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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ggtatgtgagttaaccaggaaaaaggtttttaattattttctatccatcctccaacataaaaacataaaaacataattgtttttaGGAATACAATGCCAAGCTCTCTGATTTTGGACTCGCCAAAGATGGTCCTGAAGGGGAAAAGACACACATATCTACCAGAGTCATGGGAACATATGGTTAT

Basic information

species Glycine max
transcript GLYMA18G49060.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA18G49060.1 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os01g40590.1 (Oryza sativa), 3'ss of exon 4
ggtatgtgagttaaccaggaaa--aaggtttttaattattttctatccatcctccaacataaaaacataaaa-acataattgtttttaGGAATACAATGCCAAGCTCTCTGATTTTGGACTCGCCAAAGATGGTCCTGAAGGGGAAAAGACACACATATCTACCAGAGTCATGGGAACATATGGTTAT-
 |||||  |        |  ||  ||    | | |  | | |  ||  |   |  |||||    | ||     | ||| |  |||| |||| |||||||| || ||||||||||||||||| || |||||||| ||||| || || || |||||  |||||||  ||||||||||||| ||||| ||| 
-gtatgcaaccatgtttgagaatcaaaacatattagaaatgttcatttagattgtaacattctcatatttcttaaatattcattttcagGACTACAATGCAAAACTCTCTGATTTTGGACTAGCTAAAGATGGCCCTGAGGGTGATAAAACACATGTATCTACTCGAGTCATGGGAACTTATGGATATG

upper sequence: GLYMA18G49060.1 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os09g19700.1 (Oryza sativa), 3'ss of exon 4
ggtatgtgagttaaccaggaaaaaggtttttaattattttctatccatcctccaacataaaaacataaaaacataattgttttt--aGGAATACAATGCCAAGCTCTCTGATTTTGGACTCGCCAAAGATGGTCCTGAAGGGGAAAAGACACACATATCTACCAGAGTCATGGGAACATATGGTTAT-
 ||| ||       ||  |||   | ||    |||     | |  |      || | |  ||   |  | |      |  | ||  |||| |||||||| || ||||| |||||||| || ||||||||||| |||| ||| || || || ||| | |||||  |||| |||||||||||||||||| 
-gtaagttttaagtccttgaattggattacgtattgcacaccacacgattcacatcttgtaattttgtatattatgctactcttgcagGATTACAATGCAAAACTCTCAGATTTTGGGCTTGCCAAAGATGGCCCTGTAGGTGACAAAACTCACGTGTCTACTCGAGTAATGGGAACATATGGTTATG

upper sequence: GLYMA18G49060.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G028037_T02 (Zea mays), 3'ss of exon 4
ggtatgtgagttaaccaggaaaaaggtttttaattattttctatccatcctccaacataaaaacataaaaacataattgtttttaGGAATACAATGCCAAGCTCTCTGATTTTGGACTCGCCAAAGATGGTCCTGAAGGGGAAAAGACACACATATCTACCAGAGTCATGGGAACATATGGTTAT-
     || ||  ||| |     ||   ||  || ||||    || |||      ||| |   |  |   |||||| || |||| |||| || || || || ||||||||||||||||| || |||||||| ||||| || || || |||||  | || || || ||||||||||||||||| ||| 
-----gtaagc-aactatattgaaatgttaaaaatattc---attcat------acaaatgtatttgctaacatattt-ttttcagGACTATAACGCAAAACTCTCTGATTTTGGACTTGCTAAAGATGGCCCTGAGGGTGATAAAACACATGTGTCAACTAGGGTCATGGGAACATATGGATATG

upper sequence: GLYMA18G49060.1 (Glycine max), 3'ss of exon 4
lower sequence: AT3G28690.1 (Arabidopsis thaliana), 3'ss of exon 3
ggtatgtgagttaaccaggaaa---aaggtttttaattattttctatccatcctccaacataaaaac-ataaaaacataattgtttt-taGGAATACAATGCCAAGCTCTCTGATTTTGGACTCGCCAAAGATGGTCCTGAAGGGGAAAAGACACACATATCTACCAGAGTCATGGGAACATATGGTTAT-
 ||||||  |  | |||   ||    |     | || | | | || ||  ||       |||||    | ||||| ||  |    ||  ||||||| ||||| ||||||||||||||||| || || ||||||| ||| || | | ||||  | ||| |||| ||| ||||||||||||| ||||||||| 
-gtatgtctgaaagccacttaacccgataacctcaactctgtcctttctctctatgtttataaattttagaaaaaaatgctcccattgcagGAATATAATGCAAAGCTCTCTGATTTTGGGCTTGCAAAAGATGCTCCAGACGAGAAAAAATCCCACGTATCAACCCGAGTCATGGGAACTTATGGTTATG

Mapped EST sequences

Showing partial alignments of ESTs and genomic sequences. See full alignments


 ATGC     EST sequence
 ATGC     genomic sequence (exon)
 ATGC     genomic sequence (truncated intron)


EST: gi|17400429|gb|BM177211.1|BM177211
EST:     AGACCTGTAATCTATCGTGATTTTAAGACGTCTAATATTCTATTAGATGC                         GGAATACAATGCCAAGCTCTCTGATTTTGGACTCGCCAAAGATGGTCCTGA
genomic: AGACCTGTAATCTATCGTGATTTTAAGACGTCTAATATTCTATTAGATGCggtatgtgag ... attgtttttaGGAATACAATGCCAAGCTCTCTGATTTTGGACTCGCCAAAGATGGTCCTGA
EST: gi|9820922|gb|BE556432.1|BE556432
EST:     AGACCTGTAATCTATCGTGATTTTAAGACGTCTAATATTCTATTAGATGC                         GGAATACAATGCCAAGCTCTCTGATTNTGGACTCGCCAAAGATGGTNCTGA
genomic: AGACCTGTAATCTATCGTGATTTTAAGACGTCTAATATTCTATTAGATGCggtatgtgag ... attgtttttaGGAATACAATGCCAAGCTCTCTGATTTTGGACTCGCCAAAGATGGTCCTGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

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