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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGAACAGCAAGTCAACTTTGCATGGTCCTATTGAGGAGATAGCTTGGAAAGAAGCGGGAGAAGCTGAAACATTGCTTCATGACTTGGGAATTGCAgtacggttctatccttttaagcattatcttgtcattgttgatgttcggtatgcttcttcgtttctatttatgttccctgtgcaagactcattgatgttgt...

Basic information

species Zea mays
transcript GRMZM2G044819_T03
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G044819_T03 (Zea mays), 5'ss of exon 2
lower sequence: LOC_Os01g14810.2 (Oryza sativa), 5'ss of exon 2
---GGAACAGCAAGTCAACTTTGCATGGTCCTATTGAGGAGATAGCTTGGAAAGAAGCGGGAGAAGCTGAAACATTGCTTCATGACTTGGGAATTGCAgtacggttctatccttttaagcattatcttg--tcattgttgatgttcggta-------tgctt--cttcgtttctatttatgttccctgtgcaagactcattgatgttgt
   ||||  ||||||| || |||||||| ||||| ||||||||||||||| |||||||| ||||||||||| | ||||| | ||| |||||||||||||||   |||||  || ||| ||||||| ||   || ||||||||||| ||||       |||||   | | |||||||| || |||  |     | | ||           
GTGGGAATGGCAAGTCGACATTGCATGGCCCTATAGAGGAGATAGCTTGGCAAGAAGCGAGAGAAGCTGAATCGTTGCTCCGTGAGTTGGGAATTGCAgtaatattctactctatta-gcattattttacctccttgttgatgtttggtaattggtatgctttcttccatttctattcatattctgttaaatatattcg----------
















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|148953072|gb|EE152549.2|EE152549
EST:     GGAAAGAAGCGGGAGAAGCTGAAACATTGCTTCATGACTTGGGAATTGCA                         GACCCGTTTTCAGTAAGACACTCTCCTCGTGGAATTTTCTGCACCAGGACA
genomic: GGAAAGAAGCGGGAGAAGCTGAAACATTGCTTCATGACTTGGGAATTGCAgtacggttct ... aaaaatgcagGACCCGTTTTCAGTAAGACACTCTCCTCGTGGAATTTTCTGCACCAGGACA
EST: gi|149071776|gb|EE160171.2|EE160171
EST:     GGAAAGAAGCGGGAGAAGCTGAAACATTGCTTCATGACTTGGGAATTGCA                         GACCCGTTTTCAGTAAGACACTCTCCTCGTGGAATTTTCTGCACCAGGACA
genomic: GGAAAGAAGCGGGAGAAGCTGAAACATTGCTTCATGACTTGGGAATTGCAgtacggttct ... aaaaatgcagGACCCGTTTTCAGTAAGACACTCTCCTCGTGGAATTTTCTGCACCAGGACA
EST: gi|22935698|gb|BU571973.1|BU571973
EST:     AGCGGGAGAAGCTGAAACATTGCTTCATGACTTGGGAATTGCA                         GACCCGTTTTCAGTAAGACACTCTCCTCGNGGAATTTTCTGCACCAGGACA
genomic: AGCGGGAGAAGCTGAAACATTGCTTCATGACTTGGGAATTGCAgtacggttct ... aaaaatgcagGACCCGTTTTCAGTAAGACACTCTCCTCGTGGAATTTTCTGCACCAGGACA
EST: gi|148931443|gb|EC874416.2|EC874416
EST:     GGAAAGAAGCGGGAGAAGCTGAAACATTGCTTCATGACTTGGGAATTGCA                         GACCCGTTTTCAGTAAGACACTCTCCTCGTGGAATTTTCTGCACCAGGACA
genomic: GGAAAGAAGCGGGAGAAGCTGAAACATTGCTTCATGACTTGGGAATTGCAgtacggttct ... aaaaatgcagGACCCGTTTTCAGTAAGACACTCTCCTCGTGGAATTTTCTGCACCAGGACA
EST: gi|211437118|gb|FL188840.1|FL188840
EST:     GGAAAGAAGCGGGAGAAGCTGAAACATTGCTTCATGACTTGGGAATTGCA                         GACCCGTTTTCAGTAAGACACTCTCCTCGTGGAATTTTCTGCACCAGGACA
genomic: GGAAAGAAGCGGGAGAAGCTGAAACATTGCTTCATGACTTGGGAATTGCAgtacggttct ... aaaaatgcagGACCCGTTTTCAGTAAGACACTCTCCTCGTGGAATTTTCTGCACCAGGACA
EST: gi|211437123|gb|FL188845.1|FL188845
EST:     GGAAAGAAGCGGGAGAAGCTGAAACATTGCTTCATGACTTGGGAATTGCA                         GACCCGTTTTTCAGTA-GACACTCTCCTCGTGGAATTTTCTGCACCAAGAC
genomic: GGAAAGAAGCGGGAGAAGCTGAAACATTGCTTCATGACTTGGGAATTGCAgtacggttct ... aaaaatgcagGACCCGTTTT-CAGTAAGACACTCTCCTCGTGGAATTTTCTGCACCAGGAC
EST: gi|26559582|gb|CA831817.1|CA831817
EST:     TGAAACATTGCTTCATGACTTGGGAATTGCA                         GACCCGTTTTCAGTAAGACACTCTCCTCCG-GGAATTTTCTGCACCAGGAC
genomic: TGAAACATTGCTTCATGACTTGGGAATTGCAgtacggttct ... aaaaatgcagGACCCGTTTTCAGTAAGACACTCTCCT-CGTGGAATTTTCTGCACCAGGAC
EST: gi|71446139|gb|DR827189.1|DR827189
EST:     GGAAAGAAGCGGGAGAAGCTGAAACATTGCTTCATGACTTGGGAATTGCA                         GACCCGTTTTCAGTAAGACACTCTCCTCGTGGAATTTTCTGCACCAGGACA
genomic: GGAAAGAAGCGGGAGAAGCTGAAACATTGCTTCATGACTTGGGAATTGCAgtacggttct ... aaaaatgcagGACCCGTTTTCAGTAAGACACTCTCCTCGTGGAATTTTCTGCACCAGGACA
EST: gi|87156662|gb|DY401451.1|DY401451
EST:     AGCGGGAGAAGCTGAAACATTGCTTCATGACTTGGGAATTGCA                         GACCCGTTTTCAGTAAGACACTCTCCTCGTGGAATTTTCTGCACCAGGACA
genomic: AGCGGGAGAAGCTGAAACATTGCTTCATGACTTGGGAATTGCAgtacggttct ... aaaaatgcagGACCCGTTTTCAGTAAGACACTCTCCTCGTGGAATTTTCTGCACCAGGACA
EST: gi|211437116|gb|FL188838.1|FL188838
EST:     GGAAAGAAGCGGGAGAAGCTGAAACATTGCTTCATGACTTGGGAATTGCA                         GACCCGTTTTCAGTAAGACACTCTTCTCGTGGAATTTTCTGCACCAGGACA
genomic: GGAAAGAAGCGGGAGAAGCTGAAACATTGCTTCATGACTTGGGAATTGCAgtacggttct ... aaaaatgcagGACCCGTTTTCAGTAAGACACTCTCCTCGTGGAATTTTCTGCACCAGGACA
EST: gi|148967093|gb|EE018263.2|EE018263
EST:     GGAAAGAAGCGGGAGAAGCTGAAACATTGCTTCATGACTTGGGAATTGCA                         GACCCGTTTTCAGTAAGACACTCTCCTCGTGGAATTTTCTGCACCAGGACA
genomic: GGAAAGAAGCGGGAGAAGCTGAAACATTGCTTCATGACTTGGGAATTGCAgtacggttct ... aaaaatgcagGACCCGTTTTCAGTAAGACACTCTCCTCGTGGAATTTTCTGCACCAGGACA
EST: gi|211437120|gb|FL188842.1|FL188842
EST:     GGAAAGAAGCGGGAGAAGCTGAAACATTGCTTCATGACTTGGGAATTGCA                         GACCCGTTTTCAGTAAGACACTCTCCTCGTGGAATTTTCTGCACCAGGACA
genomic: GGAAAGAAGCGGGAGAAGCTGAAACATTGCTTCATGACTTGGGAATTGCAgtacggttct ... aaaaatgcagGACCCGTTTTCAGTAAGACACTCTCCTCGTGGAATTTTCTGCACCAGGACA
EST: gi|211437117|gb|FL188839.1|FL188839
EST:     GGAAAGAAGCGGGAGAAGCTGAAACATTGCTTCATGACTTGGGAATTGCA                         GACCCGTTTTCAGTAAGACACTCTCCTCGTGGAATTTTCTGCACCCAG-AC
genomic: GGAAAGAAGCGGGAGAAGCTGAAACATTGCTTCATGACTTGGGAATTGCAgtacggttct ... aaaaatgcagGACCCGTTTTCAGTAAGACACTCTCCTCGTGGAATTTTCTGCACC-AGGAC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGAACAGCAAGTCAACTTTGCATGGTCCTATTGAGGAGATAGCTTGGAAAGAAGCGGGAGAAGCTGAAACATTGCTTCATGACTTGGGAATTGCAgtacggttctatccttttaagcattatcttgtcattgttgatgttcggtatgcttcttcgtttctatttatgttccctgtgcaagactcattgatgttgt

- - - - - - - - - - - - - - - - - - - - - - -  AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - -  AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGA