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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CTTGTTGGTAAAGATGCGCTGGCAGAATCTGACAAGATTACGCTGGAGACAGCAAAGCTTTTGAGAGAAGATTATTTGGCACAAAATGCATTCACCCCgtgagtcccctacttatttcaacacatttgatgctcatttttctccattatattttaagtatttttttgacaagtgctgtttaattatatag

Basic information

species Zea mays
transcript GRMZM2G421857_T04
intron # 17
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G421857_T02 (Zea mays), 5'ss of exon 16
lower sequence: LOC_Os02g07870.1 (Oryza sativa), 5'ss of exon 16
CTTGTTGGTAAAGATGCGCTGGCAGAATCTGACAAGATTACGCTGGAGACAGCAAAGCTTTTGAGAGAAGATTATTTGGCACAAAATGCATTCACCCCgtgagtcccctacttatttcaacacatttgatgctcatttttctccattatatttta-agtatttttttgacaagtgctgtttaattatatag
|||||||||||||| || ||||||||||||||||||||||| |||||||||||||| ||| |||||||||||||||||||||||||||||||||||||||||||     ||  |||| |       |  | || | |   ||   | ||| |  | | ||  |  ||||  | | |||||  || | | ||
CTTGTTGGTAAAGACGCACTGGCAGAATCTGACAAGATTACACTGGAGACAGCAAAACTTCTGAGAGAAGATTATTTGGCACAAAATGCATTCACCCCgtgagtgttaaacccatttga-------tagttct-actaacctgtgtcataatccatattaactaattgatcaattctgttgcatgaaacag

upper sequence: GRMZM2G421857_T02 (Zea mays), 5'ss of exon 16
lower sequence: Vv09s0054g00890.t01 (Vitis vinifera), 5'ss of exon 17
CTTGTTGGTAAAGATGCGCTGGCAGAATCTGACAAGATTACGCTGGAGACAGCAAAGCTTTTGAGAGAAGATTATTTGGCACAAAATGCATTCACCCCgtgagtcccctacttatttcaacacatttgatgctcatttttctccattatattttaagtatttttttgacaagtgctgtttaattatatag----------------------------------------------------
||||| || ||||||||  | || ||| | || || ||||| || ||||| |||||||||||||| ||||| ||| | |||||||||||||| ||||||| ||||||  | | | ||    |  |   ||  || |  || |  ||| |  ||||  || | |||    | || |   ||  ||||   |                                                    
CTTGTCGGAAAAGATGCTTTAGCTGAAACAGATAAAATTACTCTAGAGACTGCAAAGCTTTTGAGGGAAGACTATCTTGCACAAAATGCATTTACCCCgtaagtcccagattaagtttttgat-tcaaattttcgtcctttttaatttttgtttacttactatttccttatgttccccttt-ttatgctggtctagaaattctttttccacttaatatatgtatctcatgtggctgtgacag
















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|32850183|gb|CD989864.1|CD989864
EST:     ACAGCAAAGCTTTTGAGAGAAGATTATTTGGCACAAAATGCATTCACCCC                         ATATGATAAGTTCTGCCCATTCTACAAATCCGTTTGGATGATGCGCAACAT
genomic: ACAGCAAAGCTTTTGAGAGAAGATTATTTGGCACAAAATGCATTCACCCCgtgagtcccc ... aattatatagATATGATAAGTTCTGCCCATTCTACAAATCCGTTTGGATGATGCGCAACAT
EST: gi|32921243|gb|CF026055.1|CF026055
EST:     ACAGCAAAGCTTTTGAGAGAAGATTATTTGGCACAAAATGCATTCACCCC                         ATATGATAAGTTCTGCCCATTCTACAAATCCGTTTGGATGATGCGCAACAT
genomic: ACAGCAAAGCTTTTGAGAGAAGATTATTTGGCACAAAATGCATTCACCCCgtgagtcccc ... aattatatagATATGATAAGTTCTGCCCATTCTACAAATCCGTTTGGATGATGCGCAACAT
EST: gi|67026160|gb|CO454909.1|CO454909
EST:     ACAGCAAAGCTTTTGAGAGAAGATTATTTGGCACAAAATGCATTCACCCC                         ATATGATAAGTTCTGCCCATTCTACAAATCTGTTTGGATGATGCGCAACAT
genomic: ACAGCAAAGCTTTTGAGAGAAGATTATTTGGCACAAAATGCATTCACCCCgtgagtcccc ... aattatatagATATGATAAGTTCTGCCCATTCTACAAATCCGTTTGGATGATGCGCAACAT
EST: gi|32845901|gb|CD985582.1|CD985582
EST:     ACAGCAAAGCTTTTGAGAGAAGATTATTTGGCACAAAATGCATTCACCCC                         ATATGATAAGTTCTGCCCATTCTACAAATCCGTTTGGATGATGCGCAACAT
genomic: ACAGCAAAGCTTTTGAGAGAAGATTATTTGGCACAAAATGCATTCACCCCgtgagtcccc ... aattatatagATATGATAAGTTCTGCCCATTCTACAAATCCGTTTGGATGATGCGCAACAT
EST: gi|32922059|gb|CF026871.1|CF026871
EST:     ACAGCAAAGCTTTTGAGAGAAGATTATTTGGCACAAAATGCATTCACCCC                         ATATGATAAGTTCTGCCCATTCTACAAATCCGTTTGGATGATGCGCAACAT
genomic: ACAGCAAAGCTTTTGAGAGAAGATTATTTGGCACAAAATGCATTCACCCCgtgagtcccc ... aattatatagATATGATAAGTTCTGCCCATTCTACAAATCCGTTTGGATGATGCGCAACAT
EST: gi|24774168|gb|CA409422.1|CA409422
EST:     ACAGCAAAGCTTTTGAGAGAAGATTATTTGGCACAAAATGCATTCACCCC                         ATATGATAAGTTCTGCCCATTCTACAAATCCGTTTGGATGATGCGCAACAT
genomic: ACAGCAAAGCTTTTGAGAGAAGATTATTTGGCACAAAATGCATTCACCCCgtgagtcccc ... aattatatagATATGATAAGTTCTGCCCATTCTACAAATCCGTTTGGATGATGCGCAACAT
EST: gi|8368089|gb|BE051034.1|BE051034
EST:     ACAGCAAAGCTTTTGAGAGAAGATTATTTGGCACAAAATGCATTCACCCC                         ATATGATAAGTTCTGCCCATTCTACAAATCTGTTTGGATGATGCGCAACAT
genomic: ACAGCAAAGCTTTTGAGAGAAGATTATTTGGCACAAAATGCATTCACCCCgtgagtcccc ... aattatatagATATGATAAGTTCTGCCCATTCTACAAATCCGTTTGGATGATGCGCAACAT
EST: gi|32921648|gb|CF026460.1|CF026460
EST:     ACAGCAAAGCTTTTGAGAGAAGATTATTTGGCACAAAATGCATTCACCCC                         ATATGATAAGTTCTGCCCATTCTACAAATCCGTTTGGATGATGCGCAACAT
genomic: ACAGCAAAGCTTTTGAGAGAAGATTATTTGGCACAAAATGCATTCACCCCgtgagtcccc ... aattatatagATATGATAAGTTCTGCCCATTCTACAAATCCGTTTGGATGATGCGCAACAT
EST: gi|211529162|gb|FL123428.1|FL123428
EST:     ACAGCAAAGCTTTTGAGAGAAGATTATTTGGCACAAAATGCATTCACCCC                         ATATGATAAGTTCTGCCCATTCTACAAATCCGTTTGGATGATGCGCAACAT
genomic: ACAGCAAAGCTTTTGAGAGAAGATTATTTGGCACAAAATGCATTCACCCCgtgagtcccc ... aattatatagATATGATAAGTTCTGCCCATTCTACAAATCCGTTTGGATGATGCGCAACAT
EST: gi|6020503|gb|AW065431.1|AW065431
EST:     ACAGCAAAGCTTTTGAGAGAAGATTATTTGGCACAAAATGCATTCACCCC                         ATATGATAAGTTCTGCCCATTCTACAAATCCGTTTGGATGATGCGCAACAT
genomic: ACAGCAAAGCTTTTGAGAGAAGATTATTTGGCACAAAATGCATTCACCCCgtgagtcccc ... aattatatagATATGATAAGTTCTGCCCATTCTACAAATCCGTTTGGATGATGCGCAACAT
EST: gi|32849884|gb|CD989565.1|CD989565
EST:     ACAGCAAAGCTTNTGAGAGAAGATTATTTGGCACAAAATGCATTCACCCC                         ATATGATAAGTTCTGCCCATTCTACAAATCCGTTTGGATGATGCGCAACAT
genomic: ACAGCAAAGCTTTTGAGAGAAGATTATTTGGCACAAAATGCATTCACCCCgtgagtcccc ... aattatatagATATGATAAGTTCTGCCCATTCTACAAATCCGTTTGGATGATGCGCAACAT
EST: gi|211538183|gb|FL123481.1|FL123481
EST:     ACAGCAAAGCTTTTGAGARAAGATTATTTGGCACAAAATGCATTCACCCC                         ATATGATAAGTTCTGCCCATTCTACAAATCCGTTTGGATGATGCGCAACAT
genomic: ACAGCAAAGCTTTTGAGAGAAGATTATTTGGCACAAAATGCATTCACCCCgtgagtcccc ... aattatatagATATGATAAGTTCTGCCCATTCTACAAATCCGTTTGGATGATGCGCAACAT
EST: gi|32846431|gb|CD986112.1|CD986112
EST:     ACAGCAAAGCTTTTGACAGAAGATTATTTGGCACAAAATGCATTCACCCC                         ATATGATAAGTTCTGCCCATTCTACAAATCCGTTTGAATGATGCGCAACAT
genomic: ACAGCAAAGCTTTTGAGAGAAGATTATTTGGCACAAAATGCATTCACCCCgtgagtcccc ... aattatatagATATGATAAGTTCTGCCCATTCTACAAATCCGTTTGGATGATGCGCAACAT
EST: gi|24773770|gb|CA409024.1|CA409024
EST:     ACAGCAAAGCTTTTGAGAGAAGATTATTTGGCACAAAATGCATTCACCCC                         ATATGATAAGTTCTGCCCATTCTACAAATCCGTTTGGATGATGCGCAACAT
genomic: ACAGCAAAGCTTTTGAGAGAAGATTATTTGGCACAAAATGCATTCACCCCgtgagtcccc ... aattatatagATATGATAAGTTCTGCCCATTCTACAAATCCGTTTGGATGATGCGCAACAT
EST: gi|32846734|gb|CD986415.1|CD986415
EST:     ACAGCAAAGCTTTTGAGAGAAGATTATTTGGCACAAAATGCATTCACCCC                         ATATGATAAGTTCTGCCCATTCTACAAATCCGTTTGGATGATGCGCAACAT
genomic: ACAGCAAAGCTTTTGAGAGAAGATTATTTGGCACAAAATGCATTCACCCCgtgagtcccc ... aattatatagATATGATAAGTTCTGCCCATTCTACAAATCCGTTTGGATGATGCGCAACAT
EST: gi|8368090|gb|BE051035.1|BE051035
EST:     ACAGCAAAGCTTTTGAGAGAAGATTATTTGGCACAAAATGCATTCACCCC                         ATATGATAAGTTCTGCCCATTCTACAAATCTGTTTGGATGATGCGCAACAT
genomic: ACAGCAAAGCTTTTGAGAGAAGATTATTTGGCACAAAATGCATTCACCCCgtgagtcccc ... aattatatagATATGATAAGTTCTGCCCATTCTACAAATCCGTTTGGATGATGCGCAACAT
EST: gi|211156007|gb|FL123542.1|FL123542
EST:     ACAGCAAAGCTTTTGAGAGAAGATTATTTGGCACAAAATGCATTCATCCC                         ATATGATAAGTTCTGCCCATTCTACAAATCCGTTTGGATGATGCGCAACAT
genomic: ACAGCAAAGCTTTTGAGAGAAGATTATTTGGCACAAAATGCATTCACCCCgtgagtcccc ... aattatatagATATGATAAGTTCTGCCCATTCTACAAATCCGTTTGGATGATGCGCAACAT
EST: gi|8665370|gb|BE186186.1|BE186186
EST:     ACAGCAAAGCTTTTGAGAGAAGATTATTTGGCACAAAATGCATTCACCCC                         ATATGATAAGTTCTGCCCATTCTACAAATCTGTTTGGATGATGCGCAACAT
genomic: ACAGCAAAGCTTTTGAGAGAAGATTATTTGGCACAAAATGCATTCACCCCgtgagtcccc ... aattatatagATATGATAAGTTCTGCCCATTCTACAAATCCGTTTGGATGATGCGCAACAT
EST: gi|40334940|gb|CK369010.1|CK369010
EST:     ACAGCAAAGCTTTTGAGAGAAGATTATTTGGCACAAAATGCATTCACCCC                         ATATGATAAGTTCTGCCCATTCTACAAATCCGTTTGGATGATGCGCAACAT
genomic: ACAGCAAAGCTTTTGAGAGAAGATTATTTGGCACAAAATGCATTCACCCCgtgagtcccc ... aattatatagATATGATAAGTTCTGCCCATTCTACAAATCCGTTTGGATGATGCGCAACAT
EST: gi|22542087|gb|BU092525.1|BU092525
EST:     ACAGCAAAGCTTTTGAGAGAAGATTATTTGGCACAAAATGCATTCACCCC                         ATATGATAAGTTCTGCCCATTCTACAAATCCGTTTGGATGATGCGCAACAT
genomic: ACAGCAAAGCTTTTGAGAGAAGATTATTTGGCACAAAATGCATTCACCCCgtgagtcccc ... aattatatagATATGATAAGTTCTGCCCATTCTACAAATCCGTTTGGATGATGCGCAACAT
EST: gi|6227177|gb|AW155706.1|AW155706
EST:     ACAGCAAAGCTTTTGAGAGAAGATTATTTGGCACAAAATGCATTCACCCC                         ATATGATAAGTTCTGCCCATTCTACAAATCCGTTTGGATGATGCGCAACAT
genomic: ACAGCAAAGCTTTTGAGAGAAGATTATTTGGCACAAAATGCATTCACCCCgtgagtcccc ... aattatatagATATGATAAGTTCTGCCCATTCTACAAATCCGTTTGGATGATGCGCAACAT
EST: gi|32921742|gb|CF026554.1|CF026554
EST:     ACAGCAAAGCTTTTGAGAGAAGATTATTTGGCACAAAATGCATTCACCCC                         ATATGATAAGTTCTGCCCATTCTACAAATCCGTTTGGATGATGCGCAACAT
genomic: ACAGCAAAGCTTTTGAGAGAAGATTATTTGGCACAAAATGCATTCACCCCgtgagtcccc ... aattatatagATATGATAAGTTCTGCCCATTCTACAAATCCGTTTGGATGATGCGCAACAT
EST: gi|32920116|gb|CF024928.1|CF024928
EST:     ACAGCAAAGCTTTTGAGAGAAGATTATTTGGCACAAAATGCATTCACCCC                         ATATGATAAGTTCTGCCCATTCTACAAATCCGTTTGGATGATGCGCAACAT
genomic: ACAGCAAAGCTTTTGAGAGAAGATTATTTGGCACAAAATGCATTCACCCCgtgagtcccc ... aattatatagATATGATAAGTTCTGCCCATTCTACAAATCCGTTTGGATGATGCGCAACAT
EST: gi|32921546|gb|CF026358.1|CF026358
EST:     ACAGCAAAGCTTTTGAGAGAAGATTATTTGGCACAAAATGCATTCACCCC                         ATATGATAAGTTCTGCCCATTCTACAAATCCGTTTGGATGATGCGCAACAT
genomic: ACAGCAAAGCTTTTGAGAGAAGATTATTTGGCACAAAATGCATTCACCCCgtgagtcccc ... aattatatagATATGATAAGTTCTGCCCATTCTACAAATCCGTTTGGATGATGCGCAACAT
EST: gi|60352649|gb|DN219622.1|DN219622
EST:     ACAGCAAAGCTTTTGAGAGAAGATTATTTGGCACAAAATGCATTCACCCC                         ATATGATAAGTTCTGCCCATTCTACAAATCCGTTTGGATGATGCGCAACAT
genomic: ACAGCAAAGCTTTTGAGAGAAGATTATTTGGCACAAAATGCATTCACCCCgtgagtcccc ... aattatatagATATGATAAGTTCTGCCCATTCTACAAATCCGTTTGGATGATGCGCAACAT

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
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---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CTTGTTGGTAAAGATGCGCTGGCAGAATCTGACAAGATTACGCTGGAGACAGCAAAGCTTTTGAGAGAAGATTATTTGGCACAAAATGCATTCACCCCgtgagtcccctacttatttcaacacatttgatgctcatttttctccattatattttaagtatttttttgacaagtgctgtttaattatatag

- - - - - - - - - - - - - - - - - - - - - - - - -  GCAAAG