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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgtgagttaaccaggaaaaaggtttttaattattttttatccatcctccaacataaaaacataaaaacataattgtttttagGAATACAATGCCAAACTCTCTGATTTTGGACTCGCCAAAGATGGTCCTGAAGGGGAAAAGACACACATATCAACAAGAGTCATGGGAACATATGGTTATG

Basic information

species Glycine max
transcript GLYMA09G37580.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA09G37580.1 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os01g40590.1 (Oryza sativa), 3'ss of exon 4
gtatgtgagttaaccaggaaa--aaggtttttaattattttttatccatcctccaacataaaaacataaaa-acataattgtttttagGAATACAATGCCAAACTCTCTGATTTTGGACTCGCCAAAGATGGTCCTGAAGGGGAAAAGACACACATATCAACAAGAGTCATGGGAACATATGGTTATG
|||||  |        |  ||  ||    | | |  | | || ||  |   |  |||||    | ||     | ||| |  |||| |||| |||||||| |||||||||||||||||||| || |||||||| ||||| || || || |||||  |||| ||  ||||||||||||| ||||| ||||
gtatgcaaccatgtttgagaatcaaaacatattagaaatgttcatttagattgtaacattctcatatttcttaaatattcattttcagGACTACAATGCAAAACTCTCTGATTTTGGACTAGCTAAAGATGGCCCTGAGGGTGATAAAACACATGTATCTACTCGAGTCATGGGAACTTATGGATATG

upper sequence: GLYMA09G37580.1 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os09g19700.1 (Oryza sativa), 3'ss of exon 4
gtatgtgagttaaccaggaaaaaggtttttaattattttttatccatcctccaacataaaaacataaaaacataattgttttt--agGAATACAATGCCAAACTCTCTGATTTTGGACTCGCCAAAGATGGTCCTGAAGGGGAAAAGACACACATATCAACAAGAGTCATGGGAACATATGGTTATG
||| ||       ||  |||   | ||    |||       |  |      || | |  ||   |  | |      |  | ||  |||| |||||||| |||||||| |||||||| || ||||||||||| |||| ||| || || || ||| | || ||  |||| |||||||||||||||||||
gtaagttttaagtccttgaattggattacgtattgcacaccacacgattcacatcttgtaattttgtatattatgctactcttgcagGATTACAATGCAAAACTCTCAGATTTTGGGCTTGCCAAAGATGGCCCTGTAGGTGACAAAACTCACGTGTCTACTCGAGTAATGGGAACATATGGTTATG

upper sequence: GLYMA09G37580.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G028037_T02 (Zea mays), 3'ss of exon 4
gtatgtgagttaaccaggaaaaaggtttttaattattttttatccatcctccaacataaaaacataaaaacataattgtttttagGAATACAATGCCAAACTCTCTGATTTTGGACTCGCCAAAGATGGTCCTGAAGGGGAAAAGACACACATATCAACAAGAGTCATGGGAACATATGGTTATG
    || ||  ||| |     ||   ||  || ||||    || |||      ||| |   |  |   |||||| || |||| |||| || || || |||||||||||||||||||| || |||||||| ||||| || || || |||||  | ||||| || ||||||||||||||||| ||||
----gtaagc-aactatattgaaatgttaaaaatattc---attcat------acaaatgtatttgctaacatattt-ttttcagGACTATAACGCAAAACTCTCTGATTTTGGACTTGCTAAAGATGGCCCTGAGGGTGATAAAACACATGTGTCAACTAGGGTCATGGGAACATATGGATATG

upper sequence: GLYMA09G37580.1 (Glycine max), 3'ss of exon 4
lower sequence: AT5G15080.1 (Arabidopsis thaliana), 3'ss of exon 4
gtatgtgagttaaccaggaaaaaggtttttaattattttttatccatcctccaacataaaaacataaaaacataattgtttttagGAATACAATGCCAAACTCTCTGATTTTGGACTCGCCAAAGATGGTCCTGAAGGGGAAAAGACACACATATCAACAAGAGTCATGGGAACATATGGTTATG
   |  |  |     |      ||| |    |  || || |||       | ||  |   |||  | |||    |||||    |||| |||||||| ||||| || ||||||||||| |||||||||| |||||| |  |  || || ||  | || || || || ||||| |||||||| ||||
--gtacgtatctcttactctttaggatc---aacatcttatatttg----caaattttttaaccaataaatcccattgtc---agGACTACAATGCAAAACTATCAGATTTTGGACTTGCCAAAGATGCTCCTGATGAAGGCAAAACCCATGTTTCTACTAGGGTTATGGGTACATATGGCTATG

upper sequence: GLYMA09G37580.1 (Glycine max), 3'ss of exon 4
lower sequence: AT3G28690.1 (Arabidopsis thaliana), 3'ss of exon 3
gtatgtgagttaaccaggaaa---aaggtttttaattattttttatccatcctccaacataaaaac-ataaaaacataattgtttt-tagGAATACAATGCCAAACTCTCTGATTTTGGACTCGCCAAAGATGGTCCTGAAGGGGAAAAGACACACATATCAACAAGAGTCATGGGAACATATGGTTATG
||||||  |  | |||   ||    |     | || | | |  | ||  ||       |||||    | ||||| ||  |    ||  ||||||| ||||| || |||||||||||||| || || ||||||| ||| || | | ||||  | ||| |||||||  ||||||||||||| ||||||||||
gtatgtctgaaagccacttaacccgataacctcaactctgtcctttctctctatgtttataaattttagaaaaaaatgctcccattgcagGAATATAATGCAAAGCTCTCTGATTTTGGGCTTGCAAAAGATGCTCCAGACGAGAAAAAATCCCACGTATCAACCCGAGTCATGGGAACTTATGGTTATG

upper sequence: GLYMA09G37580.1 (Glycine max), 3'ss of exon 4
lower sequence: PP1S31_254V6.1 (Physcomitrella patens), 3'ss of exon 4
gtatgtgagttaaccaggaaaaaggttt-ttaattattttttatccatcctcca--acataaaaacataa---------aaacataattgttt----ttagGAATACAATGCCAAACTCTCTGATTTTGGACTCGCCAAAGATGGTCCTGAAGGGGAAAAGACACACATATCAACAAGAGTCATGGGAACATATGGTTATG
  || |    ||  ||  | | |  ||  ||   |||  | | | | |  |     || | |   |||           |||| || || ||     | |||| ||||  || || || ||||||||||| || || |||||||| |||||||| || || || ||| |||||||| | |||||||| || ||||| ||||
-aatattttgtacgcaatagagactttcgtttcgtatagtctgttccttgtatgggacttgatgtcatcctctgtcctcaaacctagttcttgggtgtcagGATTACACAGCTAAGCTATCTGATTTTGGCCTAGCGAAAGATGGGCCTGAAGGAGACAAAACTCACGTATCAACACGTGTCATGGGCACCTATGGCTATG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aattattttttatccatcctccaacataaaaacataaaaacataattgtttttagGAATACAATGCCAAACTCTCTGATTTTGGACTCGCCAAAGATGGTCCTGAAGGGGAAAAGACACACATATCAACAAGAGTCATGGGAACATATGGTTATG
 ttttaat  putative branch site (score: 3)
                                             ttgttttt  putative PPT
                      aacataaaaacataaa  TA-rich tract