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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttattattccttcaaatagtcattttagtactaatggtaaatgaaaatatgattcttatgattttttttgttacagGGAGAAAATAAAGGGTTTCTTGTCTGCAAGAAAAAGATGGCCACTTCTCCAGAAACTTTGTGTTGCTTTTGTCCTCAACCATTTCGACAATTTGTTGAAT

Basic information

species Glycine max
transcript GLYMA04G09080.1
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA04G09080.1 (Glycine max), 3'ss of exon 9
lower sequence: LOC_Os01g10150.1 (Oryza sativa), 3'ss of exon 9
gttattattccttcaaatagtcattttagtactaatggtaaatgaaaatatgattcttatgatttttt--ttgttacagGGAGAAAATAAAGGGTTTCTTGTCTGCAAGAAAAAGATGGCCACTTCTCCAGAAACTTTGTGTTGCTTTTGTCCTCAACCATTTCGACAATTTGTTGAAT
|||| | ||  || |  |  | | |||  |  |  |   |      ||| |  || || | |||  |   |      ||||||| |||||||| |||||||| ||||||||||||||||| || ||||||||| |||| ||| || || |||| | ||||||||| ||||||||||| |
gttaattttgattgattttatgacttttttgttgcta-catgcactaatttcgtt-ttgtaattcatgaatgaacttagGGAGAGAATAAAGGTTTTCTTGTTTGCAAGAAAAAGATGGCAACCTCTCCAGAATCTTTATGTGGCATTGGTCCACCACCATTTCGTCAATTTGTTGAGT

upper sequence: GLYMA04G09080.1 (Glycine max), 3'ss of exon 9
lower sequence: LOC_Os05g11140.1 (Oryza sativa), 3'ss of exon 9
gttattattccttcaaat---agtcattttagtactaatggtaaatgaaaatatgattctta-tgattttttt-------tgttacagGGAGAAAATAAAGGGTTTCTTGTCTGCAAGAAAAAGATGGCCACTTCTCCAGAAACTTTGTGTTGCTTTTGTCCTCAACCATTTCGACAATTTGTTGAAT
|| |   ||  ||  | |   | || ||||    ||  | ||     ||  | |  | |||| | |  ||| |       | ||  ||||||| |||||||| || ||||| ||||||||||| ||||| || ||||||||| ||||||| ||||| ||||| ||||| || || |||||| |||| |
gtgaagtttgtttgcagtgcgaatctttttttatctgttcgttttgcaaccttttgtccttagttacctttgtgttgatatattttagGGAGAGAATAAAGGTTTCCTTGTTTGCAAGAAAAAAATGGCGACCTCTCCAGAATCTTTGTGCTGCTTCTGTCCACAACCTTTCCGGCAATTTATTGAGT

upper sequence: GLYMA04G09080.1 (Glycine max), 3'ss of exon 9
lower sequence: GRMZM2G116151_T03 (Zea mays), 3'ss of exon 9
------gttattattccttcaaatagtcattttagtactaatggtaaatgaaaatatgattcttatgattttttttgttacagGGAGAAAATAAAGGGTTTCTTGTCTGCAAGAAAAAGATGGCCACTTCTCCAGAAACTTTGTGTTGCTTTTGTCCTCAACCATTTCGACAATTTGTTGAAT
       || |||   | || || | |   || | |||| ||      | |   |   ||| | |  |   |  || |   |||| || |||||||| || ||||||||||||||||||||||| |||||||||||| |||||||||||||||| || ||||| || ||||||||| |||| |
gtgaactttgttacaacctccaa-attttcttaattactgatccccccttac--tcaaattttcagcaaaatgatttt---agGGGGAGAATAAAGGTTTCCTTGTCTGCAAGAAAAAGATGGCAACTTCTCCAGAATCTTTGTGTTGCTTTTGCCCACAACCTTTCCGACAATTTATTGAGT

upper sequence: GLYMA04G09080.1 (Glycine max), 3'ss of exon 9
lower sequence: GRMZM2G045259_T02 (Zea mays), 3'ss of exon 9
--------------------------gttattattccttcaaatagtcattttagtactaat--ggtaaatgaaaatatgattcttatgatttttt--ttgttacagGGAGAAAATAAAGGGTTTCTTGTCTGCAAGAAAAAGATGGCCACTTCTCCAGAAACTTTGTGTTGCTTTTGTCCTCAACCATTTCGACAATTTGTTGAAT
                           || || || || | | |  |  ||||  |  || |    ||     |||| |  |   | | ||| ||   |   |  ||||||| || ||||| |||||||||||||||||||||||||| || ||||| ||  || ||||| |  | ||||| ||||| || ||  | |||||||| |
gttagtgtagttgatgttctgctcacctttttcttactcctactcttt-ttttgtttttatttaaatactcacaaattttttatctgttattcttcaatcaatttagGGAGAGAACAAAGGTTTTCTTGTCTGCAAGAAAAAGATGGCGACATCTCCGGAGTCTCTGTGTGGAATCTGTCCACAACCTTTCCGGAATTTTGTTGAGT

upper sequence: GLYMA04G09080.1 (Glycine max), 3'ss of exon 9
lower sequence: GRMZM2G158177_T01 (Zea mays), 3'ss of exon 2
---------------------------gttattattccttcaaatagtc-attttagtactaatggtaaatgaaaatatgattcttatg--atttttt--ttgttacagGGAGAAAATAAAGGGTTTCTTGTCTGCAAGAAAAAGATGGCCACTTCTCCAGAAACTTTGTGTTGCTTTTGTCCTCAACCATTTCGACAATTTGTTGAAT
                            ||||| || || | | |  |   ||||  ||  ||||   |  ||   | ||  | ||||   | | ||   |   |  ||||||| || || || |||||||||||||||||||||||||| || ||||| ||  |||||||| |  | ||||| ||||| || ||  | |||||||| |
gttagtttagttgatgttctggtcacctttattcttactcctacttttttgtttttatataaatgcccatagattgtttgtatgttatttcactcttcaatcaatttagGGAGAGAACAAGGGTTTTCTTGTCTGCAAGAAAAAGATGGCGACATCTCCGGAGTCTTTGTGTGGAATCTGTCCACAACCTTTCCGGGATTTTGTTGAGT

upper sequence: GLYMA04G09080.1 (Glycine max), 3'ss of exon 9
lower sequence: AT2G25760.2 (Arabidopsis thaliana), 3'ss of exon 9
gttattattccttcaaatagtcattttagtactaatggtaaatgaaaatatgattcttatgattttttttgtta--cagGGAGAAAATAAAGGGTTTCTTGTCTGCAAGAAAAAGATGGCCACTTCTCCAGAAACTTTGTGTTGCTTTTGTCCTCAACCATTTCGACAATTTGTTGAAT------
                 || |  ||||| | |   ||| || |     | | | || | | | ||  | | ||    ||||||| || ||||| || ||||| |||||||| |||||||||||||| ||||||||| | || ||||| ||||| ||||| ||||| || ||||| || |      
---------------gttatttgttttatttcc--tggcaactttccttgtcaatcat-taacttggtctatttgttagggagagAACAAAGGTTTCCTTGTTTGCAAGAAGAAGATGGCCACTTCCCCAGAAACTCTTTGCTGCTTCTGTCCCCAACCTTTTCGTCAGTTTGTCGAGTATGTGG

upper sequence: GLYMA04G09080.1 (Glycine max), 3'ss of exon 9
lower sequence: AT2G25760.1 (Arabidopsis thaliana), 3'ss of exon 9
gttattattccttcaaatagtcattttagtactaatggtaaatgaaaatatgattcttatgattttttttgtta--cagGGAGAAAATAAAGGGTTTCTTGTCTGCAAGAAAAAGATGGCCACTTCTCCAGAAACTTTGTGTTGCTTTTGTCCTCAACCATTTCGACAATTTGTTGAAT
|||       ||  |  || |  ||||| | |   ||| || |     | | | || | | | ||  | | ||    ||||||| || ||||| || ||||| |||||||| |||||||||||||| ||||||||| | || ||||| ||||| ||||| ||||| || ||||| || |
gttggggacactaaagttatttgttttatttcc--tggcaactttccttgtcaatcat-taacttggtctatttgttagGGAGAGAACAAAGGTTTCCTTGTTTGCAAGAAGAAGATGGCCACTTCCCCAGAAACTCTTTGCTGCTTCTGTCCCCAACCTTTTCGTCAGTTTGTCGAGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

attttagtactaatggtaaatgaaaatatgattcttatgattttttttgttacagGGAGAAAATAAAGGGTTTCTTGTCTGCAAGAAAAAGATGGCCACTTCTCCAGAAACTTTGTGTTGCTTTTGTCCTCAACCATTTCGACAATTTGTTGAAT
       tactaat  putative branch site (score: 1)
                                        ttttttttgtt  putative PPT
                taaatgaaaatatgat  TA-rich tract