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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTTATTCTACTGGAATCCCGTGATAGGATTGGTGGCAGAGTTCACACTGACTACTCTTTTGGGTTTCCGGTCGATTTGGGAGCATCTTGgtgagttccattctttttagctttcaccatgtgcccaaaagtttatcttgagggaatgtcatgaacatttttttcatcatttttattcatcag

Basic information

species Zea mays
transcript GRMZM2G000052_T02
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G000052_T01 (Zea mays), 5'ss of exon 4
lower sequence: LOC_Os04g53190.1 (Oryza sativa), 5'ss of exon 4
GTTATTCTACTGGAATCCCGTGATAGGATTGGTGGCAGAGTTCACACTGACTACTCTTTTGGGTTTCCGGTCGATTTGGGAGCATCTTGgtgagttcc------------attctttttagctttcaccatgtgcccaaaagtttatcttgagggaatgtcatgaacatttttttcatcatttttattcatcag
||| |||| || ||||| ||||| ||||| ||||| ||| |||||||||| ||||||||||| ||||| || ||| |||||||||| ||||||| | |            ||| | |  |   ||    |||    ||||||||||||| ||   | | |  | ||      || |||  | | |   ||||||
GTTGTTCTTCTAGAATCTCGTGACAGGATAGGTGGTAGAATTCACACTGATTACTCTTTTGGCTTTCCTGTTGATCTGGGAGCATCCTGgtgaggttcctctctgacaatattttctgaattatttgaaatggtggcaaaagtttatctggaaccattatttttaat-ccacttccattttgtgtgagcatcag

upper sequence: GRMZM2G000052_T01 (Zea mays), 5'ss of exon 4
lower sequence: LOC_Os04g53195.1 (Oryza sativa), 5'ss of exon 3
GTTATTCTACTGGAATCCCGTGATAGGATTGGTGGCAGAGTTCACACTGACTACTCTTTTGGGTTTCCGGTCGATTTGGGAGCATCTTGgtgagttccattctttttagctttcaccatgtgcccaaaagtttatcttgagggaatgtcatgaacatttttttcatcatttttattcatcag
||| |||| || ||||| ||||| ||||| ||||| ||| |||||||||| ||||||||||| ||||| || ||| |||||||||| ||||||| | | |         || | || || |   |  ||  |||| ||||     || ||  |                             
GTTGTTCTTCTAGAATCTCGTGACAGGATAGGTGGTAGAATTCACACTGATTACTCTTTTGGCTTTCCTGTTGATCTGGGAGCATCCTGgtgaggttcct---------ctctgacaatattttctgaa--ttat-ttgaaatggtggcaaaag----------------------------

upper sequence: GRMZM2G000052_T01 (Zea mays), 5'ss of exon 4
lower sequence: AT3G59050.1 (Arabidopsis thaliana), 5'ss of exon 2
-----------GTTATTCTACTGGAATCCCGTGATAGGATTGGTGGCAGAGTTCACACTGACTACTCTTTTGGGTTTCCGGTCGATTTGGGAGCATCTTGgtgagttccattctttttagctttcaccatgtgcccaaaagtttatcttgagggaatgtcatgaacattttttt--catcatttttattcatcag
           ||| || || |||| || ||||| || ||||||||  ||||||||||||| ||||| ||||| ||||| || ||| | || |||||||||| |  ||    ||  ||     | | | | | | |  |    | | | ||     ||||||  |       |   ||  ||  || |    |||
CTTCCTTTCAGGTTGTTGTATTGGAGTCTCGTGACAGAATTGGTGGACGAGTTCACACTGATTACTCATTTGGTTTTCCAGTTGATCTCGGTGCATCTTGgtaatatcatggctccttcaacct-atctttttcactgattgctgtttggatcttttgtcatcgatgccaactaagcaatatcgttttgtgacag

upper sequence: GRMZM2G000052_T01 (Zea mays), 5'ss of exon 4
lower sequence: AT2G43020.1 (Arabidopsis thaliana), 5'ss of exon 3
GTTATTCTACTGGAATCCCGTGATAGGATTGGTGGCAGAGTTCACACTGACTACTCTTTTGGGTTTCCGGTCGATTTGGGAGCATCTTGgtgagttcc--attctttttagctttcaccatgtgcc-caaaagtttatcttgagggaatgtcatgaacatttttttcatcatttttattcatcag
|||||  ||||||| |||||||| || ||||||||  ||||||||||||| ||||| ||||| ||||| || ||| | || ||||| |||| |  ||     |||||    || |||  |  ||        ||||   ||   ||       |   |        || |||  ||||    |||
GTTATGGTACTGGAGTCCCGTGACAGAATTGGTGGACGAGTTCACACTGATTACTCATTTGGTTTTCCTGTTGATCTTGGTGCATCATGgtaatctcacggctctttcatcctgtcattagatgatgttttggttttggtttttggttaactttaggctaacacagcaacatcgttatgtcacag

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|71764900|gb|DR962837.1|DR962837
EST:     GTTCACACTGACTACTCTTTTGGGTTTCCGGTCGATTTGGGAGCATCTTG                         GCTTCATGGGGTCTGTGAAGAAAATCCCTTGGCACCAATAATTGGAAGGCT
genomic: GTTCACACTGACTACTCTTTTGGGTTTCCGGTCGATTTGGGAGCATCTTGgtgagttcca ... tattcatcagGCTTCATGGGGTCTGTGAAGAAAATCCCTTGGCACCAATAATTGGAAGGCT
EST: gi|211121516|gb|FL031381.1|FL031381
EST:     GTTCACACTGACTACTCTTTTGGGTTTCCGGTCGATTTGGGAGCATCTTG                         GCTTCATGGGGTCTGTGAANGAAA-TCCCTTGGCACCAATAATTGGAAGGC
genomic: GTTCACACTGACTACTCTTTTGGGTTTCCGGTCGATTTGGGAGCATCTTGgtgagttcca ... tattcatcagGCTTCATGGGGTCTGTGAA-GAAAATCCCTTGGCACCAATAATTGGAAGGC
EST: gi|211442379|gb|FL324386.1|FL324386
EST:     GTTCACACTGACTACTCTTTTGGGTTTCCGGTCGATTTGGGAGCATCTTG                         GCTTCATGGGGTCTGTGAAGAAAATCCCTTGGCACCAATAATTGGAAGGCT
genomic: GTTCACACTGACTACTCTTTTGGGTTTCCGGTCGATTTGGGAGCATCTTGgtgagttcca ... tattcatcagGCTTCATGGGGTCTGTGAAGAAAATCCCTTGGCACCAATAATTGGAAGGCT
EST: gi|211300846|gb|FL383949.1|FL383949
EST:     GTTCACACTGACTACTCTTTTGGGTTTCCGGTCGATTTGGGAGCATCTTG                         GCTTCATGGGGTCTGTGAAGAAAATCCCTTGGCACCAATAATTGGAAGGCT
genomic: GTTCACACTGACTACTCTTTTGGGTTTCCGGTCGATTTGGGAGCATCTTGgtgagttcca ... tattcatcagGCTTCATGGGGTCTGTGAAGAAAATCCCTTGGCACCAATAATTGGAAGGCT
EST: gi|211514296|gb|FL420360.1|FL420360
EST:     GTTCACACTGACTACTCTTTTGGGTTTCCGGTCGATTTGGGAGCATCTTG                         GCTTCATGGGGTCTGTGAAGAAAATCCCTTGGCACCAATAATTGGAAGGCT
genomic: GTTCACACTGACTACTCTTTTGGGTTTCCGGTCGATTTGGGAGCATCTTGgtgagttcca ... tattcatcagGCTTCATGGGGTCTGTGAAGAAAATCCCTTGGCACCAATAATTGGAAGGCT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTTATTCTACTGGAATCCCGTGATAGGATTGGTGGCAGAGTTCACACTGACTACTCTTTTGGGTTTCCGGTCGATTTGGGAGCATCTTGgtgagttccattctttttagctttcaccatgtgcccaaaagtttatcttgagggaatgtcatgaacatttttttcatcatttttattcatcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCA