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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtataatagtagctttgcttatctcatgattgctatctactctttttctctgcctatctaaaactttgtgcctttctatacagGTGAACCCAGGGAATGCACCTTTAGTTGTTGGGCAGCTGCTAGATGATGAGTGCGCAGAAGATTTTATCAAAGGCTTGATCCTTTCTGTTCGTTCATTAC

Basic information

species Glycine max
transcript GLYMA02G42560.1
intron # 21
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA02G42560.1 (Glycine max), 3'ss of exon 21
lower sequence: LOC_Os12g01390.1 (Oryza sativa), 3'ss of exon 21
gtataatagtagctttgctta-tctcat--gattgctatctactctttttctctgcctatctaaaactttgtgcctttctata---cagGTGAACCCAGGGAATGCACCTTTAGTTGTTGGGCAGCTGCTAGATGATGAGTGCGCAGAAGATTTTATCAAAGGCTTGATCCTTTCTGTTCGTTCATTAC
||||   | |        | | | | ||  || |   ||| | |||  |   ||   ||| ||||   || |     | ||||    |||||||||| || ||||| || ||||||||||| ||||| || |||||||||||| | |||||||| || || || ||||| || ||||| |||||  | |
gtatgcaactcttccaattcagtgttattggagtatcatc-attctcatgtgctatgtatttaaatgcttattttcctttatattgtagGTGAACCCTGGAAATGCTCCATTAGTTGTTGGACAGCTACTTGATGATGAGTGCCCTGAAGATTTCATTAAGGGTTTGATTCTGTCTGTCCGTTCTCTCC

upper sequence: GLYMA02G42560.1 (Glycine max), 3'ss of exon 21
lower sequence: LOC_Os11g01380.1 (Oryza sativa), 3'ss of exon 21
gtataatagtagctttgctta-tctcat--gattgctatctactctttttctctgcctatctaaaactttgtgcctttctata---cagGTGAACCCAGGGAATGCACCTTTAGTTGTTGGGCAGCTGCTAGATGATGAGTGCGCAGAAGATTTTATCAAAGGCTTGATCCTTTCTGTTCGTTCATTAC
||||   | |        | | | | ||  || |   ||| | |||  |   ||   ||| ||||   || |     | ||||    |||||||||| || ||||| || ||||||||||| ||||| || |||||||||||| | |||||||| || || || ||||| || ||||| |||||  | |
gtatgcaactcttccaattcagtgttattggagtatcatc-attctcatgtgctatgtatttaaattcttattttcctttatattgtagGTGAACCCTGGAAATGCTCCATTAGTTGTTGGACAGCTACTTGATGATGAGTGCCCTGAAGATTTCATTAAGGGTTTGATTCTGTCTGTCCGTTCTCTCC

upper sequence: GLYMA02G42560.1 (Glycine max), 3'ss of exon 21
lower sequence: GRMZM2G111355_T01 (Zea mays), 3'ss of exon 1
-----------------gtataatagtagctttgcttatctcatgattgctatctactctttttctctgcctatctaaaactttgtgcctttctatacagGTGAACCCAGGGAATGCACCTTTAGTTGTTGGGCAGCTGCTAGATGATGAGTGCGCAGAAGATTTTATCAAAGGCTTGATCCTTTCTGTTCGTTCATTAC
                 || |          ||  ||    | |  || ||    |    ||   | ||   ||    || | | |    || | | |||||||| || |||||||| || || || || |||||  | || |||||||| ||| | |||||||||||||| || |||||||| |||||||||||  | |
gttcagaaggtagttgtgtgtttcgactctgttaattcgtgcgtcgttcctcataataggttgagtatgagaatggttaattcttttttcttgtttccagGTGAATCCCGGGAATGCTCCATTGGTAGTGGGGCAATTACTTGATGATGAATGCCCTGAAGATTTTATCAAGGGTTTGATCCTCTCTGTTCGTTCTCTCC

upper sequence: GLYMA02G42560.1 (Glycine max), 3'ss of exon 21
lower sequence: AT3G11130.1 (Arabidopsis thaliana), 3'ss of exon 21
gtataatagtagctttgcttatctcatgattgctatctactctttttctctgcctatctaaaactttgtgcctttctatacagGTGAACCCAGGGAATGCACCTTTAGTTGTTGGGCAGCTGCTAGATGATGAGTGCGCAGAAGATTTTATCAAAGGCTTGATCCTTTCTGTTCGTTCATTAC
||||    |||| ||   |   ||  || |   |||       |||||       |  || |  | || |      | |  ||||||| || |||||||| || |||||||| |||||| |||| ||||| || ||| | ||||||||||| |||||| | || |||||||||||||||||||
gtat----gtagtttctttagacttttgttaaatatggtaggattttcatgaaagaattata--tatgcgatcccttttgtagGTGAATCCTGGGAATGCTCCCTTAGTTGTGGGGCAGTTGCTTGATGACGAATGCCCTGAAGATTTTATAAAAGGCCTCATTCTTTCTGTTCGTTCATTAC

upper sequence: GLYMA02G42560.1 (Glycine max), 3'ss of exon 21
lower sequence: AT3G08530.1 (Arabidopsis thaliana), 3'ss of exon 21
gtataatagtagctttgcttatctc--atg-attgctatctactctttttctctgcc-tatctaaaactttgtgcctttctatacagGTGAACCCAGGGAATGCACCTTTAGTTGTTGGGCAGCTGCTAGATGATGAGTGCGCAGAAGATTTTATCAAAGGCTTGATCCTTTCTGTTCGTTCATTAC
||||||   |  ||  |  ||  |   |||  |||   |  | | ||||| | ||   ||| || |  ||||   || ||   | |||||||||| |||||||| || |||||||| |||||| |||| |||||||| ||| | ||||||||||| |||||| | || || |||||||||||||| |
gtataaggtttcctgggactacttttaatgcgttggagttcagtttttttttatgaaatatttatacgtttgattctgtc---aaagGTGAACCCTGGGAATGCTCCCTTAGTTGTCGGGCAGTTGCTTGATGATGAATGCCCTGAAGATTTTATAAAAGGCCTCATTCTCTCTGTTCGTTCATTGC

upper sequence: GLYMA02G42560.1 (Glycine max), 3'ss of exon 21
lower sequence: Vv13s0067g01290.t01 (Vitis vinifera), 3'ss of exon 21
----------------------------------------------------gtataatagtagctttgcttatctcatgattgctatctactcttt--ttctctgcctatctaaaac-tttgtgcctttctatacagGTGAACCCAGGGAATGCACCTTTAGTTGTTGGGCAGCTGCTAGATGATGAGTGCGCAGAAGATTTTATCAAAGGCTTGATCCTTTCTGTTCGTTCATTAC
                                                    | |     || | |      ||  | | |||  | | || ||||   || | ||  ||  | ||    || ||| | |||  | ||||||||||  | ||||||||||||||||| |||||||||||||||||||| ||  |||||||||| || |||||  | || |||||||| || ||  | |
gtgtgagttccttctagaattctagaattttggatcccctttgggtcatgatgaactcctgtggatgcttcaatgccctaattaat-tttagtcttcaattatttgattaaattaattgcttttgcttctcttgatagGTGAACCCTAGTAATGCACCTTTAGTTGTGGGGCAGCTGCTAGATGATGAATGTCCAGAAGATTTCATTAAAGGTCTAATTCTTTCTGTCCGGTCGCTGC

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|209718673|gb|BW662739.1|BW662739
EST:     ATCTATACACAAACAACATGGTTCGCTACATTGAAGGCTATGTTCAGAAG                         GTGAACCCAGGGAATGCACCTTTAGTTGTTGGGCAGCTGCTAGATGATGAA
genomic: ATCTATACACAAACAACATGGTTCGCTACATTGAAGGCTATGTTCAGAAGgtataatagt ... ttctatacagGTGAACCCAGGGAATGCACCTTTAGTTGTTGGGCAGCTGCTAGATGATGAG
EST: gi|209720996|gb|BW682475.1|BW682475
EST:     ATCTATACACAAACAACATGGTTCGCTACATTGAAGGCTATGTTCAGAAG                         GTGAACCCAGGGAATGCACCTTTAGTTGTTGGGCAGCTGCTAGATGATGAA
genomic: ATCTATACACAAACAACATGGTTCGCTACATTGAAGGCTATGTTCAGAAGgtataatagt ... ttctatacagGTGAACCCAGGGAATGCACCTTTAGTTGTTGGGCAGCTGCTAGATGATGAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

attgctatctactctttttctctgcctatctaaaactttgtgcctttctatacagGTGAACCCAGGGAATGCACCTTTAGTTGTTGGGCAGCTGCTAGATGATGAGTGCGCAGAAGATTTTATCAAAGGCTTGATCCTTTCTGTTCGTTCATTAC
                           atctaaa  putative branch site (score: 3)
                                   ctttgtgcctttct  CT-rich tract
                          tatctaaaa  TA-rich tract