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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgtggtttagtggttacttattgatgaccctgatctctattttatcacattactcttttgatactgaactgtttaaatttattattgcagATATGCTGATATTTATACATCTAGGGTGTCAAATTTTTTGTATTATACACCCTTCATGTATTTCCGCTCTCAGGAACAG

Basic information

species Glycine max
transcript GLYMA17G04580.1
intron # 15
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA17G04580.1 (Glycine max), 3'ss of exon 15
lower sequence: LOC_Os01g14810.1 (Oryza sativa), 3'ss of exon 15
gtatgtggtttagtggttacttattgatgaccctgatctctattttatcacattactcttttgatactg-aactgtttaaatttattattgcagATATGCTGATATTTATACATCTAGGGTGTCAAATTTTTTGTATTATACACCCTTCATGTATTTCCGCTCTCAGGAACAG
||  ||||||   |||||    | || |||   | || | |||     || |||     | ||  | || || | |||    |  |   ||||||||||||||||| || ||||| ||||| ||||||||| |  ||||||| || |||||||||||||  || || ||||||
gtgagtggtt--atggttttgcagtggtgaatattattt-tatgagcccaaattttatctgtgtaaatgcaattattttg--tcctcggtgcagATATGCTGATATATACACATCAAGGGTTTCAAATTTTCTACATTATACTCCATTCATGTATTTCCAATCACAAGAACAG

upper sequence: GLYMA17G04580.1 (Glycine max), 3'ss of exon 15
lower sequence: LOC_Os01g14810.3 (Oryza sativa), 3'ss of exon 16
gtatgtggtttagtggttacttattgatgaccctgatctctattttatcacattactcttttgatactg-aactgtttaaatttattattgcagATATGCTGATATTTATACATCTAGGGTGTCAAATTTTTTGTATTATACACCCTTCATGTATTTCCGCTCTCAGGAACAG---------------------
||  ||||||   |||||    | || |||   | || | |||     || |||     | ||  | || || | |||    |  |   ||||||||||||||||| || ||||| ||||| ||||||||| |  ||||||| || |||||||||||||  || || ||||||                     
gtgagtggtt--atggttttgcagtggtgaatattattt-tatgagcccaaattttatctgtgtaaatgcaattattttg--tcctcggtgcagATATGCTGATATATACACATCAAGGGTTTCAAATTTTCTACATTATACTCCATTCATGTATTTCCAATCACAAGAACAGGTAATTGCAAAACTCTAGATG

upper sequence: GLYMA17G04580.1 (Glycine max), 3'ss of exon 15
lower sequence: GRMZM2G044819_T02 (Zea mays), 3'ss of exon 14
gtatgtggtttagtggttacttattgatgaccctgatctctattttatcacattactcttttgatactgaactgtttaaatttattattgcagATATGCTGATATTTATACATCTAGGGTGTCAAATTTTTTGTATTATACACCCTTCATGTATTTCCGCTCTCAGGAACAG
         | ||| | ||  | ||  | |   |||     | | |     |   |    |  || |  ||||  ||     | ||  || |||||||||||||| || ||||| ||||| ||||||||| || | ||||| || |||||||||||||  ||||| ||||||
--------gtgagtcgctatattttttttatagtgaaaaaaaatgttatggacaccaaactgaatgc--aactaattttgcat-ttcctgtagATATGCTGATATATACACATCAAGGGTTTCAAATTTTCTGCACTATACTCCATTCATGTATTTCCAATCTCAAGAACAG

upper sequence: GLYMA17G04580.1 (Glycine max), 3'ss of exon 15
lower sequence: Vv05s0020g00880.t01 (Vitis vinifera), 3'ss of exon 15
----------------gtatgtggtttagtggttacttattgatgacc--ctgatctctattttatcacattactcttttgatactgaactgtttaaatttatta-ttgcagATATGCTGATATTTATACATCTAGGGTGTCAAATTTTTTGTATTATACACCCTTCATGTATTTCCGCTCTCAGGAACAG
                   | ||  ||  |  || |||||  | ||    || | ||  ||    | |   | ||   || |||     ||    | || |   | |||||| |||||||||||||| || |||||||| ||||||||  |  ||||||||||||| |||||||| | ||| |||||||||
gtatgtgcttttccttcattatgccttctttttttcttatgtaggagtaactaaacttcataaactaagggttctacctttatatgatccttacaatatcttccaattgcagGTATGCTGATATTTACACCTCTAGGGTCTCAAATTTCCTACATTATACACCCTTTATGTATTTTCACTCACAGGAACAG

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|51335476|gb|CO979342.1|CO979342
EST:     TCTCGTGCTGGGCTGTGGGATAAAAGCCACTTGATGAGACAAATTGAGAA                         ATATGCTGATATTTATACATCTAGGGTGTCAAATTTTTTGTATTATACACC
genomic: TCTCGTGCTGGGCTGTGGGATAAAAGCCACTTGATGAGACAAATTGAGAAgtatgtggtt ... attattgcagATATGCTGATATTTATACATCTAGGGTGTCAAATTTTTTGTATTATACACC
EST: gi|298169844|gb|HO018468.1|HO018468
EST:     TCTCGTGCTGGGCTGTGGGATAAAAGCCACCTGATGAGACAAATTGAGAA                         ATATGCTGATATTTATACATCTAGGGTGTCAAATTTTT-GTATTATACACC
genomic: TCTCGTGCTGGGCTGTGGGATAAAAGCCACTTGATGAGACAAATTGAGAAgtatgtggtt ... attattgcagATATGCTGATATTTATACATCTAGGGTGTCAAATTTTTTGTATTATACACC
EST: gi|58022071|gb|CX708812.1|CX708812
EST:     TCTCGTGCTGGGCTGTGGGATAAAAGCCACTTGATGAGACAAATTGAGAA                         ATATGCTGATATTTATACATCTAGGGTGTCAAATTTTTTGTATTATACACC
genomic: TCTCGTGCTGGGCTGTGGGATAAAAGCCACTTGATGAGACAAATTGAGAAgtatgtggtt ... attattgcagATATGCTGATATTTATACATCTAGGGTGTCAAATTTTTTGTATTATACACC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tctattttatcacattactcttttgatactgaactgtttaaatttattattgcagATATGCTGATATTTATACATCTAGGGTGTCAAATTTTTTGTATTATACACCCTTCATGTATTTCCGCTCTCAGGAACAG
                    ttttgat  putative branch site (score: 4)
                             tgaactgtttaaattt  TA-rich tract