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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGGCATGACATCGAGAAAAGAAGATTAAATTCACATGGTAATGTTATTGAAGCAAGAAAAGAAGGCATTGGCGGAGCAAAGgttagtggcctctgatgcagacttgatcatgtttttatgacagttgtagcaattatggtgggtgaagtgtgggtagaatttccactcttctttcaaaagt...

Basic information

species Zea mays
transcript GRMZM2G161019_T01
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G161019_T01 (Zea mays), 5'ss of exon 4
lower sequence: LOC_Os05g41120.1 (Oryza sativa), 5'ss of exon 4
AGGCATGACATCGAGAAAAGAAGATTAAATTCACATGGTAATGTTATTGAAGCAAGAAAAGAAGGCATTGGCGGAGCAAAGgttagtggcctctgatgcagacttgatcatgtttttatgacagttgtagc---aattatggtgggtgaagtgtgggtagaatttccactcttctttcaaaagt
|||||||| || || || ||  ||||| |  ||||||||||||| ||||| || ||||||||||||||||| |||||||||||| |||  | ||| |  ||      |      || |   || |  ||     | | ||     | |   ||  |   ||||| |||  |   | ||||    
AGGCATGATATAGAAAAGAGGCGATTAGACGCACATGGTAATGTCATTGAGGCTAGAAAAGAAGGCATTGGTGGAGCAAAGgttggtgatcactgctttagttacactttgaggttgagctcattaataaactaagtgattccccgcgctttgctgcgggaattaccaaacaattctcaat---
















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|71331223|gb|DR802438.1|DR802438
EST:     CACATGGTAATGTTATTGAAGCAAGAAAAGAAGGCATTGGCGGAGCAAAG                         GTCGAGAGGCCGTTGCAAAAACATGGAGGAAGGCTTGACAAAGGTGAACAA
genomic: CACATGGTAATGTTATTGAAGCAAGAAAAGAAGGCATTGGCGGAGCAAAGgttagtggcc ... ctttgtatagGTCGAGAGGCCGTTGCAAAAACATGGAGGAAGGCTTGACAAAGGTGAACAA
EST: gi|149112736|gb|EE295558.2|EE295558
EST:     CACATGGTAATGTTATTGAAGCAAGAAAAGAAGGCATTGGCGGAGCAAAG                         GTCGAGAGGCCGTTGCAAAAACATGGAGGAAGGCTTGACAAAGGTGAACAA
genomic: CACATGGTAATGTTATTGAAGCAAGAAAAGAAGGCATTGGCGGAGCAAAGgttagtggcc ... ctttgtatagGTCGAGAGGCCGTTGCAAAAACATGGAGGAAGGCTTGACAAAGGTGAACAA
EST: gi|149015010|gb|EE044754.2|EE044754
EST:     CACATGGTAATGTTATTGAAGCAAGAAAAGAAGGCATTGGCGGAGCAAAG                         GTCGAGAGGCCGTTGCAAAAACATGGAGGAAGGCTTGACAAAGGTGAACAA
genomic: CACATGGTAATGTTATTGAAGCAAGAAAAGAAGGCATTGGCGGAGCAAAGgttagtggcc ... ctttgtatagGTCGAGAGGCCGTTGCAAAAACATGGAGGAAGGCTTGACAAAGGTGAACAA
EST: gi|71772297|gb|DR970233.1|DR970233
EST:     CACATGGTAATGTTATTGAAGCAAGAAAAGAAGGCATTGGCGGAGCAAAG                         GTCGAGAGGTCGTTGCAAAAACATGGAGGAAGGCTTGACAAAGGTGAACAA
genomic: CACATGGTAATGTTATTGAAGCAAGAAAAGAAGGCATTGGCGGAGCAAAGgttagtggcc ... ctttgtatagGTCGAGAGGCCGTTGCAAAAACATGGAGGAAGGCTTGACAAAGGTGAACAA
EST: gi|149089164|gb|EE178352.2|EE178352
EST:     CACATGGTAATGTTATTGAAGCAAGAAAAGAAGGCATTGGCGGAGCAAAG                         GTCGAGAGGCCGTTGCAAAAACATGGAGGAAGGCTTGACAAAGGTGAACAA
genomic: CACATGGTAATGTTATTGAAGCAAGAAAAGAAGGCATTGGCGGAGCAAAGgttagtggcc ... ctttgtatagGTCGAGAGGCCGTTGCAAAAACATGGAGGAAGGCTTGACAAAGGTGAACAA
EST: gi|74232610|gb|DT640524.1|DT640524
EST:     CACATGGTAATGTTATTGAAGCAAGAAAAGAAGGCATTGGCGGAGCAAAG                         GTCGAGAGGCCGTTGCAAAAACATGGAGGAAGGCTTGACAAAGGTGAACAA
genomic: CACATGGTAATGTTATTGAAGCAAGAAAAGAAGGCATTGGCGGAGCAAAGgttagtggcc ... ctttgtatagGTCGAGAGGCCGTTGCAAAAACATGGAGGAAGGCTTGACAAAGGTGAACAA
EST: gi|71328273|gb|DR800766.1|DR800766
EST:     CACATGGTAATGTTATTGAAGCAAGAAAAGAAGGCATTGGCGGAGCAAAG                         GTCGAGAGGCCGTTGCAAAAACATGGAGGAAGGCTTGACAAAGGTGAACAA
genomic: CACATGGTAATGTTATTGAAGCAAGAAAAGAAGGCATTGGCGGAGCAAAGgttagtggcc ... ctttgtatagGTCGAGAGGCCGTTGCAAAAACATGGAGGAAGGCTTGACAAAGGTGAACAA
EST: gi|149104647|gb|EE290096.2|EE290096
EST:     CACATGGTAATGTTATTGAAGCAAGAAAAGACTGCATTGGCGGAGCACAG                         GTCGAGAGGCCGTTGCAAAAACATGGAGGAAGGCTTGACAAAGGTGAACAA
genomic: CACATGGTAATGTTATTGAAGCAAGAAAAGAAGGCATTGGCGGAGCAAAGgttagtggcc ... ctttgtatagGTCGAGAGGCCGTTGCAAAAACATGGAGGAAGGCTTGACAAAGGTGAACAA
EST: gi|148948260|gb|EC893776.2|EC893776
EST:     CACATGGTAATGTTATTGAAGCAAGAAAAGAAGGCATTGGCGGAGCAAAG                         GTCGAGAGGCCGTTGCAAAAACATGGAGGAAGGCTTGACAAAGGTGAACAA
genomic: CACATGGTAATGTTATTGAAGCAAGAAAAGAAGGCATTGGCGGAGCAAAGgttagtggcc ... ctttgtatagGTCGAGAGGCCGTTGCAAAAACATGGAGGAAGGCTTGACAAAGGTGAACAA
EST: gi|149071871|gb|EE160258.2|EE160258
EST:     CACATGGTAATGTTATTGAAGCAAGAAAAGAAGGCATTGGCGGAGCAAAG                         GTCGAGAGGCCGTTGCAAAAACATGGAGGAAGGCTTGACAAAGGTGAACAA
genomic: CACATGGTAATGTTATTGAAGCAAGAAAAGAAGGCATTGGCGGAGCAAAGgttagtggcc ... ctttgtatagGTCGAGAGGCCGTTGCAAAAACATGGAGGAAGGCTTGACAAAGGTGAACAA
EST: gi|86465733|gb|DY232106.1|DY232106
EST:     CACATGGTAATGTTATTGAAGCAAGAAAAGAAGGTATTGGCGGAGCAAAG                         GTCGAGAGGCCGTTGCAAAAACATGGAGGAAGGCTTGACAAAGGAGAACAA
genomic: CACATGGTAATGTTATTGAAGCAAGAAAAGAAGGCATTGGCGGAGCAAAGgttagtggcc ... ctttgtatagGTCGAGAGGCCGTTGCAAAAACATGGAGGAAGGCTTGACAAAGGTGAACAA
EST: gi|74242178|gb|DT650092.1|DT650092
EST:     CACATGGTAATGTTATTGAAGCAAGAAAAGAAGGCATTGGCGGAGCAAAG                         GTCGAGAGGCCGTTGCAAAAACATGGAGGAAGGCTTGACAAAGGTGAACAA
genomic: CACATGGTAATGTTATTGAAGCAAGAAAAGAAGGCATTGGCGGAGCAAAGgttagtggcc ... ctttgtatagGTCGAGAGGCCGTTGCAAAAACATGGAGGAAGGCTTGACAAAGGTGAACAA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AGGCATGACATCGAGAAAAGAAGATTAAATTCACATGGTAATGTTATTGAAGCAAGAAAAGAAGGCATTGGCGGAGCAAAGgttagtggcctctgatgcagacttgatcatgtttttatgacagttgtagcaattatggtgggtgaagtgtgggtagaatttccactcttctttcaaaagt

- - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - -  TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - -  AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - -  GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAAG