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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttgagttaatttacttgtactaacacatgttcttaattggattttgcattttgtatttctaccagcgattgggagtagtagaattgagtatttgacaattggcaattgatttttgacatttttgcagATGGAGAAGAATGCTGCAGCTGGAAGAACTCCTTCAAGTTTACCGATGCCTACCCCTCCACCGGCATCTTTAAATATATCTTCTCCGGATTTTGCACCTC

Basic information

species Glycine max
transcript GLYMA20G32430.1
intron # 52
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA20G32430.1 (Glycine max), 3'ss of exon 52
lower sequence: LOC_Os01g60040.2 (Oryza sativa), 3'ss of exon 50
gttgagttaatttacttgtactaacacatgttcttaattggattttgcattttgtatttctaccagcgattgggagtagtagaattgagtatttgac-aattggcaattgatttttgacatttttgcagATGGAGAAGAATGCTGCAGCTGGAAGAACTCCTTCAAGTTTACCGATGCCTACCCCTCCACCGGCATCTTTAAATATATCTTCTCCGGATTTTGCACCTC---
                                           |||||  |||  | | ||    | | ||  |  ||||    | | || ||| ||  |||||| |||    |||     |  ||||| |||||||||||||||| |||||||||||||| || ||  | ||  |  | || ||||| ||      |  |  |||| | |||||  | |||||||||    
------------------------------------------gtttgctattt-caatcctggaggtgtttaagc-tagttt--tggtgtttttaactgattggctattatcgtttttggctcatgcagGTGGAGAAGAATGCTGCTGCTGGAAGAACTCCCTCCAGCCTTCCATTATCCACACCTCCGCCAAT---TGCACCTATACCCTCTCCAAAATTTGCACCTTCAC

upper sequence: GLYMA20G32430.1 (Glycine max), 3'ss of exon 52
lower sequence: GRMZM2G009849_T02 (Zea mays), 3'ss of exon 33
gttgagttaatttacttgtactaacacatgttcttaattggattttgcattttgtatttctaccagcgattgggagtagtagaattgagtatttgacaattggcaattgatttttgacatttttgcagATGGAGAAGAATGCTGCAGCTGGAAGAACTCCTTCAAGTTTACCGATGCCTACCCCTCCACCGGCATCTTTAAATATATCTTCTCCGGATTTTGCACCTC---
                  |  |||     ||| |  |  ||| ||||   ||  |||||  |       |||   |  |||  |||||  |||| |  |         | | ||||  ||    |||| ||||||||||||| |||||||||||||| ||||| ||| | ||  || | || || || ||   | |   ||   || |||||||  | || |||||     
----------------gttggtaatctcagttttgga--ggagtttgagcttgttattttaatt-----ttgtttgaggtacgattga--atttaattac--------gttgtttgcaat----gcagGTGGAGAAGAATGCAGCAGCTGGAAGAACGCCTTCTAGTCTTCCACTGTCCACGCCACCCCCAATAGCAGCAA---TACCTTCTCCAAAATTGGCACCGTCCC

upper sequence: GLYMA20G32430.1 (Glycine max), 3'ss of exon 52
lower sequence: GRMZM2G068755_T01 (Zea mays), 3'ss of exon 51
gttgagttaatttacttgta--ctaacacatgttctta-attggattttgcattttgtatttctaccagcgattgggagtagtagaattgagtatttgacaattggcaattgatttttgacatttttgcagATGGAGAAGAATGCTGCAGCTGGAAGAACTCCTTCAAGTTTACCGATGCCTACCCCTCCACCGGCATCTTTAAATATATCTTCTCCGGATTTTGCACCTC---
               |||||  || |  ||||||        || ||  || | |||  ||  ||     | |||   |  |||  |||||   ||| |  |      |||| ||| | |      ||||| ||||||||||||| |||||||||||||  ||||| ||| | ||  |  | || || || ||   | |   ||   || |   |||  | ||||||||     
-------------gtttgtaacctcagtcatgttggggcggggggttgggcttgttgctttgttatggatg-ttgtttgacgtacgattga---tttaattac-----attg-tttgtaa------tgcagGTGGAGAAGAATGCAGCAGCTGGAAGAATGCCTTCCAGTCTTCCATTATCCACGCCGCCCCCAATAGCAGCAA---TACCCAATCCAAAATTTGCACCATCCC

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|16105237|gb|BI892977.1|BI892977
EST:     AAAATGCTAGTGAGGCATTTCGCACCTACATTAGAGATGGTCTTGCTCAG                         ATGGAGAAGAATGCTGCAGCTGGAAGAACTCCTTCAAGTTTACCGATGCCT
genomic: AAAATGCTAGTGAGGCATTTCGCACCTACATTAGAGATGGTCTTGCTCAGgttgagttaa ... atttttgcagATGGAGAAGAATGCTGCAGCTGGAAGAACTCCTTCAAGTTTACCGATGCCT
EST: gi|38193374|gb|CF922580.1|CF922580
EST:     AAAATGCTAGTGAGGCATTTCGCACCTACATTAGAGATGGTCTTGCTCAG                         ATGGAGAAGAATGCTGCAGCTGGAAGAACTCCTTCAAGTTTACCGATGCCT
genomic: AAAATGCTAGTGAGGCATTTCGCACCTACATTAGAGATGGTCTTGCTCAGgttgagttaa ... atttttgcagATGGAGAAGAATGCTGCAGCTGGAAGAACTCCTTCAAGTTTACCGATGCCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gagtagtagaattgagtatttgacaattggcaattgatttttgacatttttgcagATGGAGAAGAATGCTGCAGCTGGAAGAACTCCTTCAAGTTTACCGATGCCTACCCCTCCACCGGCATCTTTAAATATATCTTCTCCGGATTTTGCACCTC
                                      ttttgac  putative branch site (score: 3)
                                            cattttt  CT-rich tract
                                    atttttgacattttt  TA-rich tract