattttgattgattttatgacttttttgttgcta-catgcactaatttcgttttgtaattcatgaatgaacttagGGAGAGAATAAAGGTTTTCTTGTTTGCAAGAAAAAGATGGCAACCTCTCCAGAATCTTTATGTGGCATTGGTCCACCACCATTTCGTCAATTTGTTGAGT

upper sequence: GLYMA04G09070.1 (Glycine max), 3'ss of exon 9
lower sequence: LOC_Os05g11140.1 (Oryza sativa), 3'ss of exon 9
------gttattattgtctcaaatagtcatttgagtactaatggtaag----tcaaaaatatgattcttatgagattttttgttacagGGAGAAAATAAAGGATTTCTTGTCTGCAAGAAAAAGATGGCCACTTCTCCTGAAACTTTGTGTTGCTTGTGTCCTCAACCATTTCGGCAATTTGTTGAAT
       || ||       | |||  |  |||   |  |  |  |       |      |  | | | | || | |  | | ||  ||||||| |||||||| || ||||| ||||||||||| ||||| || ||||| ||| ||||||| ||||| ||||| ||||| || ||||||||| |||| |
gtgaagtttgtttgcagtgcgaatctttttttatctgttcgttttgcaaccttttgtccttagttacctttgtgttgatatattttagGGAGAGAATAAAGGTTTCCTTGTTTGCAAGAAAAAAATGGCGACCTCTCCAGAATCTTTGTGCTGCTTCTGTCCACAACCTTTCCGGCAATTTATTGAGT

upper sequence: GLYMA04G09070.1 (Glycine max), 3'ss of exon 9
lower sequence: GRMZM2G116151_T03 (Zea mays), 3'ss of exon 9
------gttattattgtctcaaatagtcatttgagtactaatggtaagtcaaaaatatgattcttatgagattttttgttacagGGAGAAAATAAAGGATTTCTTGTCTGCAAGAAAAAGATGGCCACTTCTCCTGAAACTTTGTGTTGCTTGTGTCCTCAACCATTTCGGCAATTTGTTGAAT
       || |||    ||| || | |   || | |||| ||      | |   | ||  ||      | ||  |||     |||| || |||||||| || ||||||||||||||||||||||| |||||||| ||| ||||||||||||| || || ||||| || || |||||| |||| |
gtgaactttgttacaacctccaa-attttcttaattactgatccccccttactcaaat--tttcagcaaaatgattt----tagGGGGAGAATAAAGGTTTCCTTGTCTGCAAGAAAAAGATGGCAACTTCTCCAGAATCTTTGTGTTGCTTTTGCCCACAACCTTTCCGACAATTTATTGAGT

upper sequence: GLYMA04G09070.1 (Glycine max), 3'ss of exon 9
lower sequence: GRMZM2G045259_T02 (Zea mays), 3'ss of exon 9
--------------------------gttattattgtctcaaatagtcatttgagtactaatggtaagtcaaaaatatgattcttatgagatttt--ttgttacagGGAGAAAATAAAGGATTTCTTGTCTGCAAGAAAAAGATGGCCACTTCTCCTGAAACTTTGTGTTGCTTGTGTCCTCAACCATTTCGGCAATTTGTTGAAT
                           || || ||    | | |  |  ||||  |     |    | ||| |||| |  |   | | |   ||   |   |  ||||||| || ||||| |||||||||||||||||||||||||| || ||||| ||  || ||||| |  | ||||| ||||| || ||| | |||||||| |
gttagtgtagttgatgttctgctcacctttttcttactcctactctttttttgtttttatttaaatactcacaaattttttatctgttattcttcaatcaatttagGGAGAGAACAAAGGTTTTCTTGTCTGCAAGAAAAAGATGGCGACATCTCCGGAGTCTCTGTGTGGAATCTGTCCACAACCTTTCCGGAATTTTGTTGAGT

upper sequence: GLYMA04G09070.1 (Glycine max), 3'ss of exon 9
lower sequence: GRMZM2G158177_T01 (Zea mays), 3'ss of exon 2
---------------------------gttattattg-tctcaaatagtcatttgagtactaatg---gtaagtcaaaaatatgattcttatgagattttttgttacagGGAGAAAATAAAGGATTTCTTGTCTGCAAGAAAAAGATGGCCACTTCTCCTGAAACTTTGTGTTGCTTGTGTCCTCAACCATTTCGGCAATTTGTTGAAT
                            ||||| ||  ||  |  |  |  |||   ||  ||||    ||  |      |||| |  ||      |   |   |  ||||||| || || || |||||||||||||||||||||||||| || ||||| ||  |||||||| |  | ||||| ||||| || ||| | |||||||| |
gttagtttagttgatgttctggtcacctttattcttactcctacttttttgtttttatataaatgcccatagattgtttgtatgttatttcactcttcaatcaatttagGGAGAGAACAAGGGTTTTCTTGTCTGCAAGAAAAAGATGGCGACATCTCCGGAGTCTTTGTGTGGAATCTGTCCACAACCTTTCCGGGATTTTGTTGAGT

upper sequence: GLYMA04G09070.1 (Glycine max), 3'ss of exon 9
lower sequence: AT2G25760.2 (Arabidopsis thaliana), 3'ss of exon 9
gttattattgtctcaaatagtcatttgagtactaatggtaagtcaaaaatatgattcttatgagattttttgttacagGGAGAAAATAAAGGATTTCTTGTCTGCAAGAAAAAGATGGCCACTTCTCCTGAAACTTTGTGTTGCTTGTGTCCTCAACCATTTCGGCAATTTGTTGAAT------
                 || |  ||| | | |   ||| || |          ||  |||      | | | |   ||||||| || ||||| || ||||| |||||||| |||||||||||||| || |||||| | || ||||| ||||| ||||| ||||| || ||||| || |      
---------------gttatttgttttatttcc--tggcaactttccttgtcaatcattaacttggtctatttgttagggagagAACAAAGGTTTCCTTGTTTGCAAGAAGAAGATGGCCACTTCCCCAGAAACTCTTTGCTGCTTCTGTCCCCAACCTTTTCGTCAGTTTGTCGAGTATGTGG

upper sequence: GLYMA04G09070.1 (Glycine max), 3'ss of exon 9
lower sequence: AT2G25760.1 (Arabidopsis thaliana), 3'ss of exon 9
gttattattgtctcaaatagtcatttgagtactaatggtaagtcaaaaatatgattcttatgagattttttgttacagGGAGAAAATAAAGGATTTCTTGTCTGCAAGAAAAAGATGGCCACTTCTCCTGAAACTTTGTGTTGCTTGTGTCCTCAACCATTTCGGCAATTTGTTGAAT
|||           |  || |  ||| | | |   ||| || |          ||  |||      | | | |   ||||||| || ||||| || ||||| |||||||| |||||||||||||| || |||||| | || ||||| ||||| ||||| ||||| || ||||| || |
gttggggacactaaagttatttgttttatttcc--tggcaactttccttgtcaatcattaacttggtctatttgttagGGAGAGAACAAAGGTTTCCTTGTTTGCAAGAAGAAGATGGCCACTTCCCCAGAAACTCTTTGCTGCTTCTGTCCCCAACCTTTTCGTCAGTTTGTCGAGT

upper sequence: GLYMA04G09070.1 (Glycine max), 3'ss of exon 9
lower sequence: EFJ31718 (Selaginella moellendorffii), 3'ss of exon 7
gttattattgtctcaaatagtcatttgagtactaatggtaagtcaaaaatatgattcttatgagattttttgttacagGGAGAAAATAAAGGATTTCTTGTCTGCAAGAAAAAGATGGCCACTTCTCCTGAAACTTTGTGTTGCTTGTGTCCTCAACCATTTCGGCAATTTGTTGAAT
                        |   |   |  |  ||  | |    |||  || |||   |     || ||| ||||||| |||||||||||||| |||||||| || || |||||||| || || || |  ||||| || || || || |  |||||   ||| ||| | ||| 
-----------------------gtcaggctgttttaatattttagttttattgtt-ttacatgggcgctt-ttatagGGAGACAATAAAGGATTTCTGGTCTGCAAAAAGAAAATGGCCACGTCCCCGGAGATGTTGTGCTGTTTCTGCCCGCCTCCATTCAAGCAGTTTTTGGAAA

upper sequence: GLYMA04G09070.1 (Glycine max), 3'ss of exon 9
lower sequence: EFJ38433 (Selaginella moellendorffii), 3'ss of exon 7
gttattattgtctcaaatagtcatttgagtactaatggtaagtcaaaaatatgattcttatgagattttttgttacagGGAGAAAATAAAGGATTTCTTGTCTGCAAGAAAAAGATGGCCACTTCTCCTGAAACTTTGTGTTGCTTGTGTCCTCAACCATTTCGGCAATTTGTTGAAT
                        |   |   |  |  ||  | |    |||| ||   ||| |   ||||   | ||||||| |||||||||||||| |||||||| || || |||||||| || || || |  ||||| || || || || |  |||||   ||| ||| | ||| 
-----------------------gtcaggctgttttaatatattagttttatgttttacatgggcgctttt---atagGGAGACAATAAAGGATTTCTGGTCTGCAAAAAGAAAATGGCCACATCCCCGGAGATGTTGTGCTGTTTCTGCCCGCCTCCATTCAAGCAGTTTTTGGAAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttgagtactaatggtaagtcaaaaatatgattcttatgagattttttgttacagGGAGAAAATAAAGGATTTCTTGTCTGCAAGAAAAAGATGGCCACTTCTCCTGAAACTTTGTGTTGCTTGTGTCCTCAACCATTTCGGCAATTTGTTGAAT
      tactaat  putative branch site (score: 1)
                                          ttttttgtt  putative PPT
                     aaaaatatgattctta  TA-rich tract