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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GATTTCCAGAAGGACATAGTTAGAGCAGCTGAAGGTTTGGTGTCTATTGGAAACAAACATATTGAAGTGGgtatgtgcttatgtggctcatgtcagttatccttggttaattttgtcaggttgagatttcctcagaacaaaagaaagttacattgttagtttttgttgtt...

Basic information

species Zea mays
transcript GRMZM2G179459_T02
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G179459_T02 (Zea mays), 5'ss of exon 3
lower sequence: LOC_Os07g32460.1 (Oryza sativa), 5'ss of exon 3
GATTTCCAGAAGGACATAGTTAGAGCAGCTGAAGGTTTGGTGTCTATTGGAAACAAACATATTGAAGTGGgtatgtgcttatgtggctcatgtcagttatccttggttaattttgtcaggttgagatttcctcagaacaaaagaaagttacattgttagtttttgttgtt-----
|||||||| |||||||| ||| |||| |||||||||||||| |||||||||| ||  ||| |||||||||||||||| ||   || ||    ||   | |   | | | ||| ||||| |||  ||||| |          |  |  ||  ||  ||   |  ||    |     
GATTTCCAAAAGGACATTGTTCGAGCGGCTGAAGGTTTGGTTTCTATTGGAATCAGGCATGTTGAAGTGGgtatgtggtt-catgccttccatcctctgt---tagcttattatgtcatgtttggatttgcatgcttttccatcatttt-tatgcttgaatggtgggaatattaa
















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|211127070|gb|FL125800.1|FL125800
EST:     TAGAGCAGCTGAAGGTTTGGTGTCTATTGGAAACAAAVATATTGAAGTGG                         GAACAAAATTTTCTGAGGACTGCTATAGATATGGAAGCGAAAATAATGCAA
genomic: TAGAGCAGCTGAAGGTTTGGTGTCTATTGGAAACAAACATATTGAAGTGGgtatgtgctt ... ttggccatagGAACAAAATTTTCTGAGGACTGCTATAGATATGGAAGCGAAAATAATGCAA
EST: gi|149001142|gb|EE038404.2|EE038404
EST:     TAGAGCAGCTGAAGGTTTGGTGTCTATTGGAAACAAACATATTGAAGTGG                         GAACAAAATTTTCTGAGGACTGCTATAGATATGGAAGCGAAAATAATGCAA
genomic: TAGAGCAGCTGAAGGTTTGGTGTCTATTGGAAACAAACATATTGAAGTGGgtatgtgctt ... ttggccatagGAACAAAATTTTCTGAGGACTGCTATAGATATGGAAGCGAAAATAATGCAA
EST: gi|149088736|gb|EE177860.2|EE177860
EST:     TAGAGCAGCTGAAGGTTTGGTGTCTATTGGAAACAAACATATTGAAGTGG                         GAACAAAATTTTCTGAGGACTGCTATAGATATGGAAGCGAAAATAATGCAA
genomic: TAGAGCAGCTGAAGGTTTGGTGTCTATTGGAAACAAACATATTGAAGTGGgtatgtgctt ... ttggccatagGAACAAAATTTTCTGAGGACTGCTATAGATATGGAAGCGAAAATAATGCAA
EST: gi|149032717|gb|EE154943.2|EE154943
EST:     TAGAGCAGCTGAAGGTTTGGTGTCTATTGGAAACAAACATATTGAAGTGG                         GAACAAAATTTTCTGAGGACTGCTATAGATATGGAAGCGAAAATAATGCAA
genomic: TAGAGCAGCTGAAGGTTTGGTGTCTATTGGAAACAAACATATTGAAGTGGgtatgtgctt ... ttggccatagGAACAAAATTTTCTGAGGACTGCTATAGATATGGAAGCGAAAATAATGCAA
EST: gi|148996112|gb|EE035378.2|EE035378
EST:     TAGAGCAGCTGAAGGTTTGGTGTCTATTGGAAACAAACATATTGAAGTGG                         GAACAAAATTTTCTGAGGACTGCTATAGATATGGAAGCGAAAATAATGCAA
genomic: TAGAGCAGCTGAAGGTTTGGTGTCTATTGGAAACAAACATATTGAAGTGGgtatgtgctt ... ttggccatagGAACAAAATTTTCTGAGGACTGCTATAGATATGGAAGCGAAAATAATGCAA
EST: gi|211128000|gb|FL125817.1|FL125817
EST:     TAGAGCAGCTGAAGGTTTGGTGTCTATTGGAAACAAACATATTGAAGTGG                         GAACAAAATTTTCTGAGGACTGCTATAGATATGGA
genomic: TAGAGCAGCTGAAGGTTTGGTGTCTATTGGAAACAAACATATTGAAGTGGgtatgtgctt ... ttggccatagGAACAAAATTTTCTGAGGACTGCTATAGATATGGA
EST: gi|88757167|gb|DY541308.1|DY541308
EST:     TAGAGCAGCTGAAGGTTTGGTGTCTATTGGAAACAAACATATTGAAGTGG                         GAACAAAATTTTCTGAGGACTGCTATAGATATGGAAGCGAAAATAATGCAA
genomic: TAGAGCAGCTGAAGGTTTGGTGTCTATTGGAAACAAACATATTGAAGTGGgtatgtgctt ... ttggccatagGAACAAAATTTTCTGAGGACTGCTATAGATATGGAAGCGAAAATAATGCAA
EST: gi|149013869|gb|EE043354.2|EE043354
EST:     TAGAGCAGCTGAAGGTTTGGTGTCTATTGGAAACAAACATATTGAAGTGG                         GAACAAAATTTTCTGAGGACTGCTATAGATATGGAAGCGAAAATAATGCAA
genomic: TAGAGCAGCTGAAGGTTTGGTGTCTATTGGAAACAAACATATTGAAGTGGgtatgtgctt ... ttggccatagGAACAAAATTTTCTGAGGACTGCTATAGATATGGAAGCGAAAATAATGCAA
EST: gi|93014497|gb|EB640017.1|EB640017
EST:     TAGAGCAGCTGAAGGTTTGGTGTCTATTGGAAACAAACATATTGAAGTGG                         GAACAAAATTTTCTGAGGACTGCTATAGATATGGAAGCGAAAATAATGCAA
genomic: TAGAGCAGCTGAAGGTTTGGTGTCTATTGGAAACAAACATATTGAAGTGGgtatgtgctt ... ttggccatagGAACAAAATTTTCTGAGGACTGCTATAGATATGGAAGCGAAAATAATGCAA
EST: gi|211127986|gb|FL125803.1|FL125803
EST:     TAGAGCAGCTGAAGGTTTGGTGTCTATTGGAAACAAACATATTGAAGTGG                         GAACAAAATTTTCTGAGGACTGCTATAGATATGGAAGCGAAAATAATGCAA
genomic: TAGAGCAGCTGAAGGTTTGGTGTCTATTGGAAACAAACATATTGAAGTGGgtatgtgctt ... ttggccatagGAACAAAATTTTCTGAGGACTGCTATAGATATGGAAGCGAAAATAATGCAA
EST: gi|149085767|gb|EE175287.2|EE175287
EST:     TAGAGCAGCTGAAGGTTTGGTGTCTATTGGAAACAAACATATTGAAGTGG                         GAACAAAATTTTCTGAGGACTGCTATAGATATGGAAGCGAAAATAATGCAA
genomic: TAGAGCAGCTGAAGGTTTGGTGTCTATTGGAAACAAACATATTGAAGTGGgtatgtgctt ... ttggccatagGAACAAAATTTTCTGAGGACTGCTATAGATATGGAAGCGAAAATAATGCAA
EST: gi|101389748|gb|EB816808.1|EB816808
EST:     TAGAGCAGCTGAAGGTTTGGTGTCTATTGGAAACAAACATATTGAAGTGG                         GAACAAAATTTTCTGAGGACTGCTATAGATATGGAAGCGAAAATAATGCAA
genomic: TAGAGCAGCTGAAGGTTTGGTGTCTATTGGAAACAAACATATTGAAGTGGgtatgtgctt ... ttggccatagGAACAAAATTTTCTGAGGACTGCTATAGATATGGAAGCGAAAATAATGCAA
EST: gi|211127997|gb|FL125814.1|FL125814
EST:     ARAGCAGCTGAAGGTTTGGTGTCTATTGGAAACAAACATATTGAAAGTGG                         GAACAAAATTTTCTGA
genomic: AGAGCAGCTGAAGGTTTGGTGTCTATTGGAAACAAACATATTGAA-GTGGgtatgtgctt ... ttggccatagGAACAAAATTTTCTGA
EST: gi|149086994|gb|EE176539.2|EE176539
EST:     TAGAGCAGCTGAAGGTTTGGTGTCTATTGGAAACAAACATATTGAAGTGG                         GAACAAAATTTTCTGAGGACTGCTATAGATATGGAAGCGAAAATAATGCAA
genomic: TAGAGCAGCTGAAGGTTTGGTGTCTATTGGAAACAAACATATTGAAGTGGgtatgtgctt ... ttggccatagGAACAAAATTTTCTGAGGACTGCTATAGATATGGAAGCGAAAATAATGCAA
EST: gi|6564150|gb|AW231772.1|AW231772
EST:     TAGAGCAGCTGAAGGTTTGGTGTCTATTGGAAACAAACATATTGAAGTGG                         GAACAAAATTTTCTGAGGACTGCTATAGATATGGAAGCGAAAATAATGCAA
genomic: TAGAGCAGCTGAAGGTTTGGTGTCTATTGGAAACAAACATATTGAAGTGGgtatgtgctt ... ttggccatagGAACAAAATTTTCTGAGGACTGCTATAGATATGGAAGCGAAAATAATGCAA
EST: gi|148983017|gb|EE028919.2|EE028919
EST:     TAGAGCAGCTGAAGGTTTGGTGTCTATTGGAAACAAACATATTGAAGTGG                         GAACAAAATTTTCTGAGGACTGCTATAGATATGGAAGCGAAAATAATGCAA
genomic: TAGAGCAGCTGAAGGTTTGGTGTCTATTGGAAACAAACATATTGAAGTGGgtatgtgctt ... ttggccatagGAACAAAATTTTCTGAGGACTGCTATAGATATGGAAGCGAAAATAATGCAA
EST: gi|211127992|gb|FL125809.1|FL125809
EST:     TAGAGCAGCTGAAGGTTTGGTGTCTATTGGAAACAAACATATTGAAGTGG                         GAACAAAATTTTCTGAGGACTGCTATAGATATGGAAGCGAAAATAATGCAA
genomic: TAGAGCAGCTGAAGGTTTGGTGTCTATTGGAAACAAACATATTGAAGTGGgtatgtgctt ... ttggccatagGAACAAAATTTTCTGAGGACTGCTATAGATATGGAAGCGAAAATAATGCAA
EST: gi|21843563|gb|BQ704144.1|BQ704144
EST:     TAGAGCAGCTGAAGGTTTGGTGTCTATTGGAAACAAACATATTGAAGTGG                         GAACAAAATTTTCTGAGGACTGCTATAGATATGGAAGTGAAAATAATGCAA
genomic: TAGAGCAGCTGAAGGTTTGGTGTCTATTGGAAACAAACATATTGAAGTGGgtatgtgctt ... ttggccatagGAACAAAATTTTCTGAGGACTGCTATAGATATGGAAGCGAAAATAATGCAA
EST: gi|211127995|gb|FL125812.1|FL125812
EST:     TAGAGCAGCTGAAGGTTTGGTGTCTATTGGAAACAAACATATTGAAGTGG                         GAACAAAATTTTCTGAGGACTGCTATAGATATGGAAGCGAAAATAATGCAA
genomic: TAGAGCAGCTGAAGGTTTGGTGTCTATTGGAAACAAACATATTGAAGTGGgtatgtgctt ... ttggccatagGAACAAAATTTTCTGAGGACTGCTATAGATATGGAAGCGAAAATAATGCAA
EST: gi|148951274|gb|EC896976.2|EC896976
EST:     TAGAGCAGCTGAAGGTTTGGTGTCTATTGGAAACAAACATATTGAAGTGG                         GAACAAAATTTTCTGAGGACTGCTATAGATATGGAAGCGAAAATAATGCAA
genomic: TAGAGCAGCTGAAGGTTTGGTGTCTATTGGAAACAAACATATTGAAGTGGgtatgtgctt ... ttggccatagGAACAAAATTTTCTGAGGACTGCTATAGATATGGAAGCGAAAATAATGCAA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GATTTCCAGAAGGACATAGTTAGAGCAGCTGAAGGTTTGGTGTCTATTGGAAACAAACATATTGAAGTGGgtatgtgcttatgtggctcatgtcagttatccttggttaattttgtcaggttgagatttcctcagaacaaaagaaagttacattgttagtttttgttgtt

- - - - - - - - - -  AGAGCA
- - - - - - - - - - - GAGCAG
- - - - - - - - - - - - GCAGCT
- - - - - - - - - - - -  CAGCTG
- - - - - - - - - - - - - AGCTGA
- - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGAAG