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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gcgtatggaacattccctatacatcagttgccataagtttctctaaaggatttttattctatttttaaaaataattgcctaattttaatgctcttattagGTTCCAAATCCACTCTTTGACCTTGCTGGTATTATGTGTGGGCAATTTGGTGTGCCTTTCTGGGAGTTCTTGTTTGCTACTTTGATTGGGAAAGCCATCA

Basic information

species Zea mays
transcript GRMZM2G054811_T03
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G054811_T02 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os01g57066.1 (Oryza sativa), 3'ss of exon 5
gcgtatggaacatt-ccctatacatcagttgccataagtttctctaaaggatttttattctatttttaaaaataattgcctaattttaatgctcttattagGTTCCAAATCCACTCTTTGACCTTGCTGGTATTATGTGTGGGCAATTTGGTGTGCCTTTCTGGGAGTTCTTGTTTGCTACTTTGATTGGGAAAGCCATCA
||  |  ||   |     |||  |  |  |    |   ||   ||||    |  |   |  ||  || |  |||       | |||   ||  |||| ||||||||||| ||||| ||||||||||||||||| |||||||||||||||||  | || |||||||||||||| |||||||||||||||||||| |||||||
gctaacagatggtggtgatatggagaatcttggttcttttgtactaacatctgatggataaataatttaccata-caatgaattttctttgtgcttactagGTTCCAAACCCACTGTTTGACCTTGCTGGTATAATGTGTGGGCAATTTGGCATTCCCTTCTGGGAGTTCTTCTTTGCTACTTTGATTGGGAAGGCCATCA

upper sequence: GRMZM2G054811_T02 (Zea mays), 3'ss of exon 5
lower sequence: GLYMA01G44920.1 (Glycine max), 3'ss of exon 5
gcgtatggaacattccctatacatcagttgccataagtttctctaaaggatttttattctat-ttttaaaaa----taattgcctaattttaatgctcttatt--agGTTCCAAATCCACTCTTTGACCTTGCTGGTATTATGTGTGGGCAATTTGGTGTGCCTTTCTGGGAGTTCTTGTTTGCTACTTTGATTGGGAAAGCCATCA
        | || | ||| ||  | || |||       |     | || |||| |  | |||  ||||  ||    |||    ||| |      | |  ||||  ||||||||||||| || |||||||||||||| ||||||||||| ||||||||  | || || ||| | || ||  |||| || |||||||| || || ||||
-------tagcaattcctttatttgaggtgcatcctcctctaagatagaatttattatatatactttatcaacgtgtaaacagctattaactgagattatatttcagGTTCCAAATCCTCTATTTGACCTTGCTGGCATTATGTGTGGACAATTTGGCATTCCATTTTGGAAATTTTTTCTTGCAACCTTGATTGGAAAGGCAATCA

upper sequence: GRMZM2G054811_T02 (Zea mays), 3'ss of exon 5
lower sequence: GLYMA11G00720.1 (Glycine max), 3'ss of exon 5
gcgtatggaacattccctatacatcagttgccataagtttctctaa-aggattt-ttat-tctatttttaaaaataattgcctaattttaat---gctcttatt--agGTTCCAAATCCACTCTTTGACCTTGCTGGTATTATGTGTGGGCAATTTGGTGTGCCTTTCTGGGAGTTCTTGTTTGCTACTTTGATTGGGAAAGCCATCA
           | | ||| ||  | || ||| ||     |||  || || |||| |||| | || |||   ||||  |   |   | ||||    | |  ||||  ||||||||||||| || ||||||||||| || || |||||||| ||||||||  | || || ||| | || ||  |||| || |||||||| || || || |
-------agttacttcctttatttgaggtgc-atcctcctctaaaatagcatttattatatatactttatcaaattgtaaacagctattaactgagattatatttcagGTTCCAAATCCTCTATTTGACCTTGCCGGCATCATGTGTGGACAATTTGGCATTCCATTTTGGAAATTTTTTCTTGCAACCTTGATTGGAAAGGCAATTA

upper sequence: GRMZM2G054811_T02 (Zea mays), 3'ss of exon 5
lower sequence: AT4G14950.1 (Arabidopsis thaliana), 3'ss of exon 5
----------------------------------------gcgtatggaacattccctatacatcagttgccata-agtttctctaaaggatttttattctatttttaaaa----ataattgcctaat--tttaatgctcttattagGTTCCAAATCCACTCTTTGACCTTGCTGGTATTATGTGTGGGCAATTTGGTGTGCCTTTCTGGGAGTTCTTGTTTGCTACTTTGATTGGGAAAGCCATCA
                                        ||  |||||  ||  ||  ||  |    || |||| | | ||| |       |   |||| ||  | |  |    |  ||| |  | |  ||  ||    || | |||||||||||||  | |||||||| ||||| || |||||||| ||||||||  | || || ||||| |||||  | || || || || || || || ||||
gttagtatgcatcctccaatttactttaccttctgcagtagcaaatggattatgacc-gtatttactgtgtcatataatatcttttgctttctaggattcaatgatcaggaccttaccattactcactgcttcgatttgattgt-agGTTCCAAATCCTTTGTTTGACCTCGCTGGAATAATGTGTGGACAATTTGGCATTCCGTTTTGGGAATTCTTCCTGGCGACCTTAATCGGAAAGGCGATCA

upper sequence: GRMZM2G054811_T02 (Zea mays), 3'ss of exon 5
lower sequence: Vv05s0020g03160.t01 (Vitis vinifera), 3'ss of exon 5
gcgtatggaacattccctatacatcagttgccataagtttctctaaag--gatttttattctatttttaaaaataat-tgcctaattttaatgctcttattagGTTCCAAATCCACTCTTTGACCTTGCTGGTATTATGTGTGGGCAATTTGGTGTGCCTTTCTGGGAGTTCTTGTTTGCTACTTTGATTGGGAAAGCCATCA
    | |   ||  |  |     | ||      ||||| |   ||     ||||   | | ||||  ||   |     ||  ||| | |  |  | || |||||| || ||||| || |||||||||||||| || |||||||| ||||||||  | || || ||| |||| ||  |||| || || ||||| || || || |
--tgaagatgcagactttgcgtttgagaaaaagtaagtctagatatttctgattagcaatttattgatatgtacctcctggttaactgttgtattgtt-ttagGTGCCGAATCCTCTATTTGACCTTGCTGGCATAATGTGTGGACAATTTGGGATTCCATTTTGGAAGTTTTTTCTTGCAACATTCATTGGAAAGGCAATTA

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|5928745|gb|AW055962.1|AW055962
EST:     TCTCTCACTCCCAACATCTCAACTTCTTCTCTATCTTGATTCTTGCTTCG                         GTTCCAAATCCACTCTTTGACCTTGCTGGTATTATGTGTGGGCAATTTGGT
genomic: TCTCTCACTCCCAACATCTCAACTTCTTCTCTATCTTGATTCTTGCTTCGgttggtctcc ... ctcttattagGTTCCAAATCCACTCTTTGACCTTGCTGGTATTATGTGTGGGCAATTTGGT






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aaggatttttattctatttttaaaaataattgcctaattttaatgctcttattagGTTCCAAATCCACTCTTTGACCTTGCTGGTATTATGTGTGGGCAATTTGGTGTGCCTTTCTGGGAGTTCTTGTTTGCTACTTTGATTGGGAAAGCCATCA
                                     ttttaat  putative branch site (score: 3)
                                             ctcttatt  CT-rich tract
     tttttattctattttt  TA-rich tract