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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cccatccaatccatgtatgtggcttaggaataatcgaacaagacctcactacttaagttcaccagccatgttagcagtcacttgatctatgttcttgcagGTAAGTACTGTTGAAGAGGAGGCTGCCTATAATGCTCGACTCACAAAAGATAAG

Basic information

species Zea mays
transcript GRMZM5G816356_T02
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G816356_T02 (Zea mays), 3'ss of exon 6
lower sequence: LOC_Os01g47690.2 (Oryza sativa), 3'ss of exon 6
cccatccaatccatgtatgtggcttaggaataatcgaacaagacctcactactt--aagttcaccagccatgttagcagtcacttga-tctatgttcttgcagGTAAGTACTGTTGAAGAGGAGGCTGCCTATAATGCTCGACTCACAAAAGATAAG----------------------------------------------
                                       |||  ||||||   |  ||| |||| |  || | || ||| ||||||| | | |  | |||||||||||||||||||||||||||| ||| |||||||||||||| ||||| ||||||                                              
-------------------------------------gtaagtgctcactttcttaaagctcactaatcaaggtaccaggcacttgactattttattttgcagGTAAGTACTGTTGAAGAGGAGGTTGCGTATAATGCTCGACTAACAAAGGATAAGGTACATGCTACTTTGGCTAATTCTTTACACCCATCTAACTAATAAA

upper sequence: GRMZM5G816356_T02 (Zea mays), 3'ss of exon 6
lower sequence: LOC_Os01g47690.1 (Oryza sativa), 3'ss of exon 6
cccatccaatccatgtatgtggcttaggaataatcgaacaagacctcactactt--aagttcaccagccatgttagcagtcacttgatc-tatgttcttgcagGTAAGTACTGTTGAAGAGGAGGCTGCCTATAATGCTCGACTCACAAAAGATAAG
                                       |||  ||||||   |  ||| |||| |  || | || ||| |||||||   | |  | |||||||||||||||||||||||||||| ||| |||||||||||||| ||||| ||||||
-------------------------------------gtaagtgctcactttcttaaagctcactaatcaaggtaccaggcacttgactattttattttgcagGTAAGTACTGTTGAAGAGGAGGTTGCGTATAATGCTCGACTAACAAAGGATAAG
















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|32827854|gb|CD967532.1|CD967532
EST:     TGCCAAAGGATACACTACTTTATCCTGCTCAAGACTATAAAGGTTTCACG                         GTAAGTACTGTTGAAGAGGAGGCTGCCTATAATGCTCGACTCACGAAAGAT
genomic: TGCCAAAGGATACACTACTTTATCCTGCTCATGACTATAAAGGTTTCACGgtgagtttct ... gttcttgcagGTAAGTACTGTTGAAGAGGAGGCTGCCTATAATGCTCGACTCACAAAAGAT
EST: gi|50331454|gb|CO526580.1|CO526580
EST:     TGCCAAAGGATACACTACTTTATCCTGCTCATGACTATAAAGGTTTCACG                         GTAAGTACTGTTGAAGAGGAGGCTGCCTATAATGCTCGACTCACAAAAGAT
genomic: TGCCAAAGGATACACTACTTTATCCTGCTCATGACTATAAAGGTTTCACGgtgagtttct ... gttcttgcagGTAAGTACTGTTGAAGAGGAGGCTGCCTATAATGCTCGACTCACAAAAGAT
EST: gi|28982565|gb|BQ538185.2|BQ538185
EST:     TGCCAAAGGATACACTACTTTATCCTGCTCATGACTATAAAGGTTTCACG                         GTAAGTACTGTTGAAAAGGAGGCTGCCTATAATGCTCGACTCACAAAAGAT
genomic: TGCCAAAGGATACACTACTTTATCCTGCTCATGACTATAAAGGTTTCACGgtgagtttct ... gttcttgcagGTAAGTACTGTTGAAGAGGAGGCTGCCTATAATGCTCGACTCACAAAAGAT
EST: gi|87155453|gb|DY400242.1|DY400242
EST:     TGCCAAAGGATACACTACTTTATCCTGTTCATGACTATAAAGGTTTCACG                         GTAAGTACTGTTGAAGAGGAGGCTGCCTATAATGCTCGACTCACGAAAGAT
genomic: TGCCAAAGGATACACTACTTTATCCTGCTCATGACTATAAAGGTTTCACGgtgagtttct ... gttcttgcagGTAAGTACTGTTGAAGAGGAGGCTGCCTATAATGCTCGACTCACAAAAGAT
EST: gi|211380540|gb|FL436905.1|FL436905
EST:     TGCCAAAGGATACACTACTTTATCCTGCTCATGACTATAAAGGTTTCACG                         GTAAGTACTGTTGAAGAGGAGGCTGCCTATAATGCTCGACTCACAAAAGAT
genomic: TGCCAAAGGATACACTACTTTATCCTGCTCATGACTATAAAGGTTTCACGgtgagtttct ... gttcttgcagGTAAGTACTGTTGAAGAGGAGGCTGCCTATAATGCTCGACTCACAAAAGAT
EST: gi|37383453|gb|CF628743.1|CF628743
EST:     TGCCAAAGGATACACTACTTTATCCTGCTCATGACTATAAAGGTTTCACG                         GTAAGTACTGTTGAAGAGGAGGCTGCCTATAATGCTCGACTCACGAAAGAT
genomic: TGCCAAAGGATACACTACTTTATCCTGCTCATGACTATAAAGGTTTCACGgtgagtttct ... gttcttgcagGTAAGTACTGTTGAAGAGGAGGCTGCCTATAATGCTCGACTCACAAAAGAT
EST: gi|111990479|gb|EE331905.1|EE331905
EST:     TGCCAAAGGATACACTACTTTATCCTGCTCATGACTATAAAGGTTTCACG                         GTAAGTACTGTTGAAGAGGAGGCTGCCTATAATGCTCGACTCACGAAAGAT
genomic: TGCCAAAGGATACACTACTTTATCCTGCTCATGACTATAAAGGTTTCACGgtgagtttct ... gttcttgcagGTAAGTACTGTTGAAGAGGAGGCTGCCTATAATGCTCGACTCACAAAAGAT
EST: gi|78180745|gb|DV551118.1|DV551118
EST:     TGCCAAAGGATACACTACTTTATCCTGCTCATGACTATAAAGGTTTCACG                         GTAAGTACTGTTGAAGAGGAGGCTGCCTATAATGCTCGACTCACGAAAGAT
genomic: TGCCAAAGGATACACTACTTTATCCTGCTCATGACTATAAAGGTTTCACGgtgagtttct ... gttcttgcagGTAAGTACTGTTGAAGAGGAGGCTGCCTATAATGCTCGACTCACAAAAGAT
EST: gi|93283010|gb|EB675274.1|EB675274
EST:     TGCCAAAGGATACACTACTTTATCCTGCTCATGACTATAAAGGTTTCACG                         GTAAGTACTGTTGAAGAGGAGGCTGCCTATAATGCTCGACTCACAAAAGAT
genomic: TGCCAAAGGATACACTACTTTATCCTGCTCATGACTATAAAGGTTTCACGgtgagtttct ... gttcttgcagGTAAGTACTGTTGAAGAGGAGGCTGCCTATAATGCTCGACTCACAAAAGAT
EST: gi|78106797|gb|DV525215.1|DV525215
EST:     TGCCAAAGGATACACTACTTTATCCTGCTCATGACTATAAAGGTTTCACG                         GTAAGTACTGTTGAAGAGGAGGCTGCCTATAATGCTCGACTCACAAAAGAT
genomic: TGCCAAAGGATACACTACTTTATCCTGCTCATGACTATAAAGGTTTCACGgtgagtttct ... gttcttgcagGTAAGTACTGTTGAAGAGGAGGCTGCCTATAATGCTCGACTCACAAAAGAT
EST: gi|6918329|gb|AW399859.1|AW399859
EST:     TGCCAAAGGATACACTACTTTATCCTGCTCATGACTATAAAGGTTTCACG                         GTAAGTACTGTTGAAGAGGAGGCTGCCTATAATGCTCGACTCACGAAAGAT
genomic: TGCCAAAGGATACACTACTTTATCCTGCTCATGACTATAAAGGTTTCACGgtgagtttct ... gttcttgcagGTAAGTACTGTTGAAGAGGAGGCTGCCTATAATGCTCGACTCACAAAAGAT
EST: gi|71446301|gb|DR827351.1|DR827351
EST:     TGCCAAAGGATACACTACTTTATCCTGCTCATGACTATAAAGGTTTCACG                         GTAAGTACTGTTGAAGAGGAGGCTGCCTATAATGCTCGACTCACAAAAGAT
genomic: TGCCAAAGGATACACTACTTTATCCTGCTCATGACTATAAAGGTTTCACGgtgagtttct ... gttcttgcagGTAAGTACTGTTGAAGAGGAGGCTGCCTATAATGCTCGACTCACAAAAGAT
EST: gi|78077487|gb|DV505921.1|DV505921
EST:     TGCCAAAGGATACACTACTTTATCCTGCTCATGACTATAAAGGTTTCACG                         GTAAGTACTGTTGAAGAGGAGGCGGCCTATAATGCTCGACTCACAAAAGAT
genomic: TGCCAAAGGATACACTACTTTATCCTGCTCATGACTATAAAGGTTTCACGgtgagtttct ... gttcttgcagGTAAGTACTGTTGAAGAGGAGGCTGCCTATAATGCTCGACTCACAAAAGAT
EST: gi|16917690|gb|BM073404.1|BM073404
EST:     TGCCAAAGGATACACTACTTTATCCTGCTCATGACTATAAAGGTTTCACG                         GTAAGTACTGTTGAAGAGGAGGCTGCCTATAATGCTCGACTCACAAAAGAT
genomic: TGCCAAAGGATACACTACTTTATCCTGCTCATGACTATAAAGGTTTCACGgtgagtttct ... gttcttgcagGTAAGTACTGTTGAAGAGGAGGCTGCCTATAATGCTCGACTCACAAAAGAT
EST: gi|78077488|gb|DV505922.1|DV505922
EST:     TGCCAAAGGATACACTACTTTATCCTGCTCATGACTATAAAGGTTTCACG                         GTAAGTACTGTTGAAGAGGAGGCTGCCTATAAT
genomic: TGCCAAAGGATACACTACTTTATCCTGCTCATGACTATAAAGGTTTCACGgtgagtttct ... gttcttgcagGTAAGTACTGTTGAAGAGGAGGCTGCCTATAAT
EST: gi|108953804|gb|EC364896.1|EC364896
EST:     TGCCAAAGGATACACTACTTTATCCTGCTCATGACTATAAAGGTTTCACG                         GTAAGTACTGTTGAAGAGGAGGCTGCCTATAATGCTCGACCCACCGAAAGA
genomic: TGCCAAAGGATACACTACTTTATCCTGCTCATGACTATAAAGGTTTCACGgtgagtttct ... gttcttgcagGTAAGTACTGTTGAAGAGGAGGCTGCCTATAATGCTCGACTCACA-AAAGA
EST: gi|148930115|gb|EC872441.2|EC872441
EST:     TGCCAAAGGATACACTACTTTATCCTGCTCATGACTATAAAGGTTTCACG                         GTAAGTACTGTTGAAGAGGAGGCTGCCTATAATGCT
genomic: TGCCAAAGGATACACTACTTTATCCTGCTCATGACTATAAAGGTTTCACGgtgagtttct ... gttcttgcagGTAAGTACTGTTGAAGAGGAGGCTGCCTATAATGCT
EST: gi|76911210|gb|DV164200.1|DV164200
EST:     TGCCAAAGGATACACTACTTTATCCTGCTCATGACTATAAAGGTTTCACG                         GTAAGTACTGTTGAAGAGGAGGCTGCCTATAATGCTCGACTCACAAAAGAT
genomic: TGCCAAAGGATACACTACTTTATCCTGCTCATGACTATAAAGGTTTCACGgtgagtttct ... gttcttgcagGTAAGTACTGTTGAAGAGGAGGCTGCCTATAATGCTCGACTCACAAAAGAT
EST: gi|60339336|gb|DN206309.1|DN206309
EST:     TGCCAAAGGATACACTACTTTATCCTGCTCATGACTATAAAGGTTTCACG                         GTAAGTACTGTTGAAGAGGAGGCTGCCTATAATGCTCGACTCACAAAAGAT
genomic: TGCCAAAGGATACACTACTTTATCCTGCTCATGACTATAAAGGTTTCACGgtgagtttct ... gttcttgcagGTAAGTACTGTTGAAGAGGAGGCTGCCTATAATGCTCGACTCACAAAAGAT
EST: gi|108953251|gb|EC364657.1|EC364657
EST:     TGCCAAAGGATACACTACTTTATCCTGCTCCTGACTATAAAGGTTTCACG                         GTAAGTACTGTTGAAGAGGAGGCTGCCTATAATGCTCGACTCACGAAAGAT
genomic: TGCCAAAGGATACACTACTTTATCCTGCTCATGACTATAAAGGTTTCACGgtgagtttct ... gttcttgcagGTAAGTACTGTTGAAGAGGAGGCTGCCTATAATGCTCGACTCACAAAAGAT
EST: gi|9953495|gb|BE640078.1|BE640078
EST:     TGCCAAAGGATACACTACTTTATCCTGCTCATGACTATAAAGGTTTCACG                         GTAAGTACTGTTGAAGAGGAGGCTGCCTATAATGCTCGACTCACAAAAGAT
genomic: TGCCAAAGGATACACTACTTTATCCTGCTCATGACTATAAAGGTTTCACGgtgagtttct ... gttcttgcagGTAAGTACTGTTGAAGAGGAGGCTGCCTATAATGCTCGACTCACAAAAGAT
EST: gi|91048595|gb|EB159013.1|EB159013
EST:     TGCCAAAGGATACACTACTTTATCCTGCTCATGACTATAAAGGTTTCACG                         GTAAGTACTGTTGAAGAGGAGGCTGCCTATAATGCTCGACTCACAAAAGAT
genomic: TGCCAAAGGATACACTACTTTATCCTGCTCATGACTATAAAGGTTTCACGgtgagtttct ... gttcttgcagGTAAGTACTGTTGAAGAGGAGGCTGCCTATAATGCTCGACTCACAAAAGAT
EST: gi|71446302|gb|DR827352.1|DR827352
EST:     GCCAAAGGATACACTACTTTATCCTGCTCATGACTTATAAAGGTTTCACG                         GTAAGTACTGTTTGA-GAGGAGGCTGCCTATAATGCTCG
genomic: GCCAAAGGATACACTACTTTATCCTGCTCATGACT-ATAAAGGTTTCACGgtgagtttct ... gttcttgcagGTAAGTACTGTT-GAAGAGGAGGCTGCCTATAATGCTCG
EST: gi|149098018|gb|EE183965.2|EE183965
EST:     TGCCAAAGGATACACTACTTTATCCTGCTCATGACTATAAAGGTTTCACG                         GTAAGTACTGTTGAAGAGGAGGCTGCCTATAATGCTCGACTCACAAAAGAT
genomic: TGCCAAAGGATACACTACTTTATCCTGCTCATGACTATAAAGGTTTCACGgtgagtttct ... gttcttgcagGTAAGTACTGTTGAAGAGGAGGCTGCCTATAATGCTCGACTCACAAAAGAT
EST: gi|148944080|gb|EC889165.2|EC889165
EST:     TGCCAAAGGATACACTACTTTATCCTGCTCATGACTATAAAGGTTTCACG                         GTAAGTACTGTTGAAGAGGAGGCTGCCTATAATGCTCGACTCACAAAAGAT
genomic: TGCCAAAGGATACACTACTTTATCCTGCTCATGACTATAAAGGTTTCACGgtgagtttct ... gttcttgcagGTAAGTACTGTTGAAGAGGAGGCTGCCTATAATGCTCGACTCACAAAAGAT
EST: gi|6918576|gb|AW400106.1|AW400106
EST:     TGCCAAA-GATACACTACTTTATCCTGCTCATGACTATAAAGGTTTCACG                         GTAAGTACTGTTGAAGAGGAGGCTGCCTATAATGCTCGACTCACGAAAGAT
genomic: TGCCAAAGGATACACTACTTTATCCTGCTCATGACTATAAAGGTTTCACGgtgagtttct ... gttcttgcagGTAAGTACTGTTGAAGAGGAGGCTGCCTATAATGCTCGACTCACAAAAGAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcactacttaagttcaccagccatgttagcagtcacttgatctatgttcttgcagGTAAGTACTGTTGAAGAGGAGGCTGCCTATAATGCTCGACTCACAAAAGATAAG
                                            tgttctt  CT-rich tract
       ttaagtt  TA-rich tract
















Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
cccatccaatccatgtatgtggcttaggaataatcgaacaagacctcactacttaagttcaccagccatgttagcagtcacttgatctatgttcttgcagGTAAGTACTGTTGAAGAGGAGGCTGCCTATAATGCTCGACTCACAAAAGATAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAG