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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGATGTGAGAAACAAGGAGGACGTTGTGTTGAGGATGAGATCCGCTGTCGCGAGCAAGCAGTTTGGTCAGGAGGATATAATGTGCCCTCTTGTGGCTGATgtaagctaatccatatcagcttatagggagaattttcttttttaaccagtccgctctatattccagagtggaaaaataaaaaaattcagaaacaagtaaa...

Basic information

species Zea mays
transcript GRMZM2G083095_T03
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G083095_T03 (Zea mays), 5'ss of exon 3
lower sequence: LOC_Os03g59020.1 (Oryza sativa), 5'ss of exon 3
GGATGTGAGAAACAAGGAGGACGTTGTGTTGAGGATGAGATCCGCTGTCGCGAGCAAGCAGTTTGGTCAGGAGGATATAATGTGCCCTCTTGTGGCTGATgtaagctaatccatatcagcttata--gggagaattttcttttttaaccagtccgctcta-tattccagagtggaaaaataaaaaaattcagaaacaagtaaa
||||||||| ||||||||||| |||||||||  ||||||||| || || ||||||||||| || ||||||||||||||| |||||||||||||||||||||||||  ||| | || || |||||    |  | |  |  ||| ||||| | |     ||  | ||  |   ||||     |                      
GGATGTGAGGAACAAGGAGGAGGTTGTGTTGCTGATGAGATCTGCAGTTGCGAGCAAGCAATTCGGTCAGGAGGATATATTGTGCCCTCTTGTGGCTGATgtaagacaattcttaccatcttatgtgagagggagctcatttcttaacaactaatagctggttttttaccatggattttcag---------------------
















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|211339975|gb|FL217825.1|FL217825
EST:     CGAGCAAGCAGTTTGGTCAGGAGGATATAATGTGCCCTCTTGTGGCTGAT                         GCCTGCATTCAAGTTTGCCCCAAAAATCCAGCAAACTTCAATGTCGACAAT
genomic: CGAGCAAGCAGTTTGGTCAGGAGGATATAATGTGCCCTCTTGTGGCTGATgtaagctaat ... cgatttttagGCCTGCATTCAAGTTTGCCCCAAAAATCCAGCAAACTTCAATGTCGACAAT
EST: gi|211512561|gb|FL110022.1|FL110022
EST:     CGAGCAAGCAGTTTGGTCAGGAGGATATAATGTGCCCTCTTGTGGCTGAT                         GCCTGCATTCAAGTTTGCCCCAAAAATCCAGCAAACTTCAATGTCGACAAT
genomic: CGAGCAAGCAGTTTGGTCAGGAGGATATAATGTGCCCTCTTGTGGCTGATgtaagctaat ... cgatttttagGCCTGCATTCAAGTTTGCCCCAAAAATCCAGCAAACTTCAATGTCGACAAT
EST: gi|148995430|gb|EE034628.2|EE034628
EST:     CGAGCAAGCAGTTTGGTCAGGAGGATATAATGTGCCCTCTTGTGGCTGAT                         GCCTGCATTCAAGTTTGCCCCAAAAATCCAGCAAACTTCAATGTCGACAAT
genomic: CGAGCAAGCAGTTTGGTCAGGAGGATATAATGTGCCCTCTTGTGGCTGATgtaagctaat ... cgatttttagGCCTGCATTCAAGTTTGCCCCAAAAATCCAGCAAACTTCAATGTCGACAAT
EST: gi|60358557|gb|DN225530.1|DN225530
EST:     CGAGCAAGCAGTTTGGTCAGGAGGATATAATGTGCCCTCTTGTGGCTGAT                         GCCTGCATTCAAGTTTGCCCCAAAAATCCAGCAAACTTCAATGTCGACAAT
genomic: CGAGCAAGCAGTTTGGTCAGGAGGATATAATGTGCCCTCTTGTGGCTGATgtaagctaat ... cgatttttagGCCTGCATTCAAGTTTGCCCCAAAAATCCAGCAAACTTCAATGTCGACAAT
EST: gi|71431587|gb|DR812637.1|DR812637
EST:     CGAGCAAGCAGTTTGGTCAGGAGGATATAATGTGCCCTCTTGTGGCTGAT                         GCCTGCATTNCA-GTTTGCCCCAAAAATCC
genomic: CGAGCAAGCAGTTTGGTCAGGAGGATATAATGTGCCCTCTTGTGGCTGATgtaagctaat ... cgatttttagGCCTGCATT-CAAGTTTGCCCCAAAAATCC
EST: gi|211342365|gb|FL217838.1|FL217838
EST:     CGAGCAAGCAGTTTGGTCAGGAGGATATAATGTGCCCTCTTGTGGCTGAT                         GCCTGCATTNCA-GTTTGCCCCAAAAATCC
genomic: CGAGCAAGCAGTTTGGTCAGGAGGATATAATGTGCCCTCTTGTGGCTGATgtaagctaat ... cgatttttagGCCTGCATT-CAAGTTTGCCCCAAAAATCC
EST: gi|148987524|gb|EE031386.2|EE031386
EST:     CGAGCAAGCAGTTTGGTCAGGAGGATATAATGTGCCCTCTTGTGGCTGAT                         GCCTGCATTCAAGTTTGCCCCAAAAATCCAGCAAACTTCAATGTCGACAAT
genomic: CGAGCAAGCAGTTTGGTCAGGAGGATATAATGTGCCCTCTTGTGGCTGATgtaagctaat ... cgatttttagGCCTGCATTCAAGTTTGCCCCAAAAATCCAGCAAACTTCAATGTCGACAAT
EST: gi|211339983|gb|FL217833.1|FL217833
EST:     CGAGCAAGCAGTTTGGTCAGGAGGATATAATGTGCCCTCTTGTGGCTGAT                         GCCTGCATTCAAGTTTGCCCCCAAAAATCCAGCAAACTTCAATGTCGACAA
genomic: CGAGCAAGCAGTTTGGTCAGGAGGATATAATGTGCCCTCTTGTGGCTGATgtaagctaat ... cgatttttagGCCTGCATTCAAGTTTGCCCC-AAAAATCCAGCAAACTTCAATGTCGACAA
EST: gi|22715295|gb|BU197687.1|BU197687
EST:     CGAGCAAGCAGTTTGGTCAGGAGGATATAATGTGCCCTCTTGTGGCTGAT                         GCCTGCATTCAAGTTTGCCCCAAAAATCCAGCAAACTTCAATGTCGACAAT
genomic: CGAGCAAGCAGTTTGGTCAGGAGGATATAATGTGCCCTCTTGTGGCTGATgtaagctaat ... cgatttttagGCCTGCATTCAAGTTTGCCCCAAAAATCCAGCAAACTTCAATGTCGACAAT
EST: gi|87157134|gb|DY401923.1|DY401923
EST:     CGAGCAAGCAGTTTGGTCAGGAGGATATAATGTGCCCTCTTGTGGCTGAT                         GCCTGCATTCAAGTTTGCCCCAAAAATCCAGCAAACTTCAATGTCGACAAT
genomic: CGAGCAAGCAGTTTGGTCAGGAGGATATAATGTGCCCTCTTGTGGCTGATgtaagctaat ... cgatttttagGCCTGCATTCAAGTTTGCCCCAAAAATCCAGCAAACTTCAATGTCGACAAT
EST: gi|148932523|gb|EC876316.2|EC876316
EST:     CGAGCAAGCAGTTTGGTCAGGAGGATATAATGTGCCCTCTTGTGGCTGAT                         GCCTGCATTCAAGTTTGCCCCAAAAATCCAGCAAACTTCAATGTCGANCA-
genomic: CGAGCAAGCAGTTTGGTCAGGAGGATATAATGTGCCCTCTTGTGGCTGATgtaagctaat ... cgatttttagGCCTGCATTCAAGTTTGCCCCAAAAATCCAGCAAACTTCAATGTCGA-CAA
EST: gi|211342367|gb|FL217840.1|FL217840
EST:     CGAGCAAGCAGTTTGGTCAGGAGGATATAATGTGCCCTCTTGTGGCTGAT                         GCCTGCATTCAAGTTTGCCCCAAAAATCCAGCAAACTTCAATGGTCGACA
genomic: CGAGCAAGCAGTTTGGTCAGGAGGATATAATGTGCCCTCTTGTGGCTGATgtaagctaat ... cgatttttagGCCTGCATTCAAGTTTGCCCCAAAAATCCAGCAAACTTCAATG-TCGACA
EST: gi|21760124|gb|BQ635665.1|BQ635665
EST:     CGAGCAAGCAGTTTGGTCAGGAGGATATAATGTGCCCTCTTGTGGCTGAT                         GCCTGCATTCAAGTTTGCCCCAAAAATCCAGCAAACTTCAATGTCGACAAT
genomic: CGAGCAAGCAGTTTGGTCAGGAGGATATAATGTGCCCTCTTGTGGCTGATgtaagctaat ... cgatttttagGCCTGCATTCAAGTTTGCCCCAAAAATCCAGCAAACTTCAATGTCGACAAT
EST: gi|211339978|gb|FL217828.1|FL217828
EST:     GCAAGCAGTTTTGGTCAGGAGGGATATAATGTGCCCTCTTTGTGGCTGAT                         GCTTGCATTTCAAGTTTGCCCCCAAAAATCCAGCAAACCTTCAAGGTCGA
genomic: GCAAGCAGTTT-GGTCAGGAGG-ATATAATGTGCCCTCTT-GTGGCTGATgtaagctaat ... cgatttttagGCCTGCATT-CAAGTTTGCCCC-AAAAATCCAGCAAAC-TTCAATGTCGA
EST: gi|26559613|gb|CA831848.1|CA831848
EST:     CGAGCAAGCAGTTTGGTCAGGAGGATATAATGTGCCCTCTTGTGGCTGAT                         GCCTGCATTCAAGTTTGCCCCAAAAATCCAGCAAACTTCAATGTCGACAAT
genomic: CGAGCAAGCAGTTTGGTCAGGAGGATATAATGTGCCCTCTTGTGGCTGATgtaagctaat ... cgatttttagGCCTGCATTCAAGTTTGCCCCAAAAATCCAGCAAACTTCAATGTCGACAAT
EST: gi|211342363|gb|FL217836.1|FL217836
EST:     CGAGCAAGCAGTTTGGTCAGGAGGATATAATGTGCCCTCTTGTGGCTGAT                         GCCTGCATTCAAGTTTGCCCCAAAAATCCAGCAAACTTCAATGTCGACAAT
genomic: CGAGCAAGCAGTTTGGTCAGGAGGATATAATGTGCCCTCTTGTGGCTGATgtaagctaat ... cgatttttagGCCTGCATTCAAGTTTGCCCCAAAAATCCAGCAAACTTCAATGTCGACAAT
EST: gi|22935567|gb|BU571842.1|BU571842
EST:     CGAGCAAGCAGTTTGGTCAGGAGGATATAATGTGCCCTCTTGTGGCTGAT                         GCCTGCATTCAAGTTTGCCCCAAAAATCCAGCAAACTTCAATGTCGACAAT
genomic: CGAGCAAGCAGTTTGGTCAGGAGGATATAATGTGCCCTCTTGTGGCTGATgtaagctaat ... cgatttttagGCCTGCATTCAAGTTTGCCCCAAAAATCCAGCAAACTTCAATGTCGACAAT
EST: gi|149015148|gb|EE044917.2|EE044917
EST:     CGAGCAAGCAGTTTGGTCAGGAGGATATAATGTGCCCTCTTGTGGCTGAT                         GCCTGCATTCAAGTTTGCCCCAAAAATCCAGCAAACTTNCA-TGTCGACAA
genomic: CGAGCAAGCAGTTTGGTCAGGAGGATATAATGTGCCCTCTTGTGGCTGATgtaagctaat ... cgatttttagGCCTGCATTCAAGTTTGCCCCAAAAATCCAGCAAACTT-CAATGTCGACAA
EST: gi|211512562|gb|FL110023.1|FL110023
EST:     CGAGCAAGCAGTTTGGTCAGGAGGATATAATGTGCCCTCTTGTGGCTGAT                         GCCTGCATTCAAGTTTGCCCCAAAAATCCAGCAAACTTCAATGTCGACAAT
genomic: CGAGCAAGCAGTTTGGTCAGGAGGATATAATGTGCCCTCTTGTGGCTGATgtaagctaat ... cgatttttagGCCTGCATTCAAGTTTGCCCCAAAAATCCAGCAAACTTCAATGTCGACAAT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGATGTGAGAAACAAGGAGGACGTTGTGTTGAGGATGAGATCCGCTGTCGCGAGCAAGCAGTTTGGTCAGGAGGATATAATGTGCCCTCTTGTGGCTGATgtaagctaatccatatcagcttatagggagaattttcttttttaaccagtccgctctatattccagagtggaaaaataaaaaaattcagaaacaagtaaa

- - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ggaaaaat
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aaaaaaat
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -agaaacaa