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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagaccgcgatccgttactgaattccccctgctccccccccccccccccccccccccccggcgcgcgcttgtaaataattcgaaccgtagctgaagcggtgggtcactgcattcgcagATACTTGGATATGCTTCCGAGCACCTTTGGGAGCTCCCTTTGGTTTACTGAGGAAGAGCTTGCCGAACTGGAAGGGACAACTTTGCACCGAGCTACGTTG

Basic information

species Zea mays
transcript GRMZM2G078458_T04
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G078458_T01 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os06g03676.1 (Oryza sativa), 3'ss of exon 3
gtaagaccgcgatccgttactgaattccccctgctccccccccccccccccccccccccccggcgcgcgcttgtaaataattcgaaccgtagctgaagcggtgggtcactgcattcgcagATACTTGGATATGCTTCCGAGCACCTTTGGGAGCTCCCTTTGGTTTACTGAGGAAGAGCTTGCCGAACTGGAAGGGACAACTTTGCACCGAGCTACGTTG
                                                   | |   || |  | | |  |  |||| || | || | ||   ||||    | ||| | | |  |   || || |||||||||||||| |||||||| || |||||| ||||||| || || || |||||||| ||  |||||||||| ||  | ||||| || ||  ||
--------------------------------------------gtatggtcgcaatccacatctctccatgttaaacaacttgatcagtgattgaatt--ttggtaatttctct---agGTATTTGGATATGCTTCCAAGCACCTTCGGAAGCTCCATTTGGTTCACCGAAGATGAGCTTGCTGAGTTGGAAGGGACCACACTTCACCGGGCAACCGTG
















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|71298470|gb|DR785213.1|DR785213
EST:     ATGCTCTTCCTCATGGCCGAGCGCCGACGCCCTGGCTCACTCTGGAAGCC                         ATACTTGGATATGCTTCCGAGCACCTTTGGGAGCTCCCTTTGGTTTACTGA
genomic: ATGCTCTTCCTCATGGCCGAGCGCCGACGCCCTGGCTCACTCTGGAAGCCgtaagaccgc ... gcattcgcagATACTTGGATATGCTTCCGAGCACCTTTGGGAGCTCCCTTTGGTTTACTGA
EST: gi|211047245|gb|FL354513.1|FL354513
EST:     ATGCTCTTCCTCATGGCCGAGCGCCGACGCCCTGGCTCACTCTGGAAGCC                         ATACTTGGATATGCTTCCGAGCACCTTTGGGAGCTCCCTTTGGTTTACTGA
genomic: ATGCTCTTCCTCATGGCCGAGCGCCGACGCCCTGGCTCACTCTGGAAGCCgtaagaccgc ... gcattcgcagATACTTGGATATGCTTCCGAGCACCTTTGGGAGCTCCCTTTGGTTTACTGA
EST: gi|71766035|gb|DR963972.1|DR963972
EST:     ATGCTCTTCCTCATGGCCGAGCGCCGACGCCCTGGCTCACTCTGGAAGCC                         ATACTTGGATATGCTTCCGAGCACCTTTGGGAGCTCCCTTTGGTTTACTGA
genomic: ATGCTCTTCCTCATGGCCGAGCGCCGACGCCCTGGCTCACTCTGGAAGCCgtaagaccgc ... gcattcgcagATACTTGGATATGCTTCCGAGCACCTTTGGGAGCTCCCTTTGGTTTACTGA
EST: gi|78108131|gb|DV526549.1|DV526549
EST:     ATGCTCTTCCTCATGGCCGAGCGCCGACGCCCTGGCTCACTCTGGAAGCC                         ATACTTGGATATGCTTCCGAGCACCTTTGGGAGCTCCCTTTGGTTTACTGA
genomic: ATGCTCTTCCTCATGGCCGAGCGCCGACGCCCTGGCTCACTCTGGAAGCCgtaagaccgc ... gcattcgcagATACTTGGATATGCTTCCGAGCACCTTTGGGAGCTCCCTTTGGTTTACTGA
EST: gi|101383848|gb|EB813979.1|EB813979
EST:     ATGCTCTTCCTCATGGCCGAGCGCCGACGCCCTGGCTCACTCTGGAAGCC                         ATACTTGGATATGCTTCCGAGCACCTTTGGGAGCTCCCTTTGGTTTACTGA
genomic: ATGCTCTTCCTCATGGCCGAGCGCCGACGCCCTGGCTCACTCTGGAAGCCgtaagaccgc ... gcattcgcagATACTTGGATATGCTTCCGAGCACCTTTGGGAGCTCCCTTTGGTTTACTGA
EST: gi|71319933|gb|DR796728.1|DR796728
EST:     ATGCTCTTCCTCATGGCCGAGCGCCGACGCCCTGGCTCACTCTGGAAGCC                         ATACTTGGATATGCTTCCGAGCACCTTTGGGAGCTCCCTTTGGTTTACTGA
genomic: ATGCTCTTCCTCATGGCCGAGCGCCGACGCCCTGGCTCACTCTGGAAGCCgtaagaccgc ... gcattcgcagATACTTGGATATGCTTCCGAGCACCTTTGGGAGCTCCCTTTGGTTTACTGA
EST: gi|148973503|gb|EE024603.2|EE024603
EST:     ATGCTCTTCCTCATGGCCGAGCGCCGACGCCCTGGCTCACTCTGGAAGCC                         ATACTTGGATATGCTTCCGAGCACCTTTGGGAGCTCCCTTTGGTTTACTGA
genomic: ATGCTCTTCCTCATGGCCGAGCGCCGACGCCCTGGCTCACTCTGGAAGCCgtaagaccgc ... gcattcgcagATACTTGGATATGCTTCCGAGCACCTTTGGGAGCTCCCTTTGGTTTACTGA
EST: gi|74241324|gb|DT649238.1|DT649238
EST:     ATGCTCTTCCTCATGGCCGAGCGCCGACGCCCTGGCTCACTCTGGAAGCC                         ATACTTGGATATGCTTCCGAGCACCTTTGGGAGCTCCCTTTGGTTTACTGA
genomic: ATGCTCTTCCTCATGGCCGAGCGCCGACGCCCTGGCTCACTCTGGAAGCCgtaagaccgc ... gcattcgcagATACTTGGATATGCTTCCGAGCACCTTTGGGAGCTCCCTTTGGTTTACTGA
EST: gi|71330009|gb|DR801742.1|DR801742
EST:     ATGCTCTTCCTCATGGCCGAGCGCCGACGCCCTGGCTCACTCTGGAAGCC                         ATACTTGGATATGCTTCCGAGCACCTTTGGGAGCTCCCTTTGGTTTACTGA
genomic: ATGCTCTTCCTCATGGCCGAGCGCCGACGCCCTGGCTCACTCTGGAAGCCgtaagaccgc ... gcattcgcagATACTTGGATATGCTTCCGAGCACCTTTGGGAGCTCCCTTTGGTTTACTGA
EST: gi|37421956|gb|CF648682.1|CF648682
EST:     ATGCTCTTCCTCATGGCCGAGCGCCGACGCCCTGGCTCACTCTGGAAGCC                         ATACTTGGATATGCTTCCGAGCACCTTTGGGAGCTCCCTTTGGTTTACTGA
genomic: ATGCTCTTCCTCATGGCCGAGCGCCGACGCCCTGGCTCACTCTGGAAGCCgtaagaccgc ... gcattcgcagATACTTGGATATGCTTCCGAGCACCTTTGGGAGCTCCCTTTGGTTTACTGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cgcgcttgtaaataattcgaaccgtagctgaagcggtgggtcactgcattcgcagATACTTGGATATGCTTCCGAGCACCTTTGGGAGCTCCCTTTGGTTTACTGAGGAAGAGCTTGCCGAACTGGAAGGGACAACTTTGCACCGAGCTACGTTG
     ttgtaaataatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagaccgcgatccgttactgaattccccctgctccccccccccccccccccccccccccggcgcgcgcttgtaaataattcgaaccgtagctgaagcggtgggtcactgcattcgcagATACTTGGATATGCTTCCGAGCACCTTTGGGAGCTCCCTTTGGTTTACTGAGGAAGAGCTTGCCGAACTGGAAGGGACAACTTTGCACCGAGCTACGTTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGCTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG