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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaatgaaattaactttgtttgcctttctgtcatggtcttatacatgtgttgtttactactgtcttggtttggagaagcttcagcattattatatttacatgctgtttcagGACTCGACCTTTGAGTTTGAGAGAAAGCGAAACAGACCTGAGAGATATGACAGGAATCTTGCTGAGAATGTCCTCAAGGCCATTCCAAAGATTGATAAAA

Basic information

species Glycine max
transcript GLYMA12G09090.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA12G09090.1 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os01g33050.2 (Oryza sativa), 3'ss of exon 2
---gtaaatgaaattaactttgtttgcctttctgtcatggtcttataca-tgtgttgtttactactgtcttggtttggagaagcttcagcattattatatttacatgctgtttcagGACTCGACCTTTGAGTTTGAGAGAAAGCGAAACAGACCTGAGAGATATGACAGGAATCTTGCTGAGAATGTCCTCAAGGCCATTCCAAAGATTGATAAAA
    |   |     ||  || |||     ||  ||   |  |  ||    | || |||  || ||| |||  | |  ||    | || | ||  ||    | | ||       |||||||| ||||||||||||||||| ||| | |||||||| ||| | |||||| ||||| |  |||   |    || ||||| || ||    |||   || |
gtatttgcttgttctattttcgttcagtattaagtagagagcacattttctatgctgtgaaccactttctatgctgtgaaccacatctgaatcgtt----tgaaat-------cagGACTCCACCTTTGAGTTTGAGAGGAAGAGGAACAGACCAGAGCGCTATGACCGGAATGTCACTGCACAAACTCTTAAGGCTATCCCTCTTATTACAAAGA

upper sequence: GLYMA12G09090.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv06s0061g01330.t01 (Vitis vinifera), 3'ss of exon 2
gtaaatgaaattaactttgtttgccttt---ctgtcatggtcttatacatgtgttgtttactactgtcttggt---ttggagaagcttcagcattattatatttacatgctgtttc-------agGACTCGACCTTTGAGTTTGAGAGAAAGCGAAACAGACCTGAGAGATATGACAGGAATCTTGCTGAGAATGTCCTCAAGGCCATTCCAAAGATTGATAAAA
||| |  || | | |||   ||  | ||   |||  |  |||  ||  || |     | | ||  |||  |      |   |    ||||   || || |   |   |  | || |       |||| || |||||||||||||||||||||||||| || || ||||||||||| |||||| |||||||||||   || ||||| |||   ||||| |||||| 
gtacacaaactaatcttcaattaaccttttcctgaaacagtcccatttatattcctgtaattatagtcaagaaaaactaatgcgagttcatgttttttctgggtctgtcttattcctttttaaagGATTCAACCTTTGAGTTTGAGAGAAAGCGAAATAGGCCAGAGAGATATGATAGGAATGTTGCTGAGAATACTCTGAAGGCTATTAAGAAGATCGATAAAG

upper sequence: GLYMA12G09090.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv08s0007g03850.t01 (Vitis vinifera), 3'ss of exon 3
gtaaatgaaattaactttgtttgcctttctgtcatggtcttatacatgtgttgtt----tactactgt----cttggtttggagaagcttcagcattattatatttacatgctgtttcagGACTCGACCTTTGAGTTTGAGAGAAAGCGAAACAGACCTGAGAGATATGACAGGAATCTTGCTGAGAATGTCCTCAAGGCCATTCCAAAGATTGATAAAA
||||||    || | | || ||   ||||| |  || ||||   ||   |||        | | |  |    || |||   ||   | |      ||    | ||| |||  | ||  |||| || ||||||||||||||||||||||| || || || ||||||||||||||||||||||| |||||    || ||||| |||   |||||||| ||| 
gtaaatatggttcattatggttat-tttctcttttgatcttcctcagcagttaccactgcattgccataaaactgggtggtgatctgttcttttctttgcttcttttcatatt-ttctagGATTCAACCTTTGAGTTTGAGAGAAAGCGGAATAGGCCAGAGAGATATGACAGGAATCTTGCAGAGAACACTCTAAAGGCAATTAAGAAGATTGACAAAG

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|298190182|gb|HO032303.1|HO032303
EST:     TAAAATGGACAAAGGCATATAGACGAGTGCATGGAAAGGATATGACACAG                         GACTCGACCTTTGAGTTTGAGAGAAAGCGAAACAGACCTGAGAGATATGAC
genomic: TAAAATGGACAAAGGCATATAGACGAGTGCATGGAAAGGATATGACACAGgtaaatgaaa ... gctgtttcagGACTCGACCTTTGAGTTTGAGAGAAAGCGAAACAGACCTGAGAGATATGAC
EST: gi|6070529|gb|AW099916.1|AW099916
EST:     TAAAATGGACAAAGGCATATAGACGAGTGCATGGAAAGGATATGACACAG                         GACTCGACCTTTGAGTTTGAGAGAAAGCGAAACAGACCTGAGAGATATGAC
genomic: TAAAATGGACAAAGGCATATAGACGAGTGCATGGAAAGGATATGACACAGgtaaatgaaa ... gctgtttcagGACTCGACCTTTGAGTTTGAGAGAAAGCGAAACAGACCTGAGAGATATGAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctactgtcttggtttggagaagcttcagcattattatatttacatgctgtttcagGACTCGACCTTTGAGTTTGAGAGAAAGCGAAACAGACCTGAGAGATATGACAGGAATCTTGCTGAGAATGTCCTCAAGGCCATTCCAAAGATTGATAAAA
                                              ctgtttc  CT-rich tract
                             attattatatttacat  TA-rich tract