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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgcacccgatttctctacttttttttttgttcttgacaattcctttttgtacaatatatactaacattcatgttggcaatgtggatactttgaaattcttagGTTTACCCTCATGTTGCTACTGGGTTCTCCGATACATCTGCTTTTCTCAGGGAACTGACTCTTAAGTCTATGTTAATTCTGGCTCCAAAG

Basic information

species Glycine max
transcript GLYMA09G38740.1
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA09G38740.1 (Glycine max), 3'ss of exon 11
lower sequence: LOC_Os01g60440.1 (Oryza sativa), 3'ss of exon 11
gtatgcacccgatttctctacttttttttttgttcttgacaattcctttttgtacaatatatactaacattcatgttggcaatgtggatactttgaaattcttagGTTTACCCTCATGTTGCTACTGGGTTCTCCGATACATCTGCTTTTCTCAGGGAACTGACTCTTAAGTCTATGTTAATTCTGGCTCCAAAG
                | | || |  |||    | | ||||  | | | |  | |   | ||  | |   |     || ||   |  |||  |  ||      |||||| ||| |||||||| ||||||||||| ||||| |||||||||||  | ||||||||  | ||||||||| |  |  |||| || || 
---------------gtatgctatcatttcctgtatggacatctgcatgtgtttctgga-atgttgatgct-----tgacaggataaatatctctaa---tgcagGTTTTCCCCCATGTTGCCACTGGGTTCTCTGATACTTCTGCTTTTCTTCGTGAACTGACCTTGAAGTCTATGCTTGTATTGGCACCCAAA

upper sequence: GLYMA09G38740.1 (Glycine max), 3'ss of exon 11
lower sequence: AT2G40730.1 (Arabidopsis thaliana), 3'ss of exon 11
----------------gtatgcacccgatttctctacttttttttttgttcttgacaattcctttttgtacaatatatactaacattcatgttggcaatgtggatactttgaaattcttagGTTTACCCTCATGTTGCTACTGGGTTCTCCGATACATCTGCTTTTCTCAGGGAACTGACTCTTAAGTCTATGTTAATTCTGGCTCCAAAG
                 | ||   |  |      |  |    | |  ||  |||||| | |   | | || | |  |||||    ||    ||  ||||| ||||   ||    ||  ||||| |||||||||||||||||||| ||  | |||||||||||||||||| | || ||||||||||| || ||| |  || | ||||| |||
gtaagatcagtttctcttctgtggc-aagaaaggtgttcacctatgggtgtttgacagtactgctgtcta-attgcatactt---ttagcatttacaatg-ggatgtgtt---tttactagGTATACCCTCATGTTGCTACTGGATTTGCGGATACATCTGCTTTTCTCCGAGAGCTGACTCTTAAATCGATGCTCGTTTTAGCTCCGAAG

upper sequence: GLYMA09G38740.1 (Glycine max), 3'ss of exon 11
lower sequence: Vv13s0067g03110.t01 (Vitis vinifera), 3'ss of exon 11
gtatgcacccgatttctctacttttttttttgttcttgacaattcct-ttttgtacaatatatacta-----acattcatgttggcaatgtggatactttgaaattctt----------------agGTTTACCCTCATGTTGCTACTGGGTTCTCCGATACATCTGCTTTTCTCAGGGAACTGACTCTTAAGTCTATGTTAATTCTGGCTCCAAAG
|||||     | |||||  |   |||  |    | ||  |  | | | ||||| |||  | ||| |      |  ||        |||| |||| | | | |||| |||                |||||||  |||||||||||||||||||||| || || |||||||||||  ||||| |||| ||||| || ||| | ||||| ||||| |||
gtatggtagtggtttctgaatgatttaatcaaattttagctgtccatgttttggacataagataatgcttgtatcttttcaccatcaatttggaaattctaaaatgcttggtgatgcttggcactagGTTTATACTCATGTTGCTACTGGGTTCTCAGACACGTCTGCTTTTCTTCGGGAATTGACACTTAAATCCATGCTTATTCTTGCTCCTAAG

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|17021829|gb|BM092863.1|BM092863
EST:     ATATTGATCAATATGGAGAGTCTTTATCAGCGCAAGCTGTTGATGAACAA                         GTTTACCCTCATGTTGCTACTGGGTTCTCCGATACATCTGCTTTTCTCAGG
genomic: ATATTGATCAATATGGAGAGTCGTTATCAGCGCAAGCTGTTGATGAGCAAgtatgcaccc ... aaattcttagGTTTACCCTCATGTTGCTACTGGGTTCTCCGATACATCTGCTTTTCTCAGG
EST: gi|254342248|gb|GR853385.1|GR853385
EST:     ATATTGATCAATATGGAGAGTCTTTATCAGCGCAAGCTGTTGATGAACAA                         GTTTACCCTCATGTTGCTACTGGGTTCTCCGATACATCTGCTTTTCTCAGG
genomic: ATATTGATCAATATGGAGAGTCGTTATCAGCGCAAGCTGTTGATGAGCAAgtatgcaccc ... aaattcttagGTTTACCCTCATGTTGCTACTGGGTTCTCCGATACATCTGCTTTTCTCAGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgtacaatatatactaacattcatgttggcaatgtggatactttgaaattcttagGTTTACCCTCATGTTGCTACTGGGTTCTCCGATACATCTGCTTTTCTCAGGGAACTGACTCTTAAGTCTATGTTAATTCTGGCTCCAAAG
           tactaac  putative branch site (score: 0)
                                                ttctt  putative PPT
     aatatatactaacatt  TA-rich tract