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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagaggatcataattgttggcattgttagattcattgcttacttgttttgttaaataaagatgcatgtgcaaggtacaatacagactgtgaaagtcgttggagctcttgttttgtgtatcatggcgcttttggtgaaaccccactaggcgattaattctctgtatttgcaccttccctcctagATTGCTGTGATGGGAGTGATGAATATGACAGCAATATCACCTGTAAGAACACTTGCTGGGAGGCTGGCAAAGCGGCAAGGGAGAAATTGAAGAAGAAAGT

Basic information

species Zea mays
transcript GRMZM2G052875_T01
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G052875_T01 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os01g16970.1 (Oryza sativa), 3'ss of exon 3
gtaagaggatcataattgttggcattgttagattcattgcttacttgttttgttaaataaagatgcatgtgcaaggtacaatacagactgtgaaagtcgttggagctcttgttttgtgtatcatggcgcttttggtgaaaccccactaggcgatt----aattctctgtatttgcacct---tccctcctagATTGCTGTGATGGGAGTGATGAATATGACAGCAATATCACCTGTAAGAACACTTGCTGGGAGGCTGGCAAAGCGGCAAGGGAGAAATTGAAGAAGAAAGT
|||||||||| ||||| | ||||        ||||  ||  |  ||    ||| ||   |  |    |   |||  |  | |  |      || | | |  || ||| |||||  ||  | ||| | ||||  || |||  ||| |||     ||    ||||  |  ||| ||    |   | |||| |||||||||| || ||||||||||| ||||| |||||| |||| || ||||| || |||||||||||||| |||||||||||||| ||||||||||| |||||
gtaagaggattataatcggtggcc-------attctctgtatcattcaaatgtaaacacagtaaatgtacacaaaatcaattgtaaggctagagattag--ggtgcttttgttccgtaaa-catagtgcttgagg-gaattcccgctatatttttttctaattacccatatgtgtttgtcgctgcctcttagATTGCTGCGACGGGAGTGATGAGTATGATAGCAATGTCACTTGCAAGAATACGTGCTGGGAGGCTGGTAAAGCGGCAAGGGATAAATTGAAGAAAAAAGT
















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|87153726|gb|DY398515.1|DY398515
EST:     CCACACTCCAGTCACGATCTTCTCATCACGAGTGAATGACGGCATTTGTG                         ATTGCTGTGATGGGAGTGATGAATATGACAGCAATATCACCTGTAAGAACA
genomic: CCACACTCCAGTCACGATCTTCTCATCACGAGTGAATGACGGCATTTGTGgtaagaggat ... tccctcctagATTGCTGTGATGGGAGTGATGAATATGACAGCAATATCACCTGTAAGAACA
EST: gi|211215768|gb|FL437214.1|FL437214
EST:     CCACACTCCAGTCACGATCTTCTCATCACGAGTGAATGATGGCATTTGTG                         ATTGCTGTGATGGGAGTGATGAATATGACAGCAATATCACCTGTAAGAACA
genomic: CCACACTCCAGTCACGATCTTCTCATCACGAGTGAATGACGGCATTTGTGgtaagaggat ... tccctcctagATTGCTGTGATGGGAGTGATGAATATGACAGCAATATCACCTGTAAGAACA
EST: gi|22490637|gb|BU050560.1|BU050560
EST:     CCACACTCCAGTCACGATCTTCTCATCACGAGTGAATGACGGCATTTGTG                         ATTGCTGTGATGGGAGTGATGAATATGACAGCAATATCACCTGTAAGAACA
genomic: CCACACTCCAGTCACGATCTTCTCATCACGAGTGAATGACGGCATTTGTGgtaagaggat ... tccctcctagATTGCTGTGATGGGAGTGATGAATATGACAGCAATATCACCTGTAAGAACA
EST: gi|211322390|gb|FL223767.1|FL223767
EST:     CCACACTCCAGTCACGATCTTCTCATCACGAGTGAATGACGGCATTTGTG                         ATTGCTGTGATGGGAGTGATGAATATGACAGCAATATCACCTGTAAGAACA
genomic: CCACACTCCAGTCACGATCTTCTCATCACGAGTGAATGACGGCATTTGTGgtaagaggat ... tccctcctagATTGCTGTGATGGGAGTGATGAATATGACAGCAATATCACCTGTAAGAACA
EST: gi|19057817|gb|BM736484.1|BM736484
EST:     CCACACTCCAGTCACGATCTTCTCATCACGAGTGAATGACGGCATTTGTG                         ATTGCTGTGATGGGAGTGATGAATATGACAGCAATATCACCTGTAAGAACA
genomic: CCACACTCCAGTCACGATCTTCTCATCACGAGTGAATGACGGCATTTGTGgtaagaggat ... tccctcctagATTGCTGTGATGGGAGTGATGAATATGACAGCAATATCACCTGTAAGAACA
EST: gi|31612130|gb|CD568752.1|CD568752
EST:     CCACACTCCAGTCACGATCTTCTCATCACGAGTGAATGACGGCATTTGTG                         ATTGCTGTGATGGGAGTGATGAATATGACAGCAATATCACCTGTAAGAACA
genomic: CCACACTCCAGTCACGATCTTCTCATCACGAGTGAATGACGGCATTTGTGgtaagaggat ... tccctcctagATTGCTGTGATGGGAGTGATGAATATGACAGCAATATCACCTGTAAGAACA
EST: gi|19058293|gb|BM736960.1|BM736960
EST:     CCACACTCCAGTCACGATCTTCTCATCACGAGTGAATGCCGGCATTTGTG                         ATTGCTGTGATGGGAGTGATGAATATGCCAGCAATATCACCTGTAAGAACA
genomic: CCACACTCCAGTCACGATCTTCTCATCACGAGTGAATGACGGCATTTGTGgtaagaggat ... tccctcctagATTGCTGTGATGGGAGTGATGAATATGACAGCAATATCACCTGTAAGAACA
EST: gi|211320224|gb|FL223759.1|FL223759
EST:     CCACACTCCAGTCACGATCTTCTCATCACGAGTGAATGACGGGATTTGTG                         ATTGCTGTGATGGGAGNGATGAATATGACAGCAATATCACCTGTAAGAACA
genomic: CCACACTCCAGTCACGATCTTCTCATCACGAGTGAATGACGGCATTTGTGgtaagaggat ... tccctcctagATTGCTGTGATGGGAGTGATGAATATGACAGCAATATCACCTGTAAGAACA
EST: gi|211322386|gb|FL223763.1|FL223763
EST:     CCACACTCCAGTCACGATCTTCTCATCACGAGTGAATGACGGCATTTGTG                         ATTGCTGTGATGGGAGTGATGAATATGACAGCAATATCACCTGTAAGAACA
genomic: CCACACTCCAGTCACGATCTTCTCATCACGAGTGAATGACGGCATTTGTGgtaagaggat ... tccctcctagATTGCTGTGATGGGAGTGATGAATATGACAGCAATATCACCTGTAAGAACA
EST: gi|211457195|gb|FL323091.1|FL323091
EST:     CCACACTCCAGTCACGATCTTCTCATCACGAGTGAATGATGGCATTTGTG                         ATTGCTGTGATGGGAGTGATGAATATGACAGCAATATCACCTGTAAGAACA
genomic: CCACACTCCAGTCACGATCTTCTCATCACGAGTGAATGACGGCATTTGTGgtaagaggat ... tccctcctagATTGCTGTGATGGGAGTGATGAATATGACAGCAATATCACCTGTAAGAACA
EST: gi|211322388|gb|FL223765.1|FL223765
EST:     CCACACTCCAGTCACGATCTTCTCATCACGAGTGAATGACGGCATTTGTG                         ATTGCTGTGATGGGAGTGATGAATATGACAGCAATATCACCTGTAAGAACA
genomic: CCACACTCCAGTCACGATCTTCTCATCACGAGTGAATGACGGCATTTGTGgtaagaggat ... tccctcctagATTGCTGTGATGGGAGTGATGAATATGACAGCAATATCACCTGTAAGAACA
EST: gi|211322389|gb|FL223766.1|FL223766
EST:     CCACACTCCAGTCACGATCTTCTCATCACGAGTGAATGACGGCATTTGTG                         ATTGCTGTGATGGGAGTGATGAATATGACAGCAATATCACCTGTAAGAACA
genomic: CCACACTCCAGTCACGATCTTCTCATCACGAGTGAATGACGGCATTTGTGgtaagaggat ... tccctcctagATTGCTGTGATGGGAGTGATGAATATGACAGCAATATCACCTGTAAGAACA
EST: gi|32847353|gb|CD987034.1|CD987034
EST:     CCACACTCCAGTCACGATCTTCTCATCACGAGTGAATGACGGCATTTGTG                         ATTGCTGTGATGGGAGTGATGAATATGACAGCAATATCACCTGTAAGAACA
genomic: CCACACTCCAGTCACGATCTTCTCATCACGAGTGAATGACGGCATTTGTGgtaagaggat ... tccctcctagATTGCTGTGATGGGAGTGATGAATATGACAGCAATATCACCTGTAAGAACA
EST: gi|211320227|gb|FL223762.1|FL223762
EST:     CCACACTCCAGTCACGATCTTCTCATCACGAGTGAATGACGGCATTTGTG                         ATTGCTGTGATGGGAG
genomic: CCACACTCCAGTCACGATCTTCTCATCACGAGTGAATGACGGCATTTGTGgtaagaggat ... tccctcctagATTGCTGTGATGGGAG
EST: gi|211320225|gb|FL223760.1|FL223760
EST:     CCACACTCCAGTCACGATCTTCTCATCACGAGTGAATGACGGCATTTGTG                         ATTGCTGTGATGGGAGTGATGAATATGACAGCAATATCACCTGTAAGAACA
genomic: CCACACTCCAGTCACGATCTTCTCATCACGAGTGAATGACGGCATTTGTGgtaagaggat ... tccctcctagATTGCTGTGATGGGAGTGATGAATATGACAGCAATATCACCTGTAAGAACA
EST: gi|211320223|gb|FL223758.1|FL223758
EST:     CCACACTCCAGTCACGATCTTCTCATCACGAGTGAAAGACGGCATTTGTG                         ATTGCTGTGATGGGAGTGATGAATATGACAGCAATATCACCTGTAAGAACA
genomic: CCACACTCCAGTCACGATCTTCTCATCACGAGTGAATGACGGCATTTGTGgtaagaggat ... tccctcctagATTGCTGTGATGGGAGTGATGAATATGACAGCAATATCACCTGTAAGAACA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttggtgaaaccccactaggcgattaattctctgtatttgcaccttccctcctagATTGCTGTGATGGGAGTGATGAATATGACAGCAATATCACCTGTAAGAACACTTGCTGGGAGGCTGGCAAAGCGGCAAGGGAGAAATTGAAGAAGAAAGT
                     gattaat  putative branch site (score: 3)
                                    tttgcaccttccctcc  putative PPT
                      attaattct  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagaggatcataattgttggcattgttagattcattgcttacttgttttgttaaataaagatgcatgtgcaaggtacaatacagactgtgaaagtcgttggagctcttgttttgtgtatcatggcgcttttggtgaaaccccactaggcgattaattctctgtatttgcaccttccctcctagATTGCTGTGATGGGAGTGATGAATATGACAGCAATATCACCTGTAAGAACACTTGCTGGGAGGCTGGCAAAGCGGCAAGGGAGAAATTGAAGAAGAAAGT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA