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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTCAAACAAGGAGAAGGAGGAGGACTTCATGGCGATGAAGGGCTCCAAGCTGCCACAGAGGCCAAAGAAGAGGCCCAAGCTGATGCAGAAGTGCTTGCTTgtaatgctcccttccactaattcattttataagttttcacttcattgctatgatcgtactcattcatttgaacatgtcttctgttacattttttggacaactgtag

Basic information

species Zea mays
transcript GRMZM2G024395_T03
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G024395_T03 (Zea mays), 5'ss of exon 3
lower sequence: LOC_Os03g59250.1 (Oryza sativa), 5'ss of exon 3
GTCAAACAAGGAGAAGGAGGAGGACTTCATGGCGATGAAGGGCTCCAAGCTGCCACAGAGGCCAAAGAAGAGGCCCAAGCTGATGCAGAAGTGCTTGCTTgtaatgctcccttccactaattcattttataagttttcacttcattgctatgatcgtactca-ttcatttgaacatgtc----ttctgttacattttttggacaactgtag
|| ||||||||||| || |||||||||||||| |||||||| | |||||| ||||||||||| ||||||||||| ||| ||||||||||||||||||||||||| | ||| ||| || | | || ||| | || | ||||| | |||| || ||| ||| || ||||||| |||| || || |||||
ATCCAACAAGGAGAAAGAAGAGGACTTCATGGCAATGAAGGGATGCAAGCTCCCACAGAGGCCGAAGAAGAGGCCAAAGTTGATGCAGAAGTGCTTGCTTgtaatcccttctttcacaaagat-tactgcaaaattttgttctttta-tgtgatcatgctcacttttttttaacccttccatattctgtttcattgttgggcttgttgtag

upper sequence: GRMZM2G024395_T03 (Zea mays), 5'ss of exon 3
lower sequence: EFJ29998 (Selaginella moellendorffii), 5'ss of exon 1
GTCAAACAAGGAGAAGGAGGAGGACTTCATGGCGATGAAGGGCTCCAAGCTGCCACAGAGGCCAAAGAAGAGGCCCAAGCTGATGCAGAAGTGCTTGCTTgtaatgctcccttccactaattcattttataagttttcacttcattgctatgatcgtactcattcatttgaacatgtc-ttctgttacattttttggacaactgtag
||| ||||||||||||||| || ||| ||||||| ||||| ||||||||||| ||| |||| ||| | || |||||| | ||||| |||| |||| |||| | || || ||||||| || ||| | | | | || | | | | || || ||| ||
GTCCCGCAAGGAGAAGGAGGACGATTTCCTGGCGATCAAGGGATCCAAGCTGCCGCAGCGGCCCAAGCGGCGGACCAAGCATGTCGAGAAGACATTGCACgtaag---ttcttcgtgttcttggcttgcaaagttttttttttattttttttttaatgttcttgagctaactcttttcgtttcgttgcag-----------------

upper sequence: GRMZM2G024395_T03 (Zea mays), 5'ss of exon 3
lower sequence: EFJ25046 (Selaginella moellendorffii), 5'ss of exon 1
GTCAAACAAGGAGAAGGAGGAGGACTTCATGGCGATGAAGGGCTCCAAGCTGCCACAGAGGCCAAAGAAGAGGCCCAAGCTGATGCAGAAGTGCTTGCTTgtaatgctcccttccactaattcattttataagttttcacttcattgctatgatcgtactcattcatttgaacatgtcttctgttacattttttggacaactgtag
||| ||||||||||||||| || ||| ||||||| ||||| ||||||||||| ||| |||| ||| | || |||||| | ||||| |||| |||| |||| | || || ||||||| || || | | || | | | | | || | ||||||
GTCCCGCAAGGAGAAGGAGGACGATTTCCTGGCGATCAAGGGATCCAAGCTGCCGCAGCGGCCCAAGCGGCGGACCAAGCATGTCGAGAAGACATTGCACgtaag---ttcttcgtgttcttggcttgcaaagttttttttttttttttttaatgttcttgagctaactcttttcgtttc--gttacag-----------------

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|84970271|gb|DW468621.1|DW468621
EST:     TCCCACAGAGGCCAAAGAAGAGGCCCAAGCTGATGCAGAAGTGCTTGCTT                         ATGGTGAGCCCAGGAGCTTGGTTATCAGATCTATCTCATGAGAGATATGAA
genomic: TGCCACAGAGGCCAAAGAAGAGGCCCAAGCTGATGCAGAAGTGCTTGCTTgtaatgctcc ... acaactgtagATGGTGAGCCCAGGAGCTTGGTTATCAGATCTATCTCATGAGAGATATGAA
EST: gi|78106870|gb|DV525288.1|DV525288
EST:     TGCCACAGAGGCCAAAGAAGAGGCCCAAGCTGATGCAGAAGTGCTTGCTT                         ATGGTGAGCCCAGGAGCTTGGTTATCAGATCTATCTCATGAGAGATATGAA
genomic: TGCCACAGAGGCCAAAGAAGAGGCCCAAGCTGATGCAGAAGTGCTTGCTTgtaatgctcc ... acaactgtagATGGTGAGCCCAGGAGCTTGGTTATCAGATCTATCTCATGAGAGATATGAA
EST: gi|76286625|gb|DV026193.1|DV026193
EST:     TGCCACAGAGGCCAAAGAAGAGGCCCAAGCTGATGCAGAAGTGCTTGCTT                         ATGGTGAGCCCAGGAGCTTGGTTATCAGATCTATCTCATGAGAGATATGAA
genomic: TGCCACAGAGGCCAAAGAAGAGGCCCAAGCTGATGCAGAAGTGCTTGCTTgtaatgctcc ... acaactgtagATGGTGAGCCCAGGAGCTTGGTTATCAGATCTATCTCATGAGAGATATGAA
EST: gi|93284387|gb|EB676651.1|EB676651
EST:     TGCCACAGAGGCCAAAGAAGAGGCCCAAGCTGATGCAGAAGTGCTTGCTT                         ATGGTGAGCCCAGGAGCTTGGTTATCAGATC
genomic: TGCCACAGAGGCCAAAGAAGAGGCCCAAGCTGATGCAGAAGTGCTTGCTTgtaatgctcc ... acaactgtagATGGTGAGCCCAGGAGCTTGGTTATCAGATC
EST: gi|76914671|gb|DV165630.1|DV165630
EST:     TGCCACAGAGGCCAAAGAAGAGGCCCAAGCTGATGCAGAAGTGCTTGCTT                         ATGGTGAGCCCAGGAGCTTGGTTATCAGATCTATCTCATGAGAGATATGAA
genomic: TGCCACAGAGGCCAAAGAAGAGGCCCAAGCTGATGCAGAAGTGCTTGCTTgtaatgctcc ... acaactgtagATGGTGAGCCCAGGAGCTTGGTTATCAGATCTATCTCATGAGAGATATGAA
EST: gi|71775433|gb|DR973311.1|DR973311
EST:     TGCCACAGAGGCCAAAGAAGAGGCCCAAGCTGATGCAGAAGTGCTTGCTT                         ATGGTGAGCCCAGGAGCTTGGTTATCAGATCTATCTCATGAGAGATATGAA
genomic: TGCCACAGAGGCCAAAGAAGAGGCCCAAGCTGATGCAGAAGTGCTTGCTTgtaatgctcc ... acaactgtagATGGTGAGCCCAGGAGCTTGGTTATCAGATCTATCTCATGAGAGATATGAA
EST: gi|101386838|gb|EB815436.1|EB815436
EST:     TGCCACAGAGGCCAAAGAAGAGGCCCAAGCTGATGCAGAAGTGCTTGCTT                         ATGGTGAGCTCAGGAGCTTGGTTATCAGATCTATCTCATGAGAGATAT
genomic: TGCCACAGAGGCCAAAGAAGAGGCCCAAGCTGATGCAGAAGTGCTTGCTTgtaatgctcc ... acaactgtagATGGTGAGCCCAGGAGCTTGGTTATCAGATCTATCTCATGAGAGATAT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTCAAACAAGGAGAAGGAGGAGGACTTCATGGCGATGAAGGGCTCCAAGCTGCCACAGAGGCCAAAGAAGAGGCCCAAGCTGATGCAGAAGTGCTTGCTTgtaatgctcccttccactaattcattttataagttttcacttcattgctatgatcgtactcattcatttgaacatgtcttctgttacattttttggacaactgtag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT