Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   		6  
 5'  3'   		7  
 5'  3'   		8  
 5'  3'   		9  
 5'  3'   		10  
 5'  3'   		11  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgctcttggcctagataacaaaattgggaacagaccggttttagtaaaaattaaggagtcaaccttttcacccatttgatgagttagagtctcttctcagGTTCAGCTCAACTTGCGGCTGTTGGTGCATCTACTTCCATATTCAATTTGGTATCCAAGCTGTTTAATGTGCCGCTACTTAATGTCACAACATCCTTTGT

Basic information

species Zea mays
transcript GRMZM5G890665_T02
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G890665_T02 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os12g01580.1 (Oryza sativa), 3'ss of exon 1
tgctcttggcctagataacaaaattgggaacagac-cggttttagtaaaaattaaggagtcaacc----ttttcacccatttgatgagttagagtctcttc-tcagGTTCAGCTCAACTTGCGGCTGTTGGTGCATCTACTTCCATATTCAATTTGGTATCCAAGCTGTTTAATGTGCCGCTACTTAATGTCACAACATCCTTTGT
      | |   ||| |   |  |     |||    |  | ||| |    |  ||   ||  | |    |  | |  || |||  |   |  |     |||  |||||||| || ||||||| || ||||| | ||| | ||| || ||||||||||||||||||||| | ||||| ||  | || || ||||| |||||||||||
------ttgtgaagaaacttatttcttacacatttacattcttatttgctacaaaaatgttgatcacgatactaattcacttggcggtctccaactcattcaccagGTTCAACTGAACTTGCTGCCGTTGGAGTATCCATTTCTATCTTCAATTTGGTATCCAAGCTGCTCAATGTCCCATTGCTCAACGTCACCACATCCTTTGT

upper sequence: GRMZM5G890665_T02 (Zea mays), 3'ss of exon 1
lower sequence: AT2G38330.1 (Arabidopsis thaliana), 3'ss of exon 2
tgctcttggcctagataacaaaattgggaacagaccggttttagtaaaaattaaggagtc-aaccttttcacccatttgatgagttagagtctcttctcagGTTCAGCTCAACTTGCGGCTGTTGGTGCATCTACTTCCATATTCAATTTGGTATCCAAGCTGTTTAATGTGCCGCTACTTAATGTCACAACATCCTTTGT
               ||| | | ||       |   ||||| |  ||      |    || ||  ||  ||    |   ||   |  | ||    |  ||||||| ||  || | || || || || |  ||   |||  ||||||||||||| || ||||| || ||||| ||  |||| |||||||||||||| |||||
--------------gtaa-atacttactttttgcttggtttcaacaatttcacatttttcgaaagttcacatttttaacattcatatgtgtaatgtgacagGTTCTGCGGAATTAGCTGCAGTAGGAGTGTCAGTTTCTGTATTCAATTTGGTGTCGAAGCTCTTCAATGTTCCTTTACTAAATGTCACAACATCGTTTGT
















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|9731974|gb|BE510726.1|BE510726
EST:     CGCGGACCCCATCACGGCGCTCGTCGACACTGCCTTCGTCGGGCATATCG                         GTTCAGCTCAACTTGCGGCTGTTGGTGCATCTACTTCCATATTCAATTTGG
genomic: CGCGGACCCCATCACGGCGCTCGTCGACACTGCCTTCGTCGGGCATATCGgtaacccagt ... ctcttctcagGTTCAGCTCAACTTGCGGCTGTTGGTGCATCTACTTCCATATTCAATTTGG
EST: gi|211025186|gb|FL300502.1|FL300502
EST:     CGCGGACCCCATCACGGCGCTCGTCGACACTGCCTTCGTCGGGCATATCG                         GTTCAGCTCAACTTGCGGCTGGTGGTGCATCTACTTCCATATTCAATTTGG
genomic: CGCGGACCCCATCACGGCGCTCGTCGACACTGCCTTCGTCGGGCATATCGgtaacccagt ... ctcttctcagGTTCAGCTCAACTTGCGGCTGTTGGTGCATCTACTTCCATATTCAATTTGG
EST: gi|211025188|gb|FL300504.1|FL300504
EST:     CGCGGACCCCATCACGGCGCTCGTCGACACTGCCTTCGTCGGGCATATCG                         GTTCAGCTCAACTTGCGGCTGTTGGTGCATCTACTTCCATATTCAATTTGG
genomic: CGCGGACCCCATCACGGCGCTCGTCGACACTGCCTTCGTCGGGCATATCGgtaacccagt ... ctcttctcagGTTCAGCTCAACTTGCGGCTGTTGGTGCATCTACTTCCATATTCAATTTGG
EST: gi|211025181|gb|FL300497.1|FL300497
EST:     CGCGGACCCCATCACGGCGCTCGTCGACACTGCCTTCGTCGGGCATATCG                         GTTCAGCTCAACTTGCGGCTGTTGGTGCATCTACTTCCATATTCAATTTGG
genomic: CGCGGACCCCATCACGGCGCTCGTCGACACTGCCTTCGTCGGGCATATCGgtaacccagt ... ctcttctcagGTTCAGCTCAACTTGCGGCTGTTGGTGCATCTACTTCCATATTCAATTTGG
EST: gi|211025184|gb|FL300500.1|FL300500
EST:     CGCGGACCCCATCACGGCGCTCGTCGACACTGCCTTCGTCGGGCATATCG                         GTTCAGCTCAACTTGCGGCTGTTGGTGCATCTACTTCCATATTCAATTTGG
genomic: CGCGGACCCCATCACGGCGCTCGTCGACACTGCCTTCGTCGGGCATATCGgtaacccagt ... ctcttctcagGTTCAGCTCAACTTGCGGCTGTTGGTGCATCTACTTCCATATTCAATTTGG
EST: gi|148939832|gb|EC884537.2|EC884537
EST:     CGCGGACCCCATCACGGCGCTCGTCGACACTGCCTTCGTCGGGCATATCG                         GTTCAGCTCAACTTGCGGCTGTTGGTGCATCTACTTCCATATTCAATTTGG
genomic: CGCGGACCCCATCACGGCGCTCGTCGACACTGCCTTCGTCGGGCATATCGgtaacccagt ... ctcttctcagGTTCAGCTCAACTTGCGGCTGTTGGTGCATCTACTTCCATATTCAATTTGG
EST: gi|149072460|gb|EE160737.2|EE160737
EST:     CGCGGACCCCATCACGGCGCTCGTCGACACTGCCTTCGTCGGGCATATCG                         GTTCAGCTCAACTTGCGGCTGTTGGTGCATCTACTTCCATATTCAATTTGG
genomic: CGCGGACCCCATCACGGCGCTCGTCGACACTGCCTTCGTCGGGCATATCGgtaacccagt ... ctcttctcagGTTCAGCTCAACTTGCGGCTGTTGGTGCATCTACTTCCATATTCAATTTGG
EST: gi|211025185|gb|FL300501.1|FL300501
EST:     CGCGGACCCCATCACGGCGCTCGTCGACACTGCCTTCGTCGGGCATATCG                         GTTCAGCTCAACTTGCGGCTGTTGGTGCATCTACTTCCATATTCAATTTGG
genomic: CGCGGACCCCATCACGGCGCTCGTCGACACTGCCTTCGTCGGGCATATCGgtaacccagt ... ctcttctcagGTTCAGCTCAACTTGCGGCTGTTGGTGCATCTACTTCCATATTCAATTTGG
EST: gi|211025182|gb|FL300498.1|FL300498
EST:     CGCGGACCCCATCACGGCGCTCGTCGACACTGCCTTCGTCGGGCATATCG                         GTTCAGCTCAACTTGCGGCTGTTGGTGCATCTACTTCCATATTCAATTTGG
genomic: CGCGGACCCCATCACGGCGCTCGTCGACACTGCCTTCGTCGGGCATATCGgtaacccagt ... ctcttctcagGTTCAGCTCAACTTGCGGCTGTTGGTGCATCTACTTCCATATTCAATTTGG
EST: gi|211025183|gb|FL300499.1|FL300499
EST:     CGCGGACCCCATCACGGCGCTCGTCGACACTGCCTTCGTCGGGCATATCG                         GTTCAGCTCAACTTGCGGCTGTTGGTGCATCTACTTCCATATTCAATTTGG
genomic: CGCGGACCCCATCACGGCGCTCGTCGACACTGCCTTCGTCGGGCATATCGgtaacccagt ... ctcttctcagGTTCAGCTCAACTTGCGGCTGTTGGTGCATCTACTTCCATATTCAATTTGG
EST: gi|211025191|gb|FL300507.1|FL300507
EST:     CGCGGACCCCATCACGGCGCTCGTCGACACTGCCTTCGTCGGGCATATCG                         GTTCAGCTCNACTTGCGGCTGTTGGTGCATCTACTTCCATATTCAATTTTG
genomic: CGCGGACCCCATCACGGCGCTCGTCGACACTGCCTTCGTCGGGCATATCGgtaacccagt ... ctcttctcagGTTCAGCTCAACTTGCGGCTGTTGGTGCATCTACTTCCATATTCAATTT-G
EST: gi|76935587|gb|DV174390.1|DV174390
EST:     CGCGGACCCCATCACGGCGCTCGTCGACACTGCCTTCGTCGGGCATATCG                         GTTCAGCTCAACTTGCGGCTGTTGGTGCATCTACTTCCATATTCAATTTGG
genomic: CGCGGACCCCATCACGGCGCTCGTCGACACTGCCTTCGTCGGGCATATCGgtaacccagt ... ctcttctcagGTTCAGCTCAACTTGCGGCTGTTGGTGCATCTACTTCCATATTCAATTTGG
EST: gi|149085740|gb|EE175261.2|EE175261
EST:     CGCGGACCCCATCACGGCGCTCGTCGACACTGCCTTCGTCGGGCATATCG                         GTTCAGCTCAACTTGCGGCTGTTGGTGCATCTACTTCCATATTCAATTTGG
genomic: CGCGGACCCCATCACGGCGCTCGTCGACACTGCCTTCGTCGGGCATATCGgtaacccagt ... ctcttctcagGTTCAGCTCAACTTGCGGCTGTTGGTGCATCTACTTCCATATTCAATTTGG
EST: gi|211025193|gb|FL300509.1|FL300509
EST:     CGCGGACCCCATCACGGCGCTCGTCGACACTGCCTTCGTCGGGCATATCG                         GTTCAGCTCAACTTGCGGCTGTTGGTGCATCTACTTCCATATTCAATTTGG
genomic: CGCGGACCCCATCACGGCGCTCGTCGACACTGCCTTCGTCGGGCATATCGgtaacccagt ... ctcttctcagGTTCAGCTCAACTTGCGGCTGTTGGTGCATCTACTTCCATATTCAATTTGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aaaaattaaggagtcaaccttttcacccatttgatgagttagagtctcttctcagGTTCAGCTCAACTTGCGGCTGTTGGTGCATCTACTTCCATATTCAATTTGGTATCCAAGCTGTTTAATGTGCCGCTACTTAATGTCACAACATCCTTTGT
                            atttgat  putative branch site (score: 5)
                                            tctcttctc  putative PPT
                            atttgat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgctcttggcctagataacaaaattgggaacagaccggttttagtaaaaattaaggagtcaaccttttcacccatttgatgagttagagtctcttctcagGTTCAGCTCAACTTGCGGCTGTTGGTGCATCTACTTCCATATTCAATTTGGTATCCAAGCTGTTTAATGTGCCGCTACTTAATGTCACAACATCCTTTGT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT