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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGTTTGCTACTCGTGGTGGGTGCTATCGAGCCTAGTCATGATTGACAGAGTGCATTGGATTGACAAGGAAAAGCTAACGAAATTCATACTGAACTGTCAGgtaactgttctattattcccaccactgccatttgcgtaacccgtatgtcccttgacttataacaagtactggttccaactcttctcattcatgttgatcggcag

Basic information

species Zea mays
transcript GRMZM2G124557_T04
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G124557_T04 (Zea mays), 5'ss of exon 5
lower sequence: LOC_Os08g40140.1 (Oryza sativa), 5'ss of exon 7
GGTTTGCTACTCGTGGTGGGTGCTATCGAGCCTAGTCATGATTGACAGAGTGCATTGGATTGACAAGGAAAAGCTAACGAAATTCATACTGAACTGTCAGgtaactgttctattattcccaccactgccatttgcgtaacccgtatgtcccttgacttataacaagta-------ctggttccaactcttctcattcatgttgatcggcag---------------------
 || |||||||| ||||||||||| || ||| |  | |||||||| |||||||| |||||||||||||| || ||  | ||||||||||| || || ||||||| || |  |  | ||   |  |||   |||| ||||||  | ||||| || |   |  | || ||       |  ||||| | ||||  |||| |  ||  |                           
-GTGTGCTACTCCTGGTGGGTGCTCTCAAGCTTGATAATGATTGATAGAGTGCACTGGATTGACAAGGACAAACTTGCAAAATTCATACTAAATTGCCAGgtaaatgcttga--aatcttgcatctgatttttgtgtaacc-atgtgtccattaatcaaataaaaatatctgtctcctgttcccagtctttccatttacattttttaaatatataatcttgttcattggtag

upper sequence: GRMZM2G124557_T04 (Zea mays), 5'ss of exon 5
lower sequence: AT5G12210.2 (Arabidopsis thaliana), 5'ss of exon 8
GGTTTGCTACTCGTGGTGGGTGCTATCGAGCCTAGTCATGATTGACAGAGTGCATTGGATTGACAAGGAAAAGCTAACGAAATTCATACTGAACTGTCAGgtaactgttctattattcccaccactgccatttgcgtaacccgtatgtcccttgacttataacaagtactggttccaactcttctcattcatgttgatcggcag
 |||||||| || |||||||| |||||||||||| ||||||| || ||||| || ||||| ||||| | ||||||    || ||||| ||| ||||||||||   | | | |      | |  |    ||| | ||| ||   || | |  ||   | ||   |||  ||  |  || || |    |||    ||  |    ||
-GTTTGCTATTCTTGGTGGGTCCTATCGAGCCTAATCATGATAGATAGAGTTCACTGGATCGACAAAGCAAAGCTTGTCAAGTTCATTCTGGACTGTCAGgttcgtctccaa------caagaaaattcatat-cgttactaataagccagtt--ttgattgaaagctctcatctcatctatctaaatttgaatt--tgaatag

upper sequence: GRMZM2G124557_T04 (Zea mays), 5'ss of exon 5
lower sequence: Vv12s0134g00150.t01 (Vitis vinifera), 5'ss of exon 8
GGTTTGCTACTCGTGGTGGGTGCTATCGAGCCTAGTCATGATTGACAGAGTGCATTGGATTGACAAGGAAAAGCTAACGAAATTCATACTGAACTGTCAGgtaactgttctattattcccaccactgccatttgcgtaacccgtatgtcccttgacttataacaagtactggttccaactcttctcattcatgttgatcggcag---------------------------------------
 || || ||||| ||||||||||| || ||| |  |||||||||||||||  ||||||||||||||||| ||||| |  ||||| ||| |  ||||||||||  | ||||||  | |      ||||  | ||   |      ||  | | | ||   |     | |  ||   |  ||   |||  | | | || ||   ||                                        
-GTCTGTTACTCATGGTGGGTGCTTTCAAGCTTGATCATGATTGACAGAGCTCATTGGATTGACAAGGATAAGCTCATTAAATTTATAATAGACTGTCAGgt--cagttctaa-actaaatgaactgttacttagtttcagtttaatttcatagaaaaacctagaattttgcaccttacctctctgctgctttttcatttacaaggtaaatatgatcctcagttattggctgaaaaattgcag

upper sequence: GRMZM2G124557_T04 (Zea mays), 5'ss of exon 5
lower sequence: Vv15s0024g00080.t01 (Vitis vinifera), 5'ss of exon 8
GGTTTGCTACTCGTGGTGGGTGCTATCGAGCCTAGTCATGATTGACAGAGTGCATTGGATTGACAAGGAAAAGCTAACGAAATTCATACTGAACTGTCAGgtaactgttctattattcccaccactgcc---atttgcgtaacccgtatgtc--ccttgacttataacaagtactggttccaactcttctcattcatgttgatcggcag----------------
 || || ||||| |||||||||||||| |||||  |||||||||||||||  ||||||||||||||||||||||| |  ||||||||  |  | |||||||| | |  |  | ||      |   |      |||    ||||    |       | |  |   ||   ||   | |||  ||||        |  |    ||   |||                
-GTCTGTTACTCATGGTGGGTGCTATCAAGCCTGATCATGATTGACAGAGCTCATTGGATTGACAAGGAAAAGCTCATTAAATTCATCTTAGATTGTCAGgtcagttctaaactaagtgagctgttatttagattcagataacttacacagaaatcctagcccttatttagatttagttt-aacttaaaaaggtggttaaaattctcagtttgtggaaaatgcag

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|211265935|gb|FL477027.1|FL477027
EST:     CAAGGAAAAGCTAACGAAATTCATACTGAACTGTCAG                         GACAAAGAGAACGGCGGCATTTCAGATAGGCCAGATAATGCAGTCGATATC
genomic: CAAGGAAAAGCTAACGAAATTCATACTGAACTGTCAGgtaactgttc ... tgatcggcagGACAAAGAGAACGGCGGCATTTCAGATAGACCAGATAATGCAGTCGATATC
EST: gi|166429214|gb|EG289960.1|EG289960
EST:     TGCATTGGATTGACAAGGAAAAGCTAACGAAATTCATACTGAACTGTCAG                         GACAAAGAGAACGGCGGCATTTCAGATAGACC
genomic: TGCATTGGATTGACAAGGAAAAGCTAACGAAATTCATACTGAACTGTCAGgtaactgttc ... tgatcggcagGACAAAGAGAACGGCGGCATTTCAGATAGACC
EST: gi|71443998|gb|DR825048.1|DR825048
EST:     TGCATTGGATTGACAAGGAAAAGCTAACGAAATTCATACTGAACTGTCAG                         GACAAAGAGAACGGCGGCATTTCAGATAGACCAGATAATGCAGTCGATATC
genomic: TGCATTGGATTGACAAGGAAAAGCTAACGAAATTCATACTGAACTGTCAGgtaactgttc ... tgatcggcagGACAAAGAGAACGGCGGCATTTCAGATAGACCAGATAATGCAGTCGATATC
EST: gi|166573818|gb|EG319919.1|EG319919
EST:     GCATTGGATTGACAAGGAAAAGCTAACGAAATTACATACTGAACTGTCAG                         GACAAAGAGAACGGCGGCATTTCAGATAGACCAGATAA
genomic: GCATTGGATTGACAAGGAAAAGCTAACGAAATT-CATACTGAACTGTCAGgtaactgttc ... tgatcggcagGACAAAGAGAACGGCGGCATTTCAGATAGACCAGATAA
EST: gi|89250321|gb|DY622107.1|DY622107
EST:     TGCATTGGATTGACAAGGAAAAGCTAACGAAATTCATACTGAACTGTCAG                         GACAAAGAGAACGGCGGCATTTCAGATAGACCAGATAATGCAGTCGATATC
genomic: TGCATTGGATTGACAAGGAAAAGCTAACGAAATTCATACTGAACTGTCAGgtaactgttc ... tgatcggcagGACAAAGAGAACGGCGGCATTTCAGATAGACCAGATAATGCAGTCGATATC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGTTTGCTACTCGTGGTGGGTGCTATCGAGCCTAGTCATGATTGACAGAGTGCATTGGATTGACAAGGAAAAGCTAACGAAATTCATACTGAACTGTCAGgtaactgttctattattcccaccactgccatttgcgtaacccgtatgtcccttgacttataacaagtactggttccaactcttctcattcatgttgatcggcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA